Austria

Language models hold incredible promise for enabling scientific discovery by synthesizing massive research corpora. Many complex scientific research questions have multiple plausible answers, each supported by evidence of varying strength. However, existing language models lack the capability to quantitatively and faithfully compare answer plausibility in terms of supporting evidence. To address this, we introduce Retrieve to Explain (R2E), a retrieval-based model that scores and ranks all possible answers to a research question based on evidence retrieved from a document corpus. The architecture represents each answer only in terms of its supporting evidence, with the answer itself masked. This allows us to extend feature attribution methods such as Shapley values, to transparently attribute answer scores to supporting evidence at inference time. The architecture also allows incorporation of new evidence without retraining, including non-textual data modalities templated into natural language. We developed R2E for the challenging scientific discovery task of drug target identification, a human-in-the-loop process where failures are extremely costly and explainability paramount. When predicting whether drug targets will subsequently be confirmed as efficacious in clinical trials, R2E not only matches non-explainable literature-based models but also surpasses a genetics-based target identification approach used throughout the pharmaceutical industry.

ACL 2025

Retrieve to Explain: Evidence-driven Predictions for Explainable Drug Target Identification

explanation faithfulness

healthcare applications

nlp datasets

feature attribution

human-in-the-loop

passage retrieval

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ACL 2024

The 62nd Annual Meeting of the Association for Computational Linguistics (ACL 2024) will take place in Bangkok, Thailand from August 11th to 16th, 2024. More information will be announced soon.

technical paper

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

Traditional methods for processing classical Chinese typically segment language understanding into discrete tasks, which overlook crucial background information and reduce user engagement. Large language models (LLMs) provide integrated solutions, yet they entail high computational costs and risks of generating inaccurate historical information. To tackle these challenges, we propose a novel framework, TEACH (conTrastive knowlEdge Adaptive distillation with enhanCed Historical interpretability), which focuses on classical Chinese understanding by integrating word sense disambiguation with sentence translation. This integration leverages a confidence-annotated knowledge base and a step-by-step Chain-of-Thought prompting mechanism to minimize hallucinations and improve semantic analysis. Moreover, TEACH employs contrastive distillation learning to efficiently transfer capabilities from larger models to smaller ones (e.g., Qwen2-1.5B), addressing overly liberal translations. Additionally, we introduce an innovative generation evaluation metric using iterative word alignment, enhancing LLM performance assessments by distinguishing additional information and addressing excessive translation issues. Experiments conducted on real-world datasets validate TEACH's efficacy in classical Chinese educational scenarios.

TEACH: A Contrastive Knowledge Adaptive Distillation Framework for Ancient Chinese Understanding

Large Language Models (LLMs) can correct their self-generated responses, but a decline in accuracy after self-correction is also witnessed. To have a deeper understanding of self-correction, we endeavor to decompose, evaluate, and analyze the self-correction behaviors of LLMs. By enumerating and analyzing answer correctness before and after self-correction, we decompose the self-correction capability into confidence (being confident to correct answers) and critique (turning wrong answers to correct) capabilities, and propose two metrics from a probabilistic perspective to measure these 2 capabilities, along with another metric for overall self-correction capability evaluation. Based on our decomposition and evaluation metrics, we conduct extensive experiments and draw some empirical conclusions. For example, we find different models can exhibit distinct behaviors: some models are confident while others are more critical. We also find the trade-off between the two capabilities (i.e. improving one can lead to a decline in the other) when manipulating model self-correction behavior by prompts or in-context learning. Further, we find a simple yet efficient strategy to improve self-correction capability by transforming Supervision Fine-Tuning (SFT) data format, and our strategy outperforms vanilla SFT in both capabilities and achieves much higher accuracy after self-correction.

