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Substrate Prediction for RiPP Biosynthetic Enzymes via Masked Language Modeling and Transfer Learning

Ribosomally synthesized and post-translationally modified peptide (RiPP) biosynthetic enzymes often exhibit promiscuous substrate preferences that cannot be reduced to simple rules. Large language models are promising tools for predicting such peptide fitness landscapes. However, state-of-the-art protein language models are trained on relatively few peptide sequences. A previous study comprehensively profiled the peptide substrate preferences of LazBF (a two-component serine dehydratase) and LazDEF (a three-component azole synthetase) from the lactazole biosynthetic pathway. We demonstrated that masked language modeling of LazBF substrate preferences produced language model embeddings that improved downstream classification models of both LazBF and LazDEF substrates. Similarly, masked language modeling of LazDEF substrate preferences produced embeddings that improved the performance of classification models of both LazBF and LazDEF substrates. Our results suggest that the models learned functional forms that are transferable between distinct enzymatic transformations that act within the same biosynthetic pathway. Our transfer learning method improved performance and data efficiency in data-scarce scenarios. We then fine-tuned models on each data set and showed that the fine-tuned models provided interpretable insight that we anticipate will facilitate the design of substrate libraries that are compatible with desired RiPP biosynthetic pathways.

Fast, Effective, and Self-Supervised: Transforming Masked Language Models into Universal Lexical and Sentence Encoders

Pretrained Masked Language Models (MLMs) have revolutionised NLP in recent years. However, previous work has indicated that off-the-shelf MLMs are not effective as universal lexical or sentence encoders without further task-specific fine-tuning on NLI, sentence similarity, or paraphrasing tasks using annotated task data. In this work, we demonstrate that it is possible to turn MLMs into effective universal lexical and sentence encoders even without any additional data and without any supervision. We propose an extremely simple, fast and effective contrastive learning technique, termed Mirror-BERT, which converts MLMs (e.g., BERT and RoBERTa) into such encoders in 20-30 seconds without any additional external knowledge. Mirror-BERT relies on fully identical or slightly modified string pairs as positive (i.e., synonymous) fine-tuning examples, and aims to maximise their similarity during identity fine-tuning. We report huge gains over off-the-shelf MLMs with Mirror-BERT in both lexical-level and sentence-level tasks, across different domains and different languages. Notably, in the standard sentence semantic similarity (STS) tasks, our self-supervised Mirror-BERT model even matches the performance of the task-tuned Sentence-BERT models from prior work. Finally, we delve deeper into the inner workings of MLMs, and suggest some evidence on why this simple approach can yield effective universal lexical and sentence encoders.

DrBERT: Unveiling the Potential of Masked Language Modeling Decoder in BERT pretraining

BERT (Bidirectional Encoder Representations from Transformers) has revolutionized the field of natural language processing through its exceptional performance on numerous tasks. Yet, the majority of researchers have mainly concentrated on enhancements related to the model structure, such as relative position embedding and more efficient attention mechanisms. Others have delved into pretraining tricks associated with Masked Language Modeling, including whole word masking. DeBERTa introduced an enhanced decoder adapted for BERT's encoder model for pretraining, proving to be highly effective. We argue that the design and research around enhanced masked language modeling decoders have been underappreciated. In this paper, we propose several designs of enhanced decoders and introduce DrBERT (Decoder-refined BERT), a novel method for modeling training. Typically, a pretrained BERT model is fine-tuned for specific Natural Language Understanding (NLU) tasks. In our approach, we utilize the original BERT model as the encoder, making only changes to the decoder without altering the encoder. This approach does not necessitate extensive modifications to the model's architecture and can be seamlessly integrated into existing fine-tuning pipelines and services, offering an efficient and effective enhancement strategy. Compared to other methods, while we also incur a moderate training cost for the decoder during the pretraining process, our approach does not introduce additional training costs during the fine-tuning phase. We test multiple enhanced decoder structures after pretraining and evaluate their performance on the GLUE benchmark. Our results demonstrate that DrBERT, having only undergone subtle refinements to the model structure during pretraining, significantly enhances model performance without escalating the inference time and serving budget.

Pairing interacting protein sequences using masked language modeling

Predicting which proteins interact together from amino-acid sequences is an important task. We develop a method to pair interacting protein sequences which leverages the power of protein language models trained on multiple sequence alignments, such as MSA Transformer and the EvoFormer module of AlphaFold. We formulate the problem of pairing interacting partners among the paralogs of two protein families in a differentiable way. We introduce a method called DiffPALM that solves it by exploiting the ability of MSA Transformer to fill in masked amino acids in multiple sequence alignments using the surrounding context. MSA Transformer encodes coevolution between functionally or structurally coupled amino acids. We show that it captures inter-chain coevolution, while it was trained on single-chain data, which means that it can be used out-of-distribution. Relying on MSA Transformer without fine-tuning, DiffPALM outperforms existing coevolution-based pairing methods on difficult benchmarks of shallow multiple sequence alignments extracted from ubiquitous prokaryotic protein datasets. It also outperforms an alternative method based on a state-of-the-art protein language model trained on single sequences. Paired alignments of interacting protein sequences are a crucial ingredient of supervised deep learning methods to predict the three-dimensional structure of protein complexes. DiffPALM substantially improves the structure prediction of some eukaryotic protein complexes by AlphaFold-Multimer, without significantly deteriorating any of those we tested. It also achieves competitive performance with using orthology-based pairing.

W2v-BERT: Combining Contrastive Learning and Masked Language Modeling for Self-Supervised Speech Pre-Training

Motivated by the success of masked language modeling~(MLM) in pre-training natural language processing models, we propose w2v-BERT that explores MLM for self-supervised speech representation learning. w2v-BERT is a framework that combines contrastive learning and MLM, where the former trains the model to discretize input continuous speech signals into a finite set of discriminative speech tokens, and the latter trains the model to learn contextualized speech representations via solving a masked prediction task consuming the discretized tokens. In contrast to existing MLM-based speech pre-training frameworks such as HuBERT, which relies on an iterative re-clustering and re-training process, or vq-wav2vec, which concatenates two separately trained modules, w2v-BERT can be optimized in an end-to-end fashion by solving the two self-supervised tasks~(the contrastive task and MLM) simultaneously. Our experiments show that w2v-BERT achieves competitive results compared to current state-of-the-art pre-trained models on the LibriSpeech benchmarks when using the Libri-Light~60k corpus as the unsupervised data. In particular, when compared to published models such as conformer-based wav2vec~2.0 and HuBERT, our model shows~5\% to~10\% relative WER reduction on the test-clean and test-other subsets. When applied to the Google's Voice Search traffic dataset, w2v-BERT outperforms our internal conformer-based wav2vec~2.0 by more than~30\% relatively.

ERNIE-Gram: Pre-Training with Explicitly N-Gram Masked Language Modeling for Natural Language Understanding

Coarse-grained linguistic information, such as named entities or phrases, facilitates adequately representation learning in pre-training. Previous works mainly focus on extending the objective of BERT's Masked Language Modeling (MLM) from masking individual tokens to contiguous sequences of n tokens. We argue that such contiguously masking method neglects to model the intra-dependencies and inter-relation of coarse-grained linguistic information. As an alternative, we propose ERNIE-Gram, an explicitly n-gram masking method to enhance the integration of coarse-grained information into pre-training. In ERNIE-Gram, n-grams are masked and predicted directly using explicit n-gram identities rather than contiguous sequences of n tokens. Furthermore, ERNIE-Gram employs a generator model to sample plausible n-gram identities as optional n-gram masks and predict them in both coarse-grained and fine-grained manners to enable comprehensive n-gram prediction and relation modeling. We pre-train ERNIE-Gram on English and Chinese text corpora and fine-tune on 19 downstream tasks. Experimental results show that ERNIE-Gram outperforms previous pre-training models like XLNet and RoBERTa by a large margin, and achieves comparable results with state-of-the-art methods. The source codes and pre-trained models have been released at https://github.com/PaddlePaddle/ERNIE.

It's All in The [MASK]: Simple Instruction-Tuning Enables BERT-like Masked Language Models As Generative Classifiers

While encoder-only models such as BERT and ModernBERT are ubiquitous in real-world NLP applications, their conventional reliance on task-specific classification heads can limit their applicability compared to decoder-based large language models (LLMs). In this work, we introduce ModernBERT-Large-Instruct, a 0.4B-parameter encoder model that leverages its masked language modelling (MLM) head for generative classification. Our approach employs an intentionally simple training loop and inference mechanism that requires no heavy pre-processing, heavily engineered prompting, or architectural modifications. ModernBERT-Large-Instruct exhibits strong zero-shot performance on both classification and knowledge-based tasks, outperforming similarly sized LLMs on MMLU and achieving 93% of Llama3-1B's MMLU performance with 60% less parameters. We also demonstrate that, when fine-tuned, the generative approach using the MLM head matches or even surpasses traditional classification-head methods across diverse NLU tasks.This capability emerges specifically in models trained on contemporary, diverse data mixes, with models trained on lower volume, less-diverse data yielding considerably weaker performance. Although preliminary, these results demonstrate the potential of using the original generative masked language modelling head over traditional task-specific heads for downstream tasks. Our work suggests that further exploration into this area is warranted, highlighting many avenues for future improvements.

PepMLM: Target Sequence-Conditioned Generation of Peptide Binders via Masked Language Modeling

Target proteins that lack accessible binding pockets and conformational stability have posed increasing challenges for drug development. Induced proximity strategies, such as PROTACs and molecular glues, have thus gained attention as pharmacological alternatives, but still require small molecule docking at binding pockets for targeted protein degradation (TPD). The computational design of protein-based binders presents unique opportunities to access undruggable targets, but have often relied on stable 3D structures or predictions for effective binder generation. Recently, we have leveraged the expressive latent spaces of protein language models (pLMs) for the prioritization of peptide binders from sequence alone, which we have then fused to E3 ubiquitin ligase domains, creating a CRISPR-analogous TPD system for target proteins. However, our methods rely on training discriminator models for ranking heuristically or unconditionally-derived guide peptides for their target binding capability. In this work, we introduce PepMLM, a purely target sequence-conditioned de novo generator of linear peptide binders. By employing a novel masking strategy that uniquely positions cognate peptide sequences at the terminus of target protein sequences, PepMLM tasks the state-of-the-art ESM-2 pLM to fully reconstruct the binder region, achieving low perplexities matching or improving upon previously-validated peptide-protein sequence pairs. After successful in silico benchmarking with AlphaFold-Multimer, we experimentally verify PepMLM's efficacy via fusion of model-derived peptides to E3 ubiquitin ligase domains, demonstrating endogenous degradation of target substrates in cellular models. In total, PepMLM enables the generative design of candidate binders to any target protein, without the requirement of target structure, empowering downstream programmable proteome editing applications.

Pre-training Language Model as a Multi-perspective Course Learner

ELECTRA, the generator-discriminator pre-training framework, has achieved impressive semantic construction capability among various downstream tasks. Despite the convincing performance, ELECTRA still faces the challenges of monotonous training and deficient interaction. Generator with only masked language modeling (MLM) leads to biased learning and label imbalance for discriminator, decreasing learning efficiency; no explicit feedback loop from discriminator to generator results in the chasm between these two components, underutilizing the course learning. In this study, a multi-perspective course learning (MCL) method is proposed to fetch a many degrees and visual angles for sample-efficient pre-training, and to fully leverage the relationship between generator and discriminator. Concretely, three self-supervision courses are designed to alleviate inherent flaws of MLM and balance the label in a multi-perspective way. Besides, two self-correction courses are proposed to bridge the chasm between the two encoders by creating a "correction notebook" for secondary-supervision. Moreover, a course soups trial is conducted to solve the "tug-of-war" dynamics problem of MCL, evolving a stronger pre-trained model. Experimental results show that our method significantly improves ELECTRA's average performance by 2.8% and 3.2% absolute points respectively on GLUE and SQuAD 2.0 benchmarks, and overshadows recent advanced ELECTRA-style models under the same settings. The pre-trained MCL model is available at https://huggingface.co/McmanusChen/MCL-base.

