GenAI4ELab/papercli-papers huggingface dataset:
AELC: Adaptive Entity Linking with LLM-Driven Contextualization
Authors: Fang Wang; Zhengwei Tao; Ming Wang; Minghao Hu; Xiaoying Bai
Venue: EMNLP 2025 (Findings of the Association for Computational Linguistics: EMNLP 2025)

Abstract: Entity linking (EL) focuses on accurately associating ambiguous mentions in text with corresponding entities in a knowledge graph. Traditional methods mainly rely on fine-tuning or training on specific datasets. However, they suffer from insufficient semantic comprehension, high training costs, and poor scalability. Large Language Models (LLMs) offer promising solutions for EL, but face key challenges: weak simple-prompt performance, costly fine-tuning, and limited recall and precision due to the lack of LLMs use in candidate generation. Building on this, we introduce a novel framework: **A**daptive **E**ntity **L**inking with LLM-Driven **C**ontextualization. AELC, for the first time, introduces the combination of high-density key information condensation prompt and tool-invocation strategy, using a unified format semantic filtering strategy and an adaptive iterative retrieval mechanism to dynamically optimize the candidate set, significantly enhancing both precision and coverage. Furthermore, we innovatively reformulate the EL task as a multiple-choice problem, enabling multi-round reasoning to substantially improve the model’s discriminative capability and robustness. Experiments on four public benchmark datasets demonstrate that AELC achieves state-of-the-art performance. Further ablation studies validate the effectiveness of each module.
MetaLadder: Ascending Mathematical Solution Quality via Analogical-Problem Reasoning Transfer
Authors: Honglin Lin; Zhuoshi Pan; Qizhi Pei; Xin Gao; Yu Li; Mengzhang Cai; Conghui He; Lijun Wu
Venue: EMNLP 2025 (Findings of the Association for Computational Linguistics: EMNLP 2025)

Abstract: Large Language Models (LLMs) have demonstrated promising capabilities in solving mathematical reasoning tasks, leveraging Chain-of-Thought (CoT) data as a vital component in guiding answer generation. Current paradigms typically generate CoT and answers directly for a given problem, diverging from human problem-solving strategies to some extent. Humans often solve problems by recalling analogous cases and leveraging their solutions to reason about the current task. Inspired by this cognitive process, we propose MetaLadder, a novel framework that explicitly prompts LLMs to recall and reflect on meta-problems, those structurally or semantically analogical problems, alongside their CoT solutions before addressing the target problem. Additionally, we introduce a problem-restating mechanism to enhance the model’s comprehension of the target problem by regenerating the original question, which further improves reasoning accuracy. Therefore, the model can achieve reasoning transfer from analogical problems, mimicking human-like “learning from examples” and generalization abilities. Extensive experiments on mathematical benchmarks demonstrate that our MetaLadder significantly boosts LLMs’ problem-solving accuracy, largely outperforming standard CoT-based methods (10.3% accuracy gain) and other methods.
GLProtein: Global-and-Local Structure Aware Protein Representation Learning
Authors: Yunqing Liu; Wenqi Fan; Xiaoyong Wei; Li Qing
Venue: EMNLP 2025 (Findings of the Association for Computational Linguistics: EMNLP 2025)

Abstract: Proteins are central to biological systems, participating as building blocks across all forms of life. Despite advancements in understanding protein functions through protein sequence analysis, there remains potential for further exploration in integrating protein structural information. We argue that the structural information of proteins is not only limited to their 3D information but also encompasses information from amino acid molecules (local information) to protein-protein structure similarity (global information). To address this, we propose GLProtein, the first framework in protein pre-training that incorporates both global structural similarity and local amino acid details to enhance prediction accuracy and functional insights. GLProtein innovatively combines protein-masked modelling with triplet structure similarity scoring, protein 3D distance encoding and substructure-based amino acid molecule encoding. Experimental results demonstrate that GLProtein outperforms previous methods in several bioinformatics tasks, including predicting protein-protein interactions, contact prediction, and so on.
Reward Mixology: Crafting Hybrid Signals for Reinforcement Learning Driven In-Context Learning
Authors: Changshuo Zhang; Ang Gao; Xiao Zhang; Yong Liu; Deyang Li; Fangchao Liu; Xinyu Zhang
Venue: EMNLP 2025 (Findings of the Association for Computational Linguistics: EMNLP 2025)

