ACL 2025 Papers

Large Language Models (LLMs) are revolutionizing bioinformatics, enabling advanced analysis of DNA, RNA, proteins, and single-cell data. This survey provides a systematic review of recent advancements, focusing on genomic sequence modeling, RNA structure prediction, protein function inference, and single-cell transcriptomics. Meanwhile, we also discuss several key challenges, including data scarcity, computational complexity, and cross-omics integration, and explore future directions such as multimodal learning, hybrid AI models, and clinical applications. By offering a comprehensive perspective, this paper underscores the transformative potential of LLMs in driving innovations in bioinformatics and precision medicine.

Predictive analysis is a cornerstone of modern decision-making, with applications in various domains. Large Language Models (LLMs) have emerged as powerful tools in enabling nuanced, knowledge-intensive conversations, thus aiding in complex decision-making tasks. With the burgeoning expectation to harness LLMs for predictive analysis, there is an urgent need to systematically assess their capability in this domain. However, there are no relevant evaluations in existing studies. To bridge this gap, we introduce the PredictiQ benchmark, which integrates 1130 sophisticated predictive analysis queries originating from 44 real-world datasets of 8 diverse fields. We design an evaluation protocol considering text analysis, code generation, and their alignment. Twelve renowned LLMs are evaluated, offering insights into their practical use in predictive analysis.

This study investigates the linguistic understanding of Large Language Models (LLMs) regarding signifier (form) and signified (meaning) by distinguishing two LLM assessment paradigms: psycholinguistic and neurolinguistic. Traditional psycholinguistic evaluations often reflect statistical rules that may not accurately represent LLMs’ true linguistic competence. We introduce a neurolinguistic approach, utilizing a novel method that combines minimal pair and diagnostic probing to analyze activation patterns across model layers. This method allows for a detailed examination of how LLMs represent form and meaning, and whether these representations are consistent across languages. We found: (1) Psycholinguistic and neurolinguistic methods reveal that language performance and competence are distinct; (2) Direct probability measurement may not accurately assess linguistic competence; (3) Instruction tuning won’t change much competence but improve performance; (4) LLMs exhibit higher competence and performance in form compared to meaning. Additionally, we introduce new conceptual minimal pair datasets for Chinese (COMPS-ZH) and German (COMPS-DE), complementing existing English datasets.

When adapting ICL with or without fine-tuning, we are curious about whether the instruction-tuned language model is able to achieve well-calibrated results without suffering from the problem of overconfidence (i.e., miscalibration) considering its strong instruction following ability, especially in such limited data setups. In this work, we deliver an in-depth analysis of the behavior across different choices of learning methods from the perspective of both performance and calibration. Through extensive controlled experiments, we observe that the miscalibration problem exists across all learning methods in low-resource setups. To achieve simultaneous gain for both in-task performance and calibration, we then study the potential of self-ensembling applied at different modeling stages (e.g., variations of in-context examples or variations in prompts or different ensembling strategies) to make the predictions more calibrated and have comparable or even better performance. We find that self-ensembling with max probability produces robust and calibrated predictions. Our work reveals the potential calibration problem of using ICL despite the improvements in task performance and sheds light on which learning paradigm to choose. We also provide practical guidelines for choosing learning paradigms depending on whether the data has been seen by the model before and a worthwhile solution via self-ensembling on how to enhance both task performance and calibration of LMs, which we hope could encourage further study.

Large language models (LLMs) have demonstrated remarkable capabilities across various domains, yet their application to relational deep learning (RDL) remains underexplored. Existing approaches adapt LLMs by traversing relational links between entities in a database and converting the structured data into flat text documents, but this text-based serialization disregards critical relational structures, introduces redundancy, and often exceeds standard LLM context lengths. We introduce Rel-LLM, a novel architecture that employs a graph neural network (GNN) based encoder to create structured relational prompts for LLMs within a retrieval-augmented generation (RAG) framework. Unlike traditional text-based serialization approaches, our method preserves the inherent relational structure of databases while enabling LLMs to effectively process and reason over complex entity relationships. Specifically, the GNN encoder extracts a local subgraph around an entity to build feature representations that contain relevant entity relationships and temporal dependencies. These representations are transformed into structured prompts using a denormalization process, effectively allowing the LLM to reason over relational structures. Through extensive experiments, we demonstrate that Rel-LLM outperforms existing methods on key RDL tasks, offering a scalable and efficient approach to integrating LLMs with structured data sources. Code is available at https://github.com/smiles724/Rel-LLM.