Do Not (Always) Look Right: Investigating the Capabilities of Decoder-Based Large Language Models for Sequence Labeling

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.

What Language Model Architecture and Pretraining Objective Work Best for Zero-Shot Generalization?

Large pretrained Transformer language models have been shown to exhibit zero-shot generalization, i.e. they can perform a wide variety of tasks that they were not explicitly trained on. However, the architectures and pretraining objectives used across state-of-the-art models differ significantly, and there has been limited systematic comparison of these factors. In this work, we present a large-scale evaluation of modeling choices and their impact on zero-shot generalization. In particular, we focus on text-to-text models and experiment with three model architectures (causal/non-causal decoder-only and encoder-decoder), trained with two different pretraining objectives (autoregressive and masked language modeling), and evaluated with and without multitask prompted finetuning. We train models with over 5 billion parameters for more than 170 billion tokens, thereby increasing the likelihood that our conclusions will transfer to even larger scales. Our experiments show that causal decoder-only models trained on an autoregressive language modeling objective exhibit the strongest zero-shot generalization after purely unsupervised pretraining. However, models with non-causal visibility on their input trained with a masked language modeling objective followed by multitask finetuning perform the best among our experiments. We therefore consider the adaptation of pretrained models across architectures and objectives. We find that pretrained non-causal decoder models can be adapted into performant generative causal decoder models, using autoregressive language modeling as a downstream task. Furthermore, we find that pretrained causal decoder models can be efficiently adapted into non-causal decoder models, ultimately achieving competitive performance after multitask finetuning. Code and checkpoints are available at https://github.com/bigscience-workshop/architecture-objective.

Bidirectional Language Models Are Also Few-shot Learners

Large language models such as GPT-3 (Brown et al., 2020) can perform arbitrary tasks without undergoing fine-tuning after being prompted with only a few labeled examples. An arbitrary task can be reformulated as a natural language prompt, and a language model can be asked to generate the completion, indirectly performing the task in a paradigm known as prompt-based learning. To date, emergent prompt-based learning capabilities have mainly been demonstrated for unidirectional language models. However, bidirectional language models pre-trained on denoising objectives such as masked language modeling produce stronger learned representations for transfer learning. This motivates the possibility of prompting bidirectional models, but their pre-training objectives have made them largely incompatible with the existing prompting paradigm. We present SAP (Sequential Autoregressive Prompting), a technique that enables the prompting of bidirectional models. Utilizing the machine translation task as a case study, we prompt the bidirectional mT5 model (Xue et al., 2021) with SAP and demonstrate its few-shot and zero-shot translations outperform the few-shot translations of unidirectional models like GPT-3 and XGLM (Lin et al., 2021), despite mT5's approximately 50% fewer parameters. We further show SAP is effective on question answering and summarization. For the first time, our results demonstrate prompt-based learning is an emergent property of a broader class of language models, rather than only unidirectional models.

Biomedical Language Models are Robust to Sub-optimal Tokenization

As opposed to general English, many concepts in biomedical terminology have been designed in recent history by biomedical professionals with the goal of being precise and concise. This is often achieved by concatenating meaningful biomedical morphemes to create new semantic units. Nevertheless, most modern biomedical language models (LMs) are pre-trained using standard domain-specific tokenizers derived from large scale biomedical corpus statistics without explicitly leveraging the agglutinating nature of biomedical language. In this work, we first find that standard open-domain and biomedical tokenizers are largely unable to segment biomedical terms into meaningful components. Therefore, we hypothesize that using a tokenizer which segments biomedical terminology more accurately would enable biomedical LMs to improve their performance on downstream biomedical NLP tasks, especially ones which involve biomedical terms directly such as named entity recognition (NER) and entity linking. Surprisingly, we find that pre-training a biomedical LM using a more accurate biomedical tokenizer does not improve the entity representation quality of a language model as measured by several intrinsic and extrinsic measures such as masked language modeling prediction (MLM) accuracy as well as NER and entity linking performance. These quantitative findings, along with a case study which explores entity representation quality more directly, suggest that the biomedical pre-training process is quite robust to instances of sub-optimal tokenization.

SecureBERT: A Domain-Specific Language Model for Cybersecurity

Natural Language Processing (NLP) has recently gained wide attention in cybersecurity, particularly in Cyber Threat Intelligence (CTI) and cyber automation. Increased connection and automation have revolutionized the world's economic and cultural infrastructures, while they have introduced risks in terms of cyber attacks. CTI is information that helps cybersecurity analysts make intelligent security decisions, that is often delivered in the form of natural language text, which must be transformed to machine readable format through an automated procedure before it can be used for automated security measures. This paper proposes SecureBERT, a cybersecurity language model capable of capturing text connotations in cybersecurity text (e.g., CTI) and therefore successful in automation for many critical cybersecurity tasks that would otherwise rely on human expertise and time-consuming manual efforts. SecureBERT has been trained using a large corpus of cybersecurity text.To make SecureBERT effective not just in retaining general English understanding, but also when applied to text with cybersecurity implications, we developed a customized tokenizer as well as a method to alter pre-trained weights. The SecureBERT is evaluated using the standard Masked Language Model (MLM) test as well as two additional standard NLP tasks. Our evaluation studies show that SecureBERT\url{https://github.com/ehsanaghaei/SecureBERT} outperforms existing similar models, confirming its capability for solving crucial NLP tasks in cybersecurity.

Toward Efficient Language Model Pretraining and Downstream Adaptation via Self-Evolution: A Case Study on SuperGLUE

This technical report briefly describes our JDExplore d-team's Vega v2 submission on the SuperGLUE leaderboard. SuperGLUE is more challenging than the widely used general language understanding evaluation (GLUE) benchmark, containing eight difficult language understanding tasks, including question answering, natural language inference, word sense disambiguation, coreference resolution, and reasoning. [Method] Instead of arbitrarily increasing the size of a pretrained language model (PLM), our aim is to 1) fully extract knowledge from the input pretraining data given a certain parameter budget, e.g., 6B, and 2) effectively transfer this knowledge to downstream tasks. To achieve goal 1), we propose self-evolution learning for PLMs to wisely predict the informative tokens that should be masked, and supervise the masked language modeling (MLM) process with rectified smooth labels. For goal 2), we leverage the prompt transfer technique to improve the low-resource tasks by transferring the knowledge from the foundation model and related downstream tasks to the target task. [Results] According to our submission record (Oct. 2022), with our optimized pretraining and fine-tuning strategies, our 6B Vega method achieved new state-of-the-art performance on 4/8 tasks, sitting atop the SuperGLUE leaderboard on Oct. 8, 2022, with an average score of 91.3.

L3Cube-HingCorpus and HingBERT: A Code Mixed Hindi-English Dataset and BERT Language Models

Code-switching occurs when more than one language is mixed in a given sentence or a conversation. This phenomenon is more prominent on social media platforms and its adoption is increasing over time. Therefore code-mixed NLP has been extensively studied in the literature. As pre-trained transformer-based architectures are gaining popularity, we observe that real code-mixing data are scarce to pre-train large language models. We present L3Cube-HingCorpus, the first large-scale real Hindi-English code mixed data in a Roman script. It consists of 52.93M sentences and 1.04B tokens, scraped from Twitter. We further present HingBERT, HingMBERT, HingRoBERTa, and HingGPT. The BERT models have been pre-trained on codemixed HingCorpus using masked language modelling objectives. We show the effectiveness of these BERT models on the subsequent downstream tasks like code-mixed sentiment analysis, POS tagging, NER, and LID from the GLUECoS benchmark. The HingGPT is a GPT2 based generative transformer model capable of generating full tweets. We also release L3Cube-HingLID Corpus, the largest code-mixed Hindi-English language identification(LID) dataset and HingBERT-LID, a production-quality LID model to facilitate capturing of more code-mixed data using the process outlined in this work. The dataset and models are available at https://github.com/l3cube-pune/code-mixed-nlp .

CM3: A Causal Masked Multimodal Model of the Internet

We introduce CM3, a family of causally masked generative models trained over a large corpus of structured multi-modal documents that can contain both text and image tokens. Our new causally masked approach generates tokens left to right while also masking out a small number of long token spans that are generated at the end of the string, instead of their original positions. The casual masking object provides a type of hybrid of the more common causal and masked language models, by enabling full generative modeling while also providing bidirectional context when generating the masked spans. We train causally masked language-image models on large-scale web and Wikipedia articles, where each document contains all of the text, hypertext markup, hyperlinks, and image tokens (from a VQVAE-GAN), provided in the order they appear in the original HTML source (before masking). The resulting CM3 models can generate rich structured, multi-modal outputs while conditioning on arbitrary masked document contexts, and thereby implicitly learn a wide range of text, image, and cross modal tasks. They can be prompted to recover, in a zero-shot fashion, the functionality of models such as DALL-E, GENRE, and HTLM. We set the new state-of-the-art in zero-shot summarization, entity linking, and entity disambiguation while maintaining competitive performance in the fine-tuning setting. We can generate images unconditionally, conditioned on text (like DALL-E) and do captioning all in a zero-shot setting with a single model.

Linguistic Entity Masking to Improve Cross-Lingual Representation of Multilingual Language Models for Low-Resource Languages

Multilingual Pre-trained Language models (multiPLMs), trained on the Masked Language Modelling (MLM) objective are commonly being used for cross-lingual tasks such as bitext mining. However, the performance of these models is still suboptimal for low-resource languages (LRLs). To improve the language representation of a given multiPLM, it is possible to further pre-train it. This is known as continual pre-training. Previous research has shown that continual pre-training with MLM and subsequently with Translation Language Modelling (TLM) improves the cross-lingual representation of multiPLMs. However, during masking, both MLM and TLM give equal weight to all tokens in the input sequence, irrespective of the linguistic properties of the tokens. In this paper, we introduce a novel masking strategy, Linguistic Entity Masking (LEM) to be used in the continual pre-training step to further improve the cross-lingual representations of existing multiPLMs. In contrast to MLM and TLM, LEM limits masking to the linguistic entity types nouns, verbs and named entities, which hold a higher prominence in a sentence. Secondly, we limit masking to a single token within the linguistic entity span thus keeping more context, whereas, in MLM and TLM, tokens are masked randomly. We evaluate the effectiveness of LEM using three downstream tasks, namely bitext mining, parallel data curation and code-mixed sentiment analysis using three low-resource language pairs English-Sinhala, English-Tamil, and Sinhala-Tamil. Experiment results show that continually pre-training a multiPLM with LEM outperforms a multiPLM continually pre-trained with MLM+TLM for all three tasks.

CamemBERT 2.0: A Smarter French Language Model Aged to Perfection

French language models, such as CamemBERT, have been widely adopted across industries for natural language processing (NLP) tasks, with models like CamemBERT seeing over 4 million downloads per month. However, these models face challenges due to temporal concept drift, where outdated training data leads to a decline in performance, especially when encountering new topics and terminology. This issue emphasizes the need for updated models that reflect current linguistic trends. In this paper, we introduce two new versions of the CamemBERT base model-CamemBERTav2 and CamemBERTv2-designed to address these challenges. CamemBERTav2 is based on the DeBERTaV3 architecture and makes use of the Replaced Token Detection (RTD) objective for better contextual understanding, while CamemBERTv2 is built on RoBERTa, which uses the Masked Language Modeling (MLM) objective. Both models are trained on a significantly larger and more recent dataset with longer context length and an updated tokenizer that enhances tokenization performance for French. We evaluate the performance of these models on both general-domain NLP tasks and domain-specific applications, such as medical field tasks, demonstrating their versatility and effectiveness across a range of use cases. Our results show that these updated models vastly outperform their predecessors, making them valuable tools for modern NLP systems. All our new models, as well as intermediate checkpoints, are made openly available on Huggingface.

