Austria

The recent advancements in language models have significantly catalyzed progress in computational biology. A growing body of research strives to construct unified foundation models for single-cell biology, with language models serving as the cornerstone. In this paper, we systematically review the developments in foundation language models designed specifically for single-cell biology. Our survey offers a thorough analysis of various incarnations of single-cell foundation language models, viewed through the lens of both pre-trained language models (PLMs) and large language models (LLMs). This includes an exploration of data tokenization strategies, pre-training/tuning paradigms, and downstream single-cell data analysis tasks. Additionally, we discuss the current challenges faced by these pioneering works and speculate on future research directions. Overall, this survey provides a comprehensive overview of the existing single-cell foundation language models, paving the way for future research endeavors.

ACL 2025

A Survey on Foundation Language Models for Single-cell Biology

single-cell

foundation models

llms

We are pleased to announce the Fortieth AAAI Conference on Artificial Intelligence (AAAI-26), which will be held in Singapore EXPO from January 20 to January 27, 2026.

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AAAI 2026

We are pleased to announce the Fortieth AAAI Conference on Artificial Intelligence (AAAI-26), which will be held in Singapore EXPO from January 20 to January 27, 2026.

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### Welcome to The 63rd Annual Meeting of the Association for Computational Linguistics (ACL 2025)

Message from the General Chair: 
*It is my great pleasure and honor to welcome you to the 63rd Annual Meeting of the Association for Computational Linguistics (ACL 2025), held in beautiful Vienna, Austria, from July 27 to August 1, 2025. ACL2025continues our field’s tradition of excellence in scholarship, innovation, and inclusivity, and I am deeply grateful to the many volunteers who have worked tirelessly to bring this event to life.* 
[Read more](https://drive.google.com/file/d/1GI_hvOpjswAuYdUTromfeDiPpCcqidwg/view?usp=sharing)

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Welcome to The 63rd Annual Meeting of the Association for Computational Linguistics (ACL 2025)

This paper introduces RuleArena, a novel and challenging benchmark designed to evaluate the ability of large language models (LLMs) to follow complex, real-world rules in reasoning. Covering three practical domains -- airline baggage fees, NBA transactions, and tax regulations -- RuleArena assesses LLMs' proficiency in handling intricate natural language instructions that demand long-context understanding, logical reasoning, and accurate mathematical computation. Two key attributes distinguish RuleArena from traditional rule-based reasoning benchmarks: (1) it extends beyond standard first-order logic representations, and (2) it is grounded in authentic, practical scenarios, providing insights into the suitability and reliability of LLMs for real-world applications. Our findings reveal several notable limitations in LLMs: (1) they struggle to identify and apply the appropriate rules, frequently becoming confused by similar but distinct regulations, (2) they cannot consistently perform accurate mathematical computations, even when they correctly identify the relevant rules, and (3) in general, they perform poorly in the benchmark. We also observe a significant performance boost when LLMs are provided with external tools for oracle math and logic operations. These results highlight significant challenges and promising research directions in advancing LLMs' rule-guided reasoning capabilities in real-life applications. Our codes and data are publicly available on https://github.com/skyriver-2000/rulearena.

RuleArena: A Benchmark for Rule-Guided Reasoning with LLMs in Real-World Scenarios

Specializing large language models (LLMs) for local deployment in domain-specific use cases is necessary for strong performance while meeting latency and privacy constraints. However, conventional task-specific adaptation approaches do not show simultaneous memory saving and inference speedup at deployment time. Practical compression techniques like quantization and pruning require dedicated hardware or kernel support to achieve measured inference speedup. We develop TrimLLM based on the layer-wise specialization phenomenon we empirically observed and verified on contemporary LLMs. TrimLLM reduces the depth of LLMs via progressive layer dropping. We show it retains LLMs' capacity in specific domains and achieves inference speedup irrespective of hardware and deep learning frameworks. We evaluated TrimLLM on LLMs of various sizes for inference; models adapted on medical, legal, and financial datasets all demonstrate $2.1 - 5.7\times$ inference speedup on consumer GPUs and up to $3.1\times$ speedup on A100 when compared to state-of-the-art model compression algorithms, with no loss in accuracy at $50\sim 60$\% model compression ratio.

