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VLSP 2021 - ViMRC Challenge: Vietnamese Machine Reading Comprehension

One of the emerging research trends in natural language understanding is machine reading comprehension (MRC) which is the task to find answers to human questions based on textual data. Existing Vietnamese datasets for MRC research concentrate solely on answerable questions. However, in reality, questions can be unanswerable for which the correct answer is not stated in the given textual data. To address the weakness, we provide the research community with a benchmark dataset named UIT-ViQuAD 2.0 for evaluating the MRC task and question answering systems for the Vietnamese language. We use UIT-ViQuAD 2.0 as a benchmark dataset for the challenge on Vietnamese MRC at the Eighth Workshop on Vietnamese Language and Speech Processing (VLSP 2021). This task attracted 77 participant teams from 34 universities and other organizations. In this article, we present details of the organization of the challenge, an overview of the methods employed by shared-task participants, and the results. The highest performances are 77.24% in F1-score and 67.43% in Exact Match on the private test set. The Vietnamese MRC systems proposed by the top 3 teams use XLM-RoBERTa, a powerful pre-trained language model based on the transformer architecture. The UIT-ViQuAD 2.0 dataset motivates researchers to further explore the Vietnamese machine reading comprehension task and related tasks such as question answering, question generation, and natural language inference.

L3Cube-MahaSBERT and HindSBERT: Sentence BERT Models and Benchmarking BERT Sentence Representations for Hindi and Marathi

Sentence representation from vanilla BERT models does not work well on sentence similarity tasks. Sentence-BERT models specifically trained on STS or NLI datasets are shown to provide state-of-the-art performance. However, building these models for low-resource languages is not straightforward due to the lack of these specialized datasets. This work focuses on two low-resource Indian languages, Hindi and Marathi. We train sentence-BERT models for these languages using synthetic NLI and STS datasets prepared using machine translation. We show that the strategy of NLI pre-training followed by STSb fine-tuning is effective in generating high-performance sentence-similarity models for Hindi and Marathi. The vanilla BERT models trained using this simple strategy outperform the multilingual LaBSE trained using a complex training strategy. These models are evaluated on downstream text classification and similarity tasks. We evaluate these models on real text classification datasets to show embeddings obtained from synthetic data training are generalizable to real datasets as well and thus represent an effective training strategy for low-resource languages. We also provide a comparative analysis of sentence embeddings from fast text models, multilingual BERT models (mBERT, IndicBERT, xlm-RoBERTa, MuRIL), multilingual sentence embedding models (LASER, LaBSE), and monolingual BERT models based on L3Cube-MahaBERT and HindBERT. We release L3Cube-MahaSBERT and HindSBERT, the state-of-the-art sentence-BERT models for Marathi and Hindi respectively. Our work also serves as a guide to building low-resource sentence embedding models.

DeepHateExplainer: Explainable Hate Speech Detection in Under-resourced Bengali Language

The exponential growths of social media and micro-blogging sites not only provide platforms for empowering freedom of expressions and individual voices, but also enables people to express anti-social behaviour like online harassment, cyberbullying, and hate speech. Numerous works have been proposed to utilize textual data for social and anti-social behaviour analysis, by predicting the contexts mostly for highly-resourced languages like English. However, some languages are under-resourced, e.g., South Asian languages like Bengali, that lack computational resources for accurate natural language processing (NLP). In this paper, we propose an explainable approach for hate speech detection from the under-resourced Bengali language, which we called DeepHateExplainer. Bengali texts are first comprehensively preprocessed, before classifying them into political, personal, geopolitical, and religious hates using a neural ensemble method of transformer-based neural architectures (i.e., monolingual Bangla BERT-base, multilingual BERT-cased/uncased, and XLM-RoBERTa). Important(most and least) terms are then identified using sensitivity analysis and layer-wise relevance propagation(LRP), before providing human-interpretable explanations. Finally, we compute comprehensiveness and sufficiency scores to measure the quality of explanations w.r.t faithfulness. Evaluations against machine learning~(linear and tree-based models) and neural networks (i.e., CNN, Bi-LSTM, and Conv-LSTM with word embeddings) baselines yield F1-scores of 78%, 91%, 89%, and 84%, for political, personal, geopolitical, and religious hates, respectively, outperforming both ML and DNN baselines.