Lessons learned from the evaluation of Spanish Language Models

Given the impact of language models on the field of Natural Language Processing, a number of Spanish encoder-only masked language models (aka BERTs) have been trained and released. These models were developed either within large projects using very large private corpora or by means of smaller scale academic efforts leveraging freely available data. In this paper we present a comprehensive head-to-head comparison of language models for Spanish with the following results: (i) Previously ignored multilingual models from large companies fare better than monolingual models, substantially changing the evaluation landscape of language models in Spanish; (ii) Results across the monolingual models are not conclusive, with supposedly smaller and inferior models performing competitively. Based on these empirical results, we argue for the need of more research to understand the factors underlying them. In this sense, the effect of corpus size, quality and pre-training techniques need to be further investigated to be able to obtain Spanish monolingual models significantly better than the multilingual ones released by large private companies, specially in the face of rapid ongoing progress in the field. The recent activity in the development of language technology for Spanish is to be welcomed, but our results show that building language models remains an open, resource-heavy problem which requires to marry resources (monetary and/or computational) with the best research expertise and practice.

Long-context Protein Language Model

Self-supervised training of language models (LMs) has seen great success for protein sequences in learning meaningful representations and for generative drug design. Most protein LMs are based on the Transformer architecture trained on individual proteins with short context lengths. Such protein LMs cannot extrapolate to longer proteins and protein complexes well. They also fail to account for the underlying biological mechanisms carried out by biomolecular interactions and dynamics i.e., proteins often interact with other proteins, molecules, and pathways in complex biological systems. In this work, we propose LC-PLM based on an alternative protein LM architecture, BiMamba-S, built off selective structured state-space models, to learn high-quality universal protein representations at the amino acid token level using masked language modeling. We also introduce its graph-contextual variant, LC-PLM-G, which contextualizes protein-protein interaction (PPI) graphs for a second stage of training. LC-PLM demonstrates favorable neural scaling laws, better length extrapolation capability, and a 7% to 34% improvement on protein downstream tasks than Transformer-based ESM-2. LC-PLM-G further trained within the context of PPI graphs shows promising results on protein structure and function prediction tasks. Our study demonstrates the benefit of increasing the context size with computationally efficient LM architecture (e.g. structured state space models) in learning universal protein representations and incorporating molecular interaction context contained in biological graphs.

Towards Effective Time-Aware Language Representation: Exploring Enhanced Temporal Understanding in Language Models

In the evolving field of Natural Language Processing, understanding the temporal context of text is increasingly crucial. This study investigates methods to incorporate temporal information during pre-training, aiming to achieve effective time-aware language representation for improved performance on time-related tasks. In contrast to common pre-trained models like BERT, which rely on synchronic document collections such as BookCorpus and Wikipedia, our research introduces BiTimeBERT 2.0, a novel language model pre-trained on a temporal news article collection. BiTimeBERT 2.0 utilizes this temporal news collection, focusing on three innovative pre-training objectives: Time-Aware Masked Language Modeling (TAMLM), Document Dating (DD), and Time-Sensitive Entity Replacement (TSER). Each objective targets a unique aspect of temporal information. TAMLM is designed to enhance the understanding of temporal contexts and relations, DD integrates document timestamps as chronological markers, and TSER focuses on the temporal dynamics of "Person" entities, recognizing their inherent temporal significance. The experimental results consistently demonstrate that BiTimeBERT 2.0 outperforms models like BERT and other existing pre-trained models, achieving substantial gains across a variety of downstream NLP tasks and applications where time plays a pivotal role.

LightCLIP: Learning Multi-Level Interaction for Lightweight Vision-Language Models

Vision-language pre-training like CLIP has shown promising performance on various downstream tasks such as zero-shot image classification and image-text retrieval. Most of the existing CLIP-alike works usually adopt relatively large image encoders like ResNet50 and ViT, while the lightweight counterparts are rarely discussed. In this paper, we propose a multi-level interaction paradigm for training lightweight CLIP models. Firstly, to mitigate the problem that some image-text pairs are not strictly one-to-one correspondence, we improve the conventional global instance-level alignment objective by softening the label of negative samples progressively. Secondly, a relaxed bipartite matching based token-level alignment objective is introduced for finer-grained alignment between image patches and textual words. Moreover, based on the observation that the accuracy of CLIP model does not increase correspondingly as the parameters of text encoder increase, an extra objective of masked language modeling (MLM) is leveraged for maximizing the potential of the shortened text encoder. In practice, an auxiliary fusion module injecting unmasked image embedding into masked text embedding at different network stages is proposed for enhancing the MLM. Extensive experiments show that without introducing additional computational cost during inference, the proposed method achieves a higher performance on multiple downstream tasks.

Small Models, Big Impact: Efficient Corpus and Graph-Based Adaptation of Small Multilingual Language Models for Low-Resource Languages

Low-resource languages (LRLs) face significant challenges in natural language processing (NLP) due to limited data. While current state-of-the-art large language models (LLMs) still struggle with LRLs, smaller multilingual models (mLMs) such as mBERT and XLM-R offer greater promise due to a better fit of their capacity to low training data sizes. This study systematically investigates parameter-efficient adapter-based methods for adapting mLMs to LRLs, evaluating three architectures: Sequential Bottleneck, Invertible Bottleneck, and Low-Rank Adaptation. Using unstructured text from GlotCC and structured knowledge from ConceptNet, we show that small adaptation datasets (e.g., up to 1 GB of free-text or a few MB of knowledge graph data) yield gains in intrinsic (masked language modeling) and extrinsic tasks (topic classification, sentiment analysis, and named entity recognition). We find that Sequential Bottleneck adapters excel in language modeling, while Invertible Bottleneck adapters slightly outperform other methods on downstream tasks due to better embedding alignment and larger parameter counts. Adapter-based methods match or outperform full fine-tuning while using far fewer parameters, and smaller mLMs prove more effective for LRLs than massive LLMs like LLaMA-3, GPT-4, and DeepSeek-R1-based distilled models. While adaptation improves performance, pre-training data size remains the dominant factor, especially for languages with extensive pre-training coverage.

Making the Most of your Model: Methods for Finetuning and Applying Pretrained Transformers

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.

Deep Bidirectional Language-Knowledge Graph Pretraining

Pretraining a language model (LM) on text has been shown to help various downstream NLP tasks. Recent works show that a knowledge graph (KG) can complement text data, offering structured background knowledge that provides a useful scaffold for reasoning. However, these works are not pretrained to learn a deep fusion of the two modalities at scale, limiting the potential to acquire fully joint representations of text and KG. Here we propose DRAGON (Deep Bidirectional Language-Knowledge Graph Pretraining), a self-supervised approach to pretraining a deeply joint language-knowledge foundation model from text and KG at scale. Specifically, our model takes pairs of text segments and relevant KG subgraphs as input and bidirectionally fuses information from both modalities. We pretrain this model by unifying two self-supervised reasoning tasks, masked language modeling and KG link prediction. DRAGON outperforms existing LM and LM+KG models on diverse downstream tasks including question answering across general and biomedical domains, with +5% absolute gain on average. In particular, DRAGON achieves notable performance on complex reasoning about language and knowledge (+10% on questions involving long contexts or multi-step reasoning) and low-resource QA (+8% on OBQA and RiddleSense), and new state-of-the-art results on various BioNLP tasks. Our code and trained models are available at https://github.com/michiyasunaga/dragon.

DomURLs_BERT: Pre-trained BERT-based Model for Malicious Domains and URLs Detection and Classification

Detecting and classifying suspicious or malicious domain names and URLs is fundamental task in cybersecurity. To leverage such indicators of compromise, cybersecurity vendors and practitioners often maintain and update blacklists of known malicious domains and URLs. However, blacklists frequently fail to identify emerging and obfuscated threats. Over the past few decades, there has been significant interest in developing machine learning models that automatically detect malicious domains and URLs, addressing the limitations of blacklists maintenance and updates. In this paper, we introduce DomURLs_BERT, a pre-trained BERT-based encoder adapted for detecting and classifying suspicious/malicious domains and URLs. DomURLs_BERT is pre-trained using the Masked Language Modeling (MLM) objective on a large multilingual corpus of URLs, domain names, and Domain Generation Algorithms (DGA) dataset. In order to assess the performance of DomURLs_BERT, we have conducted experiments on several binary and multi-class classification tasks involving domain names and URLs, covering phishing, malware, DGA, and DNS tunneling. The evaluations results show that the proposed encoder outperforms state-of-the-art character-based deep learning models and cybersecurity-focused BERT models across multiple tasks and datasets. The pre-training dataset, the pre-trained DomURLs_BERT encoder, and the experiments source code are publicly available.

Emerging Property of Masked Token for Effective Pre-training

Driven by the success of Masked Language Modeling (MLM), the realm of self-supervised learning for computer vision has been invigorated by the central role of Masked Image Modeling (MIM) in driving recent breakthroughs. Notwithstanding the achievements of MIM across various downstream tasks, its overall efficiency is occasionally hampered by the lengthy duration of the pre-training phase. This paper presents a perspective that the optimization of masked tokens as a means of addressing the prevailing issue. Initially, we delve into an exploration of the inherent properties that a masked token ought to possess. Within the properties, we principally dedicated to articulating and emphasizing the `data singularity' attribute inherent in masked tokens. Through a comprehensive analysis of the heterogeneity between masked tokens and visible tokens within pre-trained models, we propose a novel approach termed masked token optimization (MTO), specifically designed to improve model efficiency through weight recalibration and the enhancement of the key property of masked tokens. The proposed method serves as an adaptable solution that seamlessly integrates into any MIM approach that leverages masked tokens. As a result, MTO achieves a considerable improvement in pre-training efficiency, resulting in an approximately 50% reduction in pre-training epochs required to attain converged performance of the recent approaches.

ContraBERT: Enhancing Code Pre-trained Models via Contrastive Learning

Large-scale pre-trained models such as CodeBERT, GraphCodeBERT have earned widespread attention from both academia and industry. Attributed to the superior ability in code representation, they have been further applied in multiple downstream tasks such as clone detection, code search and code translation. However, it is also observed that these state-of-the-art pre-trained models are susceptible to adversarial attacks. The performance of these pre-trained models drops significantly with simple perturbations such as renaming variable names. This weakness may be inherited by their downstream models and thereby amplified at an unprecedented scale. To this end, we propose an approach namely ContraBERT that aims to improve the robustness of pre-trained models via contrastive learning. Specifically, we design nine kinds of simple and complex data augmentation operators on the programming language (PL) and natural language (NL) data to construct different variants. Furthermore, we continue to train the existing pre-trained models by masked language modeling (MLM) and contrastive pre-training task on the original samples with their augmented variants to enhance the robustness of the model. The extensive experiments demonstrate that ContraBERT can effectively improve the robustness of the existing pre-trained models. Further study also confirms that these robustness-enhanced models provide improvements as compared to original models over four popular downstream tasks.

Can bidirectional encoder become the ultimate winner for downstream applications of foundation models?

