Daily Papers

The incremental sequence labeling task involves continuously learning new classes over time while retaining knowledge of the previous ones. Our investigation identifies two significant semantic shifts: E2O (where the model mislabels an old entity as a non-entity) and O2E (where the model labels a non-entity or old entity as a new entity). Previous research has predominantly focused on addressing the E2O problem, neglecting the O2E issue. This negligence results in a model bias towards classifying new data samples as belonging to the new class during the learning process. To address these challenges, we propose a novel framework, Incremental Sequential Labeling without Semantic Shifts (IS3). Motivated by the identified semantic shifts (E2O and O2E), IS3 aims to mitigate catastrophic forgetting in models. As for the E2O problem, we use knowledge distillation to maintain the model's discriminative ability for old entities. Simultaneously, to tackle the O2E problem, we alleviate the model's bias towards new entities through debiased loss and optimization levels. Our experimental evaluation, conducted on three datasets with various incremental settings, demonstrates the superior performance of IS3 compared to the previous state-of-the-art method by a significant margin.The data, code, and scripts are publicly available at https://github.com/zzz47zzz/codebase-for-incremental-learning-with-llm.

Word emphasis in textual content aims at conveying the desired intention by changing the size, color, typeface, style (bold, italic, etc.), and other typographical features. The emphasized words are extremely helpful in drawing the readers' attention to specific information that the authors wish to emphasize. However, performing such emphasis using a soft keyboard for social media interactions is time-consuming and has an associated learning curve. In this paper, we propose a novel approach to automate the emphasis word detection on short written texts. To the best of our knowledge, this work presents the first lightweight deep learning approach for smartphone deployment of emphasis selection. Experimental results show that our approach achieves comparable accuracy at a much lower model size than existing models. Our best lightweight model has a memory footprint of 2.82 MB with a matching score of 0.716 on SemEval-2020 public benchmark dataset.

We consider higher-order linear-chain conditional random fields (HO-LC-CRFs) for sequence modelling, and use sum-product networks (SPNs) for representing higher-order input- and output-dependent factors. SPNs are a recently introduced class of deep models for which exact and efficient inference can be performed. By combining HO-LC-CRFs with SPNs, expressive models over both the output labels and the hidden variables are instantiated while still enabling efficient exact inference. Furthermore, the use of higher-order factors allows us to capture relations of multiple input segments and multiple output labels as often present in real-world data. These relations can not be modelled by the commonly used first-order models and higher-order models with local factors including only a single output label. We demonstrate the effectiveness of our proposed models for sequence labeling. In extensive experiments, we outperform other state-of-the-art methods in optical character recognition and achieve competitive results in phone classification.

Dialogue Act recognition associate dialogue acts (i.e., semantic labels) to utterances in a conversation. The problem of associating semantic labels to utterances can be treated as a sequence labeling problem. In this work, we build a hierarchical recurrent neural network using bidirectional LSTM as a base unit and the conditional random field (CRF) as the top layer to classify each utterance into its corresponding dialogue act. The hierarchical network learns representations at multiple levels, i.e., word level, utterance level, and conversation level. The conversation level representations are input to the CRF layer, which takes into account not only all previous utterances but also their dialogue acts, thus modeling the dependency among both, labels and utterances, an important consideration of natural dialogue. We validate our approach on two different benchmark data sets, Switchboard and Meeting Recorder Dialogue Act, and show performance improvement over the state-of-the-art methods by 2.2% and 4.1% absolute points, respectively. It is worth noting that the inter-annotator agreement on Switchboard data set is 84%, and our method is able to achieve the accuracy of about 79% despite being trained on the noisy data.

In the absence of readily available labeled data for a given sequence labeling task and language, annotation projection has been proposed as one of the possible strategies to automatically generate annotated data. Annotation projection has often been formulated as the task of transporting, on parallel corpora, the labels pertaining to a given span in the source language into its corresponding span in the target language. In this paper we present T-Projection, a novel approach for annotation projection that leverages large pretrained text-to-text language models and state-of-the-art machine translation technology. T-Projection decomposes the label projection task into two subtasks: (i) A candidate generation step, in which a set of projection candidates using a multilingual T5 model is generated and, (ii) a candidate selection step, in which the generated candidates are ranked based on translation probabilities. We conducted experiments on intrinsic and extrinsic tasks in 5 Indo-European and 8 low-resource African languages. We demostrate that T-projection outperforms previous annotation projection methods by a wide margin. We believe that T-Projection can help to automatically alleviate the lack of high-quality training data for sequence labeling tasks. Code and data are publicly available.

Real world deployments of word alignment are almost certain to cover both high and low resource languages. However, the state-of-the-art for this task recommends a different model class depending on the availability of gold alignment training data for a particular language pair. We propose BinaryAlign, a novel word alignment technique based on binary sequence labeling that outperforms existing approaches in both scenarios, offering a unifying approach to the task. Additionally, we vary the specific choice of multilingual foundation model, perform stratified error analysis over alignment error type, and explore the performance of BinaryAlign on non-English language pairs. We make our source code publicly available.

In this paper, we formulate keyphrase extraction from scholarly articles as a sequence labeling task solved using a BiLSTM-CRF, where the words in the input text are represented using deep contextualized embeddings. We evaluate the proposed architecture using both contextualized and fixed word embedding models on three different benchmark datasets (Inspec, SemEval 2010, SemEval 2017) and compare with existing popular unsupervised and supervised techniques. Our results quantify the benefits of (a) using contextualized embeddings (e.g. BERT) over fixed word embeddings (e.g. Glove); (b) using a BiLSTM-CRF architecture with contextualized word embeddings over fine-tuning the contextualized word embedding model directly, and (c) using genre-specific contextualized embeddings (SciBERT). Through error analysis, we also provide some insights into why particular models work better than others. Lastly, we present a case study where we analyze different self-attention layers of the two best models (BERT and SciBERT) to better understand the predictions made by each for the task of keyphrase extraction.

Prompt-based methods have been successfully applied to multilingual pretrained language models for zero-shot cross-lingual understanding. However, most previous studies primarily focused on sentence-level classification tasks, and only a few considered token-level labeling tasks such as Named Entity Recognition (NER) and Part-of-Speech (POS) tagging. In this paper, we propose Token-Level Prompt Decomposition (ToPro), which facilitates the prompt-based method for token-level sequence labeling tasks. The ToPro method decomposes an input sentence into single tokens and applies one prompt template to each token. Our experiments on multilingual NER and POS tagging datasets demonstrate that ToPro-based fine-tuning outperforms Vanilla fine-tuning and Prompt-Tuning in zero-shot cross-lingual transfer, especially for languages that are typologically different from the source language English. Our method also attains state-of-the-art performance when employed with the mT5 model. Besides, our exploratory study in multilingual large language models shows that ToPro performs much better than the current in-context learning method. Overall, the performance improvements show that ToPro could potentially serve as a novel and simple benchmarking method for sequence labeling tasks.

Pre-trained language models based on masked language modeling (MLM) objective excel in natural language understanding (NLU) tasks. While fine-tuned MLM-based encoders consistently outperform causal language modeling decoders of comparable size, a recent trend of scaling decoder models to multiple billion parameters resulted in large language models (LLMs), making them competitive with MLM-based encoders. Although scale amplifies their prowess in NLU tasks, LLMs fall short of SOTA results in information extraction (IE) tasks, many framed as sequence labeling (SL). However, whether this is an intrinsic limitation of LLMs or whether their SL performance can be improved remains unclear. To address this, we explore strategies to enhance the SL performance of "open" LLMs (Llama2 and Mistral) on IE tasks. We investigate bidirectional information flow within groups of decoder blocks, applying layer-wise removal or enforcement of the causal mask (CM) during LLM fine-tuning. This approach yields performance gains competitive with SOTA SL models, matching or outperforming the results of CM removal from all blocks. Our findings hold for diverse SL tasks, proving that "open" LLMs with layer-dependent CM removal outperform strong MLM-based encoders and instruction-tuned LLMs. However, we observe no effect from CM removal on a small scale when maintaining an equivalent model size, pre-training steps, and pre-training and fine-tuning data.

We present QueryNER, a manually-annotated dataset and accompanying model for e-commerce query segmentation. Prior work in sequence labeling for e-commerce has largely addressed aspect-value extraction which focuses on extracting portions of a product title or query for narrowly defined aspects. Our work instead focuses on the goal of dividing a query into meaningful chunks with broadly applicable types. We report baseline tagging results and conduct experiments comparing token and entity dropping for null and low recall query recovery. Challenging test sets are created using automatic transformations and show how simple data augmentation techniques can make the models more robust to noise. We make the QueryNER dataset publicly available.

Lately, instruction-based techniques have made significant strides in improving performance in few-shot learning scenarios. They achieve this by bridging the gap between pre-trained language models and fine-tuning for specific downstream tasks. Despite these advancements, the performance of Large Language Models (LLMs) in information extraction tasks like Named Entity Recognition (NER), using prompts or instructions, still falls short of supervised baselines. The reason for this performance gap can be attributed to the fundamental disparity between NER and LLMs. NER is inherently a sequence labeling task, where the model must assign entity-type labels to individual tokens within a sentence. In contrast, LLMs are designed as a text generation task. This distinction between semantic labeling and text generation leads to subpar performance. In this paper, we transform the NER task into a text-generation task that can be readily adapted by LLMs. This involves enhancing source sentences with task-specific instructions and answer choices, allowing for the identification of entities and their types within natural language. We harness the strength of LLMs by integrating supervised learning within them. The goal of this combined strategy is to boost the performance of LLMs in extraction tasks like NER while simultaneously addressing hallucination issues often observed in LLM-generated content. A novel corpus Contract NER comprising seven frequently observed contract categories, encompassing named entities associated with 18 distinct legal entity types is released along with our baseline models. Our models and dataset are available to the community for future research * .

Named Entity Recognition (NER) models capable of Continual Learning (CL) are realistically valuable in areas where entity types continuously increase (e.g., personal assistants). Meanwhile the learning paradigm of NER advances to new patterns such as the span-based methods. However, its potential to CL has not been fully explored. In this paper, we propose SpanKL, a simple yet effective Span-based model with Knowledge distillation (KD) to preserve memories and multi-Label prediction to prevent conflicts in CL-NER. Unlike prior sequence labeling approaches, the inherently independent modeling in span and entity level with the designed coherent optimization on SpanKL promotes its learning at each incremental step and mitigates the forgetting. Experiments on synthetic CL datasets derived from OntoNotes and Few-NERD show that SpanKL significantly outperforms previous SoTA in many aspects, and obtains the smallest gap from CL to the upper bound revealing its high practiced value. The code is available at https://github.com/Qznan/SpanKL.

Neural models that do not rely on pre-training have excelled in the keyphrase generation task with large annotated datasets. Meanwhile, new approaches have incorporated pre-trained language models (PLMs) for their data efficiency. However, there lacks a systematic study of how the two types of approaches compare and how different design choices can affect the performance of PLM-based models. To fill in this knowledge gap and facilitate a more informed use of PLMs for keyphrase extraction and keyphrase generation, we present an in-depth empirical study. Formulating keyphrase extraction as sequence labeling and keyphrase generation as sequence-to-sequence generation, we perform extensive experiments in three domains. After showing that PLMs have competitive high-resource performance and state-of-the-art low-resource performance, we investigate important design choices including in-domain PLMs, PLMs with different pre-training objectives, using PLMs with a parameter budget, and different formulations for present keyphrases. Further results show that (1) in-domain BERT-like PLMs can be used to build strong and data-efficient keyphrase generation models; (2) with a fixed parameter budget, prioritizing model depth over width and allocating more layers in the encoder leads to better encoder-decoder models; and (3) introducing four in-domain PLMs, we achieve a competitive performance in the news domain and the state-of-the-art performance in the scientific domain.

Slot Filling (SF) is one of the sub-tasks of Spoken Language Understanding (SLU) which aims to extract semantic constituents from a given natural language utterance. It is formulated as a sequence labeling task. Recently, it has been shown that contextual information is vital for this task. However, existing models employ contextual information in a restricted manner, e.g., using self-attention. Such methods fail to distinguish the effects of the context on the word representation and the word label. To address this issue, in this paper, we propose a novel method to incorporate the contextual information in two different levels, i.e., representation level and task-specific (i.e., label) level. Our extensive experiments on three benchmark datasets on SF show the effectiveness of our model leading to new state-of-the-art results on all three benchmark datasets for the task of SF.

We present bgGLUE(Bulgarian General Language Understanding Evaluation), a benchmark for evaluating language models on Natural Language Understanding (NLU) tasks in Bulgarian. Our benchmark includes NLU tasks targeting a variety of NLP problems (e.g., natural language inference, fact-checking, named entity recognition, sentiment analysis, question answering, etc.) and machine learning tasks (sequence labeling, document-level classification, and regression). We run the first systematic evaluation of pre-trained language models for Bulgarian, comparing and contrasting results across the nine tasks in the benchmark. The evaluation results show strong performance on sequence labeling tasks, but there is a lot of room for improvement for tasks that require more complex reasoning. We make bgGLUE publicly available together with the fine-tuning and the evaluation code, as well as a public leaderboard at https://bgglue.github.io/, and we hope that it will enable further advancements in developing NLU models for Bulgarian.

Recent development in Large Language Models (LLMs) and Multi-modal Large Language Models (MLLMs) have leverage Attention-based Transformer architectures and achieved superior performance and generalization capabilities. They have since covered extensive areas of traditional learning tasks. For instance, text-based tasks such as text-classification and sequence-labeling, as well as multi-modal tasks like Visual Question Answering (VQA) and Optical Character Recognition (OCR), which were previously addressed using different models, can now be tackled based on one foundation model. Consequently, the training and lightweight fine-tuning of LLMs and MLLMs, especially those based on Transformer architecture, has become particularly important. In recognition of these overwhelming needs, we develop SWIFT, a customizable one-stop infrastructure for large models. With support of over 300+ LLMs and 50+ MLLMs, SWIFT stands as the open-source framework that provide the most comprehensive support for fine-tuning large models. In particular, it is the first training framework that provides systematic support for MLLMs. In addition to the core functionalities of fine-tuning, SWIFT also integrates post-training processes such as inference, evaluation, and model quantization, to facilitate fast adoptions of large models in various application scenarios. With a systematic integration of various training techniques, SWIFT offers helpful utilities such as benchmark comparisons among different training techniques for large models. For fine-tuning models specialized in agent framework, we show that notable improvements on the ToolBench leader-board can be achieved by training with customized dataset on SWIFT, with an increase of 5.2%-21.8% in the Act.EM metric over various baseline models, a reduction in hallucination by 1.6%-14.1%, and an average performance improvement of 8%-17%.

Natural Language Processing (NLP) has seen remarkable advances in recent years, particularly with the emergence of Large Language Models that have achieved unprecedented performance across many tasks. However, these developments have mainly benefited a small number of high-resource languages such as English. The majority of languages still face significant challenges due to the scarcity of training data and computational resources. To address this issue, this thesis focuses on cross-lingual transfer learning, a research area aimed at leveraging data and models from high-resource languages to improve NLP performance for low-resource languages. Specifically, we focus on Sequence Labeling tasks such as Named Entity Recognition, Opinion Target Extraction, and Argument Mining. The research is structured around three main objectives: (1) advancing data-based cross-lingual transfer learning methods through improved translation and annotation projection techniques, (2) developing enhanced model-based transfer learning approaches utilizing state-of-the-art multilingual models, and (3) applying these methods to real-world problems while creating open-source resources that facilitate future research in low-resource NLP. More specifically, this thesis presents a new method to improve data-based transfer with T-Projection, a state-of-the-art annotation projection method that leverages text-to-text multilingual models and machine translation systems. T-Projection significantly outperforms previous annotation projection methods by a wide margin. For model-based transfer, we introduce a constrained decoding algorithm that enhances cross-lingual Sequence Labeling in zero-shot settings using text-to-text models. Finally, we develop Medical mT5, the first multilingual text-to-text medical model, demonstrating the practical impact of our research on real-world applications.

The increasing number of benchmarks for Natural Language Processing (NLP) tasks in the computational job market domain highlights the demand for methods that can handle job-related tasks such as skill extraction, skill classification, job title classification, and de-identification. While some approaches have been developed that are specific to the job market domain, there is a lack of generalized, multilingual models and benchmarks for these tasks. In this study, we introduce a language model called ESCOXLM-R, based on XLM-R, which uses domain-adaptive pre-training on the European Skills, Competences, Qualifications and Occupations (ESCO) taxonomy, covering 27 languages. The pre-training objectives for ESCOXLM-R include dynamic masked language modeling and a novel additional objective for inducing multilingual taxonomical ESCO relations. We comprehensively evaluate the performance of ESCOXLM-R on 6 sequence labeling and 3 classification tasks in 4 languages and find that it achieves state-of-the-art results on 6 out of 9 datasets. Our analysis reveals that ESCOXLM-R performs better on short spans and outperforms XLM-R on entity-level and surface-level span-F1, likely due to ESCO containing short skill and occupation titles, and encoding information on the entity-level.

We address a challenging and practical task of labeling questions in speech in real time during telephone calls to emergency medical services in English, which embeds within a broader decision support system for emergency call-takers. We propose a novel multimodal approach to real-time sequence labeling in speech. Our model treats speech and its own textual representation as two separate modalities or views, as it jointly learns from streamed audio and its noisy transcription into text via automatic speech recognition. Our results show significant gains of jointly learning from the two modalities when compared to text or audio only, under adverse noise and limited volume of training data. The results generalize to medical symptoms detection where we observe a similar pattern of improvements with multimodal learning.

Traditional approaches to Named Entity Recognition (NER) frame the task into a BIO sequence labeling problem. Although these systems often excel in the downstream task at hand, they require extensive annotated data and struggle to generalize to out-of-distribution input domains and unseen entity types. On the contrary, Large Language Models (LLMs) have demonstrated strong zero-shot capabilities. While several works address Zero-Shot NER in English, little has been done in other languages. In this paper, we define an evaluation framework for Zero-Shot NER, applying it to the Italian language. Furthermore, we introduce SLIMER-IT, the Italian version of SLIMER, an instruction-tuning approach for zero-shot NER leveraging prompts enriched with definition and guidelines. Comparisons with other state-of-the-art models, demonstrate the superiority of SLIMER-IT on never-seen-before entity tags.

Retrieval-augmented generation improves various aspects of large language models (LLMs) generation, but suffers from computational overhead caused by long contexts as well as the propagation of irrelevant retrieved information into generated responses. Context pruning deals with both aspects, by removing irrelevant parts of retrieved contexts before LLM generation. Existing context pruning approaches are however limited, and do not provide a universal model that would be both efficient and robust in a wide range of scenarios, e.g., when contexts contain a variable amount of relevant information or vary in length, or when evaluated on various domains. In this work, we close this gap and introduce Provence (Pruning and Reranking Of retrieVEd relevaNt ContExts), an efficient and robust context pruner for Question Answering, which dynamically detects the needed amount of pruning for a given context and can be used out-of-the-box for various domains. The three key ingredients of Provence are formulating the context pruning task as sequence labeling, unifying context pruning capabilities with context reranking, and training on diverse data. Our experimental results show that Provence enables context pruning with negligible to no drop in performance, in various domains and settings, at almost no cost in a standard RAG pipeline. We also conduct a deeper analysis alongside various ablations to provide insights into training context pruners for future work.

Aspect-based sentiment analysis (ABSA), a sequence labeling task, has attracted increasing attention in multilingual contexts. While previous research has focused largely on fine-tuning or training models specifically for ABSA, we evaluate large language models (LLMs) under zero-shot conditions to explore their potential to tackle this challenge with minimal task-specific adaptation. We conduct a comprehensive empirical evaluation of a series of LLMs on multilingual ABSA tasks, investigating various prompting strategies, including vanilla zero-shot, chain-of-thought (CoT), self-improvement, self-debate, and self-consistency, across nine different models. Results indicate that while LLMs show promise in handling multilingual ABSA, they generally fall short of fine-tuned, task-specific models. Notably, simpler zero-shot prompts often outperform more complex strategies, especially in high-resource languages like English. These findings underscore the need for further refinement of LLM-based approaches to effectively address ABSA task across diverse languages.

Prompt tuning, which only tunes continuous prompts with a frozen language model, substantially reduces per-task storage and memory usage at training. However, in the context of NLU, prior work reveals that prompt tuning does not perform well for normal-sized pretrained models. We also find that existing methods of prompt tuning cannot handle hard sequence labeling tasks, indicating a lack of universality. We present a novel empirical finding that properly optimized prompt tuning can be universally effective across a wide range of model scales and NLU tasks. It matches the performance of finetuning while having only 0.1%-3% tuned parameters. Our method P-Tuning v2 is an implementation of Deep Prompt Tuning li2021prefix,qin2021learning optimized and adapted for NLU. Given the universality and simplicity of P-Tuning v2, we believe it can serve as an alternative to finetuning and a strong baseline for future research.Our code and data are released at https://github.com/THUDM/P-tuning-v2.

Most pre-trained language models (PLMs) construct word representations at subword level with Byte-Pair Encoding (BPE) or its variations, by which OOV (out-of-vocab) words are almost avoidable. However, those methods split a word into subword units and make the representation incomplete and fragile. In this paper, we propose a character-aware pre-trained language model named CharBERT improving on the previous methods (such as BERT, RoBERTa) to tackle these problems. We first construct the contextual word embedding for each token from the sequential character representations, then fuse the representations of characters and the subword representations by a novel heterogeneous interaction module. We also propose a new pre-training task named NLM (Noisy LM) for unsupervised character representation learning. We evaluate our method on question answering, sequence labeling, and text classification tasks, both on the original datasets and adversarial misspelling test sets. The experimental results show that our method can significantly improve the performance and robustness of PLMs simultaneously. Pretrained models, evaluation sets, and code are available at https://github.com/wtma/CharBERT

Recent work in Dialogue Act classification has treated the task as a sequence labeling problem using hierarchical deep neural networks. We build on this prior work by leveraging the effectiveness of a context-aware self-attention mechanism coupled with a hierarchical recurrent neural network. We conduct extensive evaluations on standard Dialogue Act classification datasets and show significant improvement over state-of-the-art results on the Switchboard Dialogue Act (SwDA) Corpus. We also investigate the impact of different utterance-level representation learning methods and show that our method is effective at capturing utterance-level semantic text representations while maintaining high accuracy.

We present an approach for assessing how multilingual large language models (LLMs) learn syntax in terms of multi-formalism syntactic structures. We aim to recover constituent and dependency structures by casting parsing as sequence labeling. To do so, we select a few LLMs and study them on 13 diverse UD treebanks for dependency parsing and 10 treebanks for constituent parsing. Our results show that: (i) the framework is consistent across encodings, (ii) pre-trained word vectors do not favor constituency representations of syntax over dependencies, (iii) sub-word tokenization is needed to represent syntax, in contrast to character-based models, and (iv) occurrence of a language in the pretraining data is more important than the amount of task data when recovering syntax from the word vectors.

Despite the predominance of English in their training data, English-centric Large Language Models (LLMs) like GPT-3 and LLaMA display a remarkable ability to perform multilingual tasks, raising questions about the depth and nature of their cross-lingual capabilities. This paper introduces the decomposed prompting approach to probe the linguistic structure understanding of these LLMs in sequence labeling tasks. Diverging from the single text-to-text prompt, our method generates for each token of the input sentence an individual prompt which asks for its linguistic label. We assess our method on the Universal Dependencies part-of-speech tagging dataset for 38 languages, utilizing both English-centric and multilingual LLMs. Our findings show that decomposed prompting surpasses the iterative prompting baseline in efficacy and efficiency under zero- and few-shot settings. Further analysis reveals the influence of evaluation methods and the use of instructions in prompts. Our multilingual investigation shows that English-centric language models perform better on average than multilingual models. Our study offers insights into the multilingual transferability of English-centric LLMs, contributing to the understanding of their multilingual linguistic knowledge.

Part of speech tagging in zero-resource settings can be an effective approach for low-resource languages when no labeled training data is available. Existing systems use two main techniques for POS tagging i.e. pretrained multilingual large language models(LLM) or project the source language labels into the zero resource target language and train a sequence labeling model on it. We explore the latter approach using the off-the-shelf alignment module and train a hidden Markov model(HMM) to predict the POS tags. We evaluate transfer learning setup with English as a source language and French, German, and Spanish as target languages for part-of-speech tagging. Our conclusion is that projected alignment data in zero-resource language can be beneficial to predict POS tags.

Most pretrained language models rely on subword tokenization, which processes text as a sequence of subword tokens. However, different granularities of text, such as characters, subwords, and words, can contain different kinds of information. Previous studies have shown that incorporating multiple input granularities improves model generalization, yet very few of them outputs useful representations for each granularity. In this paper, we introduce the entanglement model, aiming to combine character and subword language models. Inspired by vision-language models, our model treats characters and subwords as separate modalities, and it generates mutually informed representations for both granularities as output. We evaluate our model on text classification, named entity recognition, and POS-tagging tasks. Notably, the entanglement model outperforms its backbone language models, particularly in the presence of noisy texts and low-resource languages. Furthermore, the entanglement model even outperforms larger pre-trained models on all English sequence labeling tasks and classification tasks. Our anonymized code is available at https://anonymous.4open.science/r/noisy-IE-A673

Research on definition extraction has been conducted for well over a decade, largely with significant constraints on the type of definitions considered. In this work, we present DeftEval, a SemEval shared task in which participants must extract definitions from free text using a term-definition pair corpus that reflects the complex reality of definitions in natural language. Definitions and glosses in free text often appear without explicit indicators, across sentences boundaries, or in an otherwise complex linguistic manner. DeftEval involved 3 distinct subtasks: 1)Sentence classification, 2) sequence labeling, and 3) relation extraction.

