Austria

Predicting the types and affinities of protein-protein interactions (PPIs) is crucial for understanding biological processes and developing novel therapeutic approaches. While encoding proteins themselves is essential, PPI networks can also provide rich prior knowledge for these predictive tasks. However, existing methods oversimplify the problem of PPI prediction in a semi-supervised manner when utilizing PPI networks, limiting their practical application. Furthermore, how to effectively use the rich prior knowledge of PPI networks for novel proteins not present in the network remains an unexplored issue. Additionally, due to inflexible architectures, most of existing methods cannot handle complexes containing an flexible number of proteins. To overcome these limitations, we introduce LLaPA (Large Language and Protein Assistant), a multimodal large language model that integrates proteins and PPI networks. LLaPA offers a more rational approach to utilizing PPI networks for PPI prediction and can fully exploit the information of PPI networks for unseen proteins. Through natural language instructions, LLaPA can accept flexible number of protein sequences and has the potential to perform various protein tasks. Experiments show that LLaPA achieves state-of-the-art performance in multi-label PPI (mPPI) type prediction and is capable of predicting the binding affinity between multiple interacting proteins based on sequence data.

ACL 2025

Large Language and Protein Assistant for Protein-Protein Interactions Prediction

multimodal large language model

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)

In the interaction between agents and their environments, agents expand their capabilities by planning and executing actions. However, LLM-based agents face substantial challenges when deployed in novel environments or required to navigate unconventional action spaces. To empower agents to autonomously explore environments, optimize workflows, and enhance their understanding of actions, we propose SynWorld, a framework that allows agents to synthesize possible scenarios with multi-step action invocation within the action space and perform Monte Carlo Tree Search (MCTS) exploration to effectively refine their action knowledge in the current environment. Our experiments demonstrate that SynWorld is an effective and general approach to learning action knowledge in new environments.

SynWorld: Virtual Scenario Synthesis for Agentic Action Knowledge Refinement

Large language models (LLMs) have been widely deployed as autonomous agents capable of following user instructions and making decisions in real-world applications. Previous studies have made notable progress in benchmarking the instruction following capabilities of LLMs in general domains, with a primary focus on their inherent commonsense knowledge. Recently, LLMs have been increasingly deployed as domain-oriented agents, which rely on domain-oriented guidelines that may conflict with their commonsense knowledge. These guidelines exhibit two key characteristics: they consist of a wide range of domain-oriented rules and are subject to frequent updates. Despite these challenges, the absence of comprehensive benchmarks for evaluating the domain-oriented guideline following capabilities of LLMs presents a significant obstacle to their effective assessment and further development. In this paper, we introduce GuideBench, a comprehensive benchmark designed to evaluate guideline following performance of LLMs. GuideBench evaluates LLMs on three critical aspects: (i) adherence to diverse rules, (ii) robustness to rule updates, and (iii) alignment with human preferences. Experimental results on a range of LLMs indicate substantial opportunities for improving their ability to follow domain-oriented guidelines. Data and code are available at Anonymous.

GuideBench: Benchmarking Domain-Oriented Guideline Following for LLM Agents

Mainstream issue-resolving frameworks predominantly rely on commercial models, leading to high costs and privacy concerns. Existing training approaches for issue resolving struggle with poor generalization and fail to fully leverage open-source development resources. We propose **S**ubtask-**o**riented **R**einforced **F**ine-**T**uning (**SoRFT**), a novel training approach to enhance the issue resolving capability of LLMs. We decomposes issue resolving into structured subtasks: file localization, function localization, line localization, and code edit generation. SoRFT consists of two training stages: (1) **rejection-sampled supervised fine-tuning**, Chain of Thought (CoT) data is filtered using ground-truth before fine-tuning the LLM, and (2) **rule-based reinforcement learning**, which leverages PPO with ground-truth based rewards. We evaluate the SoRFT-trained model on SWE-Bench Verified and SWE-Bench Lite, achieving state-of-the-art (SOTA) performance among open-source models (e.g., resolve 21.4% issues on SWE-Bench Verified with SoRFT-Qwen-7B). The experimental results demonstrate that SoRFT significantly enhances issue-resolving performance, improves model generalization, and provides a cost-efficient alternative to commercial models.

