United States

Developing effective biomedical retrieval models is important for excelling at knowledge-intensive biomedical tasks but still challenging due to the lack of sufficient publicly annotated biomedical data and computational resources. We present BMRetriever, a series of dense retrievers for enhancing biomedical retrieval via unsupervised pre-training on large biomedical corpora, followed by instruction fine-tuning on a combination of labeled datasets and synthetic pairs. Experiments on 5 biomedical tasks across 11 datasets verify BMRetriever&#39;s efficacy on various biomedical applications. BMRetriever also exhibits strong parameter efficiency, with the 410M variant outperforming baselines up to 11.7 times larger, and the 2B variant matching the performance of models with over 5B parameters. The training data and model checkpoints are released at https://huggingface.co/BMRetriever to ensure transparency, reproducibility, and application to new domains.

EMNLP 2024

BMRetriever: Tuning Large Language Models as Better Biomedical Text Retrievers

information retrieval

bi-encoder

cross-encoder

### Welcome to ACL 2023, the 61st Annual Meeting of the Association for Computational Linguistics! 
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ACL 2023

The Association for Computational Linguistics (ACL) is the premier international scientific and professional society for people working on computational problems involving human language, a field often referred to as either computational linguistics or natural language processing.

Developing effective biomedical retrieval models is important for excelling at knowledge-intensive biomedical tasks but still challenging due to the lack of sufficient publicly annotated biomedical data and computational resources. We present BMRetriever, a series of dense retrievers for enhancing biomedical retrieval via unsupervised pre-training on large biomedical corpora, followed by instruction fine-tuning on a combination of labeled datasets and synthetic pairs. Experiments on 5 biomedical tasks across 11 datasets verify BMRetriever's efficacy on various biomedical applications. BMRetriever also exhibits strong parameter efficiency, with the 410M variant outperforming baselines up to 11.7 times larger, and the 2B variant matching the performance of models with over 5B parameters. The training data and model checkpoints are released at https://huggingface.co/BMRetriever to ensure transparency, reproducibility, and application to new domains.

poster

## Welcome to EMNLP 2024! 
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offering both virtual and in-person participation in beautiful Miami. Due to a record-breaking number of submissions, we've expanded the total number of accepted papers to accommodate more cutting-edge research from around the globe.
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EMNLP 2024 will take place in Miami, Florida from Nov 12th to Nov 16th, 2024, at the Hyatt Regency Miami Hote and on Underline for remote participants.

Despite their improved capabilities in generation and reasoning, adapting large language models (LLMs) to the biomedical domain remains challenging due to their immense size and privacy concerns. In this study, we propose MedAdapter, a unified post-hoc adapter for test-time adaptation of LLMs towards biomedical applications. Instead of fine-tuning the entire LLM, MedAdapter effectively adapts the original model by fine-tuning only a small BERT-sized adapter to rank candidate solutions generated by LLMs. Experiments on four biomedical tasks across eight datasets demonstrate that MedAdapter effectively adapts both white-box and black-box LLMs in biomedical reasoning, achieving average performance improvements of 18.24% and 10.96%, respectively, without requiring extensive computational resources or sharing data with third parties. MedAdapter also yields enhanced performance when combined with train-time adaptation, highlighting a flexible and complementary solution to existing adaptation methods. Faced with the challenges of balancing model performance, computational resources, and data privacy, MedAdapter provides an efficient, privacy-preserving, cost-effective, and transparent solution for adapting LLMs to the biomedical domain.

MedAdapter: Efficient Test-Time Adaptation of Large Language Models Towards Medical Reasoning

Code generation models are not robust to small perturbations, which often lead to incorrect generations and significantly degrade the performance of these models. Although improving the robustness of code generation models is crucial to enhancing user experience in real-world applications, existing research efforts do not address this issue. To fill this gap, we propose CodeFort, a framework to improve the robustness of code generation models, generalizing a large variety of code perturbations to enrich the training data and enabling various robust training strategies, mixing data augmentation, batch augmentation, adversarial logits pairing, and contrastive learning, all carefully designed to support high-throughput training. Extensive evaluations show that we increase the average robust pass rates of baseline CodeGen models from 14.79 to 21.74. We notably decrease the robustness drop rate from 95.02% to 54.95% against code-syntax perturbations.