Abstract: In-context learning (ICL) performance heavily relies on the quality and ordering of demonstrations. Iterative selection (IS) is a promising approach to address this issue, but existing IS methods face two key challenges: the oversimplification of process reward signals that guide intermediate steps (often using single-dimensional metrics) and the lack of outcome reward signals that directly optimize final-task accuracy (relying solely on binary terminal feedback like correct/incorrect predictions). To address these issues, we propose a reinforcement learning method R-Mix which models iterative demonstration selection as a Markov Decision Process (MDP), crafting hybrid reward signals — combining outcome-based accuracy signals (i.e., outcome rewards) with process-oriented signals (i.e, process rewards) like stepwise influence and label entropy improvement. Our analysis reveals a positive but trade-off relationship between outcome rewards and process rewards, underscoring the importance of both components for effective policy optimization. We further introduce a dual-head policy architecture that explicitly decouples input-semantic relevance and label-content compatibility. Experiments across NLP benchmarks demonstrate superior performance over state-of-the-art methods, with ablation studies validating the necessity of both reward components and architectural disentanglement. Our work has deeply explored the effective potential of ICL through demonstration selection.
Can Multimodal LLMs See Materials Clearly? A Multimodal Benchmark on Materials Characterization
Authors: Zhengzhao Lai; Youbin Zheng; Zhenyang Cai; Haonan Lyu; Jingpu Yang; Hong-Qing Liang; Yan Hu; Benyou Wang
Venue: EMNLP 2025 (Findings of the Association for Computational Linguistics: EMNLP 2025)

Abstract: Materials characterization is fundamental to acquiring materials information, revealing the processing-microstructure-property relationships that guide material design and optimization. While multimodal large language models (MLLMs) have recently shown promise in generative and predictive tasks within materials science, their capacity to understand real-world characterization imaging data remains underexplored. To bridge this gap, we present MatCha, the first benchmark for materials characterization image understanding, comprising 1,500 questions that demand expert-level domain expertise. MatCha encompasses four key stages of materials research comprising 21 distinct tasks, each designed to reflect authentic challenges faced by materials scientists. Our evaluation of state-of-the-art MLLMs on MatCha reveals a significant performance gap compared to human experts. These models exhibit degradation when addressing questions requiring higher-level expertise and sophisticated visual perception. Simple few-shot and chain-of-thought prompting struggle to alleviate these limitations. These findings highlight that existing MLLMs still exhibit limited adaptability to real-world materials characterization scenarios. We hope MatCha will facilitate future research in areas such as new material discovery and autonomous scientific agents. MatCha is available at https://github.com/FreedomIntelligence/MatCha.
GRADE: Generating multi-hop QA and fine-gRAined Difficulty matrix for RAG Evaluation
Authors: Jeongsoo Lee; Daeyong Kwon; Kyohoon Jin
Venue: EMNLP 2025 (Findings of the Association for Computational Linguistics: EMNLP 2025)

Abstract: Retrieval-Augmented Generation (RAG) systems are widely adopted in knowledge-intensive NLP tasks, but current evaluations often overlook the structural complexity and multi-step reasoning required in real-world scenarios. These benchmarks overlook key factors such as the interaction between retrieval difficulty and reasoning depth. To address this gap, we propose GRADE, a novel evaluation framework that models task difficulty along two orthogonal dimensions: (1) reasoning depth, defined by the number of inference steps (hops), and (2) semantic distance between the query and its supporting evidence. We construct a synthetic multi-hop QA dataset from factual news articles by extracting knowledge graphs and augmenting them through semantic clustering to recover missing links, allowing us to generate diverse and difficulty-controlled queries. Central to our framework is a 2D difficulty matrix that combines generator-side and retriever-side difficulty. Experiments across multiple domains and models show that error rates strongly correlate with our difficulty measures, validating their diagnostic utility. GRADE enables fine-grained analysis of RAG performance and provides a scalable foundation for evaluating and improving multi-hop reasoning in real-world applications.
FusionDTI: Fine-grained Binding Discovery with Token-level Fusion for Drug-Target Interaction
Authors: Zhaohan Meng; Zaiqiao Meng; Ke Yuan; Iadh Ounis
Venue: EMNLP 2025 (Findings of the Association for Computational Linguistics: EMNLP 2025)