SoRFT: Issue Resolving with Subtask-oriented Reinforced Fine-Tuning

Automatic exploit generation (AEG) refers to the automatic discovery and exploitation of vulnerabilities against unknown targets. Traditional AEG often targets a single type of vulnerability and still relies on templates built from expert experience. To achieve intelligent exploit generation, we establish a comprehensive benchmark using Binary Exploitation (pwn) challenges in Capture the Flag (CTF) competitions and investigate the capabilities of Large Language Models (LLMs) in AEG based on the benchmark. To improve the performance of AEG, we propose PwnGPT, an LLM-based automatic exploit generation framework that automatically solves pwn challenges. The structural design of PwnGPT is divided into three main components: analysis, generation, and verification modules. With the help of a modular approach and structured problem inputs, PwnGPT can solve challenges that LLMs cannot directly solve. We evaluate PwnGPT on our benchmark and analyze the outputs of each module. Experimental results show that our framework is highly autonomous and capable of addressing various challenges. Compared to direct input LLMs, PwnGPT increases the completion rate of exploit on our benchmark from 26.3\% to 57.9\% with the OpenAI o1-preview model and from 21.1\% to 36.8\% with the GPT-4o model.

PwnGPT: Automatic Exploit Generation Based on Large Language Models

While data synthesis and distillation are promising strategies to enhance small language models, current approaches heavily rely on Large Language Models (LLMs), which suffer from high computational costs, environmental inefficiency, and potential biases inherited from monolithic architectures. In contrast, smaller LMs are more accessible and sustainable, but their individual capabilities often fall short in generating high-quality, diverse, and reliable data. Inspired by collaborative human processes (e.g., peer review), we propose a multiple small LMs involved framework, GRA, that aggregates specialized roles across small LMs to iterative refinement and quality control typically achieved by a single large LM. 
In this collaborative framework, multiple small LMs assume distinct roles—Generator, Reviewer, and Adjudicator—to simulate a peer-review-inspired data synthesis pipeline. The Generator proposes initial data samples, the Reviewer critiques their quality and diversity, and the Adjudicator resolves conflicts to finalize the output. By decomposing the synthesis process into specialized sub-tasks, collaborative small LMs can achieve data-level parity with distillation from large LMs. Through experiments across multiple benchmarks, we demonstrate that GRA-produced data matches or exceeds the quality of single large LM outputs, e.g., Qwen-2.5-72B-Instruct. Our results challenge the necessity of monolithic large models for high-quality data synthesis, advocating instead for strategic coordination of smaller agents.

A Strategic Coordination Framework of Small LMs Matches Large LMs in Data Synthesis

We introduce PaSa, an advanced Paper Search agent powered by large language models. PaSa can autonomously make a series of decisions, including invoking search tools, reading papers, and selecting relevant references, to ultimately obtain comprehensive and accurate results for complex scholar queries. We optimize PaSa using reinforcement learning with a synthetic dataset, AutoScholarQuery, which includes 35k fine-grained academic queries and corresponding papers sourced from top-tier AI conference publications. Additionally, we develop RealScholarQuery, a benchmark collecting real-world academic queries to assess PaSa performance in more realistic scenarios. Despite being trained on synthetic data, PaSa significantly outperforms existing baselines on RealScholarQuery, including Google, Google Scholar, Google with GPT-4o for paraphrased queries, ChatGPT (search-enabled GPT-4o), GPT-o1, and PaSa-GPT-4o (PaSa implemented by prompting GPT-4o). Notably, PaSa-7B surpasses the best Google-based baseline, Google with GPT-4o, by 37.78% in recall@20 and 39.90% in recall@50, and exceeds PaSa-GPT-4o by 30.36% in recall and 4.25% in precision. Model, datasets, and code are available at https://github.com/bytedance/pasa.
Demo: https://pasa-agent.ai