TopRoBERTa: Topology-Aware Authorship Attribution of Deepfake Texts

Recent advances in Large Language Models (LLMs) have enabled the generation of open-ended high-quality texts, that are non-trivial to distinguish from human-written texts. We refer to such LLM-generated texts as deepfake texts. There are currently over 11K text generation models in the huggingface model repo. As such, users with malicious intent can easily use these open-sourced LLMs to generate harmful texts and misinformation at scale. To mitigate this problem, a computational method to determine if a given text is a deepfake text or not is desired--i.e., Turing Test (TT). In particular, in this work, we investigate the more general version of the problem, known as Authorship Attribution (AA), in a multi-class setting--i.e., not only determining if a given text is a deepfake text or not but also being able to pinpoint which LLM is the author. We propose TopRoBERTa to improve existing AA solutions by capturing more linguistic patterns in deepfake texts by including a Topological Data Analysis (TDA) layer in the RoBERTa model. We show the benefits of having a TDA layer when dealing with noisy, imbalanced, and heterogeneous datasets, by extracting TDA features from the reshaped pooled_output of RoBERTa as input. We use RoBERTa to capture contextual representations (i.e., semantic and syntactic linguistic features), while using TDA to capture the shape and structure of data (i.e., linguistic structures). Finally, TopRoBERTa, outperforms the vanilla RoBERTa in 2/3 datasets, achieving up to 7\% increase in Macro F1 score.

Towards Efficient Methods in Medical Question Answering using Knowledge Graph Embeddings

In Natural Language Processing (NLP), Machine Reading Comprehension (MRC) is the task of answering a question based on a given context. To handle questions in the medical domain, modern language models such as BioBERT, SciBERT and even ChatGPT are trained on vast amounts of in-domain medical corpora. However, in-domain pre-training is expensive in terms of time and resources. In this paper, we propose a resource-efficient approach for injecting domain knowledge into a model without relying on such domain-specific pre-training. Knowledge graphs are powerful resources for accessing medical information. Building on existing work, we introduce a method using Multi-Layer Perceptrons (MLPs) for aligning and integrating embeddings extracted from medical knowledge graphs with the embedding spaces of pre-trained language models (LMs). The aligned embeddings are fused with open-domain LMs BERT and RoBERTa that are fine-tuned for two MRC tasks, span detection (COVID-QA) and multiple-choice questions (PubMedQA). We compare our method to prior techniques that rely on a vocabulary overlap for embedding alignment and show how our method circumvents this requirement to deliver better performance. On both datasets, our method allows BERT/RoBERTa to either perform on par (occasionally exceeding) with stronger domain-specific models or show improvements in general over prior techniques. With the proposed approach, we signal an alternative method to in-domain pre-training to achieve domain proficiency.

GottBERT: a pure German Language Model

Lately, pre-trained language models advanced the field of natural language processing (NLP). The introduction of Bidirectional Encoders for Transformers (BERT) and its optimized version RoBERTa have had significant impact and increased the relevance of pre-trained models. First, research in this field mainly started on English data followed by models trained with multilingual text corpora. However, current research shows that multilingual models are inferior to monolingual models. Currently, no German single language RoBERTa model is yet published, which we introduce in this work (GottBERT). The German portion of the OSCAR data set was used as text corpus. In an evaluation we compare its performance on the two Named Entity Recognition (NER) tasks Conll 2003 and GermEval 2014 as well as on the text classification tasks GermEval 2018 (fine and coarse) and GNAD with existing German single language BERT models and two multilingual ones. GottBERT was pre-trained related to the original RoBERTa model using fairseq. All downstream tasks were trained using hyperparameter presets taken from the benchmark of German BERT. The experiments were setup utilizing FARM. Performance was measured by the F_{1} score. GottBERT was successfully pre-trained on a 256 core TPU pod using the RoBERTa BASE architecture. Even without extensive hyper-parameter optimization, in all NER and one text classification task, GottBERT already outperformed all other tested German and multilingual models. In order to support the German NLP field, we publish GottBERT under the AGPLv3 license.