A common use of NLP is to facilitate the understanding of large document collections, with models based on Large Language Models (LLMs) replacing probabilistic topic models. Yet the effectiveness of LLM-based approaches in real-world applications remains under explored. This study measures the knowledge users acquire with topic models—including traditional, unsupervised and supervised LLM- based approaches—on two datasets. While LLM-based methods generate more human- readable topics and show higher average win probabilities than traditional models for data exploration, they produce overly generic topics for domain-specific datasets that do not easily allow users to learn much about the documents. Adding human supervision to LLM-based topic models improves data exploration by addressing hallucination and genericity but requires more human efforts. In contrast, traditional models like Latent Dirichlet Allocation (LDA) remain effective for exploration but are less user-friendly. This paper provides best practices—there is no one right model, the choice of models is situation-specific—and suggests potential improvements for scalable LLM- based topic models.

Existing fairness benchmarks for large language models (LLMs) primarily focus on simple tasks, such as multiple-choice questions, overlooking biases that may arise in more complex scenarios like long-text generation. To address this gap, we introduce the Long Text Fairness Test (LTF-TEST), a framework that evaluates biases in LLMs through essay-style prompts. LTF-TEST covers 14 topics and 10 demographic axes, including gender and race, resulting in 11,948 samples. By assessing both model responses and the reasoning behind them, LTF-TEST uncovers subtle biases that are difficult to detect in simple responses. In our evaluation of five recent LLMs, including GPT-4o and LLaMA3, we identify two key patterns of bias. First, these models frequently favor certain demographic groups in their responses. Second, they show excessive sensitivity toward traditionally disadvantaged groups, often providing overly protective responses while neglecting others. To mitigate these biases, we propose REGARD-FT, a finetuning approach that pairs biased prompts with neutral responses. REGARD-FT reduces gender bias by 34.6% and improves performance by 1.4 percentage points on the BBQ benchmark, offering a promising approach to addressing biases in long-text generation tasks.

Predicting video popularity is often framed as a supervised learning task, relying heavily on meta-information and aggregated engagement data. However, video popularity is shaped by complex cultural and social factors that such approaches often overlook. We argue that Large Language Models (LLMs), with their deep contextual awareness, can better capture these nuances. To bridge the gap between pixel-based video data and token-based LLMs, we convert frame-level visuals into sequential text representations using Vision-Language Models. This enables LLMs to process multimodal content—titles, frame-based descriptions, and captions—capturing both engagement intensity (view count) and geographic spread (number of countries where a video trends). On 13,639 popular videos, a supervised neural network using content embeddings achieves 80% accuracy, while our LLM-based approach reaches 82% without fine-tuning. Combining the neural network’s predictions with the LLM further improves accuracy to 85.5%. Moreover, the LLM generates interpretable, attribute-based explanations for its predictions. Manual validations confirm the quality of these hypotheses and address concerns about hallucinations in the video-to-text conversion process. Overall, our findings suggest that LLMs, equipped with text-based multimodal representations, offer a powerful, interpretable, and data-efficient solution for tasks requiring rich contextual insight, such as video popularity prediction.

In recent years, large language models have achieved significant success in generative tasks (e.g., speech cloning and audio generation) related to speech, audio, music, and other signal domains. A crucial element of these models is the discrete acoustic codecs, which serve as an intermediate representation replacing the mel-spectrogram. However, there exist several gaps between discrete codecs and downstream speech language models. Specifically, 1) Due to the reconstruction paradigm of the Codec model and the structure of residual vector quantization, the initial channel of the codebooks contains excessive information, making it challenging to directly generate acoustic tokens from weakly supervised signals such as text in downstream tasks. 2) Achieving good reconstruction performance requires the utilization of numerous codebooks, which increases the burden on downstream speech language models. Consequently, leveraging the characteristics of speech language models, we propose Language-Codec. In the Language-Codec, we introduce a Masked Channel Residual Vector Quantization (MCRVQ) mechanism along with improved fourier transform structures, refined discriminator design to address the aforementioned gaps. We compare our method with competing audio compression algorithms and observe significant outperformance across extensive evaluations. Furthermore, we also validate the efficiency of the Language-Codec on downstream speech language models. The source code and pretrained models will be open-sourced after the paper is accepted. Codes are available at https://github.com/jishengpeng/Languagecodec.