PaSa: An LLM Agent for Comprehensive Academic Paper Search

Recent advances in Large Language Models (LLMs) have yielded impressive successes on many language tasks. However, efficient processing of long contexts using LLMs remains a significant challenge. We introduce **EpMAN** -- a method for processing long contexts in an episodic memory module while holistically attending to semantically-relevant context chunks. Output from episodic attention is then used to reweigh the decoder's self-attention to the stored KV cache of the context during training and generation. When an LLM decoder is trained using **EpMAN**, its performance on multiple challenging single-hop long-context recall and question-answering benchmarks is found to be stronger and more robust across the range from 16k to 256k tokens than baseline decoders trained with self-attention, and popular retrieval-augmented generation frameworks.

EpMAN: Episodic Memory AttentioN for Generalizing to Longer Contexts

Multi-modal Large Language Models (MLLMs) integrating images, text, and speech can provide farmers with accurate diagnoses and treatment of pests and diseases, enhancing agricultural efficiency and sustainability. However, existing benchmarks lack comprehensive evaluations, particularly in multi-level reasoning, making it challenging to identify model limitations. To address this issue, we introduce Agri-CM$^3$, an expert-validated benchmark assessing MLLMs’ understanding and reasoning in agricultural management. It includes 3,939 images and 15,901 multi-level multiple-choice questions with detailed explanations. Evaluations of 45 MLLMs reveal significant gaps. Even GPT-4o achieves only 63.64\% accuracy, falling short in fine-grained reasoning tasks. Analysis across three reasoning levels and seven compositional abilities highlights key challenges in accuracy and cognitive understanding. Our study provides insights for advancing MLLMs in agricultural management, driving their development and application. Code and data are available at \url{https://github.com/HIT-Kwoo/Agri-CM3}.

Agri-CM3: A Chinese Massive Multi-modal, Multi-level Benchmark for Agricultural Understanding and Reasoning

With the impressive reasoning and text generation capabilities of large language models (LLMs), methods leveraging multiple LLMs to debate each other have garnered increasing attention. However, existing debate-based approaches remain limited in effectiveness in structured and detailed domains represented by code generation due to several reasons: 1) Reliance on different instances of the same LLM for debate, neglecting the potential benefits of integrating diverse models with varied internal knowledge for more comprehensive code generation, 2) under-utilization of test cases, and 3) reliance on third-party LLM moderators for result consolidation and decision-making, probably introducing hallucinations and judgment errors. To address these challenges, we propose DebateCoder to collect intelligence of LLMs via test case-driven debate for code generation. In DebateCoder, test cases serve as a medium for models to analyze code and identify bugs, while opposing models generate test cases to challenge each other's code during the debate process. These test cases, along with their execution results, are elaborately leveraged to refine and enhance the code through a novel contrastive analysis process. Furthermore, DebateCoder leverages test case outcomes to assess code quality and determine convergence criteria. Unlike previous approaches, DebateCoder emphasizes the collaborative improvement of both models through competitive debate and interactive analysis. Abundant experimental results on two datasets demonstrate the effectiveness of DebateCoder.

DebateCoder: Towards Collective Intelligence of LLMs via Test Case Driven LLM Debate for Code Generation

Modern zero-shot text-to-speech (TTS) systems, despite using extensive pre-training, often struggle in challenging scenarios such as tongue twisters, repeated words, code-switching, and cross-lingual synthesis, leading to intelligibility issues. To address these limitations, this paper leverages preference alignment techniques, which enable targeted construction of out-of-pretraining-distribution data to enhance performance. We introduce a new dataset, named the Intelligibility Preference Speech Dataset (INTP), and extend the Direct Preference Optimization (DPO) framework to accommodate diverse TTS architectures. After INTP alignment, in addition to intelligibility, we observe overall improvements including naturalness, similarity, and audio quality for multiple TTS models across diverse domains. Based on that, we also verify the weak-to-strong generalization ability of INTP for more intelligible models such as CosyVoice 2 and Ints. Moreover, we showcase the potential for further improvements through iterative alignment based on Ints. Audio samples are available at https://intalign.github.io/.

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