Multimodal language models can exhibit hallucinations in their outputs, which limits their reliability. The ability to automatically detect these errors is important for mitigating them, but has been less explored and existing efforts do not localize hallucinations, instead framing this as a classification task. In this work, we first pose multimodal hallucination detection as a sequence labeling task where models must localize hallucinated text spans and present a strong baseline model. Given the high cost of human annotations for this task, we propose an approach to improve the sample efficiency of these models by creating corrupted grounding data, which we use for pre-training. Leveraging phrase grounding data, we generate hallucinations to replace grounded spans and create hallucinated text. Experiments show that pre-training on this data improves sample efficiency when fine-tuning, and that the learning signal from the grounding data plays an important role in these improvements.

In the contemporary era of widespread online recruitment, resume understanding has been widely acknowledged as a fundamental and crucial task, which aims to extract structured information from resume documents automatically. Compared to the traditional rule-based approaches, the utilization of recently proposed pre-trained document understanding models can greatly enhance the effectiveness of resume understanding. The present approaches have, however, disregarded the hierarchical relations within the structured information presented in resumes, and have difficulty parsing resumes in an efficient manner. To this end, in this paper, we propose a novel model, namely ERU, to achieve efficient resume understanding. Specifically, we first introduce a layout-aware multi-modal fusion transformer for encoding the segments in the resume with integrated textual, visual, and layout information. Then, we design three self-supervised tasks to pre-train this module via a large number of unlabeled resumes. Next, we fine-tune the model with a multi-granularity sequence labeling task to extract structured information from resumes. Finally, extensive experiments on a real-world dataset clearly demonstrate the effectiveness of ERU.

Recently, prompt-based methods have achieved significant performance in few-shot learning scenarios by bridging the gap between language model pre-training and fine-tuning for downstream tasks. However, existing prompt templates are mostly designed for sentence-level tasks and are inappropriate for sequence labeling objectives. To address the above issue, we propose a multi-task instruction-based generative framework, named InstructionNER, for low-resource named entity recognition. Specifically, we reformulate the NER task as a generation problem, which enriches source sentences with task-specific instructions and answer options, then inferences the entities and types in natural language. We further propose two auxiliary tasks, including entity extraction and entity typing, which enable the model to capture more boundary information of entities and deepen the understanding of entity type semantics, respectively. Experimental results show that our method consistently outperforms other baselines on five datasets in few-shot settings.

Quotation extraction and attribution are challenging tasks, aiming at determining the spans containing quotations and attributing each quotation to the original speaker. Applying this task to news data is highly related to fact-checking, media monitoring and news tracking. Direct quotations are more traceable and informative, and therefore of great significance among different types of quotations. Therefore, this paper introduces DirectQuote, a corpus containing 19,760 paragraphs and 10,279 direct quotations manually annotated from online news media. To the best of our knowledge, this is the largest and most complete corpus that focuses on direct quotations in news texts. We ensure that each speaker in the annotation can be linked to a specific named entity on Wikidata, benefiting various downstream tasks. In addition, for the first time, we propose several sequence labeling models as baseline methods to extract and attribute quotations simultaneously in an end-to-end manner.

This paper presents a monolingual BERT model for Galician. We follow the recent trend that shows that it is feasible to build robust monolingual BERT models even for relatively low-resource languages, while performing better than the well-known official multilingual BERT (mBERT). More particularly, we release two monolingual Galician BERT models, built using 6 and 12 transformer layers, respectively; trained with limited resources (~45 million tokens on a single GPU of 24GB). We then provide an exhaustive evaluation on a number of tasks such as POS-tagging, dependency parsing and named entity recognition. For this purpose, all these tasks are cast in a pure sequence labeling setup in order to run BERT without the need to include any additional layers on top of it (we only use an output classification layer to map the contextualized representations into the predicted label). The experiments show that our models, especially the 12-layer one, outperform the results of mBERT in most tasks.

Although Indonesian is known to be the fourth most frequently used language over the internet, the research progress on this language in the natural language processing (NLP) is slow-moving due to a lack of available resources. In response, we introduce the first-ever vast resource for the training, evaluating, and benchmarking on Indonesian natural language understanding (IndoNLU) tasks. IndoNLU includes twelve tasks, ranging from single sentence classification to pair-sentences sequence labeling with different levels of complexity. The datasets for the tasks lie in different domains and styles to ensure task diversity. We also provide a set of Indonesian pre-trained models (IndoBERT) trained from a large and clean Indonesian dataset Indo4B collected from publicly available sources such as social media texts, blogs, news, and websites. We release baseline models for all twelve tasks, as well as the framework for benchmark evaluation, and thus it enables everyone to benchmark their system performances.

In this paper, we introduce the NER dataset from CLUE organization (CLUENER2020), a well-defined fine-grained dataset for named entity recognition in Chinese. CLUENER2020 contains 10 categories. Apart from common labels like person, organization, and location, it contains more diverse categories. It is more challenging than current other Chinese NER datasets and could better reflect real-world applications. For comparison, we implement several state-of-the-art baselines as sequence labeling tasks and report human performance, as well as its analysis. To facilitate future work on fine-grained NER for Chinese, we release our dataset, baselines, and leader-board.

Joint extraction of entities and relations aims to detect entity pairs along with their relations using a single model. Prior work typically solves this task in the extract-then-classify or unified labeling manner. However, these methods either suffer from the redundant entity pairs, or ignore the important inner structure in the process of extracting entities and relations. To address these limitations, in this paper, we first decompose the joint extraction task into two interrelated subtasks, namely HE extraction and TER extraction. The former subtask is to distinguish all head-entities that may be involved with target relations, and the latter is to identify corresponding tail-entities and relations for each extracted head-entity. Next, these two subtasks are further deconstructed into several sequence labeling problems based on our proposed span-based tagging scheme, which are conveniently solved by a hierarchical boundary tagger and a multi-span decoding algorithm. Owing to the reasonable decomposition strategy, our model can fully capture the semantic interdependency between different steps, as well as reduce noise from irrelevant entity pairs. Experimental results show that our method outperforms previous work by 5.2%, 5.9% and 21.5% (F1 score), achieving a new state-of-the-art on three public datasets

Large-scale pretraining followed by task-specific finetuning has achieved great success in various NLP tasks. Since finetuning all parameters of large pretrained models poses substantial computational and memory challenges, several efficient finetuning methods have been developed. Among them, low-rank adaptation (LoRA), which finetunes low-rank incremental update matrices on top of frozen pretrained weights, has proven particularly effective. Nonetheless, LoRA's uniform rank assignment across all layers, along with its reliance on an exhaustive search to find the best rank, leads to high computation costs and suboptimal finetuning performance. To address these limitations, we introduce AutoLoRA, a meta learning based framework for automatically identifying the optimal rank of each LoRA layer. AutoLoRA associates each rank-1 matrix in a low-rank update matrix with a selection variable, which determines whether the rank-1 matrix should be discarded. A meta learning based method is developed to learn these selection variables. The optimal rank is determined by thresholding the values of these variables. Our comprehensive experiments on natural language understanding, generation, and sequence labeling demonstrate the effectiveness of AutoLoRA.

The Yunshan Cup 2020 track focused on creating a framework for evaluating different methods of part-of-speech (POS). There were two tasks for this track: (1) POS tagging for the Indonesian language, and (2) POS tagging for the Lao tagging. The Indonesian dataset is comprised of 10000 sentences from Indonesian news within 29 tags. And the Lao dataset consists of 8000 sentences within 27 tags. 25 teams registered for the task. The methods of participants ranged from feature-based to neural networks using either classical machine learning techniques or ensemble methods. The best performing results achieve an accuracy of 95.82% for Indonesian and 93.03%, showing that neural sequence labeling models significantly outperform classic feature-based methods and rule-based methods.

Automatically and accurately identifying user intents and filling the associated slots from their spoken language are critical to the success of dialogue systems. Traditional methods require manually defining the DOMAIN-INTENT-SLOT schema and asking many domain experts to annotate the corresponding utterances, upon which neural models are trained. This procedure brings the challenges of information sharing hindering, out-of-schema, or data sparsity in open-domain dialogue systems. To tackle these challenges, we explore a new task of {\em automatic intent-slot induction} and propose a novel domain-independent tool. That is, we design a coarse-to-fine three-step procedure including Role-labeling, Concept-mining, And Pattern-mining (RCAP): (1) role-labeling: extracting keyphrases from users' utterances and classifying them into a quadruple of coarsely-defined intent-roles via sequence labeling; (2) concept-mining: clustering the extracted intent-role mentions and naming them into abstract fine-grained concepts; (3) pattern-mining: applying the Apriori algorithm to mine intent-role patterns and automatically inferring the intent-slot using these coarse-grained intent-role labels and fine-grained concepts. Empirical evaluations on both real-world in-domain and out-of-domain datasets show that: (1) our RCAP can generate satisfactory SLU schema and outperforms the state-of-the-art supervised learning method; (2) our RCAP can be directly applied to out-of-domain datasets and gain at least 76\% improvement of F1-score on intent detection and 41\% improvement of F1-score on slot filling; (3) our RCAP exhibits its power in generic intent-slot extractions with less manual effort, which opens pathways for schema induction on new domains and unseen intent-slot discovery for generalizable dialogue systems.

Pre-trained multilingual language models show significant performance gains for zero-shot cross-lingual model transfer on a wide range of natural language understanding (NLU) tasks. Previously, for zero-shot cross-lingual evaluation, pre-trained models are only fine-tuned on English data and tested on a variety of target languages. In this paper, we do cross-lingual evaluation on various NLU tasks (sentence classification, sequence labeling, question answering) using prompt-tuning and compare it with fine-tuning. The results show that prompt tuning achieves much better cross-lingual transfer than fine-tuning across datasets, with only 0.1% to 0.3% tuned parameters. Additionally, we demonstrate through the analysis that prompt tuning can have better cross-lingual transferability of representations on downstream tasks with better aligned decision boundaries.

This paper addresses the privacy and security concerns associated with deep neural language models, which serve as crucial components in various modern AI-based applications. These models are often used after being pre-trained and fine-tuned for specific tasks, with deployment on servers accessed through the internet. However, this introduces two fundamental risks: (a) the transmission of user inputs to the server via the network gives rise to interception vulnerabilities, and (b) privacy concerns emerge as organizations that deploy such models store user data with restricted context. To address this, we propose a novel method to adapt and fine-tune transformer-based language models on passkey-encrypted user-specific text. The original pre-trained language model first undergoes a quick adaptation (without any further pre-training) with a series of irreversible transformations applied to the tokenizer and token embeddings. This enables the model to perform inference on encrypted inputs while preventing reverse engineering of text from model parameters and intermediate outputs. After adaptation, models are fine-tuned on encrypted versions of existing training datasets. Experimental evaluation employing adapted versions of renowned models (e.g., BERT, RoBERTa) across established benchmark English and multilingual datasets for text classification and sequence labeling shows that encrypted models achieve performance parity with their original counterparts. This serves to safeguard performance, privacy, and security cohesively.

Zero-shot entity linking (EL) aims at aligning entity mentions to unseen entities to challenge the generalization ability. Previous methods largely focus on the candidate retrieval stage and ignore the essential candidate ranking stage, which disambiguates among entities and makes the final linking prediction. In this paper, we propose a read-and-select (ReS) framework by modeling the main components of entity disambiguation, i.e., mention-entity matching and cross-entity comparison. First, for each candidate, the reading module leverages mention context to output mention-aware entity representations, enabling mention-entity matching. Then, in the selecting module, we frame the choice of candidates as a sequence labeling problem, and all candidate representations are fused together to enable cross-entity comparison. Our method achieves the state-of-the-art performance on the established zero-shot EL dataset ZESHEL with a 2.55% micro-average accuracy gain, with no need for laborious multi-phase pre-training used in most of the previous work, showing the effectiveness of both mention-entity and cross-entity interaction.

Recent advances in multimodal pre-trained models have significantly improved information extraction from visually-rich documents (VrDs), in which named entity recognition (NER) is treated as a sequence-labeling task of predicting the BIO entity tags for tokens, following the typical setting of NLP. However, BIO-tagging scheme relies on the correct order of model inputs, which is not guaranteed in real-world NER on scanned VrDs where text are recognized and arranged by OCR systems. Such reading order issue hinders the accurate marking of entities by BIO-tagging scheme, making it impossible for sequence-labeling methods to predict correct named entities. To address the reading order issue, we introduce Token Path Prediction (TPP), a simple prediction head to predict entity mentions as token sequences within documents. Alternative to token classification, TPP models the document layout as a complete directed graph of tokens, and predicts token paths within the graph as entities. For better evaluation of VrD-NER systems, we also propose two revised benchmark datasets of NER on scanned documents which can reflect real-world scenarios. Experiment results demonstrate the effectiveness of our method, and suggest its potential to be a universal solution to various information extraction tasks on documents.

In this work, we present the first dataset, MailEx, for performing event extraction from conversational email threads. To this end, we first proposed a new taxonomy covering 10 event types and 76 arguments in the email domain. Our final dataset includes 1.5K email threads and ~4K emails, which are annotated with totally ~8K event instances. To understand the task challenges, we conducted a series of experiments comparing three types of approaches, i.e., fine-tuned sequence labeling, fine-tuned generative extraction, and few-shot in-context learning. Our results showed that the task of email event extraction is far from being addressed, due to challenges lying in, e.g., extracting non-continuous, shared trigger spans, extracting non-named entity arguments, and modeling the email conversational history. Our work thus suggests more future investigations in this domain-specific event extraction task.

Recent studies report that autoregressive language models can successfully solve many NLP tasks via zero- and few-shot learning paradigms, which opens up new possibilities for using the pre-trained language models. This paper introduces two autoregressive GPT-like models with 1.3 billion and 13 billion parameters trained on 60 languages from 25 language families using Wikipedia and Colossal Clean Crawled Corpus. We reproduce the GPT-3 architecture using GPT-2 sources and the sparse attention mechanism; Deepspeed and Megatron frameworks allow us to parallelize the training and inference steps effectively. The resulting models show performance on par with the recently released XGLM models by Facebook, covering more languages and enhancing NLP possibilities for low resource languages of CIS countries and Russian small nations. We detail the motivation for the choices of the architecture design, thoroughly describe the data preparation pipeline, and train five small versions of the model to choose the most optimal multilingual tokenization strategy. We measure the model perplexity in all covered languages and evaluate it on the wide spectre of multilingual tasks, including classification, generative, sequence labeling and knowledge probing. The models were evaluated with the zero-shot and few-shot methods. Furthermore, we compared the classification tasks with the state-of-the-art multilingual model XGLM. source code and the mGPT XL model are publicly released.

This work presents a new resource for borrowing identification and analyzes the performance and errors of several models on this task. We introduce a new annotated corpus of Spanish newswire rich in unassimilated lexical borrowings -- words from one language that are introduced into another without orthographic adaptation -- and use it to evaluate how several sequence labeling models (CRF, BiLSTM-CRF, and Transformer-based models) perform. The corpus contains 370,000 tokens and is larger, more borrowing-dense, OOV-rich, and topic-varied than previous corpora available for this task. Our results show that a BiLSTM-CRF model fed with subword embeddings along with either Transformer-based embeddings pretrained on codeswitched data or a combination of contextualized word embeddings outperforms results obtained by a multilingual BERT-based model.

In this work, we introduce BanglaBERT, a BERT-based Natural Language Understanding (NLU) model pretrained in Bangla, a widely spoken yet low-resource language in the NLP literature. To pretrain BanglaBERT, we collect 27.5 GB of Bangla pretraining data (dubbed `Bangla2B+') by crawling 110 popular Bangla sites. We introduce two downstream task datasets on natural language inference and question answering and benchmark on four diverse NLU tasks covering text classification, sequence labeling, and span prediction. In the process, we bring them under the first-ever Bangla Language Understanding Benchmark (BLUB). BanglaBERT achieves state-of-the-art results outperforming multilingual and monolingual models. We are making the models, datasets, and a leaderboard publicly available at https://github.com/csebuetnlp/banglabert to advance Bangla NLP.

Estimating probability distribution is one of the core issues in the NLP field. However, in both deep learning (DL) and pre-DL eras, unlike the vast applications of linear-chain CRF in sequence labeling tasks, very few works have applied tree-structure CRF to constituency parsing, mainly due to the complexity and inefficiency of the inside-outside algorithm. This work presents a fast and accurate neural CRF constituency parser. The key idea is to batchify the inside algorithm for loss computation by direct large tensor operations on GPU, and meanwhile avoid the outside algorithm for gradient computation via efficient back-propagation. We also propose a simple two-stage bracketing-then-labeling parsing approach to improve efficiency further. To improve the parsing performance, inspired by recent progress in dependency parsing, we introduce a new scoring architecture based on boundary representation and biaffine attention, and a beneficial dropout strategy. Experiments on PTB, CTB5.1, and CTB7 show that our two-stage CRF parser achieves new state-of-the-art performance on both settings of w/o and w/ BERT, and can parse over 1,000 sentences per second. We release our code at https://github.com/yzhangcs/crfpar.

This paper presents NorNE, a manually annotated corpus of named entities which extends the annotation of the existing Norwegian Dependency Treebank. Comprising both of the official standards of written Norwegian (Bokm{\aa}l and Nynorsk), the corpus contains around 600,000 tokens and annotates a rich set of entity types including persons, organizations, locations, geo-political entities, products, and events, in addition to a class corresponding to nominals derived from names. We here present details on the annotation effort, guidelines, inter-annotator agreement and an experimental analysis of the corpus using a neural sequence labeling architecture.

Arabic word segmentation is essential for a variety of NLP applications such as machine translation and information retrieval. Segmentation entails breaking words into their constituent stems, affixes and clitics. In this paper, we compare two approaches for segmenting four major Arabic dialects using only several thousand training examples for each dialect. The two approaches involve posing the problem as a ranking problem, where an SVM ranker picks the best segmentation, and as a sequence labeling problem, where a bi-LSTM RNN coupled with CRF determines where best to segment words. We are able to achieve solid segmentation results for all dialects using rather limited training data. We also show that employing Modern Standard Arabic data for domain adaptation and assuming context independence improve overall results.

Domain-specific named entity recognition (NER) on Computer Science (CS) scholarly articles is an information extraction task that is arguably more challenging for the various annotation aims that can beset the task and has been less studied than NER in the general domain. Given that significant progress has been made on NER, we believe that scholarly domain-specific NER will receive increasing attention in the years to come. Currently, progress on CS NER -- the focus of this work -- is hampered in part by its recency and the lack of a standardized annotation aim for scientific entities/terms. This work proposes a standardized task by defining a set of seven contribution-centric scholarly entities for CS NER viz., research problem, solution, resource, language, tool, method, and dataset. Following which, its main contributions are: combines existing CS NER resources that maintain their annotation focus on the set or subset of contribution-centric scholarly entities we consider; further, noting the need for big data to train neural NER models, this work additionally supplies thousands of contribution-centric entity annotations from article titles and abstracts, thus releasing a cumulative large novel resource for CS NER; and, finally, trains a sequence labeling CS NER model inspired after state-of-the-art neural architectures from the general domain NER task. Throughout the work, several practical considerations are made which can be useful to information technology designers of the digital libraries.

Sequences have become first class citizens in supervised learning thanks to the resurgence of recurrent neural networks. Many complex tasks that require mapping from or to a sequence of observations can now be formulated with the sequence-to-sequence (seq2seq) framework which employs the chain rule to efficiently represent the joint probability of sequences. In many cases, however, variable sized inputs and/or outputs might not be naturally expressed as sequences. For instance, it is not clear how to input a set of numbers into a model where the task is to sort them; similarly, we do not know how to organize outputs when they correspond to random variables and the task is to model their unknown joint probability. In this paper, we first show using various examples that the order in which we organize input and/or output data matters significantly when learning an underlying model. We then discuss an extension of the seq2seq framework that goes beyond sequences and handles input sets in a principled way. In addition, we propose a loss which, by searching over possible orders during training, deals with the lack of structure of output sets. We show empirical evidence of our claims regarding ordering, and on the modifications to the seq2seq framework on benchmark language modeling and parsing tasks, as well as two artificial tasks -- sorting numbers and estimating the joint probability of unknown graphical models.

Sequence-to-sequence models are commonly trained via maximum likelihood estimation (MLE). However, standard MLE training considers a word-level objective, predicting the next word given the previous ground-truth partial sentence. This procedure focuses on modeling local syntactic patterns, and may fail to capture long-range semantic structure. We present a novel solution to alleviate these issues. Our approach imposes global sequence-level guidance via new supervision based on optimal transport, enabling the overall characterization and preservation of semantic features. We further show that this method can be understood as a Wasserstein gradient flow trying to match our model to the ground truth sequence distribution. Extensive experiments are conducted to validate the utility of the proposed approach, showing consistent improvements over a wide variety of NLP tasks, including machine translation, abstractive text summarization, and image captioning.

This work proposes a novel adaptation of a pretrained sequence-to-sequence model to the task of document ranking. Our approach is fundamentally different from a commonly-adopted classification-based formulation of ranking, based on encoder-only pretrained transformer architectures such as BERT. We show how a sequence-to-sequence model can be trained to generate relevance labels as "target words", and how the underlying logits of these target words can be interpreted as relevance probabilities for ranking. On the popular MS MARCO passage ranking task, experimental results show that our approach is at least on par with previous classification-based models and can surpass them with larger, more-recent models. On the test collection from the TREC 2004 Robust Track, we demonstrate a zero-shot transfer-based approach that outperforms previous state-of-the-art models requiring in-dataset cross-validation. Furthermore, we find that our approach significantly outperforms an encoder-only model in a data-poor regime (i.e., with few training examples). We investigate this observation further by varying target words to probe the model's use of latent knowledge.

In this paper, we present a simple and efficient GEC sequence tagger using a Transformer encoder. Our system is pre-trained on synthetic data and then fine-tuned in two stages: first on errorful corpora, and second on a combination of errorful and error-free parallel corpora. We design custom token-level transformations to map input tokens to target corrections. Our best single-model/ensemble GEC tagger achieves an F_{0.5} of 65.3/66.5 on CoNLL-2014 (test) and F_{0.5} of 72.4/73.6 on BEA-2019 (test). Its inference speed is up to 10 times as fast as a Transformer-based seq2seq GEC system. The code and trained models are publicly available.

Encoder-decoder models have become an effective approach for sequence learning tasks like machine translation, image captioning and speech recognition, but have yet to show competitive results for handwritten text recognition. To this end, we propose an attention-based sequence-to-sequence model. It combines a convolutional neural network as a generic feature extractor with a recurrent neural network to encode both the visual information, as well as the temporal context between characters in the input image, and uses a separate recurrent neural network to decode the actual character sequence. We make experimental comparisons between various attention mechanisms and positional encodings, in order to find an appropriate alignment between the input and output sequence. The model can be trained end-to-end and the optional integration of a hybrid loss allows the encoder to retain an interpretable and usable output, if desired. We achieve competitive results on the IAM and ICFHR2016 READ data sets compared to the state-of-the-art without the use of a language model, and we significantly improve over any recent sequence-to-sequence approaches.

We present PubMed 200k RCT, a new dataset based on PubMed for sequential sentence classification. The dataset consists of approximately 200,000 abstracts of randomized controlled trials, totaling 2.3 million sentences. Each sentence of each abstract is labeled with their role in the abstract using one of the following classes: background, objective, method, result, or conclusion. The purpose of releasing this dataset is twofold. First, the majority of datasets for sequential short-text classification (i.e., classification of short texts that appear in sequences) are small: we hope that releasing a new large dataset will help develop more accurate algorithms for this task. Second, from an application perspective, researchers need better tools to efficiently skim through the literature. Automatically classifying each sentence in an abstract would help researchers read abstracts more efficiently, especially in fields where abstracts may be long, such as the medical field.

Zero-resource cross-lingual transfer approaches aim to apply supervised models from a source language to unlabelled target languages. In this paper we perform an in-depth study of the two main techniques employed so far for cross-lingual zero-resource sequence labelling, based either on data or model transfer. Although previous research has proposed translation and annotation projection (data-based cross-lingual transfer) as an effective technique for cross-lingual sequence labelling, in this paper we experimentally demonstrate that high capacity multilingual language models applied in a zero-shot (model-based cross-lingual transfer) setting consistently outperform data-based cross-lingual transfer approaches. A detailed analysis of our results suggests that this might be due to important differences in language use. More specifically, machine translation often generates a textual signal which is different to what the models are exposed to when using gold standard data, which affects both the fine-tuning and evaluation processes. Our results also indicate that data-based cross-lingual transfer approaches remain a competitive option when high-capacity multilingual language models are not available.