Over the past few decades, Artificial Intelligence(AI) has progressed from the initial machine learning stage to the deep learning stage, and now to the stage of foundational models. Foundational models have the characteristics of pre-training, transfer learning, and self-supervised learning, and pre-trained models can be fine-tuned and applied to various downstream tasks. Under the framework of foundational models, models such as Bidirectional Encoder Representations from Transformers(BERT) and Generative Pre-trained Transformer(GPT) have greatly advanced the development of natural language processing(NLP), especially the emergence of many models based on BERT. BERT broke through the limitation of only using one-way methods for language modeling in pre-training by using a masked language model. It can capture bidirectional context information to predict the masked words in the sequence, this can improve the feature extraction ability of the model. This makes the model very useful for downstream tasks, especially for specialized applications. The model using the bidirectional encoder can better understand the domain knowledge and be better applied to these downstream tasks. So we hope to help understand how this technology has evolved and improved model performance in various natural language processing tasks under the background of foundational models and reveal its importance in capturing context information and improving the model's performance on downstream tasks. This article analyzes one-way and bidirectional models based on GPT and BERT and compares their differences based on the purpose of the model. It also briefly analyzes BERT and the improvements of some models based on BERT. The model's performance on the Stanford Question Answering Dataset(SQuAD) and General Language Understanding Evaluation(GLUE) was compared.

MERT: Acoustic Music Understanding Model with Large-Scale Self-supervised Training

Self-supervised learning (SSL) has recently emerged as a promising paradigm for training generalisable models on large-scale data in the fields of vision, text, and speech. Although SSL has been proven effective in speech and audio, its application to music audio has yet to be thoroughly explored. This is primarily due to the distinctive challenges associated with modelling musical knowledge, particularly its tonal and pitched characteristics of music. To address this research gap, we propose an acoustic Music undERstanding model with large-scale self-supervised Training (MERT), which incorporates teacher models to provide pseudo labels in the masked language modelling (MLM) style acoustic pre-training. In our exploration, we identified a superior combination of teacher models, which outperforms conventional speech and audio approaches in terms of performance. This combination includes an acoustic teacher based on Residual Vector Quantization - Variational AutoEncoder (RVQ-VAE) and a musical teacher based on the Constant-Q Transform (CQT). These teachers effectively guide our student model, a BERT-style transformer encoder, to better model music audio. In addition, we introduce an in-batch noise mixture augmentation to enhance the representation robustness. Furthermore, we explore a wide range of settings to overcome the instability in acoustic language model pre-training, which allows our designed paradigm to scale from 95M to 330M parameters. Experimental results indicate that our model can generalise and perform well on 14 music understanding tasks and attains state-of-the-art (SOTA) overall scores. The code and models are online: https://github.com/yizhilll/MERT.

Model-tuning Via Prompts Makes NLP Models Adversarially Robust

In recent years, NLP practitioners have converged on the following practice: (i) import an off-the-shelf pretrained (masked) language model; (ii) append a multilayer perceptron atop the CLS token's hidden representation (with randomly initialized weights); and (iii) fine-tune the entire model on a downstream task (MLP-FT). This procedure has produced massive gains on standard NLP benchmarks, but these models remain brittle, even to mild adversarial perturbations. In this work, we demonstrate surprising gains in adversarial robustness enjoyed by Model-tuning Via Prompts (MVP), an alternative method of adapting to downstream tasks. Rather than appending an MLP head to make output prediction, MVP appends a prompt template to the input, and makes prediction via text infilling/completion. Across 5 NLP datasets, 4 adversarial attacks, and 3 different models, MVP improves performance against adversarial substitutions by an average of 8% over standard methods and even outperforms adversarial training-based state-of-art defenses by 3.5%. By combining MVP with adversarial training, we achieve further improvements in adversarial robustness while maintaining performance on unperturbed examples. Finally, we conduct ablations to investigate the mechanism underlying these gains. Notably, we find that the main causes of vulnerability of MLP-FT can be attributed to the misalignment between pre-training and fine-tuning tasks, and the randomly initialized MLP parameters.

ELECTRA: Pre-training Text Encoders as Discriminators Rather Than Generators

Masked language modeling (MLM) pre-training methods such as BERT corrupt the input by replacing some tokens with [MASK] and then train a model to reconstruct the original tokens. While they produce good results when transferred to downstream NLP tasks, they generally require large amounts of compute to be effective. As an alternative, we propose a more sample-efficient pre-training task called replaced token detection. Instead of masking the input, our approach corrupts it by replacing some tokens with plausible alternatives sampled from a small generator network. Then, instead of training a model that predicts the original identities of the corrupted tokens, we train a discriminative model that predicts whether each token in the corrupted input was replaced by a generator sample or not. Thorough experiments demonstrate this new pre-training task is more efficient than MLM because the task is defined over all input tokens rather than just the small subset that was masked out. As a result, the contextual representations learned by our approach substantially outperform the ones learned by BERT given the same model size, data, and compute. The gains are particularly strong for small models; for example, we train a model on one GPU for 4 days that outperforms GPT (trained using 30x more compute) on the GLUE natural language understanding benchmark. Our approach also works well at scale, where it performs comparably to RoBERTa and XLNet while using less than 1/4 of their compute and outperforms them when using the same amount of compute.

Fine-grained Audible Video Description

We explore a new task for audio-visual-language modeling called fine-grained audible video description (FAVD). It aims to provide detailed textual descriptions for the given audible videos, including the appearance and spatial locations of each object, the actions of moving objects, and the sounds in videos. Existing visual-language modeling tasks often concentrate on visual cues in videos while undervaluing the language and audio modalities. On the other hand, FAVD requires not only audio-visual-language modeling skills but also paragraph-level language generation abilities. We construct the first fine-grained audible video description benchmark (FAVDBench) to facilitate this research. For each video clip, we first provide a one-sentence summary of the video, ie, the caption, followed by 4-6 sentences describing the visual details and 1-2 audio-related descriptions at the end. The descriptions are provided in both English and Chinese. We create two new metrics for this task: an EntityScore to gauge the completeness of entities in the visual descriptions, and an AudioScore to assess the audio descriptions. As a preliminary approach to this task, we propose an audio-visual-language transformer that extends existing video captioning model with an additional audio branch. We combine the masked language modeling and auto-regressive language modeling losses to optimize our model so that it can produce paragraph-level descriptions. We illustrate the efficiency of our model in audio-visual-language modeling by evaluating it against the proposed benchmark using both conventional captioning metrics and our proposed metrics. We further put our benchmark to the test in video generation models, demonstrating that employing fine-grained video descriptions can create more intricate videos than using captions.

GraphCodeBERT: Pre-training Code Representations with Data Flow

Pre-trained models for programming language have achieved dramatic empirical improvements on a variety of code-related tasks such as code search, code completion, code summarization, etc. However, existing pre-trained models regard a code snippet as a sequence of tokens, while ignoring the inherent structure of code, which provides crucial code semantics and would enhance the code understanding process. We present GraphCodeBERT, a pre-trained model for programming language that considers the inherent structure of code. Instead of taking syntactic-level structure of code like abstract syntax tree (AST), we use data flow in the pre-training stage, which is a semantic-level structure of code that encodes the relation of "where-the-value-comes-from" between variables. Such a semantic-level structure is neat and does not bring an unnecessarily deep hierarchy of AST, the property of which makes the model more efficient. We develop GraphCodeBERT based on Transformer. In addition to using the task of masked language modeling, we introduce two structure-aware pre-training tasks. One is to predict code structure edges, and the other is to align representations between source code and code structure. We implement the model in an efficient way with a graph-guided masked attention function to incorporate the code structure. We evaluate our model on four tasks, including code search, clone detection, code translation, and code refinement. Results show that code structure and newly introduced pre-training tasks can improve GraphCodeBERT and achieves state-of-the-art performance on the four downstream tasks. We further show that the model prefers structure-level attentions over token-level attentions in the task of code search.

UNITER: UNiversal Image-TExt Representation Learning

Joint image-text embedding is the bedrock for most Vision-and-Language (V+L) tasks, where multimodality inputs are simultaneously processed for joint visual and textual understanding. In this paper, we introduce UNITER, a UNiversal Image-TExt Representation, learned through large-scale pre-training over four image-text datasets (COCO, Visual Genome, Conceptual Captions, and SBU Captions), which can power heterogeneous downstream V+L tasks with joint multimodal embeddings. We design four pre-training tasks: Masked Language Modeling (MLM), Masked Region Modeling (MRM, with three variants), Image-Text Matching (ITM), and Word-Region Alignment (WRA). Different from previous work that applies joint random masking to both modalities, we use conditional masking on pre-training tasks (i.e., masked language/region modeling is conditioned on full observation of image/text). In addition to ITM for global image-text alignment, we also propose WRA via the use of Optimal Transport (OT) to explicitly encourage fine-grained alignment between words and image regions during pre-training. Comprehensive analysis shows that both conditional masking and OT-based WRA contribute to better pre-training. We also conduct a thorough ablation study to find an optimal combination of pre-training tasks. Extensive experiments show that UNITER achieves new state of the art across six V+L tasks (over nine datasets), including Visual Question Answering, Image-Text Retrieval, Referring Expression Comprehension, Visual Commonsense Reasoning, Visual Entailment, and NLVR^2. Code is available at https://github.com/ChenRocks/UNITER.

Selfie: Self-supervised Pretraining for Image Embedding

We introduce a pretraining technique called Selfie, which stands for SELFie supervised Image Embedding. Selfie generalizes the concept of masked language modeling of BERT (Devlin et al., 2019) to continuous data, such as images, by making use of the Contrastive Predictive Coding loss (Oord et al., 2018). Given masked-out patches in an input image, our method learns to select the correct patch, among other "distractor" patches sampled from the same image, to fill in the masked location. This classification objective sidesteps the need for predicting exact pixel values of the target patches. The pretraining architecture of Selfie includes a network of convolutional blocks to process patches followed by an attention pooling network to summarize the content of unmasked patches before predicting masked ones. During finetuning, we reuse the convolutional weights found by pretraining. We evaluate Selfie on three benchmarks (CIFAR-10, ImageNet 32 x 32, and ImageNet 224 x 224) with varying amounts of labeled data, from 5% to 100% of the training sets. Our pretraining method provides consistent improvements to ResNet-50 across all settings compared to the standard supervised training of the same network. Notably, on ImageNet 224 x 224 with 60 examples per class (5%), our method improves the mean accuracy of ResNet-50 from 35.6% to 46.7%, an improvement of 11.1 points in absolute accuracy. Our pretraining method also improves ResNet-50 training stability, especially on low data regime, by significantly lowering the standard deviation of test accuracies across different runs.

Parameter-Efficient Neural Reranking for Cross-Lingual and Multilingual Retrieval

State-of-the-art neural (re)rankers are notoriously data-hungry which -- given the lack of large-scale training data in languages other than English -- makes them rarely used in multilingual and cross-lingual retrieval settings. Current approaches therefore commonly transfer rankers trained on English data to other languages and cross-lingual setups by means of multilingual encoders: they fine-tune all parameters of pretrained massively multilingual Transformers (MMTs, e.g., multilingual BERT) on English relevance judgments, and then deploy them in the target language(s). In this work, we show that two parameter-efficient approaches to cross-lingual transfer, namely Sparse Fine-Tuning Masks (SFTMs) and Adapters, allow for a more lightweight and more effective zero-shot transfer to multilingual and cross-lingual retrieval tasks. We first train language adapters (or SFTMs) via Masked Language Modelling and then train retrieval (i.e., reranking) adapters (SFTMs) on top, while keeping all other parameters fixed. At inference, this modular design allows us to compose the ranker by applying the (re)ranking adapter (or SFTM) trained with source language data together with the language adapter (or SFTM) of a target language. We carry out a large scale evaluation on the CLEF-2003 and HC4 benchmarks and additionally, as another contribution, extend the former with queries in three new languages: Kyrgyz, Uyghur and Turkish. The proposed parameter-efficient methods outperform standard zero-shot transfer with full MMT fine-tuning, while being more modular and reducing training times. The gains are particularly pronounced for low-resource languages, where our approaches also substantially outperform the competitive machine translation-based rankers.