Abstract: Predicting drug-target interaction (DTI) is critical in the drug discovery process. Despite remarkable advances in recent DTI models through the integration of representations from diverse drug and target encoders, such models often struggle to capture the fine-grained interactions between drugs and protein, i.e. the binding of specific drug atoms (or substructures) and key amino acids of proteins, which is crucial for understanding the binding mechanisms and optimising drug design. To address this issue, this paper introduces a novel model, called FusionDTI, which uses a token-level **Fusion** module to effectively learn fine-grained information for **D**rug-**T**arget **I**nteraction. In particular, our FusionDTI model uses the SELFIES representation of drugs to mitigate sequence fragment invalidation and incorporates the structure-aware (SA) vocabulary of target proteins to address the limitation of amino acid sequences in structural information, additionally leveraging pre-trained language models extensively trained on large-scale biomedical datasets as encoders to capture the complex information of drugs and targets. Experiments on three well-known benchmark datasets show that our proposed FusionDTI model achieves the best performance in DTI prediction compared with eight existing state-of-the-art baselines. Furthermore, our case study indicates that FusionDTI could highlight the potential binding sites, enhancing the explainability of the DTI prediction.
A Survey on Training-free Alignment of Large Language Models
Authors: Birong Pan; Yongqi Li; Weiyu Zhang; Wenpeng Lu; Mayi Xu; Shen Zhou; Yuanyuan Zhu; Ming Zhong; Tieyun Qian
Venue: EMNLP 2025 (Findings of the Association for Computational Linguistics: EMNLP 2025)

Abstract: The alignment of large language models (LLMs) aims to ensure their outputs adhere to human values, ethical standards, and legal norms. Traditional alignment methods often rely on resource-intensive fine-tuning (FT), which may suffer from knowledge degradation and face challenges in scenarios where the model accessibility or computational resources are constrained. In contrast, training-free (TF) alignment techniques—leveraging in-context learning, decoding-time adjustments, and post-generation corrections—offer a promising alternative by enabling alignment without heavily retraining LLMs, making them adaptable to both open-source and closed-source environments. This paper presents the first systematic review of TF alignment methods, categorizing them by stages of **pre-decoding**, **in-decoding**, and **post-decoding**. For each stage, we provide a detailed examination from the viewpoint of LLMs and multimodal LLMs (MLLMs), highlighting their mechanisms and limitations. Furthermore, we identify key challenges and future directions, paving the way for more inclusive and effective TF alignment techniques. By synthesizing and organizing the rapidly growing body of research, this survey offers a guidance for practitioners and advances the development of safer and more reliable LLMs.
CIVET: Systematic Evaluation of Understanding in VLMs
Authors: Massimo Rizzoli; Simone Alghisi; Olha Khomyn; Gabriel Roccabruna; Seyed Mahed Mousavi; Giuseppe Riccardi
Venue: EMNLP 2025 (Findings of the Association for Computational Linguistics: EMNLP 2025)

Abstract: While Vision-Language Models (VLMs) have achieved competitive performance in various tasks, their comprehension of the underlying structure and semantics of a scene remains understudied. To investigate the understanding of VLMs, we study their capability regarding object properties and relations in a controlled and interpretable manner. To this scope, we introduce CIVET, a novel and extensible framework for systematiC evaluatIon Via controllEd sTimuli. CIVET addresses the lack of standardized systematic evaluation for assessing VLMs’ understanding, enabling researchers to test hypotheses with statistical rigor. With CIVET, we evaluate five state-of-the-art VLMs on exhaustive sets of stimuli, free from annotation noise, dataset-specific biases, and uncontrolled scene complexity. Our findings reveal that 1) current VLMs can accurately recognize only a limited set of basic object properties; 2) their performance heavily depends on the position of the object in the scene; 3) they struggle to understand basic relations among objects. Furthermore, a comparative evaluation with human annotators reveals that VLMs still fall short of achieving human-level accuracy.
How Does Cognitive Bias Affect Large Language Models? A Case Study on the Anchoring Effect in Price Negotiation Simulations
Authors: Yoshiki Takenami; Yin Jou Huang; Yugo Murawaki; Chenhui Chu
Venue: EMNLP 2025 (Findings of the Association for Computational Linguistics: EMNLP 2025)