TrimLLM: Progressive Layer Dropping for Domain-Specific LLMs

Given the rapid progress of generative AI, there is a pressing need to systematically compare and choose between the numerous models and configurations available. The scale and versatility of such evaluations make the use of LLM-based judges a compelling solution for this challenge. Crucially, this approach requires first to validate the quality of the LLM judge itself. Previous work has focused on instance-based assessment of LLM judges, where a judge is evaluated over a set of responses, or response pairs, while being agnostic to their source systems. We argue that this setting overlooks critical factors affecting system-level ranking, such as a judge's positive or negative bias towards certain systems. To address this gap, we conduct the first large-scale study of LLM judges as system rankers. System scores are generated by aggregating judgment scores over multiple system outputs, and the judge's quality is assessed by comparing the resulting system ranking to a human-based ranking. Beyond overall judge assessment, our analysis provides a fine-grained characterization of judge behavior, including their decisiveness and bias.

JuStRank: Benchmarking LLM Judges for System Ranking

Automatic prompt engineering aims to enhance the generation quality of large language models (LLMs). Recent works utilize feedbacks generated from erroneous cases to guide the prompt optimization. During inference, they may further retrieve several semantically-related exemplars and concatenate them to the optimized prompts to improve the performance. However, those works only utilize the feedback at the current step, ignoring historical and unseleccted feedbacks which are potentially beneficial. Moreover, the selection of exemplars only considers the general semantic relationship and may not be optimal in terms of task performance and matching with the optimized prompt. In this work, we propose an Exemplar-Guided Reflection with Memory mechanism (ERM) to realize more efficient and accurate prompt optimization. Specifically, we design an exemplar-guided reflection mechanism where the feedback generation is additionally guided by the generated exemplars. We further build two kinds of memory to fully utilize the historical feedback information and support more effective exemplar retrieval. Empirical evaluations show our method surpasses previous state-of-the-arts with less optimization steps, i.e., improving F1 score by 10.1 on LIAR dataset, and reducing half of the optimization steps on ProTeGi.

Efficient and Accurate Prompt Optimization: the Benefit of Memory in Exemplar-Guided Reflection

Language model agents excel in long-session planning and reasoning, but existing benchmarks primarily focus on goal-oriented tasks with explicit objectives, neglecting creative adaptation in unfamiliar environments. To address this, we introduce EscapeBench—a benchmark suite of room escape game environments designed to challenge agents with creative reasoning, unconventional tool use, and iterative problem-solving to uncover implicit goals. Our results show that current LM models, despite employing working memory and Chain-of-Thought reasoning, achieve only 15% average progress without hints, highlighting their limitations in creativity. To bridge this gap, we propose EscapeAgent, a framework designed to enhance creative reasoning through Foresight (innovative tool use) and Reflection (identifying unsolved tasks). Experiments show that EscapeAgent can execute action chains over 1,000 steps while maintaining logical coherence. It navigates and completes games with up to 40% fewer steps and hints, performs robustly across difficulty levels, and achieves higher action success rates with more efficient and innovative puzzle-solving strategies.

EscapeBench: Towards Advancing Creative Intelligence of Language Model Agents

Cross-lingual aspect-based sentiment analysis (ABSA) involves detailed sentiment analysis in a target language by transferring knowledge from a source language with available annotated data. Most existing methods depend heavily on often unreliable translation tools to bridge the language gap. In this paper, we propose a new approach that leverages a large language model (LLM) to generate high-quality pseudo-labelled data in the target language without the need for translation tools. First, the framework trains an ABSA model to obtain predictions for unlabelled target language data. Next, LLM is prompted to generate natural sentences that better represent these noisy predictions than the original text. The ABSA model is then further fine-tuned on the resulting pseudo-labelled dataset. We demonstrate the effectiveness of this method across six languages and five backbone models, surpassing previous state-of-the-art translation-based approaches. The proposed framework also supports generative models, and we show that fine-tuned LLMs outperform smaller multilingual models.