BIOSCAN-5M: A Multimodal Dataset for Insect Biodiversity

As part of an ongoing worldwide effort to comprehend and monitor insect biodiversity, this paper presents the BIOSCAN-5M Insect dataset to the machine learning community and establish several benchmark tasks. BIOSCAN-5M is a comprehensive dataset containing multi-modal information for over 5 million insect specimens, and it significantly expands existing image-based biological datasets by including taxonomic labels, raw nucleotide barcode sequences, assigned barcode index numbers, and geographical information. We propose three benchmark experiments to demonstrate the impact of the multi-modal data types on the classification and clustering accuracy. First, we pretrain a masked language model on the DNA barcode sequences of the BIOSCAN-5M dataset, and demonstrate the impact of using this large reference library on species- and genus-level classification performance. Second, we propose a zero-shot transfer learning task applied to images and DNA barcodes to cluster feature embeddings obtained from self-supervised learning, to investigate whether meaningful clusters can be derived from these representation embeddings. Third, we benchmark multi-modality by performing contrastive learning on DNA barcodes, image data, and taxonomic information. This yields a general shared embedding space enabling taxonomic classification using multiple types of information and modalities. The code repository of the BIOSCAN-5M Insect dataset is available at {https://github.com/zahrag/BIOSCAN-5M}

Symbolic Discovery of Optimization Algorithms

We present a method to formulate algorithm discovery as program search, and apply it to discover optimization algorithms for deep neural network training. We leverage efficient search techniques to explore an infinite and sparse program space. To bridge the large generalization gap between proxy and target tasks, we also introduce program selection and simplification strategies. Our method discovers a simple and effective optimization algorithm, Lion (Evo\textbf{Lved Sign Momentum}). It is more memory-efficient than Adam as it only keeps track of the momentum. Different from adaptive optimizers, its update has the same magnitude for each parameter calculated through the sign operation. We compare Lion with widely used optimizers, such as Adam and Adafactor, for training a variety of models on different tasks. On image classification, Lion boosts the accuracy of ViT by up to 2% on ImageNet and saves up to 5x the pre-training compute on JFT. On vision-language contrastive learning, we achieve 88.3% zero-shot and 91.1% fine-tuning accuracy on ImageNet, surpassing the previous best results by 2% and 0.1%, respectively. On diffusion models, Lion outperforms Adam by achieving a better FID score and reducing the training compute by up to 2.3x. For autoregressive, masked language modeling, and fine-tuning, Lion exhibits a similar or better performance compared to Adam. Our analysis of Lion reveals that its performance gain grows with the training batch size. It also requires a smaller learning rate than Adam due to the larger norm of the update produced by the sign function. Additionally, we examine the limitations of Lion and identify scenarios where its improvements are small or not statistically significant. The implementation of Lion is publicly available.

MosaicBERT: A Bidirectional Encoder Optimized for Fast Pretraining

Although BERT-style encoder models are heavily used in NLP research, many researchers do not pretrain their own BERTs from scratch due to the high cost of training. In the past half-decade since BERT first rose to prominence, many advances have been made with other transformer architectures and training configurations that have yet to be systematically incorporated into BERT. Here, we introduce MosaicBERT, a BERT-style encoder architecture and training recipe that is empirically optimized for fast pretraining. This efficient architecture incorporates FlashAttention, Attention with Linear Biases (ALiBi), Gated Linear Units (GLU), a module to dynamically remove padded tokens, and low precision LayerNorm into the classic transformer encoder block. The training recipe includes a 30% masking ratio for the Masked Language Modeling (MLM) objective, bfloat16 precision, and vocabulary size optimized for GPU throughput, in addition to best-practices from RoBERTa and other encoder models. When pretrained from scratch on the C4 dataset, this base model achieves a downstream average GLUE (dev) score of 79.6 in 1.13 hours on 8 A100 80 GB GPUs at a cost of roughly $20. We plot extensive accuracy vs. pretraining speed Pareto curves and show that MosaicBERT base and large are consistently Pareto optimal when compared to a competitive BERT base and large. This empirical speed up in pretraining enables researchers and engineers to pretrain custom BERT-style models at low cost instead of finetune on existing generic models. We open source our model weights and code.

Mistral-SPLADE: LLMs for better Learned Sparse Retrieval

Learned Sparse Retrievers (LSR) have evolved into an effective retrieval strategy that can bridge the gap between traditional keyword-based sparse retrievers and embedding-based dense retrievers. At its core, learned sparse retrievers try to learn the most important semantic keyword expansions from a query and/or document which can facilitate better retrieval with overlapping keyword expansions. LSR like SPLADE has typically been using encoder only models with MLM (masked language modeling) style objective in conjunction with known ways of retrieval performance improvement such as hard negative mining, distillation, etc. In this work, we propose to use decoder-only model for learning semantic keyword expansion. We posit, decoder only models that have seen much higher magnitudes of data are better equipped to learn keyword expansions needed for improved retrieval. We use Mistral as the backbone to develop our Learned Sparse Retriever similar to SPLADE and train it on a subset of sentence-transformer data which is often used for training text embedding models. Our experiments support the hypothesis that a sparse retrieval model based on decoder only large language model (LLM) surpasses the performance of existing LSR systems, including SPLADE and all its variants. The LLM based model (Echo-Mistral-SPLADE) now stands as a state-of-the-art learned sparse retrieval model on the BEIR text retrieval benchmark.

EvoMoE: An Evolutional Mixture-of-Experts Training Framework via Dense-To-Sparse Gate

Mixture-of-experts (MoE) is becoming popular due to its success in improving the model quality, especially in Transformers. By routing tokens with a sparse gate to a few experts (i.e., a small pieces of the full model), MoE can easily increase the model parameters to a very large scale while keeping the computation cost in a constant level. Most existing works just initialize some random experts, set a fixed gating strategy (e.g., Top-k), and train the model from scratch in an ad-hoc way. We identify that these MoE models are suffering from the immature experts and unstable sparse gate, which are harmful to the convergence performance. In this paper, we propose an efficient end-to-end MoE training framework called EvoMoE. EvoMoE starts from training one single expert and gradually evolves into a large and sparse MoE structure. EvoMoE mainly contains two phases: the expert-diversify phase to train the base expert for a while and spawn multiple diverse experts from it, and the gate-sparsify phase to learn an adaptive sparse gate and activate a dynamic number of experts. EvoMoE naturally decouples the joint learning of both the experts and the sparse gate and focuses on learning the basic knowledge with a single expert at the early training stage. Then it diversifies the experts and continues to train the MoE with a novel Dense-to-Sparse gate (DTS-Gate). Specifically, instead of using a permanent sparse gate, DTS-Gate begins as a dense gate that routes tokens to all experts, then gradually and adaptively becomes sparser while routes to fewer experts. Evaluations are conducted on three popular models and tasks, including RoBERTa for masked language modeling task, GPT for language modeling task and Transformer for machine translation task. The results show that EvoMoE outperforms existing baselines, including Switch, BASE Layer, Hash Layer and StableMoE.

PROP: Pre-training with Representative Words Prediction for Ad-hoc Retrieval

Recently pre-trained language representation models such as BERT have shown great success when fine-tuned on downstream tasks including information retrieval (IR). However, pre-training objectives tailored for ad-hoc retrieval have not been well explored. In this paper, we propose Pre-training with Representative wOrds Prediction (PROP) for ad-hoc retrieval. PROP is inspired by the classical statistical language model for IR, specifically the query likelihood model, which assumes that the query is generated as the piece of text representative of the "ideal" document. Based on this idea, we construct the representative words prediction (ROP) task for pre-training. Given an input document, we sample a pair of word sets according to the document language model, where the set with higher likelihood is deemed as more representative of the document. We then pre-train the Transformer model to predict the pairwise preference between the two word sets, jointly with the Masked Language Model (MLM) objective. By further fine-tuning on a variety of representative downstream ad-hoc retrieval tasks, PROP achieves significant improvements over baselines without pre-training or with other pre-training methods. We also show that PROP can achieve exciting performance under both the zero- and low-resource IR settings. The code and pre-trained models are available at https://github.com/Albert-Ma/PROP.

DANCER: Entity Description Augmented Named Entity Corrector for Automatic Speech Recognition

End-to-end automatic speech recognition (E2E ASR) systems often suffer from mistranscription of domain-specific phrases, such as named entities, sometimes leading to catastrophic failures in downstream tasks. A family of fast and lightweight named entity correction (NEC) models for ASR have recently been proposed, which normally build on phonetic-level edit distance algorithms and have shown impressive NEC performance. However, as the named entity (NE) list grows, the problems of phonetic confusion in the NE list are exacerbated; for example, homophone ambiguities increase substantially. In view of this, we proposed a novel Description Augmented Named entity CorrEctoR (dubbed DANCER), which leverages entity descriptions to provide additional information to facilitate mitigation of phonetic confusion for NEC on ASR transcription. To this end, an efficient entity description augmented masked language model (EDA-MLM) comprised of a dense retrieval model is introduced, enabling MLM to adapt swiftly to domain-specific entities for the NEC task. A series of experiments conducted on the AISHELL-1 and Homophone datasets confirm the effectiveness of our modeling approach. DANCER outperforms a strong baseline, the phonetic edit-distance-based NEC model (PED-NEC), by a character error rate (CER) reduction of about 7% relatively on AISHELL-1 for named entities. More notably, when tested on Homophone that contain named entities of high phonetic confusion, DANCER offers a more pronounced CER reduction of 46% relatively over PED-NEC for named entities.

LXMERT: Learning Cross-Modality Encoder Representations from Transformers

Vision-and-language reasoning requires an understanding of visual concepts, language semantics, and, most importantly, the alignment and relationships between these two modalities. We thus propose the LXMERT (Learning Cross-Modality Encoder Representations from Transformers) framework to learn these vision-and-language connections. In LXMERT, we build a large-scale Transformer model that consists of three encoders: an object relationship encoder, a language encoder, and a cross-modality encoder. Next, to endow our model with the capability of connecting vision and language semantics, we pre-train the model with large amounts of image-and-sentence pairs, via five diverse representative pre-training tasks: masked language modeling, masked object prediction (feature regression and label classification), cross-modality matching, and image question answering. These tasks help in learning both intra-modality and cross-modality relationships. After fine-tuning from our pre-trained parameters, our model achieves the state-of-the-art results on two visual question answering datasets (i.e., VQA and GQA). We also show the generalizability of our pre-trained cross-modality model by adapting it to a challenging visual-reasoning task, NLVR2, and improve the previous best result by 22% absolute (54% to 76%). Lastly, we demonstrate detailed ablation studies to prove that both our novel model components and pre-training strategies significantly contribute to our strong results; and also present several attention visualizations for the different encoders. Code and pre-trained models publicly available at: https://github.com/airsplay/lxmert

Arabic Synonym BERT-based Adversarial Examples for Text Classification

Text classification systems have been proven vulnerable to adversarial text examples, modified versions of the original text examples that are often unnoticed by human eyes, yet can force text classification models to alter their classification. Often, research works quantifying the impact of adversarial text attacks have been applied only to models trained in English. In this paper, we introduce the first word-level study of adversarial attacks in Arabic. Specifically, we use a synonym (word-level) attack using a Masked Language Modeling (MLM) task with a BERT model in a black-box setting to assess the robustness of the state-of-the-art text classification models to adversarial attacks in Arabic. To evaluate the grammatical and semantic similarities of the newly produced adversarial examples using our synonym BERT-based attack, we invite four human evaluators to assess and compare the produced adversarial examples with their original examples. We also study the transferability of these newly produced Arabic adversarial examples to various models and investigate the effectiveness of defense mechanisms against these adversarial examples on the BERT models. We find that fine-tuned BERT models were more susceptible to our synonym attacks than the other Deep Neural Networks (DNN) models like WordCNN and WordLSTM we trained. We also find that fine-tuned BERT models were more susceptible to transferred attacks. We, lastly, find that fine-tuned BERT models successfully regain at least 2% in accuracy after applying adversarial training as an initial defense mechanism.