While contrastive learning is proven to be an effective training strategy in computer vision, Natural Language Processing (NLP) is only recently adopting it as a self-supervised alternative to Masked Language Modeling (MLM) for improving sequence representations. This paper introduces SupCL-Seq, which extends the supervised contrastive learning from computer vision to the optimization of sequence representations in NLP. By altering the dropout mask probability in standard Transformer architectures, for every representation (anchor), we generate augmented altered views. A supervised contrastive loss is then utilized to maximize the system's capability of pulling together similar samples (e.g., anchors and their altered views) and pushing apart the samples belonging to the other classes. Despite its simplicity, SupCLSeq leads to large gains in many sequence classification tasks on the GLUE benchmark compared to a standard BERTbase, including 6% absolute improvement on CoLA, 5.4% on MRPC, 4.7% on RTE and 2.6% on STSB. We also show consistent gains over self supervised contrastively learned representations, especially in non-semantic tasks. Finally we show that these gains are not solely due to augmentation, but rather to a downstream optimized sequence representation. Code: https://github.com/hooman650/SupCL-Seq

Data of sequential nature arise in many application domains in forms of, e.g. textual data, DNA sequences, and software execution traces. Different research disciplines have developed methods to learn sequence models from such datasets: (i) in the machine learning field methods such as (hidden) Markov models and recurrent neural networks have been developed and successfully applied to a wide-range of tasks, (ii) in process mining process discovery techniques aim to generate human-interpretable descriptive models, and (iii) in the grammar inference field the focus is on finding descriptive models in the form of formal grammars. Despite their different focuses, these fields share a common goal - learning a model that accurately describes the behavior in the underlying data. Those sequence models are generative, i.e, they can predict what elements are likely to occur after a given unfinished sequence. So far, these fields have developed mainly in isolation from each other and no comparison exists. This paper presents an interdisciplinary experimental evaluation that compares sequence modeling techniques on the task of next-element prediction on four real-life sequence datasets. The results indicate that machine learning techniques that generally have no aim at interpretability in terms of accuracy outperform techniques from the process mining and grammar inference fields that aim to yield interpretable models.

Ordinal regression refers to classifying object instances into ordinal categories. It has been widely studied in many scenarios, such as medical disease grading, movie rating, etc. Known methods focused only on learning inter-class ordinal relationships, but still incur limitations in distinguishing adjacent categories thus far. In this paper, we propose a simple sequence prediction framework for ordinal regression called Ord2Seq, which, for the first time, transforms each ordinal category label into a special label sequence and thus regards an ordinal regression task as a sequence prediction process. In this way, we decompose an ordinal regression task into a series of recursive binary classification steps, so as to subtly distinguish adjacent categories. Comprehensive experiments show the effectiveness of distinguishing adjacent categories for performance improvement and our new approach exceeds state-of-the-art performances in four different scenarios. Codes are available at https://github.com/wjh892521292/Ord2Seq.

This paper describes our submission to CoNLL 2018 UD Shared Task. We have extended an LSTM-based neural network designed for sequence tagging to additionally generate character-level sequences. The network was jointly trained to produce lemmas, part-of-speech tags and morphological features. Sentence segmentation, tokenization and dependency parsing were handled by UDPipe 1.2 baseline. The results demonstrate the viability of the proposed multitask architecture, although its performance still remains far from state-of-the-art.

During times of increasing antibiotic resistance and the spread of infectious diseases like COVID-19, it is important to classify genes related to antibiotic resistance. As natural language processing has advanced with transformer-based language models, many language models that learn characteristics of nucleotide sequences have also emerged. These models show good performance in classifying various features of nucleotide sequences. When classifying nucleotide sequences, not only the sequence itself, but also various background knowledge is utilized. In this study, we use not only a nucleotide sequence-based language model but also a text language model based on PubMed articles to reflect more biological background knowledge in the model. We propose a method to fine-tune the nucleotide sequence language model and the text language model based on various databases of antibiotic resistance genes. We also propose an LLM-based augmentation technique to supplement the data and an ensemble method to effectively combine the two models. We also propose a benchmark for evaluating the model. Our method achieved better performance than the nucleotide sequence language model in the drug resistance class prediction.

The ability to generate natural language sequences from source code snippets has a variety of applications such as code summarization, documentation, and retrieval. Sequence-to-sequence (seq2seq) models, adopted from neural machine translation (NMT), have achieved state-of-the-art performance on these tasks by treating source code as a sequence of tokens. We present {scriptsize CODE2SEQ}: an alternative approach that leverages the syntactic structure of programming languages to better encode source code. Our model represents a code snippet as the set of compositional paths in its abstract syntax tree (AST) and uses attention to select the relevant paths while decoding. We demonstrate the effectiveness of our approach for two tasks, two programming languages, and four datasets of up to 16M examples. Our model significantly outperforms previous models that were specifically designed for programming languages, as well as state-of-the-art NMT models. An interactive online demo of our model is available at http://code2seq.org. Our code, data and trained models are available at http://github.com/tech-srl/code2seq.

Many machine learning tasks can be expressed as the transformation---or transduction---of input sequences into output sequences: speech recognition, machine translation, protein secondary structure prediction and text-to-speech to name but a few. One of the key challenges in sequence transduction is learning to represent both the input and output sequences in a way that is invariant to sequential distortions such as shrinking, stretching and translating. Recurrent neural networks (RNNs) are a powerful sequence learning architecture that has proven capable of learning such representations. However RNNs traditionally require a pre-defined alignment between the input and output sequences to perform transduction. This is a severe limitation since finding the alignment is the most difficult aspect of many sequence transduction problems. Indeed, even determining the length of the output sequence is often challenging. This paper introduces an end-to-end, probabilistic sequence transduction system, based entirely on RNNs, that is in principle able to transform any input sequence into any finite, discrete output sequence. Experimental results for phoneme recognition are provided on the TIMIT speech corpus.

In this study, we tackle the challenge of limited labeled data for low-resource languages in ASR, focusing on Hindi. Specifically, we explore pseudo-labeling, by proposing a generic framework combining multiple ideas from existing works. Our framework integrates multiple base models for transcription and evaluators for assessing audio-transcript pairs, resulting in robust pseudo-labeling for low resource languages. We validate our approach with a new benchmark, IndicYT, comprising diverse YouTube audio files from multiple content categories. Our findings show that augmenting pseudo labeled data from YouTube with existing training data leads to significant performance improvements on IndicYT, without affecting performance on out-of-domain benchmarks, demonstrating the efficacy of pseudo-labeled data in enhancing ASR capabilities for low-resource languages. The benchmark, code and models developed as a part of this work will be made publicly available.

Named entity detection and Parts-of-speech tagging are the key tasks for many NLP applications. Although the current state of the art methods achieved near perfection for long, formal, structured text there are hindrances in deploying these models on memory-constrained devices such as mobile phones. Furthermore, the performance of these models is degraded when they encounter short, informal, and casual conversations. To overcome these difficulties, we present LiteMuL - a lightweight on-device sequence tagger that can efficiently process the user conversations using a Multi-Task Learning (MTL) approach. To the best of our knowledge, the proposed model is the first on-device MTL neural model for sequence tagging. Our LiteMuL model is about 2.39 MB in size and achieved an accuracy of 0.9433 (for NER), 0.9090 (for POS) on the CoNLL 2003 dataset. The proposed LiteMuL not only outperforms the current state of the art results but also surpasses the results of our proposed on-device task-specific models, with accuracy gains of up to 11% and model-size reduction by 50%-56%. Our model is competitive with other MTL approaches for NER and POS tasks while outshines them with a low memory footprint. We also evaluated our model on custom-curated user conversations and observed impressive results.

The sequence-to-sequence (seq2seq) task aims at generating the target sequence based on the given input source sequence. Traditionally, most of the seq2seq task is resolved by the Encoder-Decoder framework which requires an encoder to encode the source sequence and a decoder to generate the target text. Recently, a bunch of new approaches have emerged that apply decoder-only language models directly to the seq2seq task. Despite the significant advancements in applying language models to the seq2seq task, there is still a lack of thorough analysis on the effectiveness of the decoder-only language model architecture. This paper aims to address this gap by conducting a detailed comparison between the encoder-decoder architecture and the decoder-only language model framework through the analysis of a regularized encoder-decoder structure. This structure is designed to replicate all behaviors in the classical decoder-only language model but has an encoder and a decoder making it easier to be compared with the classical encoder-decoder structure. Based on the analysis, we unveil the attention degeneration problem in the language model, namely, as the generation step number grows, less and less attention is focused on the source sequence. To give a quantitative understanding of this problem, we conduct a theoretical sensitivity analysis of the attention output with respect to the source input. Grounded on our analysis, we propose a novel partial attention language model to solve the attention degeneration problem. Experimental results on machine translation, summarization, and data-to-text generation tasks support our analysis and demonstrate the effectiveness of our proposed model.

The task of Grammatical Error Correction (GEC) has received remarkable attention with wide applications in Natural Language Processing (NLP) in recent years. While one of the key principles of GEC is to keep the correct parts unchanged and avoid over-correction, previous sequence-to-sequence (seq2seq) models generate results from scratch, which are not guaranteed to follow the original sentence structure and may suffer from the over-correction problem. In the meantime, the recently proposed sequence tagging models can overcome the over-correction problem by only generating edit operations, but are conditioned on human designed language-specific tagging labels. In this paper, we combine the pros and alleviate the cons of both models by proposing a novel Sequence-to-Action~(S2A) module. The S2A module jointly takes the source and target sentences as input, and is able to automatically generate a token-level action sequence before predicting each token, where each action is generated from three choices named SKIP, COPY and GENerate. Then the actions are fused with the basic seq2seq framework to provide final predictions. We conduct experiments on the benchmark datasets of both English and Chinese GEC tasks. Our model consistently outperforms the seq2seq baselines, while being able to significantly alleviate the over-correction problem as well as holding better generality and diversity in the generation results compared to the sequence tagging models.

The parallels between protein sequences and natural language in their sequential structures have inspired the application of large language models (LLMs) to protein understanding. Despite the success of LLMs in NLP, their effectiveness in comprehending protein sequences remains an open question, largely due to the absence of datasets linking protein sequences to descriptive text. Researchers have then attempted to adapt LLMs for protein understanding by integrating a protein sequence encoder with a pre-trained LLM. However, this adaptation raises a fundamental question: "Can LLMs, originally designed for NLP, effectively comprehend protein sequences as a form of language?" Current datasets fall short in addressing this question due to the lack of a direct correlation between protein sequences and corresponding text descriptions, limiting the ability to train and evaluate LLMs for protein understanding effectively. To bridge this gap, we introduce ProteinLMDataset, a dataset specifically designed for further self-supervised pretraining and supervised fine-tuning (SFT) of LLMs to enhance their capability for protein sequence comprehension. Specifically, ProteinLMDataset includes 17.46 billion tokens for pretraining and 893,000 instructions for SFT. Additionally, we present ProteinLMBench, the first benchmark dataset consisting of 944 manually verified multiple-choice questions for assessing the protein understanding capabilities of LLMs. ProteinLMBench incorporates protein-related details and sequences in multiple languages, establishing a new standard for evaluating LLMs' abilities in protein comprehension. The large language model InternLM2-7B, pretrained and fine-tuned on the ProteinLMDataset, outperforms GPT-4 on ProteinLMBench, achieving the highest accuracy score. The dataset and the benchmark are available at https://huggingface.co/datasets/tsynbio/ProteinLMBench.

Conditional language models are predominantly trained with maximum likelihood estimation (MLE), giving probability mass to sparsely observed target sequences. While MLE trained models assign high probability to plausible sequences given the context, the model probabilities often do not accurately rank-order generated sequences by quality. This has been empirically observed in beam search decoding as output quality degrading with large beam sizes, and decoding strategies benefiting from heuristics such as length normalization and repetition-blocking. In this work, we introduce sequence likelihood calibration (SLiC) where the likelihood of model generated sequences are calibrated to better align with reference sequences in the model's latent space. With SLiC, decoding heuristics become unnecessary and decoding candidates' quality significantly improves regardless of the decoding method. Furthermore, SLiC shows no sign of diminishing returns with model scale, and presents alternative ways to improve quality with limited training and inference budgets. With SLiC, we exceed or match SOTA results on a wide range of generation tasks spanning abstractive summarization, question generation, abstractive question answering and data-to-text generation, even with modest-sized models.

In this paper, we propose a variety of Long Short-Term Memory (LSTM) based models for sequence tagging. These models include LSTM networks, bidirectional LSTM (BI-LSTM) networks, LSTM with a Conditional Random Field (CRF) layer (LSTM-CRF) and bidirectional LSTM with a CRF layer (BI-LSTM-CRF). Our work is the first to apply a bidirectional LSTM CRF (denoted as BI-LSTM-CRF) model to NLP benchmark sequence tagging data sets. We show that the BI-LSTM-CRF model can efficiently use both past and future input features thanks to a bidirectional LSTM component. It can also use sentence level tag information thanks to a CRF layer. The BI-LSTM-CRF model can produce state of the art (or close to) accuracy on POS, chunking and NER data sets. In addition, it is robust and has less dependence on word embedding as compared to previous observations.

Several recent works have suggested to represent semantic relations with questions and answers, decomposing textual information into separate interrogative natural language statements. In this paper, we consider three QA-based semantic tasks - namely, QA-SRL, QANom and QADiscourse, each targeting a certain type of predication - and propose to regard them as jointly providing a comprehensive representation of textual information. To promote this goal, we investigate how to best utilize the power of sequence-to-sequence (seq2seq) pre-trained language models, within the unique setup of semi-structured outputs, consisting of an unordered set of question-answer pairs. We examine different input and output linearization strategies, and assess the effect of multitask learning and of simple data augmentation techniques in the setting of imbalanced training data. Consequently, we release the first unified QASem parsing tool, practical for downstream applications who can benefit from an explicit, QA-based account of information units in a text.

Named entity recognition (NER) suffers from the scarcity of annotated training data, especially for low-resource languages without labeled data. Cross-lingual NER has been proposed to alleviate this issue by transferring knowledge from high-resource languages to low-resource languages via aligned cross-lingual representations or machine translation results. However, the performance of cross-lingual NER methods is severely affected by the unsatisfactory quality of translation or label projection. To address these problems, we propose a Cross-lingual Entity Projection framework (CROP) to enable zero-shot cross-lingual NER with the help of a multilingual labeled sequence translation model. Specifically, the target sequence is first translated into the source language and then tagged by a source NER model. We further adopt a labeled sequence translation model to project the tagged sequence back to the target language and label the target raw sentence. Ultimately, the whole pipeline is integrated into an end-to-end model by the way of self-training. Experimental results on two benchmarks demonstrate that our method substantially outperforms the previous strong baseline by a large margin of +3~7 F1 scores and achieves state-of-the-art performance.

The extreme multi-label classification (XMC) task aims at tagging content with a subset of labels from an extremely large label set. The label vocabulary is typically defined in advance by domain experts and assumed to capture all necessary tags. However in real world scenarios this label set, although large, is often incomplete and experts frequently need to refine it. To develop systems that simplify this process, we introduce the task of open vocabulary XMC (OXMC): given a piece of content, predict a set of labels, some of which may be outside of the known tag set. Hence, in addition to not having training data for some labels - as is the case in zero-shot classification - models need to invent some labels on-the-fly. We propose GROOV, a fine-tuned seq2seq model for OXMC that generates the set of labels as a flat sequence and is trained using a novel loss independent of predicted label order. We show the efficacy of the approach, experimenting with popular XMC datasets for which GROOV is able to predict meaningful labels outside the given vocabulary while performing on par with state-of-the-art solutions for known labels.

This paper describes our study on using mutilingual BERT embeddings and some new neural models for improving sequence tagging tasks for the Vietnamese language. We propose new model architectures and evaluate them extensively on two named entity recognition datasets of VLSP 2016 and VLSP 2018, and on two part-of-speech tagging datasets of VLSP 2010 and VLSP 2013. Our proposed models outperform existing methods and achieve new state-of-the-art results. In particular, we have pushed the accuracy of part-of-speech tagging to 95.40% on the VLSP 2010 corpus, to 96.77% on the VLSP 2013 corpus; and the F1 score of named entity recognition to 94.07% on the VLSP 2016 corpus, to 90.31% on the VLSP 2018 corpus. Our code and pre-trained models viBERT and vELECTRA are released as open source to facilitate adoption and further research.

Electronic Theses and Dissertations (ETDs) contain domain knowledge that can be used for many digital library tasks, such as analyzing citation networks and predicting research trends. Automatic metadata extraction is important to build scalable digital library search engines. Most existing methods are designed for born-digital documents, so they often fail to extract metadata from scanned documents such as for ETDs. Traditional sequence tagging methods mainly rely on text-based features. In this paper, we propose a conditional random field (CRF) model that combines text-based and visual features. To verify the robustness of our model, we extended an existing corpus and created a new ground truth corpus consisting of 500 ETD cover pages with human validated metadata. Our experiments show that CRF with visual features outperformed both a heuristic and a CRF model with only text-based features. The proposed model achieved 81.3%-96% F1 measure on seven metadata fields. The data and source code are publicly available on Google Drive (https://tinyurl.com/y8kxzwrp) and a GitHub repository (https://github.com/lamps-lab/ETDMiner/tree/master/etd_crf), respectively.

In industry deep learning application, our manually labeled data has a certain number of noisy data. To solve this problem and achieve more than 90 score in dev dataset, we present a simple method to find the noisy data and re-label the noisy data by human, given the model predictions as references in human labeling. In this paper, we illustrate our idea for a broad set of deep learning tasks, includes classification, sequence tagging, object detection, sequence generation, click-through rate prediction. The dev dataset evaluation results and human evaluation results verify our idea.

Sequential recommendation aims to model dynamic user behavior from historical interactions. Existing methods rely on either explicit item IDs or general textual features for sequence modeling to understand user preferences. While promising, these approaches still struggle to model cold-start items or transfer knowledge to new datasets. In this paper, we propose to model user preferences and item features as language representations that can be generalized to new items and datasets. To this end, we present a novel framework, named Recformer, which effectively learns language representations for sequential recommendation. Specifically, we propose to formulate an item as a "sentence" (word sequence) by flattening item key-value attributes described by text so that an item sequence for a user becomes a sequence of sentences. For recommendation, Recformer is trained to understand the "sentence" sequence and retrieve the next "sentence". To encode item sequences, we design a bi-directional Transformer similar to the model Longformer but with different embedding layers for sequential recommendation. For effective representation learning, we propose novel pretraining and finetuning methods which combine language understanding and recommendation tasks. Therefore, Recformer can effectively recommend the next item based on language representations. Extensive experiments conducted on six datasets demonstrate the effectiveness of Recformer for sequential recommendation, especially in low-resource and cold-start settings.

Dense retrieval methods have demonstrated promising performance in multilingual information retrieval, where queries and documents can be in different languages. However, dense retrievers typically require a substantial amount of paired data, which poses even greater challenges in multilingual scenarios. This paper introduces UMR, an Unsupervised Multilingual dense Retriever trained without any paired data. Our approach leverages the sequence likelihood estimation capabilities of multilingual language models to acquire pseudo labels for training dense retrievers. We propose a two-stage framework which iteratively improves the performance of multilingual dense retrievers. Experimental results on two benchmark datasets show that UMR outperforms supervised baselines, showcasing the potential of training multilingual retrievers without paired data, thereby enhancing their practicality. Our source code, data, and models are publicly available at https://github.com/MiuLab/UMR

Training keyphrase generation (KPG) models require a large amount of annotated data, which can be prohibitively expensive and often limited to specific domains. In this study, we first demonstrate that large distribution shifts among different domains severely hinder the transferability of KPG models. We then propose a three-stage pipeline, which gradually guides KPG models' learning focus from general syntactical features to domain-related semantics, in a data-efficient manner. With Domain-general Phrase pre-training, we pre-train Sequence-to-Sequence models with generic phrase annotations that are widely available on the web, which enables the models to generate phrases in a wide range of domains. The resulting model is then applied in the Transfer Labeling stage to produce domain-specific pseudo keyphrases, which help adapt models to a new domain. Finally, we fine-tune the model with limited data with true labels to fully adapt it to the target domain. Our experiment results show that the proposed process can produce good-quality keyphrases in new domains and achieve consistent improvements after adaptation with limited in-domain annotated data. All code and datasets are available at https://github.com/memray/OpenNMT-kpg-release.

Protein modeling is an increasingly popular area of machine learning research. Semi-supervised learning has emerged as an important paradigm in protein modeling due to the high cost of acquiring supervised protein labels, but the current literature is fragmented when it comes to datasets and standardized evaluation techniques. To facilitate progress in this field, we introduce the Tasks Assessing Protein Embeddings (TAPE), a set of five biologically relevant semi-supervised learning tasks spread across different domains of protein biology. We curate tasks into specific training, validation, and test splits to ensure that each task tests biologically relevant generalization that transfers to real-life scenarios. We benchmark a range of approaches to semi-supervised protein representation learning, which span recent work as well as canonical sequence learning techniques. We find that self-supervised pretraining is helpful for almost all models on all tasks, more than doubling performance in some cases. Despite this increase, in several cases features learned by self-supervised pretraining still lag behind features extracted by state-of-the-art non-neural techniques. This gap in performance suggests a huge opportunity for innovative architecture design and improved modeling paradigms that better capture the signal in biological sequences. TAPE will help the machine learning community focus effort on scientifically relevant problems. Toward this end, all data and code used to run these experiments are available at https://github.com/songlab-cal/tape.

Recent research on sequence labelling has been exploring different strategies to mitigate the lack of manually annotated data for the large majority of the world languages. Among others, the most successful approaches have been based on (i) the cross-lingual transfer capabilities of multilingual pre-trained language models (model-transfer), (ii) data translation and label projection (data-transfer) and (iii), prompt-based learning by reusing the mask objective to exploit the few-shot capabilities of pre-trained language models (few-shot). Previous work seems to conclude that model-transfer outperforms data-transfer methods and that few-shot techniques based on prompting are superior to updating the model's weights via fine-tuning. In this paper, we empirically demonstrate that, for Argument Mining, a sequence labelling task which requires the detection of long and complex discourse structures, previous insights on cross-lingual transfer or few-shot learning do not apply. Contrary to previous work, we show that for Argument Mining data transfer obtains better results than model-transfer and that fine-tuning outperforms few-shot methods. Regarding the former, the domain of the dataset used for data-transfer seems to be a deciding factor, while, for few-shot, the type of task (length and complexity of the sequence spans) and sampling method prove to be crucial.

We present a neural transducer model with visual attention that learns to generate LaTeX markup of a real-world math formula given its image. Applying sequence modeling and transduction techniques that have been very successful across modalities such as natural language, image, handwriting, speech and audio; we construct an image-to-markup model that learns to produce syntactically and semantically correct LaTeX markup code over 150 words long and achieves a BLEU score of 89%; improving upon the previous state-of-art for the Im2Latex problem. We also demonstrate with heat-map visualization how attention helps in interpreting the model and can pinpoint (detect and localize) symbols on the image accurately despite having been trained without any bounding box data.

In recent years, large language models (LLMs) have achieved state-of-the-art results in various biological sequence analysis tasks, such as sequence classification, structure prediction, and function prediction. Similar to advancements in AI for other scientific fields, deeper research into biological LLMs has begun to focus on using these models to rediscover important existing biological laws or uncover entirely new patterns in biological sequences.This study leverages GPT-like LLMs to utilize language transfer capabilities to rediscover the genetic code rules of the central dogma. In our experimental design, we transformed the central dogma into a binary classification problem of aligning DNA sequences with protein sequences, where positive examples are matching DNA and protein sequences, and negative examples are non-matching pairs.We first trained a GPT-2 model from scratch using a dataset comprising protein sequences, DNA sequences, and sequences from languages such as English and Chinese. Subsequently, we fine-tuned the model using the English similarity judgment dataset from PAWS-X. When tested on a dataset for DNA and protein sequence alignment judgment, the fine-tuned model achieved a classification accuracy of 76%. The study also analyzed factors contributing to this zero-shot capability, including model training stability and types of training data.This research demonstrates that LLMs can, through the transfer of natural language capabilities and solely relying on the analysis of sequences themselves, rediscover the central dogma without prior knowledge of it. This study opens a new door for AI-driven biological research.

Breakthroughs in deep learning and memory networks have made major advances in natural language understanding. Language is sequential and information carried through the sequence can be captured through memory networks. Learning the sequence is one of the key aspects in learning the language. However, memory networks are not capable of holding infinitely long sequences in their memories and are limited by various constraints such as the vanishing or exploding gradient problem. Therefore, natural language understanding models are affected when presented with long sequential text. We introduce Long Term Memory network (LTM) to learn from infinitely long sequences. LTM gives priority to the current inputs to allow it to have a high impact. Language modeling is an important factor in natural language understanding. LTM was tested in language modeling, which requires long term memory. LTM is tested on Penn Tree bank dataset, Google Billion Word dataset and WikiText-2 dataset. We compare LTM with other language models which require long term memory.