CodeFort: Robust Training for Code Generation Models

We present LoCoVQA, a dynamic benchmark generator for evaluating long-context reasoning in vision language models (VLMs). LoCoVQA augments test examples for mathematical reasoning, VQA, and character recognition tasks with increasingly long visual contexts composed of both in-distribution and out-of-distribution distractor images.

Across these tasks, a diverse set of VLMs rapidly lose performance as the visual context length grows, often exhibiting a striking logarithmic decay trend. This test assesses how well VLMs can ignore irrelevant information when answering queries---a task that is quite easy for language models (LMs) in the text domain---demonstrating that current state-of-the-art VLMs lack this essential capability for many long-context applications.

Losing Visual Needles in Image Haystacks: Vision Language Models are Easily Distracted in Short and Long Contexts

In this paper, we study an under-explored area of language and vocabulary learning: keyword mnemonics, a technique for memorizing vocabulary through memorable associations with a target word via a verbal cue. Typically, creating verbal cues requires extensive human effort and is quite time-consuming, necessitating an automated method that is more scalable. We propose a novel overgenerate-and-rank method via prompting large language models (LLMs) to generate verbal cues and then ranking them according to psycholinguistic measures and takeaways from a pilot user study. To assess cue quality, we conduct both an automated evaluation of imageability and coherence, as well as a human evaluation involving English teachers and learners. Results show that LLM-generated mnemonics are comparable to human-generated ones in terms of imageability, coherence, and perceived usefulness, but there remains plenty of room for improvement due to the diversity in background and preference among language learners.

Exploring Automated Keyword Mnemonics Generation with Large Language Models via Overgenerate-and-Rank

To ensure that math curriculum is grade-appropriate and aligns with critical skills or concepts in accordance with educational standards, pedagogical experts can spend months carefully reviewing published math problems. Drawing inspiration from this process, our work presents a novel angle for evaluating language models' (LMs) mathematical abilities, by investigating whether they can discern skills and concepts enabled by math content. We contribute two datasets: one consisting of 385 fine-grained descriptions of K-12 math skills and concepts, or *standards*, from Achieve the Core (*ATC*), and another of 9.9K math problems labeled with these standards (*MathFish*). We develop two tasks for evaluating LMs' abilities to assess math problems: (1) verifying whether a problem aligns with a given standard, and (2) tagging a problem with all aligned standards. Working with experienced teachers, we find that LMs struggle to tag and verify standards linked to problems, and instead predict labels that are close to ground truth, but differ in subtle ways. We also show that LMs often generate problems that do not fully align with standards described in prompts, suggesting the need for careful scrutiny on use cases involving LMs for generating curricular materials. Finally, we categorize problems in GSM8k using math standards, allowing us to better understand why some problems are more difficult to solve for models than others.

Evaluating Language Model Math Reasoning via Grounding in Educational Curricula

Large Language Models (LLMs) and Large Vision Language Models (LVLMs) exhibit advanced proficiency in language reasoning and comprehension across a wide array of languages. While their performance is notably robust in well-resourced languages, their capabilities in low-resource languages, such as Bahasa Melayu (hereinafter referred to as $\textit{Malay}$), remain less explored due to a scarcity of dedicated studies and benchmarks. To enhance our understanding of LLMs/LVLMs performance
in Malay, we introduce the first multi-task language understanding benchmark specifically for this language, named MalayMMLU. This
benchmark comprises 24,213 questions spanning both primary (Year 1-6) and secondary (Form 1-5) education levels in Malaysia, encompassing 5 broad topics that further divided into 22 subjects. We conducted an empirical evaluation of 44 LLMs/LVLMs, assessing their proficiency in both Malay and the nuanced contexts of Malaysian culture using this benchmark. The benchmark and evaluation code are available at https://github.com/UMxYTL-AI-Labs/MalayMMLU.