Confidence v.s. Critique: A Decomposition of Self-Correction Capability for LLMs

In this work, we propose ProtoLens, a novel prototype-based model that provides fine-grained, sub-sentence level interpretability for text classification. ProtoLens uses a Prototype-aware Span Extraction module to identify relevant text spans associated with learned prototypes and a Prototype Alignment mechanism to ensure prototypes are semantically meaningful throughout training. By aligning the prototype embeddings with human-understandable examples, ProtoLens provides interpretable predictions while maintaining competitive accuracy. Extensive experiments demonstrate that ProtoLens outperforms both prototype-based and non-interpretable baselines on multiple text classification benchmarks. Code and data are available at \url{https://github.com/weibowen555/ProtoLens}.

ProtoLens: Advancing Prototype Learning for Fine-Grained Interpretability in Text Classification

Temporal Knowledge Graphs (TKGs) are vital for event prediction, yet current methods face limitations. Graph neural networks mainly depend on structural information, often overlooking semantic understanding and requiring high computational costs. Meanwhile, Large Language Models (LLMs) support zero-shot reasoning but lack sufficient capabilities to grasp the laws of historical event development. To tackle these challenges, we introduce a training-free Analogical Replay (AnRe) reasoning framework. Our approach retrieves similar events for queries through semantic-driven clustering and builds comprehensive historical contexts using a dual history extraction module that integrates long-term and short-term history. It then uses LLMs to generate analogical reasoning examples as contextual inputs, enabling the model to deeply understand historical patterns of similar events and improve its ability to predict unknown ones. Our experiments on four benchmarks show that AnRe significantly exceeds traditional training and existing LLM-based methods. Further ablation studies also confirm the effectiveness of the dual history extraction and analogical replay mechanisms.

AnRe: Analogical Replay for Temporal Knowledge Graph Forecasting

Retrieval-Augmented Generation (RAG), while serving as a viable complement to large language models (LLMs), often overlooks the crucial aspect of text chunking within its pipeline. This paper initially introduces a dual-metric evaluation method, comprising Boundary Clarity and Chunk Stickiness, to enable the direct quantification of chunking quality. Leveraging this assessment method, we highlight the inherent limitations of traditional and semantic chunking in handling complex contextual nuances, thereby substantiating the necessity of integrating LLMs into chunking process. To address the inherent trade-off between computational efficiency and chunking precision in LLM-based approaches, we devise the granularity-aware Mixture-of-Chunkers (MoC) framework, which consists of a three-stage processing mechanism. Notably, our objective is to guide the chunker towards generating a structured list of chunking regular expressions, which are subsequently employed to extract chunks from the original text. Extensive experiments demonstrate that both our proposed metrics and the MoC framework effectively settle challenges of the chunking task, revealing the chunking kernel while enhancing the performance of the RAG system.

MoC: Mixtures of Text Chunking Learners for Retrieval-Augmented Generation System

Recent advancements in long chain-of-thoughts (long CoTs) have significantly improved the reasoning capabilities of large language models (LLMs). Existing work finds that the capability of long CoT reasoning can be efficiently elicited by tuning on only a few examples and can easily transfer to other tasks. This motivates us to investigate whether long CoT reasoning is a general capability for LLMs. In this work, we conduct an empirical analysis for this question from the perspective of representation. We find that LLMs do encode long CoT reasoning as a general capability, with a clear distinction from vanilla CoTs. Furthermore, domain-specific representations are also required for the effective transfer of long CoT reasoning. Inspired by these findings, we propose GLORE, a novel representation engineering method to unleash the general long CoT reasoning capabilities of LLMs. Extensive experiments demonstrate the effectiveness and efficiency of GLORE in both in-domain and cross-domain scenarios. The code is available at https://github.com/txy77/GLoRE.

Unlocking General Long Chain-of-Thought Reasoning Capabilities of Large Language Models via Representation Engineering

Multimodal large language models (MLLMs) have enabled LLM-based agents to directly interact with application user interfaces (UIs), enhancing agents' performance in complex tasks. However, these agents often suffer from high latency and low reliability due to the extensive sequential UI interactions. To address this issue, we propose AXIS, a novel LLM-based agents framework that prioritize actions through application programming interfaces (APIs) over UI actions. This framework also facilitates the creation and expansion of APIs through automated exploration of applications. Our experiments on Microsoft Word demonstrate that AXIS reduces task completion time by 65%-70% and cognitive workload by 38%-53%, while maintaining accuracy of 97%-98% compared to humans. Our work contributes to a new human-agent-computer interaction (HACI) framework and explores a fresh UI design principle for application providers to turn applications into agents in the era of LLMs, paving the way towards an agent-centric operating system (Agent OS). The code and dataset will be available at https://aka.ms/haci_axis.