Modern sequence models (e.g., Transformers, linear RNNs, etc.) emerged as dominant backbones of recent deep learning frameworks, mainly due to their efficiency, representational power, and/or ability to capture long-range dependencies. Adopting these sequence models for graph-structured data has recently gained popularity as the alternative to Message Passing Neural Networks (MPNNs). There is, however, a lack of a common foundation about what constitutes a good graph sequence model, and a mathematical description of the benefits and deficiencies in adopting different sequence models for learning on graphs. To this end, we first present Graph Sequence Model (GSM), a unifying framework for adopting sequence models for graphs, consisting of three main steps: (1) Tokenization, which translates the graph into a set of sequences; (2) Local Encoding, which encodes local neighborhoods around each node; and (3) Global Encoding, which employs a scalable sequence model to capture long-range dependencies within the sequences. This framework allows us to understand, evaluate, and compare the power of different sequence model backbones in graph tasks. Our theoretical evaluations of the representation power of Transformers and modern recurrent models through the lens of global and local graph tasks show that there are both negative and positive sides for both types of models. Building on this observation, we present GSM++, a fast hybrid model that uses the Hierarchical Affinity Clustering (HAC) algorithm to tokenize the graph into hierarchical sequences, and then employs a hybrid architecture of Transformer to encode these sequences. Our theoretical and experimental results support the design of GSM++, showing that GSM++ outperforms baselines in most benchmark evaluations.

This project aims to investigate a novel sequence generation method inspired by the AlphaGo paradigm, adapting it for use with large language models (LLMs). The proposed approach involves creating search trees of different possible completions and evaluating these completions based on model confidence. By considering various paths in the search tree and scoring them according to the model's confidence in each completion, we can generate diverse and high-quality sequences. This research explores the implementation of this paradigm by using confidence as a proxy for response quality akin to beam search vijayakumar2016diverse. The primary goal of this paper is to outline the paradigm and demonstrate its potential, rather than focusing on achieving perfect results. The paper will outline the reasons why we believe this paradigm has the potential to improve LLMs in the following manners: 1) increase output quality, 2) decrease errors, 3) eliminate or reduce the compound error problems, 4) generate diverse and creative completions, 5) allow for iterative problem-solving, and 6) self-training. We expect this approach to yield a set of diverse and coherent sequences, offering insights into balancing exploration and exploitation in sequence generation. Potential applications include creative text generation tasks, such as storytelling and content creation, as well as other natural language processing domains, like machine translation and automated summarization. The goal is that the model will be far more effective as it will be able to consider many possible variations allowing it to find the ideal completion. This research aims to contribute to the understanding of effective search strategies in sequence generation and their impact on generating high-quality, varied textual outputs.

Recently, sequence-to-sequence (seq2seq) models with the Transformer architecture have achieved remarkable performance on various conditional text generation tasks, such as machine translation. However, most of them are trained with teacher forcing with the ground truth label given at each time step, without being exposed to incorrectly generated tokens during training, which hurts its generalization to unseen inputs, that is known as the "exposure bias" problem. In this work, we propose to mitigate the conditional text generation problem by contrasting positive pairs with negative pairs, such that the model is exposed to various valid or incorrect perturbations of the inputs, for improved generalization. However, training the model with naive contrastive learning framework using random non-target sequences as negative examples is suboptimal, since they are easily distinguishable from the correct output, especially so with models pretrained with large text corpora. Also, generating positive examples requires domain-specific augmentation heuristics which may not generalize over diverse domains. To tackle this problem, we propose a principled method to generate positive and negative samples for contrastive learning of seq2seq models. Specifically, we generate negative examples by adding small perturbations to the input sequence to minimize its conditional likelihood, and positive examples by adding large perturbations while enforcing it to have a high conditional likelihood. Such "hard" positive and negative pairs generated using our method guides the model to better distinguish correct outputs from incorrect ones. We empirically show that our proposed method significantly improves the generalization of the seq2seq on three text generation tasks - machine translation, text summarization, and question generation.

We present an elegant and effective approach for addressing limitations in existing multi-label classification models by incorporating interaction matching, a concept shown to be useful for ad-hoc search result ranking. By performing soft n-gram interaction matching, we match labels with natural language descriptions (which are common to have in most multi-labeling tasks). Our approach can be used to enhance existing multi-label classification approaches, which are biased toward frequently-occurring labels. We evaluate our approach on two challenging tasks: automatic medical coding of clinical notes and automatic labeling of entities from software tutorial text. Our results show that our method can yield up to an 11% relative improvement in macro performance, with most of the gains stemming labels that appear infrequently in the training set (i.e., the long tail of labels).

We present a self-supervised learning framework, COCO-LM, that pretrains Language Models by COrrecting and COntrasting corrupted text sequences. Following ELECTRA-style pretraining, COCO-LM employs an auxiliary language model to corrupt text sequences, upon which it constructs two new tasks for pretraining the main model. The first token-level task, Corrective Language Modeling, is to detect and correct tokens replaced by the auxiliary model, in order to better capture token-level semantics. The second sequence-level task, Sequence Contrastive Learning, is to align text sequences originated from the same source input while ensuring uniformity in the representation space. Experiments on GLUE and SQuAD demonstrate that COCO-LM not only outperforms recent state-of-the-art pretrained models in accuracy, but also improves pretraining efficiency. It achieves the MNLI accuracy of ELECTRA with 50% of its pretraining GPU hours. With the same pretraining steps of standard base/large-sized models, COCO-LM outperforms the previous best models by 1+ GLUE average points.

Textual label names (descriptions) are typically semantically rich in many natural language understanding (NLU) tasks. In this paper, we incorporate the prompting methodology, which is widely used to enrich model input, into the label side for the first time. Specifically, we propose a Mask Matching method, which equips an input with a prompt and its label with another, and then makes predictions by matching their mask representations. We evaluate our method extensively on 8 NLU tasks with 14 datasets. The experimental results show that Mask Matching significantly outperforms its counterparts of fine-tuning and conventional prompt-tuning, setting up state-of-the-art performances in several datasets. Mask Matching is particularly good at handling NLU tasks with large label counts and informative label names. As pioneering efforts that investigate the label-side prompt, we also discuss open issues for future study.

Neural sequence models are widely used to model time-series data. Equally ubiquitous is the usage of beam search (BS) as an approximate inference algorithm to decode output sequences from these models. BS explores the search space in a greedy left-right fashion retaining only the top-B candidates - resulting in sequences that differ only slightly from each other. Producing lists of nearly identical sequences is not only computationally wasteful but also typically fails to capture the inherent ambiguity of complex AI tasks. To overcome this problem, we propose Diverse Beam Search (DBS), an alternative to BS that decodes a list of diverse outputs by optimizing for a diversity-augmented objective. We observe that our method finds better top-1 solutions by controlling for the exploration and exploitation of the search space - implying that DBS is a better search algorithm. Moreover, these gains are achieved with minimal computational or memory over- head as compared to beam search. To demonstrate the broad applicability of our method, we present results on image captioning, machine translation and visual question generation using both standard quantitative metrics and qualitative human studies. Further, we study the role of diversity for image-grounded language generation tasks as the complexity of the image changes. We observe that our method consistently outperforms BS and previously proposed techniques for diverse decoding from neural sequence models.

Building a general-purpose task model similar to ChatGPT has been an important research direction for gene large language models. Instruction fine-tuning is a key component in building ChatGPT, but existing instructions are primarily based on natural language. Natural language and gene sequences have significant differences in tokenization and encoding. Therefore, constructing a multilingual model that can handle both natural language and gene sequences is crucial for solving this problem.In this paper, we expand the capabilities of the LLaMA large language model to include gene language. This involves expanding the vocabulary using the Byte Pair Encoding (BPE) method, specifically tailored for DNA and protein sequences, and conducting further pre-training on these sequences. We then convert various downstream gene task data into a unified format for instruction fine-tuning and further fine-tune the model on this data.Our study demonstrates that a mixed model of gene and natural language, fine-tuned with instructions, achieves results comparable to the current state-of-the-art (SOTA) in tasks such as gene classification and gene sequence interaction. This provides a promising direction for building a unified large language model for gene tasks.

Set-of-Mark (SoM) Prompting unleashes the visual grounding capability of GPT-4V, by enabling the model to associate visual objects with tags inserted on the image. These tags, marked with alphanumerics, can be indexed via text tokens for easy reference. Despite the extraordinary performance from GPT-4V, we observe that other Multimodal Large Language Models (MLLMs) struggle to understand these visual tags. To promote the learning of SoM prompting for open-source models, we propose a new learning paradigm: "list items one by one," which asks the model to enumerate and describe all visual tags placed on the image following the alphanumeric orders of tags. By integrating our curated dataset with other visual instruction tuning datasets, we are able to equip existing MLLMs with the SoM prompting ability. Furthermore, we evaluate our finetuned SoM models on five MLLM benchmarks. We find that this new dataset, even in a relatively small size (10k-30k images with tags), significantly enhances visual reasoning capabilities and reduces hallucinations for MLLMs. Perhaps surprisingly, these improvements persist even when the visual tags are omitted from input images during inference. This suggests the potential of "list items one by one" as a new paradigm for training MLLMs, which strengthens the object-text alignment through the use of visual tags in the training stage. Finally, we conduct analyses by probing trained models to understand the working mechanism of SoM. Our code and data are available at https://github.com/zzxslp/SoM-LLaVA.

Pre-trained LLMs have demonstrated substantial capabilities across a range of conventional natural language processing (NLP) tasks, such as summarization and entity recognition. In this paper, we explore the application of LLMs in the generation of high-quality protein sequences. Specifically, we adopt a suite of pre-trained LLMs, including Mistral-7B1, Llama-2-7B2, Llama-3-8B3, and gemma-7B4, to produce valid protein sequences. All of these models are publicly available.5 Unlike previous work in this field, our approach utilizes a relatively small dataset comprising 42,000 distinct human protein sequences. We retrain these models to process protein-related data, ensuring the generation of biologically feasible protein structures. Our findings demonstrate that even with limited data, the adapted models exhibit efficiency comparable to established protein-focused models such as ProGen varieties, ProtGPT2, and ProLLaMA, which were trained on millions of protein sequences. To validate and quantify the performance of our models, we conduct comparative analyses employing standard metrics such as pLDDT, RMSD, TM-score, and REU. Furthermore, we commit to making the trained versions of all four models publicly available, fostering greater transparency and collaboration in the field of computational biology.

Given an input sequence (or prefix), modern language models often assign high probabilities to output sequences that are repetitive, incoherent, or irrelevant to the prefix; as such, model-generated text also contains such artifacts. To address these issues we present RankGen, a 1.2B parameter encoder model for English that scores model generations given a prefix. RankGen can be flexibly incorporated as a scoring function in beam search and used to decode from any pretrained language model. We train RankGen using large-scale contrastive learning to map a prefix close to the ground-truth sequence that follows it and far away from two types of negatives: (1) random sequences from the same document as the prefix, and (2) sequences generated from a large language model conditioned on the prefix. Experiments across four different language models (345M-11B parameters) and two domains show that RankGen significantly outperforms decoding algorithms like nucleus, top-k, and typical sampling, as well as contrastive decoding and search, on both automatic metrics (85.0 vs 77.3 MAUVE over nucleus) as well as human evaluations with English writers (74.5% human preference over nucleus sampling). Analysis reveals that RankGen outputs are more relevant to the prefix and improve continuity and coherence compared to baselines. We release our model checkpoints, code, and human preference data with explanations to facilitate future research.

Weak supervision (WS) frameworks are a popular way to bypass hand-labeling large datasets for training data-hungry models. These approaches synthesize multiple noisy but cheaply-acquired estimates of labels into a set of high-quality pseudolabels for downstream training. However, the synthesis technique is specific to a particular kind of label, such as binary labels or sequences, and each new label type requires manually designing a new synthesis algorithm. Instead, we propose a universal technique that enables weak supervision over any label type while still offering desirable properties, including practical flexibility, computational efficiency, and theoretical guarantees. We apply this technique to important problems previously not tackled by WS frameworks including learning to rank, regression, and learning in hyperbolic space. Theoretically, our synthesis approach produces a consistent estimators for learning some challenging but important generalizations of the exponential family model. Experimentally, we validate our framework and show improvement over baselines in diverse settings including real-world learning-to-rank and regression problems along with learning on hyperbolic manifolds.

Effective training of today's large language models (LLMs) depends on large batches and long sequences for throughput and accuracy. To handle variable-length sequences on hardware accelerators, it is common practice to introduce padding tokens, so that all sequences in a batch have the same length. We show in this paper that the variation in sequence lengths in common NLP datasets is such that up to 50% of all tokens can be padding. In less common, but not extreme, cases (e.g. GLUE-cola with sequence length 128), the ratio is up to 89%. Existing methods to address the resulting inefficiency are complicated by the need to avoid cross-contamination in self-attention, by a reduction in accuracy when sequence ordering information is lost, or by customized kernel implementations only valid for specific accelerators. This paper introduces a new formalization of sequence packing in the context of the well-studied bin packing problem, and presents new algorithms based on this formulation which, for example, confer a 2x speedup for phase 2 pre-training in BERT. We show how existing models can be adapted to ensure mathematical equivalence between the original and packed models, meaning that packed models can be trained with existing pre-training and fine-tuning practices.

Large-scale datasets are essential to modern day deep learning. Advocates argue that understanding these methods requires dataset transparency (e.g. "dataset curation, motivation, composition, collection process, etc..."). However, almost no one has suggested the release of the detailed definitions and visual category examples provided to annotators - information critical to understanding the structure of the annotations present in each dataset. These labels are at the heart of public datasets, yet few datasets include the instructions that were used to generate them. We introduce a new task, Labeling Instruction Generation, to address missing publicly available labeling instructions. In Labeling Instruction Generation, we take a reasonably annotated dataset and: 1) generate a set of examples that are visually representative of each category in the dataset; 2) provide a text label that corresponds to each of the examples. We introduce a framework that requires no model training to solve this task and includes a newly created rapid retrieval system that leverages a large, pre-trained vision and language model. This framework acts as a proxy to human annotators that can help to both generate a final labeling instruction set and evaluate its quality. Our framework generates multiple diverse visual and text representations of dataset categories. The optimized instruction set outperforms our strongest baseline across 5 folds by 7.06 mAP for NuImages and 12.9 mAP for COCO.

In this paper we address the challenge of extracting scientific references from patents. We approach the problem as a sequence labelling task and investigate the merits of BERT models to the extraction of these long sequences. References in patents to scientific literature are relevant to study the connection between science and industry. Most prior work only uses the front-page citations for this analysis, which are provided in the metadata of patent archives. In this paper we build on prior work using Conditional Random Fields (CRF) and Flair for reference extraction. We improve the quality of the training data and train three BERT-based models on the labelled data (BERT, bioBERT, sciBERT). We find that the improved training data leads to a large improvement in the quality of the trained models. In addition, the BERT models beat CRF and Flair, with recall scores around 97% obtained with cross validation. With the best model we label a large collection of 33 thousand patents, extract the citations, and match them to publications in the Web of Science database. We extract 50% more references than with the old training data and methods: 735 thousand references in total. With these patent-publication links, follow-up research will further analyze which types of scientific work lead to inventions.

Pre-trained Programming Language Models (PPLMs) achieved many recent states of the art results for many code-related software engineering tasks. Though some studies use data flow or propose tree-based models that utilize Abstract Syntax Tree (AST), most PPLMs do not fully utilize the rich syntactical information in source code. Still, the input is considered a sequence of tokens. There are two issues; the first is computational inefficiency due to the quadratic relationship between input length and attention complexity. Second, any syntactical information, when needed as an extra input to the current PPLMs, requires the model to be pre-trained from scratch, wasting all the computational resources already used for pre-training the current models. In this work, we propose Named Entity Recognition (NER) adapters, lightweight modules that can be inserted into Transformer blocks to learn type information extracted from the AST. These adapters can be used with current PPLMs such as CodeBERT, GraphCodeBERT, and CodeT5. We train the NER adapters using a novel Token Type Classification objective function (TTC). We insert our proposed work in CodeBERT, building CodeBERTER, and evaluate the performance on two tasks of code refinement and code summarization. CodeBERTER improves the accuracy of code refinement from 16.4 to 17.8 while using 20% of training parameter budget compared to the fully fine-tuning approach, and the BLEU score of code summarization from 14.75 to 15.90 while reducing 77% of training parameters compared to the fully fine-tuning approach.

Recently, substantial progress has been made in text ranking based on pretrained language models such as BERT. However, there are limited studies on how to leverage more powerful sequence-to-sequence models such as T5. Existing attempts usually formulate text ranking as classification and rely on postprocessing to obtain a ranked list. In this paper, we propose RankT5 and study two T5-based ranking model structures, an encoder-decoder and an encoder-only one, so that they not only can directly output ranking scores for each query-document pair, but also can be fine-tuned with "pairwise" or "listwise" ranking losses to optimize ranking performances. Our experiments show that the proposed models with ranking losses can achieve substantial ranking performance gains on different public text ranking data sets. Moreover, when fine-tuned with listwise ranking losses, the ranking model appears to have better zero-shot ranking performance on out-of-domain data sets compared to the model fine-tuned with classification losses.

Generative pre-trained Transformer (GPT) has demonstrates its great success in natural language processing and related techniques have been adapted into molecular modeling. Considering that text is the most important record for scientific discovery, in this paper, we propose MolXPT, a unified language model of text and molecules pre-trained on SMILES (a sequence representation of molecules) wrapped by text. Briefly, we detect the molecule names in each sequence and replace them to the corresponding SMILES. In this way, the SMILES could leverage the information from surrounding text, and vice versa. The above wrapped sequences, text sequences from PubMed and SMILES sequences from PubChem are all fed into a language model for pre-training. Experimental results demonstrate that MolXPT outperforms strong baselines of molecular property prediction on MoleculeNet, performs comparably to the best model in text-molecule translation while using less than half of its parameters, and enables zero-shot molecular generation without finetuning.

Neural sequence-to-sequence models provide a competitive approach to the task of mapping a question in natural language to an SQL query, also referred to as text-to-SQL generation. The Byte-Pair Encoding algorithm (BPE) has previously been used to improve machine translation (MT) between natural languages. In this work, we adapt BPE for text-to-SQL generation. As the datasets for this task are rather small compared to MT, we present a novel stopping criterion that prevents overfitting the BPE encoding to the training set. Additionally, we present AST BPE, which is a version of BPE that uses the Abstract Syntax Tree (AST) of the SQL statement to guide BPE merges and therefore produce BPE encodings that generalize better. We improved the accuracy of a strong attentive seq2seq baseline on five out of six English text-to-SQL tasks while reducing training time by more than 50% on four of them due to the shortened targets. Finally, on two of these tasks we exceeded previously reported accuracies.

This thesis provides methods and analysis of models which make progress on this goal. The techniques outlined are task agnostic, and should provide benefit when used with nearly any transformer LM. We introduce two new finetuning methods which add new capabilities to the models they are used on. The first adds a recurrence mechanism, which removes the fixed-window sized constraint and improves the efficiency of a transformer decoder. The second allows masked language models (MLMs) to be used for initialization of both the encoder and decoder of a non-autoregressive sequence-to-sequence transformer, opening up generative applications of models which were previously only used for natural language understanding tasks. We also introduce two new techniques for improving the quality of predictions of any transformer decoder without additional finetuning. One, hidden state optimization, can be applied to any transformer decoder to improve the quality of predictions at inference time, especially for few-shot classification. The other, conditional beam search, allows practitioners to search for natural language generation (NLG) model outputs with high likelihood while conditioning on the event that the output is not degenerate (e.g. empty, repetitive, etc.). Finally, we provide theoretical and empirical insights on the divergence of model-likelihood and output quality which has widely been observed in prior work. These insights apply to any model which represents a distribution over text, and apply to language models which are not transformers or even autoregressive. We argue that the NLP community has, to some extent, misunderstood the implications of these findings, and encourage a point of view which has more nuance.

Recent years have seen a paradigm shift in NLP towards using pretrained language models ({PLM}) for a wide range of tasks. However, there are many difficult design decisions to represent structures (e.g. tagged text, coreference chains) in a way such that they can be captured by PLMs. Prior work on structured prediction with PLMs typically flattens the structured output into a sequence, which limits the quality of structural information being learned and leads to inferior performance compared to classic discriminative models. In this work, we describe an approach to model structures as sequences of actions in an autoregressive manner with PLMs, allowing in-structure dependencies to be learned without any loss. Our approach achieves the new state-of-the-art on all the structured prediction tasks we looked at, namely, named entity recognition, end-to-end relation extraction, and coreference resolution.

The rapid expansion of genomic sequence data calls for new methods to achieve robust sequence representations. Existing techniques often neglect intricate structural details, emphasizing mainly contextual information. To address this, we developed k-mer embeddings that merge contextual and structural string information by enhancing De Bruijn graphs with structural similarity connections. Subsequently, we crafted a self-supervised method based on Contrastive Learning that employs a heterogeneous Graph Convolutional Network encoder and constructs positive pairs based on node similarities. Our embeddings consistently outperform prior techniques for Edit Distance Approximation and Closest String Retrieval tasks.

Recent large-scale neural autoregressive sequence models have shown impressive performances on a variety of natural language generation tasks. However, their generated sequences often exhibit degenerate properties such as non-termination, undesirable repetition, and premature termination, when generated with decoding algorithms such as greedy search, beam search, top-k sampling, and nucleus sampling. In this paper, we focus on the problem of non-terminating sequences resulting from an incomplete decoding algorithm. We first define an incomplete probable decoding algorithm which includes greedy search, top-k sampling, and nucleus sampling, beyond the incomplete decoding algorithm originally put forward by Welleck et al. (2020). We then propose a non-monotonic self-terminating language model, which significantly relaxes the constraint of monotonically increasing termination probability in the originally proposed self-terminating language model by Welleck et al. (2020), to address the issue of non-terminating sequences when using incomplete probable decoding algorithms. We prove that our proposed model prevents non-terminating sequences when using not only incomplete probable decoding algorithms but also beam search. We empirically validate our model on sequence completion tasks with various architectures.

Intelligently extracting and linking complex scientific information from unstructured text is a challenging endeavor particularly for those inexperienced with natural language processing. Here, we present a simple sequence-to-sequence approach to joint named entity recognition and relation extraction for complex hierarchical information in scientific text. The approach leverages a pre-trained large language model (LLM), GPT-3, that is fine-tuned on approximately 500 pairs of prompts (inputs) and completions (outputs). Information is extracted either from single sentences or across sentences in abstracts/passages, and the output can be returned as simple English sentences or a more structured format, such as a list of JSON objects. We demonstrate that LLMs trained in this way are capable of accurately extracting useful records of complex scientific knowledge for three representative tasks in materials chemistry: linking dopants with their host materials, cataloging metal-organic frameworks, and general chemistry/phase/morphology/application information extraction. This approach represents a simple, accessible, and highly-flexible route to obtaining large databases of structured knowledge extracted from unstructured text. An online demo is available at http://www.matscholar.com/info-extraction.

Annotated data has become the most important bottleneck in training accurate machine learning models, especially for areas that require domain expertise. A recent approach to deal with the above issue proposes using natural language explanations instead of labeling individual data points, thereby increasing human annotators' efficiency as well as decreasing costs substantially. This paper focuses on the task of turning these natural language descriptions into Python labeling functions by following a novel approach to semantic parsing with pre-trained text-to-text Transformers. In a series of experiments our approach achieves a new state of the art on the semantic parsing benchmark CoNaLa, surpassing the previous best approach by 3.7 BLEU points. Furthermore, on a manually constructed dataset of natural language descriptions-labeling functions pairs we achieve a BLEU of 0.39. Our approach can be regarded as a stepping stone towards models that are taught how to label in natural language, instead of being provided specific labeled samples. Our code, constructed dataset and models are available at https://github.com/ypapanik/t5-for-code-generation.

Large Language Models (LLMs), including GPT-x and LLaMA2, have achieved remarkable performance in multiple Natural Language Processing (NLP) tasks. Under the premise that protein sequences constitute the protein language, Protein Large Language Models (ProLLMs) trained on protein corpora excel at de novo protein sequence generation. However, as of now, unlike LLMs in NLP, no ProLLM is capable of multiple tasks in the Protein Language Processing (PLP) field. This prompts us to delineate the inherent limitations in current ProLLMs: (i) the lack of natural language capabilities, (ii) insufficient instruction understanding, and (iii) high training resource demands. To address these challenges, we introduce a training framework to transform any general LLM into a ProLLM capable of handling multiple PLP tasks. Specifically, our framework utilizes low-rank adaptation and employs a two-stage training approach, and it is distinguished by its universality, low overhead, and scalability. Through training under this framework, we propose the ProLLaMA model, the first known ProLLM to handle multiple PLP tasks simultaneously. Experiments show that ProLLaMA achieves state-of-the-art results in the unconditional protein sequence generation task. In the controllable protein sequence generation task, ProLLaMA can design novel proteins with desired functionalities. In the protein property prediction task, ProLLaMA achieves nearly 100\% accuracy across many categories. The latter two tasks are beyond the reach of other ProLLMs. Code is available at https://github.com/Lyu6PosHao/ProLLaMA.