Findings of the Second BabyLM Challenge: Sample-Efficient Pretraining on Developmentally Plausible Corpora

The BabyLM Challenge is a community effort to close the data-efficiency gap between human and computational language learners. Participants compete to optimize language model training on a fixed language data budget of 100 million words or less. This year, we released improved text corpora, as well as a vision-and-language corpus to facilitate research into cognitively plausible vision language models. Submissions were compared on evaluation tasks targeting grammatical ability, (visual) question answering, pragmatic abilities, and grounding, among other abilities. Participants could submit to a 10M-word text-only track, a 100M-word text-only track, and/or a 100M-word and image multimodal track. From 31 submissions employing diverse methods, a hybrid causal-masked language model architecture outperformed other approaches. No submissions outperformed the baselines in the multimodal track. In follow-up analyses, we found a strong relationship between training FLOPs and average performance across tasks, and that the best-performing submissions proposed changes to the training data, training objective, and model architecture. This year's BabyLM Challenge shows that there is still significant room for innovation in this setting, in particular for image-text modeling, but community-driven research can yield actionable insights about effective strategies for small-scale language modeling.

Composable Sparse Fine-Tuning for Cross-Lingual Transfer

Fine-tuning the entire set of parameters of a large pretrained model has become the mainstream approach for transfer learning. To increase its efficiency and prevent catastrophic forgetting and interference, techniques like adapters and sparse fine-tuning have been developed. Adapters are modular, as they can be combined to adapt a model towards different facets of knowledge (e.g., dedicated language and/or task adapters). Sparse fine-tuning is expressive, as it controls the behavior of all model components. In this work, we introduce a new fine-tuning method with both these desirable properties. In particular, we learn sparse, real-valued masks based on a simple variant of the Lottery Ticket Hypothesis. Task-specific masks are obtained from annotated data in a source language, and language-specific masks from masked language modeling in a target language. Both these masks can then be composed with the pretrained model. Unlike adapter-based fine-tuning, this method neither increases the number of parameters at inference time nor alters the original model architecture. Most importantly, it outperforms adapters in zero-shot cross-lingual transfer by a large margin in a series of multilingual benchmarks, including Universal Dependencies, MasakhaNER, and AmericasNLI. Based on an in-depth analysis, we additionally find that sparsity is crucial to prevent both 1) interference between the fine-tunings to be composed and 2) overfitting. We release the code and models at https://github.com/cambridgeltl/composable-sft.

Structural Self-Supervised Objectives for Transformers

This thesis focuses on improving the pre-training of natural language models using unsupervised raw data to make them more efficient and aligned with downstream applications. In the first part, we introduce three alternative pre-training objectives to BERT's Masked Language Modeling (MLM), namely Random Token Substitution (RTS), Cluster-based Random Token Substitution (C-RTS), and Swapped Language Modeling (SLM). These objectives involve token swapping instead of masking, with RTS and C-RTS aiming to predict token originality and SLM predicting the original token values. Results show that RTS and C-RTS require less pre-training time while maintaining performance comparable to MLM. Surprisingly, SLM outperforms MLM on certain tasks despite using the same computational budget. In the second part, we proposes self-supervised pre-training tasks that align structurally with downstream applications, reducing the need for labeled data. We use large corpora like Wikipedia and CC-News to train models to recognize if text spans originate from the same paragraph or document in several ways. By doing continuous pre-training, starting from existing models like RoBERTa, ELECTRA, DeBERTa, BART, and T5, we demonstrate significant performance improvements in tasks like Fact Verification, Answer Sentence Selection, and Summarization. These improvements are especially pronounced when limited annotation data is available. The proposed objectives also achieve state-of-the-art results on various benchmark datasets, including FEVER (dev set), ASNQ, WikiQA, and TREC-QA, as well as enhancing the quality of summaries. Importantly, these techniques can be easily integrated with other methods without altering the internal structure of Transformer models, making them versatile for various NLP applications.

Cross-Modal Implicit Relation Reasoning and Aligning for Text-to-Image Person Retrieval

Text-to-image person retrieval aims to identify the target person based on a given textual description query. The primary challenge is to learn the mapping of visual and textual modalities into a common latent space. Prior works have attempted to address this challenge by leveraging separately pre-trained unimodal models to extract visual and textual features. However, these approaches lack the necessary underlying alignment capabilities required to match multimodal data effectively. Besides, these works use prior information to explore explicit part alignments, which may lead to the distortion of intra-modality information. To alleviate these issues, we present IRRA: a cross-modal Implicit Relation Reasoning and Aligning framework that learns relations between local visual-textual tokens and enhances global image-text matching without requiring additional prior supervision. Specifically, we first design an Implicit Relation Reasoning module in a masked language modeling paradigm. This achieves cross-modal interaction by integrating the visual cues into the textual tokens with a cross-modal multimodal interaction encoder. Secondly, to globally align the visual and textual embeddings, Similarity Distribution Matching is proposed to minimize the KL divergence between image-text similarity distributions and the normalized label matching distributions. The proposed method achieves new state-of-the-art results on all three public datasets, with a notable margin of about 3%-9% for Rank-1 accuracy compared to prior methods.

Towards Zero-Shot Multimodal Machine Translation

Current multimodal machine translation (MMT) systems rely on fully supervised data (i.e models are trained on sentences with their translations and accompanying images). However, this type of data is costly to collect, limiting the extension of MMT to other language pairs for which such data does not exist. In this work, we propose a method to bypass the need for fully supervised data to train MMT systems, using multimodal English data only. Our method, called ZeroMMT, consists in adapting a strong text-only machine translation (MT) model by training it on a mixture of two objectives: visually conditioned masked language modelling and the Kullback-Leibler divergence between the original and new MMT outputs. We evaluate on standard MMT benchmarks and the recently released CoMMuTE, a contrastive benchmark aiming to evaluate how well models use images to disambiguate English sentences. We obtain disambiguation performance close to state-of-the-art MMT models trained additionally on fully supervised examples. To prove that our method generalizes to languages with no fully supervised training data available, we extend the CoMMuTE evaluation dataset to three new languages: Arabic, Russian and Chinese. We further show that we can control the trade-off between disambiguation capabilities and translation fidelity at inference time using classifier-free guidance and without any additional data. Our code, data and trained models are publicly accessible.

VCR: Visual Caption Restoration

We introduce Visual Caption Restoration (VCR), a novel vision-language task that challenges models to accurately restore partially obscured texts using pixel-level hints within images. This task stems from the observation that text embedded in images is intrinsically different from common visual elements and natural language due to the need to align the modalities of vision, text, and text embedded in images. While numerous works have integrated text embedded in images into visual question-answering tasks, approaches to these tasks generally rely on optical character recognition or masked language modeling, thus reducing the task to mainly text-based processing. However, text-based processing becomes ineffective in VCR as accurate text restoration depends on the combined information from provided images, context, and subtle cues from the tiny exposed areas of masked texts. We develop a pipeline to generate synthetic images for the VCR task using image-caption pairs, with adjustable caption visibility to control the task difficulty. With this pipeline, we construct a dataset for VCR called VCR-Wiki using images with captions from Wikipedia, comprising 2.11M English and 346K Chinese entities in both easy and hard split variants. Our results reveal that current vision language models significantly lag behind human performance in the VCR task, and merely fine-tuning the models on our dataset does not lead to notable improvements. We release VCR-Wiki and the data construction code to facilitate future research.

Mask-Enhanced Autoregressive Prediction: Pay Less Attention to Learn More

Large Language Models (LLMs) are discovered to suffer from accurately retrieving key information. To address this, we propose Mask-Enhanced Autoregressive Prediction (MEAP), a simple yet effective training paradigm that seamlessly integrates Masked Language Modeling (MLM) into Next-Token Prediction (NTP) to enhance the latter's in-context retrieval capabilities. Specifically, MEAP first randomly masks a small fraction of input tokens and then directly performs the standard next-token prediction autoregressive using a decoder-only Transformer. MEAP eliminates the need for bidirectional attention or encoder-decoder architectures for MLM, incurring no additional computational overhead during pre-training or inference. Intensive experiments demonstrate that MEAP substantially outperforms NTP on key information retrieval and long-context reasoning tasks, while performing on par or better on commonsense reasoning tasks. The benefits of MEAP also extend to supervised fine-tuning, where it shows remarkable advantages in lost-in-the-middle scenarios, outperforming NTP by 11.77 percentage points. Our analysis indicates that MEAP's effectiveness arises from its ability to promote more distinguishable attention scores by concentrating on a reduced set of non-masked tokens. This mechanism improves the model's focus on task-relevant signals while mitigating the influence of peripheral context. These findings position MEAP as a promising training paradigm for large language models.

SciPrompt: Knowledge-augmented Prompting for Fine-grained Categorization of Scientific Topics

Prompt-based fine-tuning has become an essential method for eliciting information encoded in pre-trained language models for a variety of tasks, including text classification. For multi-class classification tasks, prompt-based fine-tuning under low-resource scenarios has resulted in performance levels comparable to those of fully fine-tuning methods. Previous studies have used crafted prompt templates and verbalizers, mapping from the label terms space to the class space, to solve the classification problem as a masked language modeling task. However, cross-domain and fine-grained prompt-based fine-tuning with an automatically enriched verbalizer remains unexplored, mainly due to the difficulty and costs of manually selecting domain label terms for the verbalizer, which requires humans with domain expertise. To address this challenge, we introduce SciPrompt, a framework designed to automatically retrieve scientific topic-related terms for low-resource text classification tasks. To this end, we select semantically correlated and domain-specific label terms within the context of scientific literature for verbalizer augmentation. Furthermore, we propose a new verbalization strategy that uses correlation scores as additional weights to enhance the prediction performance of the language model during model tuning. Our method outperforms state-of-the-art, prompt-based fine-tuning methods on scientific text classification tasks under few and zero-shot settings, especially in classifying fine-grained and emerging scientific topics.

S2SNet: A Pretrained Neural Network for Superconductivity Discovery

Superconductivity allows electrical current to flow without any energy loss, and thus making solids superconducting is a grand goal of physics, material science, and electrical engineering. More than 16 Nobel Laureates have been awarded for their contribution to superconductivity research. Superconductors are valuable for sustainable development goals (SDGs), such as climate change mitigation, affordable and clean energy, industry, innovation and infrastructure, and so on. However, a unified physics theory explaining all superconductivity mechanism is still unknown. It is believed that superconductivity is microscopically due to not only molecular compositions but also the geometric crystal structure. Hence a new dataset, S2S, containing both crystal structures and superconducting critical temperature, is built upon SuperCon and Material Project. Based on this new dataset, we propose a novel model, S2SNet, which utilizes the attention mechanism for superconductivity prediction. To overcome the shortage of data, S2SNet is pre-trained on the whole Material Project dataset with Masked-Language Modeling (MLM). S2SNet makes a new state-of-the-art, with out-of-sample accuracy of 92% and Area Under Curve (AUC) of 0.92. To the best of our knowledge, S2SNet is the first work to predict superconductivity with only information of crystal structures. This work is beneficial to superconductivity discovery and further SDGs. Code and datasets are available in https://github.com/zjuKeLiu/S2SNet

Understanding Augmentation-based Self-Supervised Representation Learning via RKHS Approximation and Regression

Data augmentation is critical to the empirical success of modern self-supervised representation learning, such as contrastive learning and masked language modeling. However, a theoretical understanding of the exact role of augmentation remains limited. Recent work has built the connection between self-supervised learning and the approximation of the top eigenspace of a graph Laplacian operator, suggesting that learning a linear probe atop such representation can be connected to RKHS regression. Building on this insight, this work delves into a statistical analysis of augmentation-based pretraining. Starting from the isometry property, a geometric characterization of the target function given by the augmentation, we disentangle the effects of the model and the augmentation, and prove two generalization bounds that are free of model complexity. Our first bound works for an arbitrary encoder, where the prediction error is decomposed as the sum of an estimation error incurred by fitting a linear probe with RKHS regression, and an approximation error entailed by RKHS approximation. Our second bound specifically addresses the case where the encoder is near-optimal, that is it approximates the top-d eigenspace of the RKHS induced by the augmentation. A key ingredient in our analysis is the augmentation complexity, which we use to quantitatively compare different augmentations and analyze their impact on downstream performance.