AXIS: Efficient Human-Agent-Computer Interaction with API-First LLM-Based Agents

Recent advancements in large language models (LLMs) have highlighted the risk of misusing them, raising the need for accurate detection of LLM-generated content. In response, a viable solution is to inject imperceptible identifiers into LLMs, known as watermarks. Our research extends the existing watermarking methods by proposing the novel Sampling One Then Accepting (STA-1) method. STA-1 is an unbiased watermark that preserves the original token distribution in expectation and has a lower risk of producing unsatisfactory outputs in low-entropy scenarios compared to existing unbiased watermarks. In watermark detection, STA-1 does not require prompts or a white-box LLM, provides statistical guarantees, demonstrates high efficiency in detection time, and remains robust against various watermarking attacks. Experimental results on low-entropy and high-entropy datasets demonstrate that STA-1 achieves the above properties simultaneously, making it a desirable solution for watermarking LLMs. Implementation codes for this study are available online.

Watermarking Large Language Models: An Unbiased and Low-risk Method

Recent advancements in LLMs unlearning have shown remarkable success in removing unwanted data-model influences while preserving the model's utility for legitimate knowledge. Despite these strides, sparse Mixture-of-Experts (MoE) LLMs--a key subset of the LLM family--have remained unexplored in the context of unlearning. As MoE LLMs are celebrated for their exceptional performance, we ask:How can unlearning be performed effectively and efficiently on MoE LLMs? Our pilot study shows that the dynamic routing nature of MoE LLMs introduces unique challenges, leading to excessive forgetting, uncontrolled knowledge erasure and substantial utility drops when existing unlearning methods are applied. To address this, we propose a novel Selected-Expert Unlearning Framework (SEUF). Through expert attribution, unlearning is concentrated on the most actively engaged experts for the specified knowledge. Concurrently, an anchor loss is applied to the router to stabilize the active state of this targeted expert, ensuring focused and controlled unlearning. SEUF is compatible with various standard unlearning algorithms. Extensive experiments demonstrate that SEUF enhances both forget quality up to 5% and model utility by 35% on MoE LLMs across various benchmarks and LLM architectures (compared to standard unlearning algorithms), while only unlearning 0.06% of the model parameters.

SEUF: Is Unlearning One Expert Enough for Mixture-of-Experts LLMs?

Spatial transcriptomic technologies enable measuring gene expression profile and spatial information of cells in tissues simultaneously. Clustering of captured cells/spots in the spatial transcriptomic data is crucial for understanding tissue niches and uncovering disease-related changes.
Current methods to cluster spatial transcriptomic data encounter obstacles, including inefficiency in handling multi-replicate data, lack of prior knowledge incorporation, and producing uninterpretable cluster labels.
We introduce a novel approach, LLMiniST, to identify spatial niche using a zero-shot large language models (LLMs) by transforming spatial transcriptomic data into spatial context prompts, leveraging gene expression of neighboring cells/spots, cell type composition, tissue information, and external knowledge. 
The model was further enhanced using a two-stage fine-tuning strategy for improved generalizability. We also develop a user-friendly annotation tool to accelerate the creation of well-annotated spatial dataset for fine-tuning.
Comprehensive method performance evaluations showed that both zero-shot and fine-tunned LLMiniST had superior performance than current non-LLM methods in many circumstances. 
Notably, the two-stage fine-tuning strategy facilitated substantial cross-subject generalizability. 
The results demonstrate the feasibility of LLMs for tissue niche identification using spatial transcriptomic data and the potential of LLMs as a scalable solution to efficiently integrate minimal human guidance for improved performance in large-scale datasets.

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TEACH: A Contrastive Knowledge Adaptive Distillation Framework for Ancient Chinese Understanding

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