When applying automated speech recognition (ASR) for Belgian Dutch (Van Dyck et al. 2021), the output consists of an unsegmented stream of words, without any punctuation. A next step is to perform segmentation and insert punctuation, making the ASR output more readable and easy to manually correct. As far as we know there is no publicly available punctuation insertion system for Dutch that functions at a usable level. The model we present here is an extension of the models of Guhr et al. (2021) for Dutch and is made publicly available. We trained a sequence classification model, based on the Dutch language model RobBERT (Delobelle et al. 2020). For every word in the input sequence, the models predicts a punctuation marker that follows the word. We have also extended a multilingual model, for cases where the language is unknown or where code switching applies. When performing the task of segmentation, the application of the best models onto out of domain test data, a sliding window of 200 words of the ASR output stream is sent to the classifier, and segmentation is applied when the system predicts a segmenting punctuation sign with a ratio above threshold. Results show to be much better than a machine translation baseline approach.

Recently, the usefulness of self-supervised representation learning (SSRL) methods has been confirmed in various downstream tasks. Many of these models, as exemplified by HuBERT and WavLM, use pseudo-labels generated from spectral features or the model's own representation features. From previous studies, it is known that the pseudo-labels contain semantic information. However, the masked prediction task, the learning criterion of HuBERT, focuses on local contextual information and may not make effective use of global semantic information such as speaker, theme of speech, and so on. In this paper, we propose a new approach to enrich the semantic representation of HuBERT. We apply topic model to pseudo-labels to generate a topic label for each utterance. An auxiliary topic classification task is added to HuBERT by using topic labels as teachers. This allows additional global semantic information to be incorporated in an unsupervised manner. Experimental results demonstrate that our method achieves comparable or better performance than the baseline in most tasks, including automatic speech recognition and five out of the eight SUPERB tasks. Moreover, we find that topic labels include various information about utterance, such as gender, speaker, and its theme. This highlights the effectiveness of our approach in capturing multifaceted semantic nuances.

Patent examiners need to solve a complex information retrieval task when they assess the novelty and inventive step of claims made in a patent application. Given a claim, they search for prior art, which comprises all relevant publicly available information. This time-consuming task requires a deep understanding of the respective technical domain and the patent-domain-specific language. For these reasons, we address the computer-assisted search for prior art by creating a training dataset for supervised machine learning called PatentMatch. It contains pairs of claims from patent applications and semantically corresponding text passages of different degrees from cited patent documents. Each pair has been labeled by technically-skilled patent examiners from the European Patent Office. Accordingly, the label indicates the degree of semantic correspondence (matching), i.e., whether the text passage is prejudicial to the novelty of the claimed invention or not. Preliminary experiments using a baseline system show that PatentMatch can indeed be used for training a binary text pair classifier on this challenging information retrieval task. The dataset is available online: https://hpi.de/naumann/s/patentmatch.

Do state-of-the-art natural language understanding models care about word order - one of the most important characteristics of a sequence? Not always! We found 75% to 90% of the correct predictions of BERT-based classifiers, trained on many GLUE tasks, remain constant after input words are randomly shuffled. Despite BERT embeddings are famously contextual, the contribution of each individual word to downstream tasks is almost unchanged even after the word's context is shuffled. BERT-based models are able to exploit superficial cues (e.g. the sentiment of keywords in sentiment analysis; or the word-wise similarity between sequence-pair inputs in natural language inference) to make correct decisions when tokens are arranged in random orders. Encouraging classifiers to capture word order information improves the performance on most GLUE tasks, SQuAD 2.0 and out-of-samples. Our work suggests that many GLUE tasks are not challenging machines to understand the meaning of a sentence.

In-context learning is a recent paradigm in natural language understanding, where a large pre-trained language model (LM) observes a test instance and a few training examples as its input, and directly decodes the output without any update to its parameters. However, performance has been shown to strongly depend on the selected training examples (termed prompt). In this work, we propose an efficient method for retrieving prompts for in-context learning using annotated data and a LM. Given an input-output pair, we estimate the probability of the output given the input and a candidate training example as the prompt, and label training examples as positive or negative based on this probability. We then train an efficient dense retriever from this data, which is used to retrieve training examples as prompts at test time. We evaluate our approach on three sequence-to-sequence tasks where language utterances are mapped to meaning representations, and find that it substantially outperforms prior work and multiple baselines across the board.

Deep Neural Networks (DNNs) are powerful models that have achieved excellent performance on difficult learning tasks. Although DNNs work well whenever large labeled training sets are available, they cannot be used to map sequences to sequences. In this paper, we present a general end-to-end approach to sequence learning that makes minimal assumptions on the sequence structure. Our method uses a multilayered Long Short-Term Memory (LSTM) to map the input sequence to a vector of a fixed dimensionality, and then another deep LSTM to decode the target sequence from the vector. Our main result is that on an English to French translation task from the WMT'14 dataset, the translations produced by the LSTM achieve a BLEU score of 34.8 on the entire test set, where the LSTM's BLEU score was penalized on out-of-vocabulary words. Additionally, the LSTM did not have difficulty on long sentences. For comparison, a phrase-based SMT system achieves a BLEU score of 33.3 on the same dataset. When we used the LSTM to rerank the 1000 hypotheses produced by the aforementioned SMT system, its BLEU score increases to 36.5, which is close to the previous best result on this task. The LSTM also learned sensible phrase and sentence representations that are sensitive to word order and are relatively invariant to the active and the passive voice. Finally, we found that reversing the order of the words in all source sentences (but not target sentences) improved the LSTM's performance markedly, because doing so introduced many short term dependencies between the source and the target sentence which made the optimization problem easier.

The integration of molecule and language has garnered increasing attention in molecular science. Recent advancements in Language Models (LMs) have demonstrated potential for the comprehensive modeling of molecule and language. However, existing works exhibit notable limitations. Most existing works overlook the modeling of 3D information, which is crucial for understanding molecular structures and also functions. While some attempts have been made to leverage external structure encoding modules to inject the 3D molecular information into LMs, there exist obvious difficulties that hinder the integration of molecular structure and language text, such as modality alignment and separate tuning. To bridge this gap, we propose 3D-MolT5, a unified framework designed to model both 1D molecular sequence and 3D molecular structure. The key innovation lies in our methodology for mapping fine-grained 3D substructure representations (based on 3D molecular fingerprints) to a specialized 3D token vocabulary for 3D-MolT5. This 3D structure token vocabulary enables the seamless combination of 1D sequence and 3D structure representations in a tokenized format, allowing 3D-MolT5 to encode molecular sequence (SELFIES), molecular structure, and text sequences within a unified architecture. Alongside, we further introduce 1D and 3D joint pre-training to enhance the model's comprehension of these diverse modalities in a joint representation space and better generalize to various tasks for our foundation model. Through instruction tuning on multiple downstream datasets, our proposed 3D-MolT5 shows superior performance than existing methods in molecular property prediction, molecule captioning, and text-based molecule generation tasks. Our code will be available on GitHub soon.

Despite the effectiveness of recurrent neural network language models, their maximum likelihood estimation suffers from two limitations. It treats all sentences that do not match the ground truth as equally poor, ignoring the structure of the output space. Second, it suffers from "exposure bias": during training tokens are predicted given ground-truth sequences, while at test time prediction is conditioned on generated output sequences. To overcome these limitations we build upon the recent reward augmented maximum likelihood approach \ie sequence-level smoothing that encourages the model to predict sentences close to the ground truth according to a given performance metric. We extend this approach to token-level loss smoothing, and propose improvements to the sequence-level smoothing approach. Our experiments on two different tasks, image captioning and machine translation, show that token-level and sequence-level loss smoothing are complementary, and significantly improve results.

The complex nature of big biological systems pushed some scientists to classify its understanding under the inconceivable missions. Different leveled challenges complicated this task, one of is the prediction of a protein's function. In recent years, significant progress has been made in this field through the development of various machine learning approaches. However, most existing methods formulate the task as a multi-classification problem, i.e assigning predefined labels to proteins. In this work, we propose a novel approach, Prot2Text, which predicts a protein function's in a free text style, moving beyond the conventional binary or categorical classifications. By combining Graph Neural Networks(GNNs) and Large Language Models(LLMs), in an encoder-decoder framework, our model effectively integrates diverse data types including proteins' sequences, structures, and textual annotations. This multimodal approach allows for a holistic representation of proteins' functions, enabling the generation of detailed and accurate descriptions. To evaluate our model, we extracted a multimodal protein dataset from SwissProt, and demonstrate empirically the effectiveness of Prot2Text. These results highlight the transformative impact of multimodal models, specifically the fusion of GNNs and LLMs, empowering researchers with powerful tools for more accurate prediction of proteins' functions. The code, the models and a demo will be publicly released.

Large language models (LLMs) have shown impressive ability for open-domain NLP tasks. However, LLMs are sometimes too footloose for natural language understanding (NLU) tasks which always have restricted output and input format. Their performances on NLU tasks are highly related to prompts or demonstrations and are shown to be poor at performing several representative NLU tasks, such as event extraction and entity typing. To this end, we present SeqGPT, a bilingual (i.e., English and Chinese) open-source autoregressive model specially enhanced for open-domain natural language understanding. We express all NLU tasks with two atomic tasks, which define fixed instructions to restrict the input and output format but still ``open'' for arbitrarily varied label sets. The model is first instruction-tuned with extremely fine-grained labeled data synthesized by ChatGPT and then further fine-tuned by 233 different atomic tasks from 152 datasets across various domains. The experimental results show that SeqGPT has decent classification and extraction ability, and is capable of performing language understanding tasks on unseen domains. We also conduct empirical studies on the scaling of data and model size as well as on the transfer across tasks. Our model is accessible at https://github.com/Alibaba-NLP/SeqGPT.

Keyphrase Generation (KPG) is a longstanding task in NLP with widespread applications. The advent of sequence-to-sequence (seq2seq) pre-trained language models (PLMs) has ushered in a transformative era for KPG, yielding promising performance improvements. However, many design decisions remain unexplored and are often made arbitrarily. This paper undertakes a systematic analysis of the influence of model selection and decoding strategies on PLM-based KPG. We begin by elucidating why seq2seq PLMs are apt for KPG, anchored by an attention-driven hypothesis. We then establish that conventional wisdom for selecting seq2seq PLMs lacks depth: (1) merely increasing model size or performing task-specific adaptation is not parameter-efficient; (2) although combining in-domain pre-training with task adaptation benefits KPG, it does partially hinder generalization. Regarding decoding, we demonstrate that while greedy search achieves strong F1 scores, it lags in recall compared with sampling-based methods. Based on these insights, we propose DeSel, a likelihood-based decode-select algorithm for seq2seq PLMs. DeSel improves greedy search by an average of 4.7% semantic F1 across five datasets. Our collective findings pave the way for deeper future investigations into PLM-based KPG.

We study automatic question generation for sentences from text passages in reading comprehension. We introduce an attention-based sequence learning model for the task and investigate the effect of encoding sentence- vs. paragraph-level information. In contrast to all previous work, our model does not rely on hand-crafted rules or a sophisticated NLP pipeline; it is instead trainable end-to-end via sequence-to-sequence learning. Automatic evaluation results show that our system significantly outperforms the state-of-the-art rule-based system. In human evaluations, questions generated by our system are also rated as being more natural (i.e., grammaticality, fluency) and as more difficult to answer (in terms of syntactic and lexical divergence from the original text and reasoning needed to answer).

This paper presents a computationally efficient machine-learned method for natural language response suggestion. Feed-forward neural networks using n-gram embedding features encode messages into vectors which are optimized to give message-response pairs a high dot-product value. An optimized search finds response suggestions. The method is evaluated in a large-scale commercial e-mail application, Inbox by Gmail. Compared to a sequence-to-sequence approach, the new system achieves the same quality at a small fraction of the computational requirements and latency.

Playlists have become a significant part of our listening experience because of the digital cloud-based services such as Spotify, Pandora, Apple Music. Owing to the meteoric rise in the usage of playlists, recommending playlists is crucial to music services today. Although there has been a lot of work done in playlist prediction, the area of playlist representation hasn't received that level of attention. Over the last few years, sequence-to-sequence models, especially in the field of natural language processing, have shown the effectiveness of learned embeddings in capturing the semantic characteristics of sequences. We can apply similar concepts to music to learn fixed length representations for playlists and use those representations for downstream tasks such as playlist discovery, browsing, and recommendation. In this work, we formulate the problem of learning a fixed-length playlist representation in an unsupervised manner, using Sequence-to-sequence (Seq2seq) models, interpreting playlists as sentences and songs as words. We compare our model with two other encoding architectures for baseline comparison. We evaluate our work using the suite of tasks commonly used for assessing sentence embeddings, along with a few additional tasks pertaining to music, and a recommendation task to study the traits captured by the playlist embeddings and their effectiveness for the purpose of music recommendation.

In this paper, we study semantic role labelling (SRL), a subtask of semantic parsing of natural language sentences and its application for the Vietnamese language. We present our effort in building Vietnamese PropBank, the first Vietnamese SRL corpus and a software system for labelling semantic roles of Vietnamese texts. In particular, we present a novel constituent extraction algorithm in the argument candidate identification step which is more suitable and more accurate than the common node-mapping method. In the machine learning part, our system integrates distributed word features produced by two recent unsupervised learning models in two learned statistical classifiers and makes use of integer linear programming inference procedure to improve the accuracy. The system is evaluated in a series of experiments and achieves a good result, an F_1 score of 74.77%. Our system, including corpus and software, is available as an open source project for free research and we believe that it is a good baseline for the development of future Vietnamese SRL systems.

Language model based pre-trained models such as BERT have provided significant gains across different NLP tasks. In this paper, we study different types of transformer based pre-trained models such as auto-regressive models (GPT-2), auto-encoder models (BERT), and seq2seq models (BART) for conditional data augmentation. We show that prepending the class labels to text sequences provides a simple yet effective way to condition the pre-trained models for data augmentation. Additionally, on three classification benchmarks, pre-trained Seq2Seq model outperforms other data augmentation methods in a low-resource setting. Further, we explore how different pre-trained model based data augmentation differs in-terms of data diversity, and how well such methods preserve the class-label information.

This paper presents Okapi, a new dataset for Natural Language to executable web Application Programming Interfaces (NL2API). This dataset is in English and contains 22,508 questions and 9,019 unique API calls, covering three domains. We define new compositional generalization tasks for NL2API which explore the models' ability to extrapolate from simple API calls in the training set to new and more complex API calls in the inference phase. Also, the models are required to generate API calls that execute correctly as opposed to the existing approaches which evaluate queries with placeholder values. Our dataset is different than most of the existing compositional semantic parsing datasets because it is a non-synthetic dataset studying the compositional generalization in a low-resource setting. Okapi is a step towards creating realistic datasets and benchmarks for studying compositional generalization alongside the existing datasets and tasks. We report the generalization capabilities of sequence-to-sequence baseline models trained on a variety of the SCAN and Okapi datasets tasks. The best model achieves 15\% exact match accuracy when generalizing from simple API calls to more complex API calls. This highlights some challenges for future research. Okapi dataset and tasks are publicly available at https://aka.ms/nl2api/data.

Machine learning is widely used to analyze biological sequence data. Non-sequential models such as SVMs or feed-forward neural networks are often used although they have no natural way of handling sequences of varying length. Recurrent neural networks such as the long short term memory (LSTM) model on the other hand are designed to handle sequences. In this study we demonstrate that LSTM networks predict the subcellular location of proteins given only the protein sequence with high accuracy (0.902) outperforming current state of the art algorithms. We further improve the performance by introducing convolutional filters and experiment with an attention mechanism which lets the LSTM focus on specific parts of the protein. Lastly we introduce new visualizations of both the convolutional filters and the attention mechanisms and show how they can be used to extract biological relevant knowledge from the LSTM networks.

We propose a new strategy for applying large pre-trained language models to novel tasks when labeled training data is limited. Rather than apply the model in a typical zero-shot or few-shot fashion, we treat the model as the basis for labeling functions in a weak supervision framework. To create a classifier, we first prompt the model to answer multiple distinct queries about an example and define how the possible responses should be mapped to votes for labels and abstentions. We then denoise these noisy label sources using the Snorkel system and train an end classifier with the resulting training data. Our experimental evaluation shows that prompting large language models within a weak supervision framework can provide significant gains in accuracy. On the WRENCH weak supervision benchmark, this approach can significantly improve over zero-shot performance, an average 19.5% reduction in errors. We also find that this approach produces classifiers with comparable or superior accuracy to those trained from hand-engineered rules.

Learning effective protein representations is critical in a variety of tasks in biology such as predicting protein functions. Recent sequence representation learning methods based on Protein Language Models (PLMs) excel in sequence-based tasks, but their direct adaptation to tasks involving protein structures remains a challenge. In contrast, structure-based methods leverage 3D structural information with graph neural networks and geometric pre-training methods show potential in function prediction tasks, but still suffers from the limited number of available structures. To bridge this gap, our study undertakes a comprehensive exploration of joint protein representation learning by integrating a state-of-the-art PLM (ESM-2) with distinct structure encoders (GVP, GearNet, CDConv). We introduce three representation fusion strategies and explore different pre-training techniques. Our method achieves significant improvements over existing sequence- and structure-based methods, setting new state-of-the-art for function annotation. This study underscores several important design choices for fusing protein sequence and structure information. Our implementation is available at https://github.com/DeepGraphLearning/ESM-GearNet.

The recently introduced continuous Skip-gram model is an efficient method for learning high-quality distributed vector representations that capture a large number of precise syntactic and semantic word relationships. In this paper we present several extensions that improve both the quality of the vectors and the training speed. By subsampling of the frequent words we obtain significant speedup and also learn more regular word representations. We also describe a simple alternative to the hierarchical softmax called negative sampling. An inherent limitation of word representations is their indifference to word order and their inability to represent idiomatic phrases. For example, the meanings of "Canada" and "Air" cannot be easily combined to obtain "Air Canada". Motivated by this example, we present a simple method for finding phrases in text, and show that learning good vector representations for millions of phrases is possible.

Learning effective protein representations is critical in a variety of tasks in biology such as predicting protein function or structure. Existing approaches usually pretrain protein language models on a large number of unlabeled amino acid sequences and then finetune the models with some labeled data in downstream tasks. Despite the effectiveness of sequence-based approaches, the power of pretraining on known protein structures, which are available in smaller numbers only, has not been explored for protein property prediction, though protein structures are known to be determinants of protein function. In this paper, we propose to pretrain protein representations according to their 3D structures. We first present a simple yet effective encoder to learn the geometric features of a protein. We pretrain the protein graph encoder by leveraging multiview contrastive learning and different self-prediction tasks. Experimental results on both function prediction and fold classification tasks show that our proposed pretraining methods outperform or are on par with the state-of-the-art sequence-based methods, while using much less pretraining data. Our implementation is available at https://github.com/DeepGraphLearning/GearNet.

Motivation: The development of novel compounds targeting proteins of interest is one of the most important tasks in the pharmaceutical industry. Deep generative models have been applied to targeted molecular design and have shown promising results. Recently, target-specific molecule generation has been viewed as a translation between the protein language and the chemical language. However, such a model is limited by the availability of interacting protein-ligand pairs. On the other hand, large amounts of unlabeled protein sequences and chemical compounds are available and have been used to train language models that learn useful representations. In this study, we propose exploiting pretrained biochemical language models to initialize (i.e. warm start) targeted molecule generation models. We investigate two warm start strategies: (i) a one-stage strategy where the initialized model is trained on targeted molecule generation (ii) a two-stage strategy containing a pre-finetuning on molecular generation followed by target specific training. We also compare two decoding strategies to generate compounds: beam search and sampling. Results: The results show that the warm-started models perform better than a baseline model trained from scratch. The two proposed warm-start strategies achieve similar results to each other with respect to widely used metrics from benchmarks. However, docking evaluation of the generated compounds for a number of novel proteins suggests that the one-stage strategy generalizes better than the two-stage strategy. Additionally, we observe that beam search outperforms sampling in both docking evaluation and benchmark metrics for assessing compound quality. Availability and implementation: The source code is available at https://github.com/boun-tabi/biochemical-lms-for-drug-design and the materials are archived in Zenodo at https://doi.org/10.5281/zenodo.6832145

Integer sequences are of central importance to the modeling of concepts admitting complete finitary descriptions. We introduce a novel view on the learning of such concepts and lay down a set of benchmarking tasks aimed at conceptual understanding by machine learning models. These tasks indirectly assess model ability to abstract, and challenge them to reason both interpolatively and extrapolatively from the knowledge gained by observing representative examples. To further aid research in knowledge representation and reasoning, we present FACT, the Finitary Abstraction Comprehension Toolkit. The toolkit surrounds a large dataset of integer sequences comprising both organic and synthetic entries, a library for data pre-processing and generation, a set of model performance evaluation tools, and a collection of baseline model implementations, enabling the making of the future advancements with ease.

Named Entity Recognition (NER) is a foundational NLP task that aims to provide class labels like Person, Location, Organisation, Time, and Number to words in free text. Named Entities can also be multi-word expressions where the additional I-O-B annotation information helps label them during the NER annotation process. While English and European languages have considerable annotated data for the NER task, Indian languages lack on that front -- both in terms of quantity and following annotation standards. This paper releases a significantly sized standard-abiding Hindi NER dataset containing 109,146 sentences and 2,220,856 tokens, annotated with 11 tags. We discuss the dataset statistics in all their essential detail and provide an in-depth analysis of the NER tag-set used with our data. The statistics of tag-set in our dataset show a healthy per-tag distribution, especially for prominent classes like Person, Location and Organisation. Since the proof of resource-effectiveness is in building models with the resource and testing the model on benchmark data and against the leader-board entries in shared tasks, we do the same with the aforesaid data. We use different language models to perform the sequence labelling task for NER and show the efficacy of our data by performing a comparative evaluation with models trained on another dataset available for the Hindi NER task. Our dataset helps achieve a weighted F1 score of 88.78 with all the tags and 92.22 when we collapse the tag-set, as discussed in the paper. To the best of our knowledge, no available dataset meets the standards of volume (amount) and variability (diversity), as far as Hindi NER is concerned. We fill this gap through this work, which we hope will significantly help NLP for Hindi. We release this dataset with our code and models at https://github.com/cfiltnlp/HiNER

Current protein language models (PLMs) learn protein representations mainly based on their sequences, thereby well capturing co-evolutionary information, but they are unable to explicitly acquire protein functions, which is the end goal of protein representation learning. Fortunately, for many proteins, their textual property descriptions are available, where their various functions are also described. Motivated by this fact, we first build the ProtDescribe dataset to augment protein sequences with text descriptions of their functions and other important properties. Based on this dataset, we propose the ProtST framework to enhance Protein Sequence pre-training and understanding by biomedical Texts. During pre-training, we design three types of tasks, i.e., unimodal mask prediction, multimodal representation alignment and multimodal mask prediction, to enhance a PLM with protein property information with different granularities and, at the same time, preserve the PLM's original representation power. On downstream tasks, ProtST enables both supervised learning and zero-shot prediction. We verify the superiority of ProtST-induced PLMs over previous ones on diverse representation learning benchmarks. Under the zero-shot setting, we show the effectiveness of ProtST on zero-shot protein classification, and ProtST also enables functional protein retrieval from a large-scale database without any function annotation.

Recently, prompt-tuning has achieved promising results for specific few-shot classification tasks. The core idea of prompt-tuning is to insert text pieces (i.e., templates) into the input and transform a classification task into a masked language modeling problem. However, for relation extraction, determining an appropriate prompt template requires domain expertise, and it is cumbersome and time-consuming to obtain a suitable label word. Furthermore, there exists abundant semantic and prior knowledge among the relation labels that cannot be ignored. To this end, we focus on incorporating knowledge among relation labels into prompt-tuning for relation extraction and propose a Knowledge-aware Prompt-tuning approach with synergistic optimization (KnowPrompt). Specifically, we inject latent knowledge contained in relation labels into prompt construction with learnable virtual type words and answer words. Then, we synergistically optimize their representation with structured constraints. Extensive experimental results on five datasets with standard and low-resource settings demonstrate the effectiveness of our approach. Our code and datasets are available in https://github.com/zjunlp/KnowPrompt for reproducibility.

Due to the difficulty of collecting exhaustive multi-label annotations, multi-label datasets often contain partial labels. We consider an extreme of this weakly supervised learning problem, called single positive multi-label learning (SPML), where each multi-label training image has only one positive label. Traditionally, all unannotated labels are assumed as negative labels in SPML, which introduces false negative labels and causes model training to be dominated by assumed negative labels. In this work, we choose to treat all unannotated labels from an alternative perspective, i.e. acknowledging they are unknown. Hence, we propose entropy-maximization (EM) loss to attain a special gradient regime for providing proper supervision signals. Moreover, we propose asymmetric pseudo-labeling (APL), which adopts asymmetric-tolerance strategies and a self-paced procedure, to cooperate with EM loss and then provide more precise supervision. Experiments show that our method significantly improves performance and achieves state-of-the-art results on all four benchmarks. Code is available at https://github.com/Correr-Zhou/SPML-AckTheUnknown.