Language has become a prominent modality in computer vision with the rise of LLMs. Despite supporting long context-lengths, their effectiveness in handling long-term information gradually declines with input length. This becomes critical, especially in applications such as long-form video understanding. In this paper, we introduce a Language Repository (LangRepo) for LLMs, that maintains concise and structured information as an interpretable (i.e., all-textual) representation. Our repository is updated iteratively based on multi-scale video chunks. We introduce write and read operations that focus on pruning redundancies in text, and extracting information at various temporal scales. The proposed framework is evaluated on zero-shot visual question-answering benchmarks, showing state-of-the-art performance at its scale. Our code is available at https://github.com/kkahatapitiya/LangRepo.

This work concerns the path-star task, a minimal example of searching over a graph. The graph, G, is star-shaped with D arms radiating from a start node, s. A language model (LM) is given G, s, and a target node, t, which ends one of the arms and is tasked with generating the arm containing t. The minimal nature of this task means only a single choice needs to be made: which of the arms contains?Decoder-only LMs fail to solve this elementary task above 1/D chance due to a learned shortcut that absorbs training supervision. We show how this pathology is caused by excess supervision and present a series of solutions demonstrating that the task is solvable via decoder-only LMs. We find that the task’s minimal nature causes its difficulty, as it prevents task decomposition. Our solutions provide insight into the pathology and its implications for LMs trained via next-token prediction.

We explore the ability of large language models (LLMs) to engage in subtle deception through strategically phrasing and intentionally manipulating information. This harmful behavior can be hard to detect, unlike blatant lying or unintentional hallucination. We build a simple testbed mimicking a legislative environment where a corporate lobbyist module is proposing amendments to bills that benefit a specific company while evading identification of this benefactor. We use real-world legislative bills matched with potentially affected companies to ground these interactions. Our results show that LLM lobbyists can draft subtle phrasing to avoid such identification by strong LLM-based detectors. Further optimization of the phrasing using LLM-based re-planning and re-sampling increases deception rates by up to 40 percentage points.Our human evaluations to verify the quality of deceptive generations and their retention of self-serving intent show significant coherence with our automated metrics and also help in identifying certain strategies of deceptive phrasing.This study highlights the risk of LLMs’ capabilities for strategic phrasing through seemingly neutral language to attain self-serving goals. This calls for future research to uncover and protect against such subtle deception.

Large language models (LLMs) may exhibit unintended or undesirable behaviors. Recent works have concentrated on aligning LLMs to mitigate harmful outputs. Despite these efforts, some anomalies indicate that even a well-conducted alignment process can be easily circumvented, whether intentionally or accidentally. Does alignment fine-tuning yield have robust effects on models, or are its impacts merely superficial? In this work, we make the first exploration of this phenomenon from both theoretical and empirical perspectives. Empirically, we demonstrate the elasticity of post-alignment models, i.e., the tendency to revert to the behavior distribution formed during the pre-training phase upon further fine-tuning. Leveraging compression theory, we formally deduce that fine-tuning disproportionately undermines alignment relative to pre-training, potentially by orders of magnitude. We validate the presence of elasticity through experiments on models of varying types and scales. Specifically, we find that model performance declines rapidly before reverting to the pre-training distribution, after which the rate of decline drops significantly. Furthermore, we further reveal that elasticity positively correlates with the increased model size and the expansion of pre-training data. Our findings underscore the need to address the inherent elasticity of LLMs to mitigate their resistance to alignment.

This paper presents elaborate testing of various LLMs on their generalization capacities. We finetune six encoder models that have been pretrained with very different data (varying in size, language, and period) on a challenging event detection task in Early Modern Dutch archival texts. Each model is finetuned with 5 seeds on 15 different data splits, resulting in 450 finetuned models. We also pre-train a domain-specific Language Model on the target domain and fine-tune and evaluate it in the same way to provide an upper bound. Our experimental setup allows us to look at underresearched aspects of generalizability, namely i) shifts at multiple places in a modeling pipeline, ii) temporal and crosslingual shifts and iii) generalization over different initializations. The results show that none of the models reaches domain-specific model performance, demonstrating their incapacity to generalize. mBERT reaches highest F1 performance, and is relatively stable over different seeds and datasplits, contrary to XLM-R. We find that contemporary Dutch models do not generalize well to Early Modern Dutch as they underperform compared to crosslingual as well as historical models. We conclude that encoder LLMs lack temporal generalization capacities and that bigger models are not better, since even a model pre-trained with five hundred GPUs on 2.5 terabytes of training data (XLM-R) underperforms considerably compared to our domain-specific model, pre-trained on one GPU and 6 GB of data. All our code, data, and the domain-specific model are openly available.