Bio-xLSTM: Generative modeling, representation and in-context learning of biological and chemical sequences

Language models for biological and chemical sequences enable crucial applications such as drug discovery, protein engineering, and precision medicine. Currently, these language models are predominantly based on Transformer architectures. While Transformers have yielded impressive results, their quadratic runtime dependency on the sequence length complicates their use for long genomic sequences and in-context learning on proteins and chemical sequences. Recently, the recurrent xLSTM architecture has been shown to perform favorably compared to Transformers and modern state-space model (SSM) architectures in the natural language domain. Similar to SSMs, xLSTMs have a linear runtime dependency on the sequence length and allow for constant-memory decoding at inference time, which makes them prime candidates for modeling long-range dependencies in biological and chemical sequences. In this work, we tailor xLSTM towards these domains and propose a suite of architectural variants called Bio-xLSTM. Extensive experiments in three large domains, genomics, proteins, and chemistry, were performed to assess xLSTM's ability to model biological and chemical sequences. The results show that models based on Bio-xLSTM a) can serve as proficient generative models for DNA, protein, and chemical sequences, b) learn rich representations for those modalities, and c) can perform in-context learning for proteins and small molecules.

Libra: Leveraging Temporal Images for Biomedical Radiology Analysis

Radiology report generation (RRG) is a challenging task, as it requires a thorough understanding of medical images, integration of multiple temporal inputs, and accurate report generation. Effective interpretation of medical images, such as chest X-rays (CXRs), demands sophisticated visual-language reasoning to map visual findings to structured reports. Recent studies have shown that multimodal large language models (MLLMs) can acquire multimodal capabilities by aligning with pre-trained vision encoders. However, current approaches predominantly focus on single-image analysis or utilise rule-based symbolic processing to handle multiple images, thereby overlooking the essential temporal information derived from comparing current images with prior ones. To overcome this critical limitation, we introduce Libra, a temporal-aware MLLM tailored for CXR report generation using temporal images. Libra integrates a radiology-specific image encoder with a MLLM and utilises a novel Temporal Alignment Connector to capture and synthesise temporal information of images across different time points with unprecedented precision. Extensive experiments show that Libra achieves new state-of-the-art performance among the same parameter scale MLLMs for RRG tasks on the MIMIC-CXR. Specifically, Libra improves the RadCliQ metric by 12.9% and makes substantial gains across all lexical metrics compared to previous models.

xLSTM-UNet can be an Effective 2D \& 3D Medical Image Segmentation Backbone with Vision-LSTM (ViL) better than its Mamba Counterpart

Convolutional Neural Networks (CNNs) and Vision Transformers (ViT) have been pivotal in biomedical image segmentation, yet their ability to manage long-range dependencies remains constrained by inherent locality and computational overhead. To overcome these challenges, in this technical report, we first propose xLSTM-UNet, a UNet structured deep learning neural network that leverages Vision-LSTM (xLSTM) as its backbone for medical image segmentation. xLSTM is a recently proposed as the successor of Long Short-Term Memory (LSTM) networks and have demonstrated superior performance compared to Transformers and State Space Models (SSMs) like Mamba in Neural Language Processing (NLP) and image classification (as demonstrated in Vision-LSTM, or ViL implementation). Here, xLSTM-UNet we designed extend the success in biomedical image segmentation domain. By integrating the local feature extraction strengths of convolutional layers with the long-range dependency capturing abilities of xLSTM, xLSTM-UNet offers a robust solution for comprehensive image analysis. We validate the efficacy of xLSTM-UNet through experiments. Our findings demonstrate that xLSTM-UNet consistently surpasses the performance of leading CNN-based, Transformer-based, and Mamba-based segmentation networks in multiple datasets in biomedical segmentation including organs in abdomen MRI, instruments in endoscopic images, and cells in microscopic images. With comprehensive experiments performed, this technical report highlights the potential of xLSTM-based architectures in advancing biomedical image analysis in both 2D and 3D. The code, models, and datasets are publicly available at http://tianrun-chen.github.io/xLSTM-UNet/{http://tianrun-chen.github.io/xLSTM-Unet/}