MalayMMLU: A Multitask Benchmark for the Low-Resource Malay Language

High-quality text generation capability of latest Large Language Models (LLMs) causes concerns about their misuse (e.g., in massive generation/spread of disinformation). Machine-generated text (MGT) detection is important to cope with such threats. However, it is susceptible to authorship obfuscation (AO) methods, such as paraphrasing, which can cause MGTs to evade detection. So far, this was evaluated only in monolingual settings. Thus, the susceptibility of recently proposed multilingual detectors is still unknown. We fill this gap by comprehensively benchmarking the performance of 10 well-known AO methods, attacking 37 MGT detection methods against MGTs in 11 languages (i.e., 10 × 37 × 11 = 4,070 combinations). We also evaluate the effect of data augmentation on adversarial robustness using obfuscated texts. The results indicate that all tested AO methods can cause evasion of automated detection in all tested languages, where homoglyph attacks are especially successful. However, some of the AO methods severely damaged the text, making it no longer readable or easily recognizable by humans (e.g., changed language, weird characters).

Authorship Obfuscation in Multilingual Machine-Generated Text Detection

Deep neural networks (DNNs) have made significant progress in recognizing visual elements and generating descriptive text in image-captioning tasks. However, their improved performance comes from increased computational burden and inference latency. Early Exit (EE) strategies can be used to enhance their efficiency, but their adaptation presents challenges in image captioning as it requires varying levels of semantic information for accurate predictions. To overcome this, we introduce CapEEN to improve the performance of EE strategies using knowledge distillation. Inference in CapEEN is completed at intermediary layers if prediction confidence exceeds a predefined value learned from the training data. To account for real-world deployments, where target distributions could drift from that of training samples, we introduce a variant A-CapEEN to adapt the thresholds on the fly using Multi-armed bandits framework. Experiments on the MS COCO and Flickr30k datasets show that CapEEN gains speedup of $1.77\times$ while maintaining competitive performance compared to the final layer, and A-CapEEN additionally offers robustness against distortions. The source code is available at https://github.com/Div290/CapEEN.

CapEEN: Image Captioning with Early Exits and Knowledge Distillation

With the expansion of pre-trained language model usage in recent years, the importance of datasets for performing tasks in specialized domains has significantly increased. Therefore, we have built a Korean dataset called ESG-Kor to automatically extract Environmental, Social, and Governance (ESG) information, which has recently gained importance. ESG-Kor is a dataset consisting of a total of 118,946 sentences that extracted information on each ESG component from Korean companies' sustainability reports and manually labeled it according to objective rules provided by ESG evaluation agencies. To verify the effectiveness and applicability of the ESG-Kor dataset, classification performance was confirmed using several Korean pre-trained language models, and significant performance was obtained. Additionally, by extending the ESG classification model to documents of small and medium enterprises and extracting information based on ESG key issues and in-depth analysis, we demonstrated potential and practical use cases in the ESG field.

ESG-Kor: A Korean Dataset for ESG-related Information Extraction and Practical Use Cases

In recent years, Graph Neural Networks (GNNs) have become successful in molecular property prediction tasks such as toxicity analysis. However, due to the black-box nature of GNNs, their outputs can be concerning in high-stakes decision-making scenarios, e.g., drug discovery. Facing such an issue, Graph Counterfactual Explanation (GCE) has emerged as a promising approach to improve GNN transparency. However, current GCE methods usually fail to take domain-specific knowledge into consideration, which can result in outputs that are not easily comprehensible by humans. To address this challenge, we propose a novel GCE method, LLM-GCE, to unleash the power of large language models (LLMs) in explaining GNNs for molecular property prediction. Specifically, we utilize an autoencoder to generate the counterfactual graph topology from a set of counterfactual text pairs (CTPs) based on an input graph. Meanwhile, we also incorporate a CTP dynamic feedback module to mitigate LLM hallucination, which provides intermediate feedback derived from the generated counterfactuals as an attempt to give more faithful guidance. Extensive experiments demonstrate the superior performance of LLM-GCE. Our code is released on https://github.com/YinhanHe123/new\_LLM4GNNExplanation.

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MedAdapter: Efficient Test-Time Adaptation of Large Language Models Towards Medical Reasoning

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