LMs’ alignment with human reading behavior (i.e. psychometric predictive power; PPP) is known to improve during pretraining up to a tipping point, beyond which it either plateaus or degrades. Various factors, such as word frequency, recency bias in attention, and context size, have been theorized to affect PPP, yet there is no current account that explains why such a tipping point exists, and how it interacts with LMs’ pretraining dynamics more generally. We hypothesize that the underlying factor is a pretraining phase transition, characterized by the rapid emergence of specialized attention heads. We conduct a series of correlational and causal experiments to show that such a phase transition is responsible for the tipping point in PPP. We then show that, rather than producing attention patterns that contribute to the degradation in PPP, phase transitions alter the subsequent learning dynamics of the model, such that further training keeps damaging PPP.

Some statements have one well-defined continuation (e.g., “the Eiffel Tower is in [Paris]"), whereas others have a natural distribution over multiple options (e.g., “the weighted coin flip was [Heads/Tails].") We argue that language model (LM) outputs should capture these natural distributions. Our work specifically tests whether LM output probabilities are calibrated to numeric information within their textual contexts. For example, if the context (the prompt) concerns two equally likely options (e.g., heads or tails for a fair coin), the LM output probabilities should also be equal. Likewise, in a context with nonuniformly likely events (e.g., rolling a pair with two dice) an LM should output proportionate probabilities. However, we find that even in simple settings, the best LMs (1) are poorly calibrated and (2) have systematic biases: artifacts like word identity, word order, and word frequency all impact calibration. For example, ‘gpt-4o-mini‘ often picks the first of two options presented in the prompt regardless of the options’ implied likelihoods, whereas ‘Llama-3.1-8B‘ picks the second. Models do not allocate probability mass among valid options in a calibrated manner.

Large language models (LLMs) present novel opportunities in public opinion research by predicting survey responses in advance during the early stages of survey design. Prior methods steer LLMs via descriptions of subpopulations as LLMs’ input prompt, yet such prompt engineering approaches have struggled to faithfully predict the distribution of survey responses from human subjects. In this work, we propose directly fine-tuning LLMs to predict response distributions by leveraging unique structural characteristics of survey data. To enable fine-tuning, we curate SubPOP, a significantly scaled dataset of 3,362 questions and 70K subpopulation-response pairs from well-established public opinion surveys. We show that fine-tuning on SubPOP greatly improves the match between LLM predictions and human responses across various subpopulations, reducing the LLM-human gap by up to 46% compared to baselines, and achieves strong generalization to unseen surveys and subpopulations. Our findings highlight the potential of survey-based fine-tuning to improve opinion prediction for diverse, real-world subpopulations and therefore enable more efficient survey designs.

Limited availability of multilingual text corpora for training language models often leads to poor performance on downstream tasks due to undertrained representation spaces for languages other than English. This ‘under-representation’ has motivated recent cross-lingual transfer methods to leverage the English representation space by e.g. mixing English and ‘non-English’ tokens at the input level or extending model parameters to accommodate new languages. However, these approaches often come at the cost of increased computational complexity. We propose Fusion for Language Representations (FLARE) in adapters, a novel method that enhances representation quality and downstream performance for languages other than English while maintaining parameter efficiency. FLARE integrates source and target language representations within low-rank (LoRA) adapters using lightweight linear transformations, maintaining parameter efficiency while improving transfer performance. A series of experiments across representative cross-lingual natural language understanding tasks, including natural language inference, question-answering and sentiment analysis, demonstrate FLARE’s effectiveness. FLARE achieves performance improvements of 4.9% for Llama 3.1 and 2.2% for Gemma 2 compared to standard LoRA fine-tuning on question-answering tasks, as measured by the exact match metric.

Multimodal summarization (MS) combines text and visuals to generate summaries. Recently, many-to-many multimodal summarization (M3S) garnered interest as it enables a unified model for multilingual and cross-lingual MS. Existing methods have made progress by facilitating the transfer of common multimodal summarization knowledge. While, prior M3S models that fully share parameters neglect the language-specific knowledge learning, where potential interference between languages may limit the flexible adaptation of MS modes across different language combinations and hinder further collaborative improvements in joint M3S training. Based on this observation, we propose Language Constrained Multimodal Hyper Adapter (LCMHA) for M3S. LCMHA integrates language-specific multimodal adapters into multilingual pre-trained backbones via a language constrained hypernetwork, enabling relaxed parameter sharing that enhances language-specific learning while preserving shared MS knowledge learning. In addition, a language-regularized hypernetwork is designed to balance intra- and inter-language learning, generating language-specific adaptation weights and enhancing the retention of distinct language features through the regularization of generated parameters. Experimental results on the M3Sum benchmark show LCMHA’s effectiveness and scalability across multiple multilingual pre-trained backbones.