GEM: Empowering MLLM for Grounded ECG Understanding with Time Series and Images

While recent multimodal large language models (MLLMs) have advanced automated ECG interpretation, they still face two key limitations: (1) insufficient multimodal synergy between time series signals and visual ECG representations, and (2) limited explainability in linking diagnoses to granular waveform evidence. We introduce GEM, the first MLLM unifying ECG time series, 12-lead ECG images and text for grounded and clinician-aligned ECG interpretation. GEM enables feature-grounded analysis, evidence-driven reasoning, and a clinician-like diagnostic process through three core innovations: a dual-encoder framework extracting complementary time series and image features, cross-modal alignment for effective multimodal understanding, and knowledge-guided instruction generation for generating high-granularity grounding data (ECG-Grounding) linking diagnoses to measurable parameters (e.g., QRS/PR Intervals). Additionally, we propose the Grounded ECG Understanding task, a clinically motivated benchmark designed to comprehensively assess the MLLM's capability in grounded ECG understanding. Experimental results on both existing and our proposed benchmarks show GEM significantly improves predictive performance (CSN 7.4% uparrow), explainability (22.7% uparrow), and grounding (24.8% uparrow), making it more suitable for real-world clinical applications. GitHub repository: https://github.com/lanxiang1017/GEM.git

EHRSHOT: An EHR Benchmark for Few-Shot Evaluation of Foundation Models

While the general machine learning (ML) community has benefited from public datasets, tasks, and models, the progress of ML in healthcare has been hampered by a lack of such shared assets. The success of foundation models creates new challenges for healthcare ML by requiring access to shared pretrained models to validate performance benefits. We help address these challenges through three contributions. First, we publish a new dataset, EHRSHOT, which contains deidentified structured data from the electronic health records (EHRs) of 6,739 patients from Stanford Medicine. Unlike MIMIC-III/IV and other popular EHR datasets, EHRSHOT is longitudinal and not restricted to ICU/ED patients. Second, we publish the weights of CLMBR-T-base, a 141M parameter clinical foundation model pretrained on the structured EHR data of 2.57M patients. We are one of the first to fully release such a model for coded EHR data; in contrast, most prior models released for clinical data (e.g. GatorTron, ClinicalBERT) only work with unstructured text and cannot process the rich, structured data within an EHR. We provide an end-to-end pipeline for the community to validate and build upon its performance. Third, we define 15 few-shot clinical prediction tasks, enabling evaluation of foundation models on benefits such as sample efficiency and task adaptation. Our model and dataset are available via a research data use agreement from the Stanford AIMI Center. Code to reproduce our results are available at our Github repo: https://github.com/som-shahlab/ehrshot-benchmark

DeBERTaV3: Improving DeBERTa using ELECTRA-Style Pre-Training with Gradient-Disentangled Embedding Sharing

This paper presents a new pre-trained language model, DeBERTaV3, which improves the original DeBERTa model by replacing mask language modeling (MLM) with replaced token detection (RTD), a more sample-efficient pre-training task. Our analysis shows that vanilla embedding sharing in ELECTRA hurts training efficiency and model performance. This is because the training losses of the discriminator and the generator pull token embeddings in different directions, creating the "tug-of-war" dynamics. We thus propose a new gradient-disentangled embedding sharing method that avoids the tug-of-war dynamics, improving both training efficiency and the quality of the pre-trained model. We have pre-trained DeBERTaV3 using the same settings as DeBERTa to demonstrate its exceptional performance on a wide range of downstream natural language understanding (NLU) tasks. Taking the GLUE benchmark with eight tasks as an example, the DeBERTaV3 Large model achieves a 91.37% average score, which is 1.37% over DeBERTa and 1.91% over ELECTRA, setting a new state-of-the-art (SOTA) among the models with a similar structure. Furthermore, we have pre-trained a multi-lingual model mDeBERTa and observed a larger improvement over strong baselines compared to English models. For example, the mDeBERTa Base achieves a 79.8% zero-shot cross-lingual accuracy on XNLI and a 3.6% improvement over XLM-R Base, creating a new SOTA on this benchmark. We have made our pre-trained models and inference code publicly available at https://github.com/microsoft/DeBERTa.