LACA: Improving Cross-lingual Aspect-Based Sentiment Analysis with LLM Data Augmentation

Given a semi-structured knowledge base (SKB), where text documents are interconnected by relations, how can we effectively retrieve relevant information to answer user questions?
Retrieval-Augmented Generation (RAG) retrieves documents to assist large language models (LLMs) in question answering; while Graph RAG (GRAG) uses structured knowledge bases as its knowledge source.
However, many questions require both textual and relational information from SKB — referred to as "hybrid" questions — which complicates the retrieval process and underscores the need for a hybrid retrieval method that leverages both information.

In this paper, through our empirical analysis, we identify key insights that show why existing methods may struggle with hybrid question answering (HQA) over SKB. 
Based on these insights, we propose HybGRAG for HQA, consisting of a retriever bank and a critic module, with the following advantages:
1. Agentic, it automatically refines the output by incorporating feedback from the critic module, 
2. Adaptive, it solves hybrid questions requiring both textual and relational information with the retriever bank,
3. Interpretable, it justifies decision making with intuitive refinement path, and
4. Effective, it surpasses all baselines on HQA benchmarks.

In experiments on the STaRK benchmark, HybGRAG achieves significant performance gains, with an average relative improvement in Hit@1 of 51%.

HybGRAG: Hybrid Retrieval-Augmented Generation on Textual and Relational Knowledge Bases

Clinical coding is crucial for healthcare billing and data analysis. Manual clinical coding is labour-intensive and error-prone, which has motivated research towards full automation of the process. However, our analysis, based on US English electronic health records and automated coding research using these records, shows that widely used evaluation methods are not aligned with real clinical contexts. For example, evaluations that focus on the top 50 most common codes are an oversimplification, as there are thousands of codes used in practice. This position paper aims to align AI coding research more closely with practical challenges of clinical coding. Based on our analysis, we offer eight specific recommendations, suggesting ways to improve current evaluation methods. Additionally, we propose new AI-based methods beyond automated coding, suggesting alternative approaches to assist clinical coders in their workflows.

Aligning AI Research with the Needs of Clinical Coding Workflows: Eight Recommendations Based on US Data Analysis and Critical Review

Multimodal punchlines, which involve humor or sarcasm conveyed in image-caption pairs, are a popular way of communication on online multimedia platforms. With the rapid development of multimodal large language models (MLLMs), it is essential to assess their ability to effectively comprehend these punchlines. However, existing benchmarks on punchline comprehension suffer from three major limitations: 1) language shortcuts that allow models to solely rely on text, 2) lack of question diversity, and 3) narrow focus on a specific domain of multimodal content (e.g., cartoon). To address these limitations, we introduce a multimodal **Punch**line comprehension **Bench**mark, named **PunchBench**, which is tailored for accurate and comprehensive evaluation of punchline comprehension. To enhance the evaluation accuracy, we generate synonymous and antonymous captions by modifying original captions, which mitigates the impact of shortcuts in the captions. To provide a comprehensive evaluation, PunchBench incorporates diverse question formats and image-captions from various domains. On this basis, we conduct extensive evaluations and reveal a significant gap between state-of-the-art MLLMs and humans in punchline comprehension. To improve punchline comprehension, we propose Simple-to-Complex Chain-of-Question (SC-CoQ) strategy, enabling the models to incrementally address complicated questions by first mastering simple ones. SC-CoQ effectively enhances the performance of various MLLMs on PunchBench, surpassing in-context learning and chain-of-thought.

PunchBench: Benchmarking MLLMs in Multimodal Punchline Comprehension

Code generation, the automatic creation of source code from natural language descriptions, has garnered significant attention due to its potential to streamline software development. Inspired by research that links task-personality alignment with improved development outcomes, we conduct an empirical study on personality-guided code generation using large language models (LLMs). Specifically, we investigate how emulating personality traits appropriate to the coding tasks affects LLM performance. We extensively evaluate this approach using seven widely adopted LLMs across four representative datasets. Our results show that personality guidance significantly enhances code generation accuracy, with improved pass rates in 23 out of 28 LLM-dataset combinations. Notably, in 11 cases, the improvement exceeds 5%, and in 5 instances, it surpasses 10%, with the highest gain reaching 12.9%. Additionally, personality guidance can be easily integrated with other prompting strategies to further boost performance.

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RuleArena: A Benchmark for Rule-Guided Reasoning with LLMs in Real-World Scenarios

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