Protein language models have shown remarkable success in learning biological information from protein sequences. However, most existing models are limited by either autoencoding or autoregressive pre-training objectives, which makes them struggle to handle protein understanding and generation tasks concurrently. We propose a unified protein language model, xTrimoPGLM, to address these two types of tasks simultaneously through an innovative pre-training framework. Our key technical contribution is an exploration of the compatibility and the potential for joint optimization of the two types of objectives, which has led to a strategy for training xTrimoPGLM at an unprecedented scale of 100 billion parameters and 1 trillion training tokens. Our extensive experiments reveal that 1) xTrimoPGLM significantly outperforms other advanced baselines in 18 protein understanding benchmarks across four categories. The model also facilitates an atomic-resolution view of protein structures, leading to an advanced 3D structural prediction model that surpasses existing language model-based tools. 2) xTrimoPGLM not only can generate de novo protein sequences following the principles of natural ones, but also can perform programmable generation after supervised fine-tuning (SFT) on curated sequences. These results highlight the substantial capability and versatility of xTrimoPGLM in understanding and generating protein sequences, contributing to the evolving landscape of foundation models in protein science.

We present the Charles University system for the MRL~2023 Shared Task on Multi-lingual Multi-task Information Retrieval. The goal of the shared task was to develop systems for named entity recognition and question answering in several under-represented languages. Our solutions to both subtasks rely on the translate-test approach. We first translate the unlabeled examples into English using a multilingual machine translation model. Then, we run inference on the translated data using a strong task-specific model. Finally, we project the labeled data back into the original language. To keep the inferred tags on the correct positions in the original language, we propose a method based on scoring the candidate positions using a label-sensitive translation model. In both settings, we experiment with finetuning the classification models on the translated data. However, due to a domain mismatch between the development data and the shared task validation and test sets, the finetuned models could not outperform our baselines.

In this paper, we present Neural Phrase-based Machine Translation (NPMT). Our method explicitly models the phrase structures in output sequences using Sleep-WAke Networks (SWAN), a recently proposed segmentation-based sequence modeling method. To mitigate the monotonic alignment requirement of SWAN, we introduce a new layer to perform (soft) local reordering of input sequences. Different from existing neural machine translation (NMT) approaches, NPMT does not use attention-based decoding mechanisms. Instead, it directly outputs phrases in a sequential order and can decode in linear time. Our experiments show that NPMT achieves superior performances on IWSLT 2014 German-English/English-German and IWSLT 2015 English-Vietnamese machine translation tasks compared with strong NMT baselines. We also observe that our method produces meaningful phrases in output languages.

Proteins are essential macromolecules defined by their amino acid sequences, which determine their three-dimensional structures and, consequently, their functions in all living organisms. Therefore, generative protein modeling necessitates a multimodal approach to simultaneously model, understand, and generate both sequences and structures. However, existing methods typically use separate models for each modality, limiting their ability to capture the intricate relationships between sequence and structure. This results in suboptimal performance in tasks that requires joint understanding and generation of both modalities. In this paper, we introduce DPLM-2, a multimodal protein foundation model that extends discrete diffusion protein language model (DPLM) to accommodate both sequences and structures. To enable structural learning with the language model, 3D coordinates are converted to discrete tokens using a lookup-free quantization-based tokenizer. By training on both experimental and high-quality synthetic structures, DPLM-2 learns the joint distribution of sequence and structure, as well as their marginals and conditionals. We also implement an efficient warm-up strategy to exploit the connection between large-scale evolutionary data and structural inductive biases from pre-trained sequence-based protein language models. Empirical evaluation shows that DPLM-2 can simultaneously generate highly compatible amino acid sequences and their corresponding 3D structures eliminating the need for a two-stage generation approach. Moreover, DPLM-2 demonstrates competitive performance in various conditional generation tasks, including folding, inverse folding, and scaffolding with multimodal motif inputs, as well as providing structure-aware representations for predictive tasks.

Titles of short sections within long documents support readers by guiding their focus towards relevant passages and by providing anchor-points that help to understand the progression of the document. The positive effects of section titles are even more pronounced when measured on readers with less developed reading abilities, for example in communities with limited labeled text resources. We, therefore, aim to develop techniques to generate section titles in low-resource environments. In particular, we present an extractive pipeline for section title generation by first selecting the most salient sentence and then applying deletion-based compression. Our compression approach is based on a Semi-Markov Conditional Random Field that leverages unsupervised word-representations such as ELMo or BERT, eliminating the need for a complex encoder-decoder architecture. The results show that this approach leads to competitive performance with sequence-to-sequence models with high resources, while strongly outperforming it with low resources. In a human-subject study across subjects with varying reading abilities, we find that our section titles improve the speed of completing comprehension tasks while retaining similar accuracy.

This paper describes our submission to the shared task on word/phrase level Quality Estimation (QE) in the First Conference on Statistical Machine Translation (WMT16). The objective of the shared task was to predict if the given word/phrase is a correct/incorrect (OK/BAD) translation in the given sentence. In this paper, we propose a novel approach for word level Quality Estimation using Recurrent Neural Network Language Model (RNN-LM) architecture. RNN-LMs have been found very effective in different Natural Language Processing (NLP) applications. RNN-LM is mainly used for vector space language modeling for different NLP problems. For this task, we modify the architecture of RNN-LM. The modified system predicts a label (OK/BAD) in the slot rather than predicting the word. The input to the system is a word sequence, similar to the standard RNN-LM. The approach is language independent and requires only the translated text for QE. To estimate the phrase level quality, we use the output of the word level QE system.

Pretext training followed by task-specific fine-tuning has been a successful approach in vision and language domains. This paper proposes a self-supervised pretext training framework tailored to event sequence data. We introduce a novel alignment verification task that is specialized to event sequences, building on good practices in masked reconstruction and contrastive learning. Our pretext tasks unlock foundational representations that are generalizable across different down-stream tasks, including next-event prediction for temporal point process models, event sequence classification, and missing event interpolation. Experiments on popular public benchmarks demonstrate the potential of the proposed method across different tasks and data domains.

We introduce a protein language model for determining the complete sequence of a peptide based on measurement of a limited set of amino acids. To date, protein sequencing relies on mass spectrometry, with some novel edman degregation based platforms able to sequence non-native peptides. Current protein sequencing techniques face limitations in accurately identifying all amino acids, hindering comprehensive proteome analysis. Our method simulates partial sequencing data by selectively masking amino acids that are experimentally difficult to identify in protein sequences from the UniRef database. This targeted masking mimics real-world sequencing limitations. We then modify and finetune a ProtBert derived transformer-based model, for a new downstream task predicting these masked residues, providing an approximation of the complete sequence. Evaluating on three bacterial Escherichia species, we achieve per-amino-acid accuracy up to 90.5% when only four amino acids ([KCYM]) are known. Structural assessment using AlphaFold and TM-score validates the biological relevance of our predictions. The model also demonstrates potential for evolutionary analysis through cross-species performance. This integration of simulated experimental constraints with computational predictions offers a promising avenue for enhancing protein sequence analysis, potentially accelerating advancements in proteomics and structural biology by providing a probabilistic reconstruction of the complete protein sequence from limited experimental data.

We propose KnowGL, a tool that allows converting text into structured relational data represented as a set of ABox assertions compliant with the TBox of a given Knowledge Graph (KG), such as Wikidata. We address this problem as a sequence generation task by leveraging pre-trained sequence-to-sequence language models, e.g. BART. Given a sentence, we fine-tune such models to detect pairs of entity mentions and jointly generate a set of facts consisting of the full set of semantic annotations for a KG, such as entity labels, entity types, and their relationships. To showcase the capabilities of our tool, we build a web application consisting of a set of UI widgets that help users to navigate through the semantic data extracted from a given input text. We make the KnowGL model available at https://huggingface.co/ibm/knowgl-large.

Phrase representations play an important role in data science and natural language processing, benefiting various tasks like Entity Alignment, Record Linkage, Fuzzy Joins, and Paraphrase Classification. The current state-of-the-art method involves fine-tuning pre-trained language models for phrasal embeddings using contrastive learning. However, we have identified areas for improvement. First, these pre-trained models tend to be unnecessarily complex and require to be pre-trained on a corpus with context sentences. Second, leveraging the phrase type and morphology gives phrase representations that are both more precise and more flexible. We propose an improved framework to learn phrase representations in a context-free fashion. The framework employs phrase type classification as an auxiliary task and incorporates character-level information more effectively into the phrase representation. Furthermore, we design three granularities of data augmentation to increase the diversity of training samples. Our experiments across a wide range of tasks show that our approach generates superior phrase embeddings compared to previous methods while requiring a smaller model size. The code is available at \faGithub~ https://github.com/tigerchen52/PEARL abstract

Semantic search for candidate retrieval is an important yet neglected problem in retrieval-based Chatbots, which aims to select a bunch of candidate responses efficiently from a large pool. The existing bottleneck is to ensure the model architecture having two points: 1) rich interactions between a query and a response to produce query-relevant responses; 2) ability of separately projecting the query and the response into latent spaces to apply efficiently in semantic search during online inference. To tackle this problem, we propose a novel approach, called Multitask-based Semantic Search Neural Network (MSSNN) for candidate retrieval, which accomplishes query-response interactions through multi-tasks. The method employs a Seq2Seq modeling task to learn a good query encoder, and then performs a word prediction task to build response embeddings, finally conducts a simple matching model to form the dot-product scorer. Experimental studies have demonstrated the potential of the proposed approach.

In this paper, we generalize text infilling (e.g., masked language models) by proposing Sequence Span Rewriting (SSR) as a self-supervised sequence-to-sequence (seq2seq) pre-training objective. SSR provides more fine-grained learning signals for text representations by supervising the model to rewrite imperfect spans to ground truth, and it is more consistent than text infilling with many downstream seq2seq tasks that rewrite a source sentences into a target sentence. Our experiments with T5 models on various seq2seq tasks show that SSR can substantially improve seq2seq pre-training. Moreover, we observe SSR is especially helpful to improve pre-training a small-size seq2seq model with a powerful imperfect span generator, which indicates a new perspective of transferring knowledge from a large model to a smaller model for seq2seq pre-training.

A major challenge in structured prediction is to represent the interdependencies within output structures. When outputs are structured as sequences, linear-chain conditional random fields (CRFs) are a widely used model class which can learn local dependencies in the output. However, the CRF's Markov assumption makes it impossible for CRFs to represent distributions with nonlocal dependencies, and standard CRFs are unable to respect nonlocal constraints of the data (such as global arity constraints on output labels). We present a generalization of CRFs that can enforce a broad class of constraints, including nonlocal ones, by specifying the space of possible output structures as a regular language L. The resulting regular-constrained CRF (RegCCRF) has the same formal properties as a standard CRF, but assigns zero probability to all label sequences not in L. Notably, RegCCRFs can incorporate their constraints during training, while related models only enforce constraints during decoding. We prove that constrained training is never worse than constrained decoding, and show empirically that it can be substantially better in practice. Additionally, we demonstrate a practical benefit on downstream tasks by incorporating a RegCCRF into a deep neural model for semantic role labeling, exceeding state-of-the-art results on a standard dataset.

With the advent of Transformers, large language models (LLMs) have saturated well-known NLP benchmarks and leaderboards with high aggregate performance. However, many times these models systematically fail on tail data or rare groups not obvious in aggregate evaluation. Identifying such problematic data groups is even more challenging when there are no explicit labels (e.g., ethnicity, gender, etc.) and further compounded for NLP datasets due to the lack of visual features to characterize failure modes (e.g., Asian males, animals indoors, waterbirds on land, etc.). This paper introduces an interactive Systematic Error Analysis and Labeling (\seal) tool that uses a two-step approach to first identify high error slices of data and then, in the second step, introduce methods to give human-understandable semantics to those underperforming slices. We explore a variety of methods for coming up with coherent semantics for the error groups using language models for semantic labeling and a text-to-image model for generating visual features. SEAL toolkit and demo screencast is available at https://huggingface.co/spaces/nazneen/seal.

Content metadata plays a very important role in movie recommender systems as it provides valuable information about various aspects of a movie such as genre, cast, plot synopsis, box office summary, etc. Analyzing the metadata can help understand the user preferences to generate personalized recommendations and item cold starting. In this talk, we will focus on one particular type of metadata - genre labels. Genre labels associated with a movie or a TV series help categorize a collection of titles into different themes and correspondingly setting up the audience expectation. We present some of the challenges associated with using genre label information and propose a new way of examining the genre information that we call as the Genre Spectrum. The Genre Spectrum helps capture the various nuanced genres in a title and our offline and online experiments corroborate the effectiveness of the approach. Furthermore, we also talk about applications of LLMs in augmenting content metadata which could eventually be used to achieve effective organization of recommendations in user's 2-D home-grid.

Annotating training data for sequence tagging of texts is usually very time-consuming. Recent advances in transfer learning for natural language processing in conjunction with active learning open the possibility to significantly reduce the necessary annotation budget. We are the first to thoroughly investigate this powerful combination for the sequence tagging task. We conduct an extensive empirical study of various Bayesian uncertainty estimation methods and Monte Carlo dropout options for deep pre-trained models in the active learning framework and find the best combinations for different types of models. Besides, we also demonstrate that to acquire instances during active learning, a full-size Transformer can be substituted with a distilled version, which yields better computational performance and reduces obstacles for applying deep active learning in practice.

The goal of text generation is to make machines express in human language. It is one of the most important yet challenging tasks in natural language processing (NLP). Since 2014, various neural encoder-decoder models pioneered by Seq2Seq have been proposed to achieve the goal by learning to map input text to output text. However, the input text alone often provides limited knowledge to generate the desired output, so the performance of text generation is still far from satisfaction in many real-world scenarios. To address this issue, researchers have considered incorporating various forms of knowledge beyond the input text into the generation models. This research direction is known as knowledge-enhanced text generation. In this survey, we present a comprehensive review of the research on knowledge enhanced text generation over the past five years. The main content includes two parts: (i) general methods and architectures for integrating knowledge into text generation; (ii) specific techniques and applications according to different forms of knowledge data. This survey can have broad audiences, researchers and practitioners, in academia and industry.

Countless learning tasks require dealing with sequential data. Image captioning, speech synthesis, and music generation all require that a model produce outputs that are sequences. In other domains, such as time series prediction, video analysis, and musical information retrieval, a model must learn from inputs that are sequences. Interactive tasks, such as translating natural language, engaging in dialogue, and controlling a robot, often demand both capabilities. Recurrent neural networks (RNNs) are connectionist models that capture the dynamics of sequences via cycles in the network of nodes. Unlike standard feedforward neural networks, recurrent networks retain a state that can represent information from an arbitrarily long context window. Although recurrent neural networks have traditionally been difficult to train, and often contain millions of parameters, recent advances in network architectures, optimization techniques, and parallel computation have enabled successful large-scale learning with them. In recent years, systems based on long short-term memory (LSTM) and bidirectional (BRNN) architectures have demonstrated ground-breaking performance on tasks as varied as image captioning, language translation, and handwriting recognition. In this survey, we review and synthesize the research that over the past three decades first yielded and then made practical these powerful learning models. When appropriate, we reconcile conflicting notation and nomenclature. Our goal is to provide a self-contained explication of the state of the art together with a historical perspective and references to primary research.

Many tasks in natural language processing require the extraction of relationship information for a given condition, such as event argument extraction, relation extraction, and task-oriented semantic parsing. Recent works usually propose sophisticated models for each task independently and pay less attention to the commonality of these tasks and to have a unified framework for all the tasks. In this work, we propose to take a unified view of all these tasks and introduce TAGPRIME to address relational structure extraction problems. TAGPRIME is a sequence tagging model that appends priming words about the information of the given condition (such as an event trigger) to the input text. With the self-attention mechanism in pre-trained language models, the priming words make the output contextualized representations contain more information about the given condition, and hence become more suitable for extracting specific relationships for the condition. Extensive experiments and analyses on three different tasks that cover ten datasets across five different languages demonstrate the generality and effectiveness of TAGPRIME.

This paper surveys and organizes research works in a new paradigm in natural language processing, which we dub "prompt-based learning". Unlike traditional supervised learning, which trains a model to take in an input x and predict an output y as P(y|x), prompt-based learning is based on language models that model the probability of text directly. To use these models to perform prediction tasks, the original input x is modified using a template into a textual string prompt x' that has some unfilled slots, and then the language model is used to probabilistically fill the unfilled information to obtain a final string x, from which the final output y can be derived. This framework is powerful and attractive for a number of reasons: it allows the language model to be pre-trained on massive amounts of raw text, and by defining a new prompting function the model is able to perform few-shot or even zero-shot learning, adapting to new scenarios with few or no labeled data. In this paper we introduce the basics of this promising paradigm, describe a unified set of mathematical notations that can cover a wide variety of existing work, and organize existing work along several dimensions, e.g.the choice of pre-trained models, prompts, and tuning strategies. To make the field more accessible to interested beginners, we not only make a systematic review of existing works and a highly structured typology of prompt-based concepts, but also release other resources, e.g., a website http://pretrain.nlpedia.ai/ including constantly-updated survey, and paperlist.

Modern recommender systems leverage large-scale retrieval models consisting of two stages: training a dual-encoder model to embed queries and candidates in the same space, followed by an Approximate Nearest Neighbor (ANN) search to select top candidates given a query's embedding. In this paper, we propose a new single-stage paradigm: a generative retrieval model which autoregressively decodes the identifiers for the target candidates in one phase. To do this, instead of assigning randomly generated atomic IDs to each item, we generate Semantic IDs: a semantically meaningful tuple of codewords for each item that serves as its unique identifier. We use a hierarchical method called RQ-VAE to generate these codewords. Once we have the Semantic IDs for all the items, a Transformer based sequence-to-sequence model is trained to predict the Semantic ID of the next item. Since this model predicts the tuple of codewords identifying the next item directly in an autoregressive manner, it can be considered a generative retrieval model. We show that our recommender system trained in this new paradigm improves the results achieved by current SOTA models on the Amazon dataset. Moreover, we demonstrate that the sequence-to-sequence model coupled with hierarchical Semantic IDs offers better generalization and hence improves retrieval of cold-start items for recommendations.

Sequence modeling is a crucial area across various domains, including Natural Language Processing (NLP), speech recognition, time series forecasting, music generation, and bioinformatics. Recurrent Neural Networks (RNNs) and Long Short Term Memory Networks (LSTMs) have historically dominated sequence modeling tasks like Machine Translation, Named Entity Recognition (NER), etc. However, the advancement of transformers has led to a shift in this paradigm, given their superior performance. Yet, transformers suffer from O(N^2) attention complexity and challenges in handling inductive bias. Several variations have been proposed to address these issues which use spectral networks or convolutions and have performed well on a range of tasks. However, they still have difficulty in dealing with long sequences. State Space Models(SSMs) have emerged as promising alternatives for sequence modeling paradigms in this context, especially with the advent of S4 and its variants, such as S4nd, Hippo, Hyena, Diagnol State Spaces (DSS), Gated State Spaces (GSS), Linear Recurrent Unit (LRU), Liquid-S4, Mamba, etc. In this survey, we categorize the foundational SSMs based on three paradigms namely, Gating architectures, Structural architectures, and Recurrent architectures. This survey also highlights diverse applications of SSMs across domains such as vision, video, audio, speech, language (especially long sequence modeling), medical (including genomics), chemical (like drug design), recommendation systems, and time series analysis, including tabular data. Moreover, we consolidate the performance of SSMs on benchmark datasets like Long Range Arena (LRA), WikiText, Glue, Pile, ImageNet, Kinetics-400, sstv2, as well as video datasets such as Breakfast, COIN, LVU, and various time series datasets. The project page for Mamba-360 work is available on this webpage.https://github.com/badripatro/mamba360.

Precise geocoding and time normalization for text requires that location and time phrases be identified. Many state-of-the-art geoparsers and temporal parsers suffer from low recall. Categories commonly missed by parsers are: nouns used in a non- spatiotemporal sense, adjectival and adverbial phrases, prepositional phrases, and numerical phrases. We collected and annotated data set by querying commercial web searches API with such spatiotemporal expressions as were missed by state-of-the- art parsers. Due to the high cost of sentence annotation, active learning was used to label training data, and a new strategy was designed to better select training examples to reduce labeling cost. For the learning algorithm, we applied an average perceptron trained Featurized Hidden Markov Model (FHMM). Five FHMM instances were used to create an ensemble, with the output phrase selected by voting. Our ensemble model was tested on a range of sequential labeling tasks, and has shown competitive performance. Our contributions include (1) an new dataset annotated with named entities and expanded spatiotemporal expressions; (2) a comparison of inference algorithms for ensemble models showing the superior accuracy of Belief Propagation over Viterbi Decoding; (3) a new example re-weighting method for active ensemble learning that 'memorizes' the latest examples trained; (4) a spatiotemporal parser that jointly recognizes expanded spatiotemporal expressions as well as named entities.

Recent work attributes progress in NLP to large language models (LMs) with increased model size and large quantities of pretraining data. Despite this, current state-of-the-art LMs for Hebrew are both under-parameterized and under-trained compared to LMs in other languages. Additionally, previous work on pretrained Hebrew LMs focused on encoder-only models. While the encoder-only architecture is beneficial for classification tasks, it does not cater well for sub-word prediction tasks, such as Named Entity Recognition, when considering the morphologically rich nature of Hebrew. In this paper we argue that sequence-to-sequence generative architectures are more suitable for LLMs in the case of morphologically rich languages (MRLs) such as Hebrew. We demonstrate that by casting tasks in the Hebrew NLP pipeline as text-to-text tasks, we can leverage powerful multilingual, pretrained sequence-to-sequence models as mT5, eliminating the need for a specialized, morpheme-based, separately fine-tuned decoder. Using this approach, our experiments show substantial improvements over previously published results on existing Hebrew NLP benchmarks. These results suggest that multilingual sequence-to-sequence models present a promising building block for NLP for MRLs.

Prompting is used to guide or steer a language model in generating an appropriate response that is consistent with the desired outcome. Chaining is a strategy used to decompose complex tasks into smaller, manageable components. In this study, we utilize prompt chaining for extensive legal document classification tasks, which present difficulties due to their intricate domain-specific language and considerable length. Our approach begins with the creation of a concise summary of the original document, followed by a semantic search for related exemplar texts and their corresponding annotations from a training corpus. Finally, we prompt for a label - based on the task - to assign, by leveraging the in-context learning from the few-shot prompt. We demonstrate that through prompt chaining, we can not only enhance the performance over zero-shot, but also surpass the micro-F1 score achieved by larger models, such as ChatGPT zero-shot, using smaller models.

Semantic parsing models with applications in task oriented dialog systems require efficient sequence to sequence (seq2seq) architectures to be run on-device. To this end, we propose a projection based encoder-decoder model referred to as pQRNN-MAtt. Studies based on projection methods were restricted to encoder-only models, and we believe this is the first study extending it to seq2seq architectures. The resulting quantized models are less than 3.5MB in size and are well suited for on-device latency critical applications. We show that on MTOP, a challenging multilingual semantic parsing dataset, the average model performance surpasses LSTM based seq2seq model that uses pre-trained embeddings despite being 85x smaller. Furthermore, the model can be an effective student for distilling large pre-trained models such as T5/BERT.

Neural sequence models can generate highly fluent sentences, but recent studies have also shown that they are also prone to hallucinate additional content not supported by the input. These variety of fluent but wrong outputs are particularly problematic, as it will not be possible for users to tell they are being presented incorrect content. To detect these errors, we propose a task to predict whether each token in the output sequence is hallucinated (not contained in the input) and collect new manually annotated evaluation sets for this task. We also introduce a method for learning to detect hallucinations using pretrained language models fine tuned on synthetic data that includes automatically inserted hallucinations Experiments on machine translation (MT) and abstractive summarization demonstrate that our proposed approach consistently outperforms strong baselines on all benchmark datasets. We further demonstrate how to use the token-level hallucination labels to define a fine-grained loss over the target sequence in low-resource MT and achieve significant improvements over strong baseline methods. We also apply our method to word-level quality estimation for MT and show its effectiveness in both supervised and unsupervised settings. Codes and data available at https://github.com/violet-zct/fairseq-detect-hallucination.

In recent years, Transformers have become the de-facto architecture for sequence modeling on text and a variety of multi-dimensional data, such as images and video. However, the use of self-attention layers in a Transformer incurs prohibitive compute and memory complexity that scales quadratically w.r.t. the sequence length. A recent architecture, Mamba, based on state space models has been shown to achieve comparable performance for modeling text sequences, while scaling linearly with the sequence length. In this work, we present Mamba-ND, a generalized design extending the Mamba architecture to arbitrary multi-dimensional data. Our design alternatively unravels the input data across different dimensions following row-major orderings. We provide a systematic comparison of Mamba-ND with several other alternatives, based on prior multi-dimensional extensions such as Bi-directional LSTMs and S4ND. Empirically, we show that Mamba-ND demonstrates performance competitive with the state-of-the-art on a variety of multi-dimensional benchmarks, including ImageNet-1K classification, HMDB-51 action recognition, and ERA5 weather forecasting.