Abstract: Cognitive biases, well studied in humans, can also be observed in LLMs, affecting their reliability in real-world applications. This paper investigates the anchoring effect in LLM-driven price negotiations. To this end, we instructed seller LLM agents to apply the anchoring effect and evaluated negotiations using not only an objective metric but also a subjective metric. Experimental results show that LLMs are influenced by the anchoring effect like humans. Additionally, we investigated the relationship between the anchoring effect and factors such as reasoning and personality. It was shown that reasoning models are less prone to the anchoring effect, suggesting that the long chain of thought mitigates the effect. However, we found no significant correlation between personality traits and susceptibility to the anchoring effect. These findings contribute to a deeper understanding of cognitive biases in LLMs and to the realization of safe and responsible application of LLMs in society.
Enhancing Speech-to-Speech Dialogue Modeling with End-to-End Retrieval-Augmented Generation
Authors: Pengchao Feng; Ziyang Ma; Wenxi Chen; Yao Li; Sheng Wang; Kai Yu; Xie Chen
Venue: EMNLP 2025 (Findings of the Association for Computational Linguistics: EMNLP 2025)

Abstract: End-to-end speech-to-speech (S2S) dialogue systems have recently garnered increasing research attention for their lower latency and more natural integration of nonverbal cues such as emotion and speaker identity. However, these systems face key challenges, particularly in incorporating external knowledge, a capability commonly addressed by Retrieval-Augmented Generation (RAG) in text-based large language models (LLMs). The core difficulty lies in the modality gap between input speech and retrieved textual knowledge, which hinders effective integration of information. To address this issue, we propose a novel end-to-end RAG framework that directly retrieves relevant textual knowledge from speech queries. Experimental results demonstrate that our method significantly improves the performance of end-to-end S2S dialogue systems while achieving higher retrieval efficiency. Although the overall performance still lags behind the SOTA cascaded models, our framework offers a promising direction for enhancing knowledge integration in end-to-end S2S systems. Our code and dataset are released.
Backdoor-Powered Prompt Injection Attacks Nullify Defense Methods
Authors: Yulin Chen; Haoran Li; Yuan Sui; Yangqiu Song; Bryan Hooi
Venue: EMNLP 2025 (Findings of the Association for Computational Linguistics: EMNLP 2025)

Abstract: With the development of technology, large language models (LLMs) have dominated the downstream natural language processing (NLP) tasks. However, because of the LLMs’ instruction-following abilities and inability to distinguish the instructions in the data content, such as web pages from search engines, the LLMs are vulnerable to prompt injection attacks. These attacks trick the LLMs into deviating from the original input instruction and executing the attackers’ target instruction. Recently, various instruction hierarchy defense strategies are proposed to effectively defend against prompt injection attacks via fine-tuning.In this paper, we explore more vicious attacks that nullify the prompt injection defense methods, even the instruction hierarchy: backdoor-powered prompt injection attacks, where the attackers utilize the backdoor attack for prompt injection attack purposes. Specifically, the attackers poison the supervised fine-tuning samples and insert the backdoor into the model. Once the trigger is activated, the backdoored model executes the injected instruction surrounded by the trigger. We construct a benchmark for comprehensive evaluation. Our experiments demonstrate that backdoor-powered prompt injection attacks are more harmful than previous prompt injection attacks, nullifying existing prompt injection defense methods, even the instruction hierarchy techniques.
Path-enhanced Pre-trained Language Model for Knowledge Graph Completion
Authors: Hao Wang; Dandan Song; Zhijing Wu; Yuhang Tian; Pan Yang
Venue: EMNLP 2025 (Findings of the Association for Computational Linguistics: EMNLP 2025)