FACTIFY-5WQA: 5W Aspect-based Fact Verification through Question Answering

Automatic fact verification has received significant attention recently. Contemporary automatic fact-checking systems focus on estimating truthfulness using numerical scores which are not human-interpretable. A human fact-checker generally follows several logical steps to verify a verisimilitude claim and conclude whether its truthful or a mere masquerade. Popular fact-checking websites follow a common structure for fact categorization such as half true, half false, false, pants on fire, etc. Therefore, it is necessary to have an aspect-based (delineating which part(s) are true and which are false) explainable system that can assist human fact-checkers in asking relevant questions related to a fact, which can then be validated separately to reach a final verdict. In this paper, we propose a 5W framework (who, what, when, where, and why) for question-answer-based fact explainability. To that end, we present a semi-automatically generated dataset called FACTIFY-5WQA, which consists of 391, 041 facts along with relevant 5W QAs - underscoring our major contribution to this paper. A semantic role labeling system has been utilized to locate 5Ws, which generates QA pairs for claims using a masked language model. Finally, we report a baseline QA system to automatically locate those answers from evidence documents, which can serve as a baseline for future research in the field. Lastly, we propose a robust fact verification system that takes paraphrased claims and automatically validates them. The dataset and the baseline model are available at https: //github.com/ankuranii/acl-5W-QA

SSM-DTA: Breaking the Barriers of Data Scarcity in Drug-Target Affinity Prediction

Accurate prediction of Drug-Target Affinity (DTA) is of vital importance in early-stage drug discovery, facilitating the identification of drugs that can effectively interact with specific targets and regulate their activities. While wet experiments remain the most reliable method, they are time-consuming and resource-intensive, resulting in limited data availability that poses challenges for deep learning approaches. Existing methods have primarily focused on developing techniques based on the available DTA data, without adequately addressing the data scarcity issue. To overcome this challenge, we present the SSM-DTA framework, which incorporates three simple yet highly effective strategies: (1) A multi-task training approach that combines DTA prediction with masked language modeling (MLM) using paired drug-target data. (2) A semi-supervised training method that leverages large-scale unpaired molecules and proteins to enhance drug and target representations. This approach differs from previous methods that only employed molecules or proteins in pre-training. (3) The integration of a lightweight cross-attention module to improve the interaction between drugs and targets, further enhancing prediction accuracy. Through extensive experiments on benchmark datasets such as BindingDB, DAVIS, and KIBA, we demonstrate the superior performance of our framework. Additionally, we conduct case studies on specific drug-target binding activities, virtual screening experiments, drug feature visualizations, and real-world applications, all of which showcase the significant potential of our work. In conclusion, our proposed SSM-DTA framework addresses the data limitation challenge in DTA prediction and yields promising results, paving the way for more efficient and accurate drug discovery processes. Our code is available at https://github.com/QizhiPei/SSM-DTA{Github}.

PepTune: De Novo Generation of Therapeutic Peptides with Multi-Objective-Guided Discrete Diffusion

Peptide therapeutics, a major class of medicines, have achieved remarkable success across diseases such as diabetes and cancer, with landmark examples such as GLP-1 receptor agonists revolutionizing the treatment of type-2 diabetes and obesity. Despite their success, designing peptides that satisfy multiple conflicting objectives, such as target binding affinity, solubility, and membrane permeability, remains a major challenge. Classical drug development and structure-based design are ineffective for such tasks, as they fail to optimize global functional properties critical for therapeutic efficacy. Existing generative frameworks are largely limited to continuous spaces, unconditioned outputs, or single-objective guidance, making them unsuitable for discrete sequence optimization across multiple properties. To address this, we present PepTune, a multi-objective discrete diffusion model for the simultaneous generation and optimization of therapeutic peptide SMILES. Built on the Masked Discrete Language Model (MDLM) framework, PepTune ensures valid peptide structures with state-dependent masking schedules and penalty-based objectives. To guide the diffusion process, we propose a Monte Carlo Tree Search (MCTS)-based strategy that balances exploration and exploitation to iteratively refine Pareto-optimal sequences. MCTS integrates classifier-based rewards with search-tree expansion, overcoming gradient estimation challenges and data sparsity inherent to discrete spaces. Using PepTune, we generate diverse, chemically-modified peptides optimized for multiple therapeutic properties, including target binding affinity, membrane permeability, solubility, hemolysis, and non-fouling characteristics on various disease-relevant targets. In total, our results demonstrate that MCTS-guided discrete diffusion is a powerful and modular approach for multi-objective sequence design in discrete state spaces.

Starbucks: Improved Training for 2D Matryoshka Embeddings

Effective approaches that can scale embedding model depth (i.e. layers) and embedding size allow for the creation of models that are highly scalable across different computational resources and task requirements. While the recently proposed 2D Matryoshka training approach can efficiently produce a single embedding model such that its sub-layers and sub-dimensions can measure text similarity, its effectiveness is significantly worse than if smaller models were trained separately. To address this issue, we propose Starbucks, a new training strategy for Matryoshka-like embedding models, which encompasses both the fine-tuning and pre-training phases. For the fine-tuning phase, we discover that, rather than sampling a random sub-layer and sub-dimensions for each training steps, providing a fixed list of layer-dimension pairs, from small size to large sizes, and computing the loss across all pairs significantly improves the effectiveness of 2D Matryoshka embedding models, bringing them on par with their separately trained counterparts. To further enhance performance, we introduce a new pre-training strategy, which applies masked autoencoder language modelling to sub-layers and sub-dimensions during pre-training, resulting in a stronger backbone for subsequent fine-tuning of the embedding model. Experimental results on both semantic text similarity and retrieval benchmarks demonstrate that the proposed pre-training and fine-tuning strategies significantly improved the effectiveness over 2D Matryoshka models, enabling Starbucks models to perform more efficiently and effectively than separately trained models.

Beyond 512 Tokens: Siamese Multi-depth Transformer-based Hierarchical Encoder for Long-Form Document Matching

Many natural language processing and information retrieval problems can be formalized as the task of semantic matching. Existing work in this area has been largely focused on matching between short texts (e.g., question answering), or between a short and a long text (e.g., ad-hoc retrieval). Semantic matching between long-form documents, which has many important applications like news recommendation, related article recommendation and document clustering, is relatively less explored and needs more research effort. In recent years, self-attention based models like Transformers and BERT have achieved state-of-the-art performance in the task of text matching. These models, however, are still limited to short text like a few sentences or one paragraph due to the quadratic computational complexity of self-attention with respect to input text length. In this paper, we address the issue by proposing the Siamese Multi-depth Transformer-based Hierarchical (SMITH) Encoder for long-form document matching. Our model contains several innovations to adapt self-attention models for longer text input. In order to better capture sentence level semantic relations within a document, we pre-train the model with a novel masked sentence block language modeling task in addition to the masked word language modeling task used by BERT. Our experimental results on several benchmark datasets for long-form document matching show that our proposed SMITH model outperforms the previous state-of-the-art models including hierarchical attention, multi-depth attention-based hierarchical recurrent neural network, and BERT. Comparing to BERT based baselines, our model is able to increase maximum input text length from 512 to 2048. We will open source a Wikipedia based benchmark dataset, code and a pre-trained checkpoint to accelerate future research on long-form document matching.

Cross-lingual Argument Mining in the Medical Domain

Nowadays the medical domain is receiving more and more attention in applications involving Artificial Intelligence. Clinicians have to deal with an enormous amount of unstructured textual data to make a conclusion about patients' health in their everyday life. Argument mining helps to provide a structure to such data by detecting argumentative components in the text and classifying the relations between them. However, as it is the case for many tasks in Natural Language Processing in general and in medical text processing in particular, the large majority of the work on computational argumentation has been done only for English. This is also the case with the only dataset available for argumentation in the medical domain, namely, the annotated medical data of abstracts of Randomized Controlled Trials (RCT) from the MEDLINE database. In order to mitigate the lack of annotated data for other languages, we empirically investigate several strategies to perform argument mining and classification in medical texts for a language for which no annotated data is available. This project shows that automatically translating and project annotations from English to a target language (Spanish) is an effective way to generate annotated data without manual intervention. Furthermore, our experiments demonstrate that the translation and projection approach outperforms zero-shot cross-lingual approaches using a large masked multilingual language model. Finally, we show how the automatically generated data in Spanish can also be used to improve results in the original English evaluation setting.

E-ViLM: Efficient Video-Language Model via Masked Video Modeling with Semantic Vector-Quantized Tokenizer

To build scalable models for challenging real-world tasks, it is important to learn from diverse, multi-modal data in various forms (e.g., videos, text, and images). Among the existing works, a plethora of them have focused on leveraging large but cumbersome cross-modal architectures. Regardless of their effectiveness, larger architectures unavoidably prevent the models from being extended to real-world applications, so building a lightweight VL architecture and an efficient learning schema is of great practical value. In this paper, we propose an Efficient Video-Language Model (dubbed as E-ViLM) and a masked video modeling (MVM) schema, assisted with a semantic vector-quantized tokenizer. In particular, our E-ViLM learns to reconstruct the semantic labels of masked video regions, produced by the pre-trained vector-quantized tokenizer, which discretizes the continuous visual signals into labels. We show that with our simple MVM task and regular VL pre-training modelings, our E-ViLM, despite its compactness, is able to learn expressive representations from Video-Language corpus and generalize well to extensive Video-Language tasks including video question answering, text-to-video retrieval, etc. In particular, our E-ViLM obtains obvious efficiency improvements by reaching competing performances with faster inference speed, i.e., our model reaches 39.3% Top-1 accuracy on the MSRVTT benchmark, retaining 91.4% of the accuracy of state-of-the-art larger VL architecture with only 15% parameters and 94.8% fewer GFLOPs. We also provide extensive ablative studies that validate the effectiveness of our proposed learning schema for E-ViLM.

DetectGPT-SC: Improving Detection of Text Generated by Large Language Models through Self-Consistency with Masked Predictions

General large language models (LLMs) such as ChatGPT have shown remarkable success, but it has also raised concerns among people about the misuse of AI-generated texts. Therefore, an important question is how to detect whether the texts are generated by ChatGPT or by humans. Existing detectors are built on the assumption that there is a distribution gap between human-generated and AI-generated texts. These gaps are typically identified using statistical information or classifiers. In contrast to prior research methods, we find that large language models such as ChatGPT exhibit strong self-consistency in text generation and continuation. Self-consistency capitalizes on the intuition that AI-generated texts can still be reasoned with by large language models using the same logical reasoning when portions of the texts are masked, which differs from human-generated texts. Using this observation, we subsequently proposed a new method for AI-generated texts detection based on self-consistency with masked predictions to determine whether a text is generated by LLMs. This method, which we call DetectGPT-SC. We conducted a series of experiments to evaluate the performance of DetectGPT-SC. In these experiments, we employed various mask scheme, zero-shot, and simple prompt for completing masked texts and self-consistency predictions. The results indicate that DetectGPT-SC outperforms the current state-of-the-art across different tasks.