Recently, model-based retrieval has emerged as a new paradigm in text retrieval that discards the index in the traditional retrieval model and instead memorizes the candidate corpora using model parameters. This design employs a sequence-to-sequence paradigm to generate document identifiers, which enables the complete capture of the relevance between queries and documents and simplifies the classic indexretrieval-rerank pipeline. Despite its attractive qualities, there remain several major challenges in model-based retrieval, including the discrepancy between pre-training and fine-tuning, and the discrepancy between training and inference. To deal with the above challenges, we propose a novel two-stage model-based retrieval approach called TOME, which makes two major technical contributions, including the utilization of tokenized URLs as identifiers and the design of a two-stage generation architecture. We also propose a number of training strategies to deal with the training difficulty as the corpus size increases. Extensive experiments and analysis on MS MARCO and Natural Questions demonstrate the effectiveness of our proposed approach, and we investigate the scaling laws of TOME by examining various influencing factors.

The RNN transducer is a promising end-to-end model candidate. We compare the original training criterion with the full marginalization over all alignments, to the commonly used maximum approximation, which simplifies, improves and speeds up our training. We also generalize from the original neural network model and study more powerful models, made possible due to the maximum approximation. We further generalize the output label topology to cover RNN-T, RNA and CTC. We perform several studies among all these aspects, including a study on the effect of external alignments. We find that the transducer model generalizes much better on longer sequences than the attention model. Our final transducer model outperforms our attention model on Switchboard 300h by over 6% relative WER.

Definition Extraction (DE) is one of the well-known topics in Information Extraction that aims to identify terms and their corresponding definitions in unstructured texts. This task can be formalized either as a sentence classification task (i.e., containing term-definition pairs or not) or a sequential labeling task (i.e., identifying the boundaries of the terms and definitions). The previous works for DE have only focused on one of the two approaches, failing to model the inter-dependencies between the two tasks. In this work, we propose a novel model for DE that simultaneously performs the two tasks in a single framework to benefit from their inter-dependencies. Our model features deep learning architectures to exploit the global structures of the input sentences as well as the semantic consistencies between the terms and the definitions, thereby improving the quality of the representation vectors for DE. Besides the joint inference between sentence classification and sequential labeling, the proposed model is fundamentally different from the prior work for DE in that the prior work has only employed the local structures of the input sentences (i.e., word-to-word relations), and not yet considered the semantic consistencies between terms and definitions. In order to implement these novel ideas, our model presents a multi-task learning framework that employs graph convolutional neural networks and predicts the dependency paths between the terms and the definitions. We also seek to enforce the consistency between the representations of the terms and definitions both globally (i.e., increasing semantic consistency between the representations of the entire sentences and the terms/definitions) and locally (i.e., promoting the similarity between the representations of the terms and the definitions).

Complex chemical structures, like drugs, are usually defined by SMILES strings as a sequence of molecules and bonds. These SMILES strings are used in different complex machine learning-based drug-related research and representation works. Escaping from complex representation, in this work, we pose a single question: What if we treat drug SMILES as conventional sentences and engage in text classification for drug classification? Our experiments affirm the possibility with very competitive scores. The study explores the notion of viewing each atom and bond as sentence components, employing basic NLP methods to categorize drug types, proving that complex problems can also be solved with simpler perspectives. The data and code are available here: https://github.com/azminewasi/Drug-Classification-NLP.

The success of the GPT series proves that GPT can extract general information from sequences, thereby benefiting all downstream tasks. This motivates us to use pre-trained models to explore the hidden information in DNA sequences. However, data and task requirements in DNA sequence analysis are complexity and diversity as DNA relevant data includes different types of information, such as sequences, expression levels, etc, while there is currently no model specifically designed for these characteristics. Hereby, we present DNAGPT, a generalized foundation model pre-trained on over 10 billion base pairs from 9 species which can be fine-tuned for any DNA sequence analysis task. Our model can simultaneously process or output DNA sequences and numbers. In addition, our unique token design allows users to design prompts according to their own task requirements, making it applicable to any type of task. We have evaluated our model on classification, regression, and generation tasks. We demonstrate that DNAGPT benefits from pre-training, and therefore can bring performance gains to any downstream task. Our model is not only a new attempt in the field of genomes analysis, but also provides a new direction for the application of foundation models in biology.

Labeling training data has become one of the major roadblocks to using machine learning. Among various weak supervision paradigms, programmatic weak supervision (PWS) has achieved remarkable success in easing the manual labeling bottleneck by programmatically synthesizing training labels from multiple potentially noisy supervision sources. This paper presents a comprehensive survey of recent advances in PWS. In particular, we give a brief introduction of the PWS learning paradigm, and review representative approaches for each component within PWS's learning workflow. In addition, we discuss complementary learning paradigms for tackling limited labeled data scenarios and how these related approaches can be used in conjunction with PWS. Finally, we identify several critical challenges that remain under-explored in the area to hopefully inspire future research directions in the field.

Novel Class Discovery (NCD) is a growing field where we are given during training a labeled set of known classes and an unlabeled set of different classes that must be discovered. In recent years, many methods have been proposed to address this problem, and the field has begun to mature. In this paper, we provide a comprehensive survey of the state-of-the-art NCD methods. We start by formally defining the NCD problem and introducing important notions. We then give an overview of the different families of approaches, organized by the way they transfer knowledge from the labeled set to the unlabeled set. We find that they either learn in two stages, by first extracting knowledge from the labeled data only and then applying it to the unlabeled data, or in one stage by conjointly learning on both sets. For each family, we describe their general principle and detail a few representative methods. Then, we briefly introduce some new related tasks inspired by the increasing number of NCD works. We also present some common tools and techniques used in NCD, such as pseudo labeling, self-supervised learning and contrastive learning. Finally, to help readers unfamiliar with the NCD problem differentiate it from other closely related domains, we summarize some of the closest areas of research and discuss their main differences.

As a step toward better document-level understanding, we explore classification of a sequence of sentences into their corresponding categories, a task that requires understanding sentences in context of the document. Recent successful models for this task have used hierarchical models to contextualize sentence representations, and Conditional Random Fields (CRFs) to incorporate dependencies between subsequent labels. In this work, we show that pretrained language models, BERT (Devlin et al., 2018) in particular, can be used for this task to capture contextual dependencies without the need for hierarchical encoding nor a CRF. Specifically, we construct a joint sentence representation that allows BERT Transformer layers to directly utilize contextual information from all words in all sentences. Our approach achieves state-of-the-art results on four datasets, including a new dataset of structured scientific abstracts.

Empirical Risk Minimization (ERM) is fragile in scenarios with insufficient labeled samples. A vanilla extension of ERM to unlabeled samples is Entropy Minimization (EntMin), which employs the soft-labels of unlabeled samples to guide their learning. However, EntMin emphasizes prediction discriminability while neglecting prediction diversity. To alleviate this issue, in this paper, we rethink the guidance information to utilize unlabeled samples. By analyzing the learning objective of ERM, we find that the guidance information for labeled samples in a specific category is the corresponding label encoding. Inspired by this finding, we propose a Label-Encoding Risk Minimization (LERM). It first estimates the label encodings through prediction means of unlabeled samples and then aligns them with their corresponding ground-truth label encodings. As a result, the LERM ensures both prediction discriminability and diversity, and it can be integrated into existing methods as a plugin. Theoretically, we analyze the relationships between LERM and ERM as well as EntMin. Empirically, we verify the superiority of the LERM under several label insufficient scenarios. The codes are available at https://github.com/zhangyl660/LERM.

Understanding search queries is a hard problem as it involves dealing with "word salad" text ubiquitously issued by users. However, if a query resembles a well-formed question, a natural language processing pipeline is able to perform more accurate interpretation, thus reducing downstream compounding errors. Hence, identifying whether or not a query is well formed can enhance query understanding. Here, we introduce a new task of identifying a well-formed natural language question. We construct and release a dataset of 25,100 publicly available questions classified into well-formed and non-wellformed categories and report an accuracy of 70.7% on the test set. We also show that our classifier can be used to improve the performance of neural sequence-to-sequence models for generating questions for reading comprehension.

This open access book provides a comprehensive overview of the state of the art in research and applications of Foundation Models and is intended for readers familiar with basic Natural Language Processing (NLP) concepts. Over the recent years, a revolutionary new paradigm has been developed for training models for NLP. These models are first pre-trained on large collections of text documents to acquire general syntactic knowledge and semantic information. Then, they are fine-tuned for specific tasks, which they can often solve with superhuman accuracy. When the models are large enough, they can be instructed by prompts to solve new tasks without any fine-tuning. Moreover, they can be applied to a wide range of different media and problem domains, ranging from image and video processing to robot control learning. Because they provide a blueprint for solving many tasks in artificial intelligence, they have been called Foundation Models. After a brief introduction to basic NLP models the main pre-trained language models BERT, GPT and sequence-to-sequence transformer are described, as well as the concepts of self-attention and context-sensitive embedding. Then, different approaches to improving these models are discussed, such as expanding the pre-training criteria, increasing the length of input texts, or including extra knowledge. An overview of the best-performing models for about twenty application areas is then presented, e.g., question answering, translation, story generation, dialog systems, generating images from text, etc. For each application area, the strengths and weaknesses of current models are discussed, and an outlook on further developments is given. In addition, links are provided to freely available program code. A concluding chapter summarizes the economic opportunities, mitigation of risks, and potential developments of AI.

Traditional sequence-to-sequence (seq2seq) models and other variations of the attention-mechanism such as hierarchical attention have been applied to the text summarization problem. Though there is a hierarchy in the way humans use language by forming paragraphs from sentences and sentences from words, hierarchical models have usually not worked that much better than their traditional seq2seq counterparts. This effect is mainly because either the hierarchical attention mechanisms are too sparse using hard attention or noisy using soft attention. In this paper, we propose a method based on extracting the highlights of a document; a key concept that is conveyed in a few sentences. In a typical text summarization dataset consisting of documents that are 800 tokens in length (average), capturing long-term dependencies is very important, e.g., the last sentence can be grouped with the first sentence of a document to form a summary. LSTMs (Long Short-Term Memory) proved useful for machine translation. However, they often fail to capture long-term dependencies while modeling long sequences. To address these issues, we have adapted Neural Semantic Encoders (NSE) to text summarization, a class of memory-augmented neural networks by improving its functionalities and proposed a novel hierarchical NSE that outperforms similar previous models significantly. The quality of summarization was improved by augmenting linguistic factors, namely lemma, and Part-of-Speech (PoS) tags, to each word in the dataset for improved vocabulary coverage and generalization. The hierarchical NSE model on factored dataset outperformed the state-of-the-art by nearly 4 ROUGE points. We further designed and used the first GPU-based self-critical Reinforcement Learning model.

We present the first approach to automated audio captioning. We employ an encoder-decoder scheme with an alignment model in between. The input to the encoder is a sequence of log mel-band energies calculated from an audio file, while the output is a sequence of words, i.e. a caption. The encoder is a multi-layered, bi-directional gated recurrent unit (GRU) and the decoder a multi-layered GRU with a classification layer connected to the last GRU of the decoder. The classification layer and the alignment model are fully connected layers with shared weights between timesteps. The proposed method is evaluated using data drawn from a commercial sound effects library, ProSound Effects. The resulting captions were rated through metrics utilized in machine translation and image captioning fields. Results from metrics show that the proposed method can predict words appearing in the original caption, but not always correctly ordered.

State-of-the-art language models are autoregressive and operate on subword units known as tokens. Specifically, one must encode the conditioning string into a list of tokens before passing to the language models for next-token prediction. We show that popular encoding schemes, such as maximum prefix encoding (MPE) and byte-pair-encoding (BPE), induce a sampling bias that cannot be mitigated with more training or data. To counter this universal problem, for each encoding scheme above, we propose a novel algorithm to obtain unbiased estimates from any language model trained on tokenized data. Our methods do not require finetuning the model, and the complexity, defined as the number of model runs, scales linearly with the sequence length in the case of MPE. As a result, we show that one can simulate token-free behavior from a tokenized language model. We empirically verify the correctness of our method through a Markov-chain setup, where it accurately recovers the transition probabilities, as opposed to the conventional method of directly prompting tokens into the language model.

Name tagging is a key component of Information Extraction (IE), particularly in scientific domains such as biomedicine and chemistry, where large language models (LLMs), e.g., ChatGPT, fall short. We investigate the applicability of transfer learning for enhancing a name tagging model trained in the biomedical domain (the source domain) to be used in the chemical domain (the target domain). A common practice for training such a model in a few-shot learning setting is to pretrain the model on the labeled source data, and then, to finetune it on a hand-full of labeled target examples. In our experiments we observed that such a model is prone to mis-labeling the source entities, which can often appear in the text, as the target entities. To alleviate this problem, we propose a model to transfer the knowledge from the source domain to the target domain, however, at the same time, to project the source entities and target entities into separate regions of the feature space. This diminishes the risk of mis-labeling the source entities as the target entities. Our model consists of two stages: 1) entity grouping in the source domain, which incorporates knowledge from annotated events to establish relations between entities, and 2) entity discrimination in the target domain, which relies on pseudo labeling and contrastive learning to enhance discrimination between the entities in the two domains. We carry out our extensive experiments across three source and three target datasets, and demonstrate that our method outperforms the baselines, in some scenarios by 5\% absolute value.

The output structure of database-like tables, consisting of values structured in horizontal rows and vertical columns identifiable by name, can cover a wide range of NLP tasks. Following this constatation, we propose a framework for text-to-table neural models applicable to problems such as extraction of line items, joint entity and relation extraction, or knowledge base population. The permutation-based decoder of our proposal is a generalized sequential method that comprehends information from all cells in the table. The training maximizes the expected log-likelihood for a table's content across all random permutations of the factorization order. During the content inference, we exploit the model's ability to generate cells in any order by searching over possible orderings to maximize the model's confidence and avoid substantial error accumulation, which other sequential models are prone to. Experiments demonstrate a high practical value of the framework, which establishes state-of-the-art results on several challenging datasets, outperforming previous solutions by up to 15%.

Sequence modeling has demonstrated state-of-the-art performance on natural language and document understanding tasks. However, it is challenging to correctly serialize tokens in form-like documents in practice due to their variety of layout patterns. We propose FormNet, a structure-aware sequence model to mitigate the suboptimal serialization of forms. First, we design Rich Attention that leverages the spatial relationship between tokens in a form for more precise attention score calculation. Second, we construct Super-Tokens for each word by embedding representations from their neighboring tokens through graph convolutions. FormNet therefore explicitly recovers local syntactic information that may have been lost during serialization. In experiments, FormNet outperforms existing methods with a more compact model size and less pre-training data, establishing new state-of-the-art performance on CORD, FUNSD and Payment benchmarks.

In this paper, we propose a novel neural network model called RNN Encoder-Decoder that consists of two recurrent neural networks (RNN). One RNN encodes a sequence of symbols into a fixed-length vector representation, and the other decodes the representation into another sequence of symbols. The encoder and decoder of the proposed model are jointly trained to maximize the conditional probability of a target sequence given a source sequence. The performance of a statistical machine translation system is empirically found to improve by using the conditional probabilities of phrase pairs computed by the RNN Encoder-Decoder as an additional feature in the existing log-linear model. Qualitatively, we show that the proposed model learns a semantically and syntactically meaningful representation of linguistic phrases.

Learning specific hands-on skills such as cooking, car maintenance, and home repairs increasingly happens via instructional videos. The user experience with such videos is known to be improved by meta-information such as time-stamped annotations for the main steps involved. Generating such annotations automatically is challenging, and we describe here two relevant contributions. First, we construct and release a new dense video captioning dataset, Video Timeline Tags (ViTT), featuring a variety of instructional videos together with time-stamped annotations. Second, we explore several multimodal sequence-to-sequence pretraining strategies that leverage large unsupervised datasets of videos and caption-like texts. We pretrain and subsequently finetune dense video captioning models using both YouCook2 and ViTT. We show that such models generalize well and are robust over a wide variety of instructional videos.

The core of video understanding tasks, such as recognition, captioning, and tracking, is to automatically detect objects or actions in a video and analyze their temporal evolution. Despite sharing a common goal, different tasks often rely on distinct model architectures and annotation formats. In contrast, natural language processing benefits from a unified output space, i.e., text sequences, which simplifies the training of powerful foundational language models, such as GPT-3, with extensive training corpora. Inspired by this, we seek to unify the output space of video understanding tasks by using languages as labels and additionally introducing time and box tokens. In this way, a variety of video tasks could be formulated as video-grounded token generation. This enables us to address various types of video tasks, including classification (such as action recognition), captioning (covering clip captioning, video question answering, and dense video captioning), and localization tasks (such as visual object tracking) within a fully shared encoder-decoder architecture, following a generative framework. Through comprehensive experiments, we demonstrate such a simple and straightforward idea is quite effective and can achieve state-of-the-art or competitive results on seven video benchmarks, providing a novel perspective for more universal video understanding. Code is available at https://github.com/wangjk666/OmniVid.

Self-supervised representation learning of biological sequence embeddings alleviates computational resource constraints on downstream tasks while circumventing expensive experimental label acquisition. However, existing methods mostly borrow directly from large language models designed for NLP, rather than with bioinformatics philosophies in mind. Recently, contrastive mutual information maximization methods have achieved state-of-the-art representations for ImageNet. In this perspective piece, we discuss how viewing evolution as natural sequence augmentation and maximizing information across phylogenetic "noisy channels" is a biologically and theoretically desirable objective for pretraining encoders. We first provide a review of current contrastive learning literature, then provide an illustrative example where we show that contrastive learning using evolutionary augmentation can be used as a representation learning objective which maximizes the mutual information between biological sequences and their conserved function, and finally outline rationale for this approach.

Automatically classifying electronic health records (EHRs) into diagnostic codes has been challenging to the NLP community. State-of-the-art methods treated this problem as a multilabel classification problem and proposed various architectures to model this problem. However, these systems did not leverage the superb performance of pretrained language models, which achieved superb performance on natural language understanding tasks. Prior work has shown that pretrained language models underperformed on this task with the regular finetuning scheme. Therefore, this paper aims at analyzing the causes of the underperformance and developing a framework for automatic ICD coding with pretrained language models. We spotted three main issues through the experiments: 1) large label space, 2) long input sequences, and 3) domain mismatch between pretraining and fine-tuning. We propose PLMICD, a framework that tackles the challenges with various strategies. The experimental results show that our proposed framework can overcome the challenges and achieves state-of-the-art performance in terms of multiple metrics on the benchmark MIMIC data. The source code is available at https://github.com/MiuLab/PLM-ICD

Autoregressive modeling has been a huge success in the field of natural language processing (NLP). Recently, autoregressive models have emerged as a significant area of focus in computer vision, where they excel in producing high-quality visual content. Autoregressive models in NLP typically operate on subword tokens. However, the representation strategy in computer vision can vary in different levels, i.e., pixel-level, token-level, or scale-level, reflecting the diverse and hierarchical nature of visual data compared to the sequential structure of language. This survey comprehensively examines the literature on autoregressive models applied to vision. To improve readability for researchers from diverse research backgrounds, we start with preliminary sequence representation and modeling in vision. Next, we divide the fundamental frameworks of visual autoregressive models into three general sub-categories, including pixel-based, token-based, and scale-based models based on the strategy of representation. We then explore the interconnections between autoregressive models and other generative models. Furthermore, we present a multi-faceted categorization of autoregressive models in computer vision, including image generation, video generation, 3D generation, and multi-modal generation. We also elaborate on their applications in diverse domains, including emerging domains such as embodied AI and 3D medical AI, with about 250 related references. Finally, we highlight the current challenges to autoregressive models in vision with suggestions about potential research directions. We have also set up a Github repository to organize the papers included in this survey at: https://github.com/ChaofanTao/Autoregressive-Models-in-Vision-Survey.

Reviewing contracts is a time-consuming procedure that incurs large expenses to companies and social inequality to those who cannot afford it. In this work, we propose "document-level natural language inference (NLI) for contracts", a novel, real-world application of NLI that addresses such problems. In this task, a system is given a set of hypotheses (such as "Some obligations of Agreement may survive termination.") and a contract, and it is asked to classify whether each hypothesis is "entailed by", "contradicting to" or "not mentioned by" (neutral to) the contract as well as identifying "evidence" for the decision as spans in the contract. We annotated and release the largest corpus to date consisting of 607 annotated contracts. We then show that existing models fail badly on our task and introduce a strong baseline, which (1) models evidence identification as multi-label classification over spans instead of trying to predict start and end tokens, and (2) employs more sophisticated context segmentation for dealing with long documents. We also show that linguistic characteristics of contracts, such as negations by exceptions, are contributing to the difficulty of this task and that there is much room for improvement.

Information extraction(IE) is a crucial subfield within natural language processing. In this study, we introduce a Sentence Classification and Named Entity Recognition Multi-task (SCNM) approach that combines Sentence Classification (SC) and Named Entity Recognition (NER). We develop a Sentence-to-Label Generation (SLG) framework for SCNM and construct a Wikipedia dataset containing both SC and NER. Using a format converter, we unify input formats and employ a generative model to generate SC-labels, NER-labels, and associated text segments. We propose a Constraint Mechanism (CM) to improve generated format accuracy. Our results show SC accuracy increased by 1.13 points and NER by 1.06 points in SCNM compared to standalone tasks, with CM raising format accuracy from 63.61 to 100. The findings indicate mutual reinforcement effects between SC and NER, and integration enhances both tasks' performance.

Part-of-Speech (POS) tagging is an important component of the NLP pipeline, but many low-resource languages lack labeled data for training. An established method for training a POS tagger in such a scenario is to create a labeled training set by transferring from high-resource languages. In this paper, we propose a novel method for transferring labels from multiple high-resource source to low-resource target languages. We formalize POS tag projection as graph-based label propagation. Given translations of a sentence in multiple languages, we create a graph with words as nodes and alignment links as edges by aligning words for all language pairs. We then propagate node labels from source to target using a Graph Neural Network augmented with transformer layers. We show that our propagation creates training sets that allow us to train POS taggers for a diverse set of languages. When combined with enhanced contextualized embeddings, our method achieves a new state-of-the-art for unsupervised POS tagging of low-resource languages.

Multi-label classification problems with thousands of classes are hard to solve with in-context learning alone, as language models (LMs) might lack prior knowledge about the precise classes or how to assign them, and it is generally infeasible to demonstrate every class in a prompt. We propose a general program, Infer--Retrieve--Rank, that defines multi-step interactions between LMs and retrievers to efficiently tackle such problems. We implement this program using the DSPy programming model, which specifies in-context systems in a declarative manner, and use DSPy optimizers to tune it towards specific datasets by bootstrapping only tens of few-shot examples. Our primary extreme classification program, optimized separately for each task, attains state-of-the-art results across three benchmarks (HOUSE, TECH, TECHWOLF). We apply the same program to a benchmark with vastly different characteristics and attain competitive performance as well (BioDEX). Unlike prior work, our proposed solution requires no finetuning, is easily applicable to new tasks, alleviates prompt engineering, and requires only tens of labeled examples. Our code is public at https://github.com/KarelDO/xmc.dspy.

Even though term-based methods such as BM25 provide strong baselines in ranking, under certain conditions they are dominated by large pre-trained masked language models (MLMs) such as BERT. To date, the source of their effectiveness remains unclear. Is it their ability to truly understand the meaning through modeling syntactic aspects? We answer this by manipulating the input order and position information in a way that destroys the natural sequence order of query and passage and shows that the model still achieves comparable performance. Overall, our results highlight that syntactic aspects do not play a critical role in the effectiveness of re-ranking with BERT. We point to other mechanisms such as query-passage cross-attention and richer embeddings that capture word meanings based on aggregated context regardless of the word order for being the main attributions for its superior performance.

For sequence models with large vocabularies, a majority of network parameters lie in the input and output layers. In this work, we describe a new method, DeFINE, for learning deep token representations efficiently. Our architecture uses a hierarchical structure with novel skip-connections which allows for the use of low dimensional input and output layers, reducing total parameters and training time while delivering similar or better performance versus existing methods. DeFINE can be incorporated easily in new or existing sequence models. Compared to state-of-the-art methods including adaptive input representations, this technique results in a 6% to 20% drop in perplexity. On WikiText-103, DeFINE reduces the total parameters of Transformer-XL by half with minimal impact on performance. On the Penn Treebank, DeFINE improves AWD-LSTM by 4 points with a 17% reduction in parameters, achieving comparable performance to state-of-the-art methods with fewer parameters. For machine translation, DeFINE improves the efficiency of the Transformer model by about 1.4 times while delivering similar performance.

In this paper, we introduce a multi-label lazy learning approach to deal with automatic semantic indexing in large document collections in the presence of complex and structured label vocabularies with high inter-label correlation. The proposed method is an evolution of the traditional k-Nearest Neighbors algorithm which uses a large autoencoder trained to map the large label space to a reduced size latent space and to regenerate the predicted labels from this latent space. We have evaluated our proposal in a large portion of the MEDLINE biomedical document collection which uses the Medical Subject Headings (MeSH) thesaurus as a controlled vocabulary. In our experiments we propose and evaluate several document representation approaches and different label autoencoder configurations.