Abstract: Pre-trained language models (PLMs) have achieved remarkable knowledge graph completion(KGC) success. However, most methods derive KGC results mainly from triple-level and text-described learning, which lack the capability to capture long-term relational and structural information. Moreover, the absence of a visible reasoning process leads to poor interpretability and credibility of the completions. In this paper, we propose a path-enhanced pre-trained language model-based knowledge graph completion method (PEKGC), which employs multi-view generation to infer missing facts in triple-level and path-level simultaneously to address lacking long-term relational information and interpretability issues. Furthermore, a neighbor selector module is proposed to filter neighbor triples to provide the adjacent structural information. Besides, we propose a fact-level re-evaluation and a heuristic fusion ranking strategy for candidate answers to fuse multi-view predictions. Extensive experiments on the benchmark datasets demonstrate that our model significantly improves the performance of the KGC task.
Zero-shot Cross-lingual NER via Mitigating Language Difference: An Entity-aligned Translation Perspective
Authors: Zhihao Zhang; Sophia Yat Mei Lee; Dong Zhang; Shoushan Li; Guodong Zhou
Venue: EMNLP 2025 (Findings of the Association for Computational Linguistics: EMNLP 2025)

Abstract: Cross-lingual Named Entity Recognition (CL-NER) aims to transfer knowledge from high-resource languages to low-resource languages. However, existing zero-shot CL-NER (ZCL-NER) approaches primarily focus on Latin script language (LSL), where shared linguistic features facilitate effective knowledge transfer. In contrast, for non-Latin script language (NSL), such as Chinese and Japanese, performance often degrades due to deep structural differences. To address these challenges, we propose an entity-aligned translation (EAT) approach. Leveraging large language models (LLMs), EAT employs a dual-translation strategy to align entities between NSL and English. In addition, we fine-tune LLMs using multilingual Wikipedia data to enhance the entity alignment from source to target languages.
Zero-Shot Cross-Domain Aspect-Based Sentiment Analysis via Domain-Contextualized Chain-of-Thought Reasoning
Authors: Chuming Shen; Wei Wei; Dong Wang; Zhong-Hao Wang
Venue: EMNLP 2025 (Findings of the Association for Computational Linguistics: EMNLP 2025)

Abstract: Cross-domain aspect-based sentiment analysis (ABSA) aims at learning specific knowledge from a source domain to perform various ABSA tasks on a target domain. Recent works mainly focus on how to use domain adaptation techniques to transfer the domain-agnostic features from the labeled source domain to the unlabeled target domain. However, it would be unwise to manually collect a large number of unlabeled data from the target domain, where such data may not be available owing to the facts like data security concerns in banking or insurance. To alleviate this issue, we propose ZeroABSA, a unified zero-shot learning framework for cross-domain ABSA that effectively eliminates dependency on target-domain annotations. Specifically, ZeroABSA consists of two novel components, namely, (1) A hybrid data augmentation module leverages large language models (LLMs) to synthesize high-quality, domain-adaptive target-domain data, by evaluating the generated samples across vocabulary richness, semantic coherence and sentiment/domain consistency, followed by iterative refinement; (2) A domain-aware chain-of-thought (COT) prompting strategy trains models on augmented data while explicitly modeling domain-invariant reasoning to bridge the well-known cross-domain gap. Extensive evaluations across four diverse domains demonstrate that ZeroABSA surpasses the-state-of-the-arts, which effectively advances the practicality of cross-domain ABSA in real-world scenarios where labeled target-domain data is unavailable.
Tree of Agents: Improving Long-Context Capabilities of Large Language Models through Multi-Perspective Reasoning
Authors: Song Yu; Xiaofei Xu; Ke Deng; Li Li; Lin Tian
Venue: EMNLP 2025 (Findings of the Association for Computational Linguistics: EMNLP 2025)

Abstract: Large language models (LLMs) face persistent challenges when handling long-context tasks, most notably the “lost in the middle” issue, where information located in the middle of a long input tends to be underutilized. Some existing methods that reduce input have the risk of discarding key information, while others that extend context windows often lead to attention dispersion. To address these limitations, we propose Tree of Agents (TOA), a multi-agent reasoning framework that segments the input into chunks processed by independent agents. Each agent generates its local cognition, then agents dynamically exchange information for collaborative reasoning along tree-structured paths. TOA enables agents to probe different reasoning orders for multi-perspective understanding, effectively mitigating position bias and reducing hallucinations. To improve processing efficiency, we incorporate prefix-hash caching and adaptive pruning strategies, achieving significant performance improvements with comparable API overhead. Experiments show that TOA, powered by compact LLaMA3.1-8B, significantly outperforms multiple baselines and demonstrates comparable performance to the latest and much larger commercial models, such as Gemini1.5-pro, on various long-context tasks. Code is available at https://github.com/Aireduce952/Tree-of-Agents.