Masked Thought: Simply Masking Partial Reasoning Steps Can Improve Mathematical Reasoning Learning of Language Models

In reasoning tasks, even a minor error can cascade into inaccurate results, leading to suboptimal performance of large language models in such domains. Earlier fine-tuning approaches sought to mitigate this by leveraging more precise supervisory signals from human labeling, larger models, or self-sampling, although at a high cost. Conversely, we develop a method that avoids external resources, relying instead on introducing perturbations to the input. Our training approach randomly masks certain tokens within the chain of thought, a technique we found to be particularly effective for reasoning tasks. When applied to fine-tuning with GSM8K, this method achieved a 5% improvement in accuracy over standard supervised fine-tuning with a few codes modified and no additional labeling effort. Furthermore, it is complementary to existing methods. When integrated with related data augmentation methods, it leads to an average improvement of 3% improvement in GSM8K accuracy and 1% improvement in MATH accuracy across five datasets of various quality and size, as well as two base models. We further investigate the mechanisms behind this improvement through case studies and quantitative analysis, suggesting that our approach may provide superior support for the model in capturing long-distance dependencies, especially those related to questions. This enhancement could deepen understanding of premises in questions and prior steps. Our code is available at Github.

RetroMAE v2: Duplex Masked Auto-Encoder For Pre-Training Retrieval-Oriented Language Models

To better support retrieval applications such as web search and question answering, growing effort is made to develop retrieval-oriented language models. Most of the existing works focus on improving the semantic representation capability for the contextualized embedding of [CLS] token. However, recent study shows that the ordinary tokens besides [CLS] may provide extra information, which helps to produce a better representation effect. As such, it's necessary to extend the current methods where all contextualized embeddings can be jointly pre-trained for the retrieval tasks. With this motivation, we propose a new pre-training method: duplex masked auto-encoder, a.k.a. DupMAE, which targets on improving the semantic representation capacity for the contextualized embeddings of both [CLS] and ordinary tokens. It introduces two decoding tasks: one is to reconstruct the original input sentence based on the [CLS] embedding, the other one is to minimize the bag-of-words loss (BoW) about the input sentence based on the entire ordinary tokens' embeddings. The two decoding losses are added up to train a unified encoding model. The embeddings from [CLS] and ordinary tokens, after dimension reduction and aggregation, are concatenated as one unified semantic representation for the input. DupMAE is simple but empirically competitive: with a small decoding cost, it substantially contributes to the model's representation capability and transferability, where remarkable improvements are achieved on MS MARCO and BEIR benchmarks.

Scaling up Masked Diffusion Models on Text

Masked diffusion models (MDMs) have shown promise in language modeling, yet their scalability and effectiveness in core language tasks, such as text generation and language understanding, remain underexplored. This paper establishes the first scaling law for MDMs, demonstrating a scaling rate comparable to autoregressive models (ARMs) and a relatively small compute gap. Motivated by their scalability, we train a family of MDMs with up to 1.1 billion (B) parameters to systematically evaluate their performance against ARMs of comparable or larger sizes. Fully leveraging the probabilistic formulation of MDMs, we propose a simple yet effective unsupervised classifier-free guidance that effectively exploits large-scale unpaired data, boosting performance for conditional inference. In language understanding, the 1.1B MDM outperforms the 1.1B TinyLlama model trained on the same data across four of eight zero-shot benchmarks. Notably, it achieves competitive math reasoning ability with the 7B Llama-2 model on the GSM8K dataset. In text generation, MDMs with 16 times more pre-training time offer a flexible trade-off against ARMs with the accelerated sampling technique KV-Cache: MDMs match ARMs in performance while being 1.4 times faster during sampling. Moreover, MDMs address challenging tasks for ARMs by effectively handling bidirectional reasoning and adapting to temporal shifts in data. Notably, a 1.1B MDM breaks the reverse curse encountered by much larger ARMs with significantly more data and computation, such as 13B Llama-2 and 175B GPT-3. Our code is available at https://github.com/ML-GSAI/SMDM.

Fine-Tuning Language Models with Just Forward Passes

Fine-tuning language models (LMs) has yielded success on diverse downstream tasks, but as LMs grow in size, backpropagation requires a prohibitively large amount of memory. Zeroth-order (ZO) methods can in principle estimate gradients using only two forward passes but are theorized to be catastrophically slow for optimizing large models. In this work, we propose a memory-efficient zerothorder optimizer (MeZO), adapting the classical ZO-SGD method to operate in-place, thereby fine-tuning LMs with the same memory footprint as inference. For example, with a single A100 80GB GPU, MeZO can train a 30-billion parameter model, whereas fine-tuning with backpropagation can train only a 2.7B LM with the same budget. We conduct comprehensive experiments across model types (masked and autoregressive LMs), model scales (up to 66B), and downstream tasks (classification, multiple-choice, and generation). Our results demonstrate that (1) MeZO significantly outperforms in-context learning and linear probing; (2) MeZO achieves comparable performance to fine-tuning with backpropagation across multiple tasks, with up to 12x memory reduction; (3) MeZO is compatible with both full-parameter and parameter-efficient tuning techniques such as LoRA and prefix tuning; (4) MeZO can effectively optimize non-differentiable objectives (e.g., maximizing accuracy or F1). We support our empirical findings with theoretical insights, highlighting how adequate pre-training and task prompts enable MeZO to fine-tune huge models, despite classical ZO analyses suggesting otherwise.

Masked Diffusion Models are Secretly Time-Agnostic Masked Models and Exploit Inaccurate Categorical Sampling

Masked diffusion models (MDMs) have emerged as a popular research topic for generative modeling of discrete data, thanks to their superior performance over other discrete diffusion models, and are rivaling the auto-regressive models (ARMs) for language modeling tasks. The recent effort in simplifying the masked diffusion framework further leads to alignment with continuous-space diffusion models and more principled training and sampling recipes. In this paper, however, we reveal that both training and sampling of MDMs are theoretically free from the time variable, arguably the key signature of diffusion models, and are instead equivalent to masked models. The connection on the sampling aspect is drawn by our proposed first-hitting sampler (FHS). Specifically, we show that the FHS is theoretically equivalent to MDMs' original generation process while significantly alleviating the time-consuming categorical sampling and achieving a 20times speedup. In addition, our investigation raises doubts about whether MDMs can truly beat ARMs. We identify, for the first time, an underlying numerical issue, even with the commonly used 32-bit floating-point precision, which results in inaccurate categorical sampling. We show that the numerical issue lowers the effective temperature both theoretically and empirically, and the resulting decrease in token diversity makes previous evaluations, which assess the generation quality solely through the incomplete generative perplexity metric, somewhat unfair.

Forward-Backward Reasoning in Large Language Models for Mathematical Verification

Chain-of-Thought (CoT) prompting in large language models (LLMs) has shown promising performance on mathematical reasoning tasks. Recently, Self-Consistency samples a diverse set of reasoning chains with different answers and chooses the answer by majority voting. Though effective, its performance cannot be further improved by sampling more reasoning chains. To address this problem, we propose to integrate backward reasoning into answer verification. We first mask a number in the question by {bf x}. The LLM is then asked to predict the masked number with a candidate answer A embedded in the template: ``If we know the answer to the above question is {A}, what is the value of unknown variable {bf x}?'' The LLM is expected to predict the masked number successfully if the provided candidate answer is correct. To further improve performance, we propose FOBAR (FOrward-BAckward Reasoning) to combine forward and backward reasoning for verifying candidate answers. Experiments are performed on six standard mathematical data sets and three LLMs (text-davinci-003, GPT-3.5-Turbo, GPT-4). Results show that FOBAR achieves state-of-the-art performance. In particular, FOBAR outperforms Self-Consistency which uses forward reasoning alone, demonstrating that combining forward and forward reasoning is better. It also outperforms existing verification methods, verifying the effectiveness of using the simple template in backward reasoning and the proposed combination.

Circuit Representation Learning with Masked Gate Modeling and Verilog-AIG Alignment

Understanding the structure and function of circuits is crucial for electronic design automation (EDA). Circuits can be formulated as And-Inverter graphs (AIGs), enabling efficient implementation of representation learning through graph neural networks (GNNs). Masked modeling paradigms have been proven effective in graph representation learning. However, masking augmentation to original circuits will destroy their logical equivalence, which is unsuitable for circuit representation learning. Moreover, existing masked modeling paradigms often prioritize structural information at the expense of abstract information such as circuit function. To address these limitations, we introduce MGVGA, a novel constrained masked modeling paradigm incorporating masked gate modeling (MGM) and Verilog-AIG alignment (VGA). Specifically, MGM preserves logical equivalence by masking gates in the latent space rather than in the original circuits, subsequently reconstructing the attributes of these masked gates. Meanwhile, large language models (LLMs) have demonstrated an excellent understanding of the Verilog code functionality. Building upon this capability, VGA performs masking operations on original circuits and reconstructs masked gates under the constraints of equivalent Verilog codes, enabling GNNs to learn circuit functions from LLMs. We evaluate MGVGA on various logic synthesis tasks for EDA and show the superior performance of MGVGA compared to previous state-of-the-art methods. Our code is available at https://github.com/wuhy68/MGVGA.

Evaluating Dialect Robustness of Language Models via Conversation Understanding

With an evergrowing number of LLMs reporting superlative performance for English, their ability to perform equitably for different dialects of English (i.e., dialect robustness) needs to be ascertained. Specifically, we use English language (US English or Indian English) conversations between humans who play the word-guessing game of `taboo'. We formulate two evaluative tasks: target word prediction (TWP) (i.e.predict the masked target word in a conversation) and target word selection (TWS) (i.e., select the most likely masked target word in a conversation, from among a set of candidate words). Extending MD3, an existing dialectic dataset of taboo-playing conversations, we introduce M-MD3, a target-word-masked version of MD3 with the USEng and IndEng subsets. We add two subsets: AITrans (where dialectic information is removed from IndEng) and AIGen (where LLMs are prompted to generate conversations). Our evaluation uses pre-trained and fine-tuned versions of two closed-source (GPT-4/3.5) and two open-source LLMs (Mistral and Gemma). LLMs perform significantly better for US English than Indian English for both TWP and TWS, for all settings. While GPT-based models perform the best, the comparatively smaller models work more equitably for short conversations (<8 turns). Our results on AIGen and AITrans (the best and worst-performing subset) respectively show that LLMs may learn a dialect of their own based on the composition of the training data, and that dialect robustness is indeed a challenging task. Our evaluation methodology exhibits a novel way to examine attributes of language models using pre-existing dialogue datasets.

4M: Massively Multimodal Masked Modeling

Current machine learning models for vision are often highly specialized and limited to a single modality and task. In contrast, recent large language models exhibit a wide range of capabilities, hinting at a possibility for similarly versatile models in computer vision. In this paper, we take a step in this direction and propose a multimodal training scheme called 4M. It consists of training a single unified Transformer encoder-decoder using a masked modeling objective across a wide range of input/output modalities - including text, images, geometric, and semantic modalities, as well as neural network feature maps. 4M achieves scalability by unifying the representation space of all modalities through mapping them into discrete tokens and performing multimodal masked modeling on a small randomized subset of tokens. 4M leads to models that exhibit several key capabilities: (1) they can perform a diverse set of vision tasks out of the box, (2) they excel when fine-tuned for unseen downstream tasks or new input modalities, and (3) they can function as a generative model that can be conditioned on arbitrary modalities, enabling a wide variety of expressive multimodal editing capabilities with remarkable flexibility. Through experimental analyses, we demonstrate the potential of 4M for training versatile and scalable foundation models for vision tasks, setting the stage for further exploration in multimodal learning for vision and other domains.

Peptide Sequencing Via Protein Language Models

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.