In the field of language modeling, models augmented with retrieval components have emerged as a promising solution to address several challenges faced in the natural language processing (NLP) field, including knowledge grounding, interpretability, and scalability. Despite the primary focus on NLP, we posit that the paradigm of retrieval-enhancement can be extended to a broader spectrum of machine learning (ML) such as computer vision, time series prediction, and computational biology. Therefore, this work introduces a formal framework of this paradigm, Retrieval-Enhanced Machine Learning (REML), by synthesizing the literature in various domains in ML with consistent notations which is missing from the current literature. Also, we found that while a number of studies employ retrieval components to augment their models, there is a lack of integration with foundational Information Retrieval (IR) research. We bridge this gap between the seminal IR research and contemporary REML studies by investigating each component that comprises the REML framework. Ultimately, the goal of this work is to equip researchers across various disciplines with a comprehensive, formally structured framework of retrieval-enhanced models, thereby fostering interdisciplinary future research.

Deep learning approaches to natural language processing have made great strides in recent years. While these models produce symbols that convey vast amounts of diverse knowledge, it is unclear how such symbols are grounded in data from the world. In this paper, we explore the development of a private language for visual data representation by training emergent language (EL) encoders/decoders in both i) a traditional referential game environment and ii) a contrastive learning environment utilizing a within-class matching training paradigm. An additional classification layer utilizing neural machine translation and random forest classification was used to transform symbolic representations (sequences of integer symbols) to class labels. These methods were applied in two experiments focusing on object recognition and action recognition. For object recognition, a set of sketches produced by human participants from real imagery was used (Sketchy dataset) and for action recognition, 2D trajectories were generated from 3D motion capture systems (MOVI dataset). In order to interpret the symbols produced for data in each experiment, gradient-weighted class activation mapping (Grad-CAM) methods were used to identify pixel regions indicating semantic features which contribute evidence towards symbols in learned languages. Additionally, a t-distributed stochastic neighbor embedding (t-SNE) method was used to investigate embeddings learned by CNN feature extractors.

Research on question answering with knowledge base has recently seen an increasing use of deep architectures. In this extended abstract, we study the application of the neural machine translation paradigm for question parsing. We employ a sequence-to-sequence model to learn graph patterns in the SPARQL graph query language and their compositions. Instead of inducing the programs through question-answer pairs, we expect a semi-supervised approach, where alignments between questions and queries are built through templates. We argue that the coverage of language utterances can be expanded using late notable works in natural language generation.

The integration of biomolecular modeling with natural language (BL) has emerged as a promising interdisciplinary area at the intersection of artificial intelligence, chemistry and biology. This approach leverages the rich, multifaceted descriptions of biomolecules contained within textual data sources to enhance our fundamental understanding and enable downstream computational tasks such as biomolecule property prediction. The fusion of the nuanced narratives expressed through natural language with the structural and functional specifics of biomolecules described via various molecular modeling techniques opens new avenues for comprehensively representing and analyzing biomolecules. By incorporating the contextual language data that surrounds biomolecules into their modeling, BL aims to capture a holistic view encompassing both the symbolic qualities conveyed through language as well as quantitative structural characteristics. In this review, we provide an extensive analysis of recent advancements achieved through cross modeling of biomolecules and natural language. (1) We begin by outlining the technical representations of biomolecules employed, including sequences, 2D graphs, and 3D structures. (2) We then examine in depth the rationale and key objectives underlying effective multi-modal integration of language and molecular data sources. (3) We subsequently survey the practical applications enabled to date in this developing research area. (4) We also compile and summarize the available resources and datasets to facilitate future work. (5) Looking ahead, we identify several promising research directions worthy of further exploration and investment to continue advancing the field. The related resources and contents are updating in https://github.com/QizhiPei/Awesome-Biomolecule-Language-Cross-Modeling.

Automatic International Classification of Diseases (ICD) coding aims to assign multiple ICD codes to a medical note with average length of 3,000+ tokens. This task is challenging due to a high-dimensional space of multi-label assignment (tens of thousands of ICD codes) and the long-tail challenge: only a few codes (common diseases) are frequently assigned while most codes (rare diseases) are infrequently assigned. This study addresses the long-tail challenge by adapting a prompt-based fine-tuning technique with label semantics, which has been shown to be effective under few-shot setting. To further enhance the performance in medical domain, we propose a knowledge-enhanced longformer by injecting three domain-specific knowledge: hierarchy, synonym, and abbreviation with additional pretraining using contrastive learning. Experiments on MIMIC-III-full, a benchmark dataset of code assignment, show that our proposed method outperforms previous state-of-the-art method in 14.5% in marco F1 (from 10.3 to 11.8, P<0.001). To further test our model on few-shot setting, we created a new rare diseases coding dataset, MIMIC-III-rare50, on which our model improves marco F1 from 17.1 to 30.4 and micro F1 from 17.2 to 32.6 compared to previous method.

Common language models typically predict the next word given the context. In this work, we propose a method that improves language modeling by learning to align the given context and the following phrase. The model does not require any linguistic annotation of phrase segmentation. Instead, we define syntactic heights and phrase segmentation rules, enabling the model to automatically induce phrases, recognize their task-specific heads, and generate phrase embeddings in an unsupervised learning manner. Our method can easily be applied to language models with different network architectures since an independent module is used for phrase induction and context-phrase alignment, and no change is required in the underlying language modeling network. Experiments have shown that our model outperformed several strong baseline models on different data sets. We achieved a new state-of-the-art performance of 17.4 perplexity on the Wikitext-103 dataset. Additionally, visualizing the outputs of the phrase induction module showed that our model is able to learn approximate phrase-level structural knowledge without any annotation.

Translating training data into many languages has emerged as a practical solution for improving cross-lingual transfer. For tasks that involve span-level annotations, such as information extraction or question answering, an additional label projection step is required to map annotated spans onto the translated texts. Recently, a few efforts have utilized a simple mark-then-translate method to jointly perform translation and projection by inserting special markers around the labeled spans in the original sentence. However, as far as we are aware, no empirical analysis has been conducted on how this approach compares to traditional annotation projection based on word alignment. In this paper, we present an extensive empirical study across 57 languages and three tasks (QA, NER, and Event Extraction) to evaluate the effectiveness and limitations of both methods, filling an important gap in the literature. Experimental results show that our optimized version of mark-then-translate, which we call EasyProject, is easily applied to many languages and works surprisingly well, outperforming the more complex word alignment-based methods. We analyze several key factors that affect the end-task performance, and show EasyProject works well because it can accurately preserve label span boundaries after translation. We will publicly release all our code and data.

Training models on low-resource named entity recognition tasks has been shown to be a challenge, especially in industrial applications where deploying updated models is a continuous effort and crucial for business operations. In such cases there is often an abundance of unlabeled data, while labeled data is scarce or unavailable. Pre-trained language models trained to extract contextual features from text were shown to improve many natural language processing (NLP) tasks, including scarcely labeled tasks, by leveraging transfer learning. However, such models impose a heavy memory and computational burden, making it a challenge to train and deploy such models for inference use. In this work-in-progress we combined the effectiveness of transfer learning provided by pre-trained masked language models with a semi-supervised approach to train a fast and compact model using labeled and unlabeled examples. Preliminary evaluations show that the compact models can achieve competitive accuracy with 36x compression rate when compared with a state-of-the-art pre-trained language model, and run significantly faster in inference, allowing deployment of such models in production environments or on edge devices.

Alignment is the most critical step in building large language models (LLMs) that meet human needs. With the rapid development of LLMs gradually surpassing human capabilities, traditional alignment methods based on human-annotation are increasingly unable to meet the scalability demands. Therefore, there is an urgent need to explore new sources of automated alignment signals and technical approaches. In this paper, we systematically review the recently emerging methods of automated alignment, attempting to explore how to achieve effective, scalable, automated alignment once the capabilities of LLMs exceed those of humans. Specifically, we categorize existing automated alignment methods into 4 major categories based on the sources of alignment signals and discuss the current status and potential development of each category. Additionally, we explore the underlying mechanisms that enable automated alignment and discuss the essential factors that make automated alignment technologies feasible and effective from the fundamental role of alignment.

In multi-label classification, each example in a dataset may be annotated as belonging to one or more classes (or none of the classes). Example applications include image (or document) tagging where each possible tag either applies to a particular image (or document) or not. With many possible classes to consider, data annotators are likely to make errors when labeling such data in practice. Here we consider algorithms for finding mislabeled examples in multi-label classification datasets. We propose an extension of the Confident Learning framework to this setting, as well as a label quality score that ranks examples with label errors much higher than those which are correctly labeled. Both approaches can utilize any trained classifier. After demonstrating that our methodology empirically outperforms other algorithms for label error detection, we apply our approach to discover many label errors in the CelebA image tagging dataset.

The Russian Drug Reaction Corpus (RuDReC) is a new partially annotated corpus of consumer reviews in Russian about pharmaceutical products for the detection of health-related named entities and the effectiveness of pharmaceutical products. The corpus itself consists of two parts, the raw one and the labelled one. The raw part includes 1.4 million health-related user-generated texts collected from various Internet sources, including social media. The labelled part contains 500 consumer reviews about drug therapy with drug- and disease-related information. Labels for sentences include health-related issues or their absence. The sentences with one are additionally labelled at the expression level for identification of fine-grained subtypes such as drug classes and drug forms, drug indications, and drug reactions. Further, we present a baseline model for named entity recognition (NER) and multi-label sentence classification tasks on this corpus. The macro F1 score of 74.85% in the NER task was achieved by our RuDR-BERT model. For the sentence classification task, our model achieves the macro F1 score of 68.82% gaining 7.47% over the score of BERT model trained on Russian data. We make the RuDReC corpus and pretrained weights of domain-specific BERT models freely available at https://github.com/cimm-kzn/RuDReC

Sequence-to-sequence (seq2seq) learning is a popular fashion for large-scale pretraining language models. However, the prior seq2seq pretraining models generally focus on reconstructive objectives on the decoder side and neglect the effect of encoder-side supervision, which we argue may lead to sub-optimal performance. To verify our hypothesis, we first empirically study the functionalities of the encoder and decoder in seq2seq pretrained language models, and find that the encoder takes an important but under-exploitation role than the decoder regarding the downstream performance and neuron activation. Therefore, we propose an encoding-enhanced seq2seq pretraining strategy, namely E2S2, which improves the seq2seq models via integrating more efficient self-supervised information into the encoders. Specifically, E2S2 adopts two self-supervised objectives on the encoder side from two aspects: 1) locally denoising the corrupted sentence (denoising objective); and 2) globally learning better sentence representations (contrastive objective). With the help of both objectives, the encoder can effectively distinguish the noise tokens and capture high-level (i.e. syntactic and semantic) knowledge, thus strengthening the ability of seq2seq model to accurately achieve the conditional generation. On a large diversity of downstream natural language understanding and generation tasks, E2S2 dominantly improves the performance of its powerful backbone models, e.g. BART and T5. For example, upon BART backbone, we achieve +1.1% averaged gain on the general language understanding evaluation (GLUE) benchmark and +1.75% F_0.5 score improvement on CoNLL2014 dataset. We also provide in-depth analyses to show the improvement stems from better linguistic representation. We hope that our work will foster future self-supervision research on seq2seq language model pretraining.

Automatically summarizing patients' main problems from daily progress notes using natural language processing methods helps to battle against information and cognitive overload in hospital settings and potentially assists providers with computerized diagnostic decision support. Problem list summarization requires a model to understand, abstract, and generate clinical documentation. In this work, we propose a new NLP task that aims to generate a list of problems in a patient's daily care plan using input from the provider's progress notes during hospitalization. We investigate the performance of T5 and BART, two state-of-the-art seq2seq transformer architectures, in solving this problem. We provide a corpus built on top of progress notes from publicly available electronic health record progress notes in the Medical Information Mart for Intensive Care (MIMIC)-III. T5 and BART are trained on general domain text, and we experiment with a data augmentation method and a domain adaptation pre-training method to increase exposure to medical vocabulary and knowledge. Evaluation methods include ROUGE, BERTScore, cosine similarity on sentence embedding, and F-score on medical concepts. Results show that T5 with domain adaptive pre-training achieves significant performance gains compared to a rule-based system and general domain pre-trained language models, indicating a promising direction for tackling the problem summarization task.

The ability to learn new concepts sequentially is a major weakness for modern neural networks, which hinders their use in non-stationary environments. Their propensity to fit the current data distribution to the detriment of the past acquired knowledge leads to the catastrophic forgetting issue. In this work we tackle the problem of Spoken Language Understanding applied to a continual learning setting. We first define a class-incremental scenario for the SLURP dataset. Then, we propose three knowledge distillation (KD) approaches to mitigate forgetting for a sequence-to-sequence transformer model: the first KD method is applied to the encoder output (audio-KD), and the other two work on the decoder output, either directly on the token-level (tok-KD) or on the sequence-level (seq-KD) distributions. We show that the seq-KD substantially improves all the performance metrics, and its combination with the audio-KD further decreases the average WER and enhances the entity prediction metric.

In this work we focus on multi-turn passage retrieval as a crucial component of conversational search. One of the key challenges in multi-turn passage retrieval comes from the fact that the current turn query is often underspecified due to zero anaphora, topic change, or topic return. Context from the conversational history can be used to arrive at a better expression of the current turn query, defined as the task of query resolution. In this paper, we model the query resolution task as a binary term classification problem: for each term appearing in the previous turns of the conversation decide whether to add it to the current turn query or not. We propose QuReTeC (Query Resolution by Term Classification), a neural query resolution model based on bidirectional transformers. We propose a distant supervision method to automatically generate training data by using query-passage relevance labels. Such labels are often readily available in a collection either as human annotations or inferred from user interactions. We show that QuReTeC outperforms state-of-the-art models, and furthermore, that our distant supervision method can be used to substantially reduce the amount of human-curated data required to train QuReTeC. We incorporate QuReTeC in a multi-turn, multi-stage passage retrieval architecture and demonstrate its effectiveness on the TREC CAsT dataset.

In-context learning (ICL) has revolutionized the capabilities of transformer models in NLP. In our project, we extend the understanding of the mechanisms underpinning ICL by exploring whether transformers can learn from sequential, non-textual function class data distributions. We introduce a novel sliding window sequential function class and employ toy-sized transformers with a GPT-2 architecture to conduct our experiments. Our analysis indicates that these models can indeed leverage ICL when trained on non-textual sequential function classes. Additionally, our experiments with randomized y-label sequences highlights that transformers retain some ICL capabilities even when the label associations are obfuscated. We provide evidence that transformers can reason with and understand sequentiality encoded within function classes, as reflected by the effective learning of our proposed tasks. Our results also show that the performance deteriorated with increasing randomness in the labels, though not to the extent one might expect, implying a potential robustness of learned sequentiality against label noise. Future research may want to look into how previous explanations of transformers, such as induction heads and task vectors, relate to sequentiality in ICL in these toy examples. Our investigation lays the groundwork for further research into how transformers process and perceive sequential data.

The task of annotating data into concise summaries poses a significant challenge across various domains, frequently requiring the allocation of significant time and specialized knowledge by human experts. Despite existing efforts to use large language models for annotation tasks, significant problems such as limited applicability to unlabeled data, the absence of self-supervised methods, and the lack of focus on complex structured data still persist. In this work, we propose a GPT self-supervision annotation method, which embodies a generating-recovering paradigm that leverages the one-shot learning capabilities of the Generative Pretrained Transformer (GPT). The proposed approach comprises a one-shot tuning phase followed by a generation phase. In the one-shot tuning phase, we sample a data from the support set as part of the prompt for GPT to generate a textual summary, which is then used to recover the original data. The alignment score between the recovered and original data serves as a self-supervision navigator to refine the process. In the generation stage, the optimally selected one-shot sample serves as a template in the prompt and is applied to generating summaries from challenging datasets. The annotation performance is evaluated by tuning several human feedback reward networks and by calculating alignment scores between original and recovered data at both sentence and structure levels. Our self-supervised annotation method consistently achieves competitive scores, convincingly demonstrating its robust strength in various data-to-summary annotation tasks.

Transforming unstructured text into structured and meaningful forms, organized by useful category labels, is a fundamental step in text mining for downstream analysis and application. However, most existing methods for producing label taxonomies and building text-based label classifiers still rely heavily on domain expertise and manual curation, making the process expensive and time-consuming. This is particularly challenging when the label space is under-specified and large-scale data annotations are unavailable. In this paper, we address these challenges with Large Language Models (LLMs), whose prompt-based interface facilitates the induction and use of large-scale pseudo labels. We propose TnT-LLM, a two-phase framework that employs LLMs to automate the process of end-to-end label generation and assignment with minimal human effort for any given use-case. In the first phase, we introduce a zero-shot, multi-stage reasoning approach which enables LLMs to produce and refine a label taxonomy iteratively. In the second phase, LLMs are used as data labelers that yield training samples so that lightweight supervised classifiers can be reliably built, deployed, and served at scale. We apply TnT-LLM to the analysis of user intent and conversational domain for Bing Copilot (formerly Bing Chat), an open-domain chat-based search engine. Extensive experiments using both human and automatic evaluation metrics demonstrate that TnT-LLM generates more accurate and relevant label taxonomies when compared against state-of-the-art baselines, and achieves a favorable balance between accuracy and efficiency for classification at scale. We also share our practical experiences and insights on the challenges and opportunities of using LLMs for large-scale text mining in real-world applications.

Idiomatic expressions have always been a bottleneck for language comprehension and natural language understanding, specifically for tasks like Machine Translation(MT). MT systems predominantly produce literal translations of idiomatic expressions as they do not exhibit generic and linguistically deterministic patterns which can be exploited for comprehension of the non-compositional meaning of the expressions. These expressions occur in parallel corpora used for training, but due to the comparatively high occurrences of the constituent words of idiomatic expressions in literal context, the idiomatic meaning gets overpowered by the compositional meaning of the expression. State of the art Metaphor Detection Systems are able to detect non-compositional usage at word level but miss out on idiosyncratic phrasal idiomatic expressions. This creates a dire need for a dataset with a wider coverage and higher occurrence of commonly occurring idiomatic expressions, the spans of which can be used for Metaphor Detection. With this in mind, we present our English Possible Idiomatic Expressions(EPIE) corpus containing 25206 sentences labelled with lexical instances of 717 idiomatic expressions. These spans also cover literal usages for the given set of idiomatic expressions. We also present the utility of our dataset by using it to train a sequence labelling module and testing on three independent datasets with high accuracy, precision and recall scores.

Large language models (LLMs) have achieved impressive success in text-formatted learning problems, and most popular LLMs have been deployed in a black-box fashion. Meanwhile, fine-tuning is usually necessary for a specific downstream task to obtain better performance, and this functionality is provided by the owners of the black-box LLMs. To fine-tune a black-box LLM, labeled data are always required to adjust the model parameters. However, in many real-world applications, LLMs can label textual datasets with even better quality than skilled human annotators, motivating us to explore the possibility of fine-tuning black-box LLMs with unlabeled data. In this paper, we propose unsupervised prompt learning for classification with black-box LLMs, where the learning parameters are the prompt itself and the pseudo labels of unlabeled data. Specifically, the prompt is modeled as a sequence of discrete tokens, and every token has its own to-be-learned categorical distribution. On the other hand, for learning the pseudo labels, we are the first to consider the in-context learning (ICL) capabilities of LLMs: we first identify reliable pseudo-labeled data using the LLM, and then assign pseudo labels to other unlabeled data based on the prompt, allowing the pseudo-labeled data to serve as in-context demonstrations alongside the prompt. Those in-context demonstrations matter: previously, they are involved when the prompt is used for prediction while they are not involved when the prompt is trained; thus, taking them into account during training makes the prompt-learning and prompt-using stages more consistent. Experiments on benchmark datasets show the effectiveness of our proposed algorithm. After unsupervised prompt learning, we can use the pseudo-labeled dataset for further fine-tuning by the owners of the black-box LLMs.

Machine learning, notably deep learning, has significantly propelled molecular investigations within the biochemical sphere. Traditionally, modeling for such research has centered around a handful of paradigms. For instance, the prediction paradigm is frequently deployed for tasks such as molecular property prediction. To enhance the generation and decipherability of purely data-driven models, scholars have integrated biochemical domain knowledge into these molecular study models. This integration has sparked a surge in paradigm transfer, which is solving one molecular learning task by reformulating it as another one. With the emergence of Large Language Models, these paradigms have demonstrated an escalating trend towards harmonized unification. In this work, we delineate a literature survey focused on knowledge-informed molecular learning from the perspective of paradigm transfer. We classify the paradigms, scrutinize their methodologies, and dissect the contribution of domain knowledge. Moreover, we encapsulate prevailing trends and identify intriguing avenues for future exploration in molecular learning.

Few-shot named entity recognition (NER) detects named entities within text using only a few annotated examples. One promising line of research is to leverage natural language descriptions of each entity type: the common label PER might, for example, be verbalized as ''person entity.'' In an initial label interpretation learning phase, the model learns to interpret such verbalized descriptions of entity types. In a subsequent few-shot tagset extension phase, this model is then given a description of a previously unseen entity type (such as ''music album'') and optionally a few training examples to perform few-shot NER for this type. In this paper, we systematically explore the impact of a strong semantic prior to interpret verbalizations of new entity types by massively scaling up the number and granularity of entity types used for label interpretation learning. To this end, we leverage an entity linking benchmark to create a dataset with orders of magnitude of more distinct entity types and descriptions as currently used datasets. We find that this increased signal yields strong results in zero- and few-shot NER in in-domain, cross-domain, and even cross-lingual settings. Our findings indicate significant potential for improving few-shot NER through heuristical data-based optimization.

Neural sequence-to-sequence models are currently the dominant approach in several natural language processing tasks, but require large parallel corpora. We present a sequence-to-sequence-to-sequence autoencoder (SEQ^3), consisting of two chained encoder-decoder pairs, with words used as a sequence of discrete latent variables. We apply the proposed model to unsupervised abstractive sentence compression, where the first and last sequences are the input and reconstructed sentences, respectively, while the middle sequence is the compressed sentence. Constraining the length of the latent word sequences forces the model to distill important information from the input. A pretrained language model, acting as a prior over the latent sequences, encourages the compressed sentences to be human-readable. Continuous relaxations enable us to sample from categorical distributions, allowing gradient-based optimization, unlike alternatives that rely on reinforcement learning. The proposed model does not require parallel text-summary pairs, achieving promising results in unsupervised sentence compression on benchmark datasets.

In this work, we aim to connect two research areas: instruction models and retrieval-based models. While instruction-tuned Large Language Models (LLMs) excel at extracting information from text, they are not suitable for semantic retrieval. Similarity search over embedding vectors allows to index and query vectors, but the similarity reflected in the embedding is sub-optimal for many use cases. We identify the task of retrieving sentences based on abstract descriptions of their content. We demonstrate the inadequacy of current text embeddings and propose an alternative model that significantly improves when used in standard nearest neighbor search. The model is trained using positive and negative pairs sourced through prompting an a large language model (LLM). While it is easy to source the training material from an LLM, the retrieval task cannot be performed by the LLM directly. This demonstrates that data from LLMs can be used not only for distilling more efficient specialized models than the original LLM, but also for creating new capabilities not immediately possible using the original model.

Protein language models are a powerful tool for learning protein representations through pre-training on vast protein sequence datasets. However, traditional protein language models lack explicit structural supervision, despite its relevance to protein function. To address this issue, we introduce the integration of remote homology detection to distill structural information into protein language models without requiring explicit protein structures as input. We evaluate the impact of this structure-informed training on downstream protein function prediction tasks. Experimental results reveal consistent improvements in function annotation accuracy for EC number and GO term prediction. Performance on mutant datasets, however, varies based on the relationship between targeted properties and protein structures. This underscores the importance of considering this relationship when applying structure-aware training to protein function prediction tasks. Code and model weights are available at https://github.com/DeepGraphLearning/esm-s.

Sequence generation applications require satisfying semantic constraints, such as ensuring that programs are correct, using certain keywords, or avoiding undesirable content. Language models, whether fine-tuned or prompted with few-shot demonstrations, frequently violate these constraints, and lack a mechanism to iteratively revise their outputs. Moreover, some powerful language models are of extreme scale or inaccessible, making it inefficient, if not infeasible, to update their parameters for task-specific adaptation. We present Self-Correction, an approach that decouples an imperfect base generator (an off-the-shelf language model or supervised sequence-to-sequence model) from a separate corrector that learns to iteratively correct imperfect generations. To train the corrector, we propose an online training procedure that can use either scalar or natural language feedback on intermediate imperfect generations. We show that Self-Correction improves upon the base generator in three diverse generation tasks - mathematical program synthesis, lexically-constrained generation, and toxicity control - even when the corrector is much smaller than the base generator.

In drug-discovery-related tasks such as virtual screening, machine learning is emerging as a promising way to predict molecular properties. Conventionally, molecular fingerprints (numerical representations of molecules) are calculated through rule-based algorithms that map molecules to a sparse discrete space. However, these algorithms perform poorly for shallow prediction models or small datasets. To address this issue, we present SMILES Transformer. Inspired by Transformer and pre-trained language models from natural language processing, SMILES Transformer learns molecular fingerprints through unsupervised pre-training of the sequence-to-sequence language model using a huge corpus of SMILES, a text representation system for molecules. We performed benchmarks on 10 datasets against existing fingerprints and graph-based methods and demonstrated the superiority of the proposed algorithms in small-data settings where pre-training facilitated good generalization. Moreover, we define a novel metric to concurrently measure model accuracy and data efficiency.