China

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.

EMNLP 2025

GLProtein: Global-and-Local Structure Aware Protein Representation Learning

protein representation learning

protein structure

protein pretraining

protein language model

poster

## Welcome!
"I am excited to welcome you to this year’s edition of the Conference on Empirical Methods in Natural Language Processing! Importantly, it marks the 30th edition of EMNLP. With over 8,000 submissions, more than 3,000 accepted papers, and thousands of attendees, we have come a long way from that first
workshop, which had 14 accepted papers. As the field looks ahead, Suzhou is the fitting location for celebrating this milestone: rooted in a long literary tradition, yet modern and forward-looking, and home to a large share of the NLP community."<br>

*Message from the General Chair, Dirk Hovy*

[**Link to Conference Handbook**](https://drive.google.com/file/d/1johU5QqVVYO4RfH7QcIORr7qrVBdzdwC/view?usp=sharing)





<br>

Celebrate 30 Years of EMNLP! 
EMNLP 2025 will be held in Suzhou, China from November 5th to November 9th, 2025.

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.

FusionDTI: Fine-grained Binding Discovery with Token-level Fusion for Drug-Target Interaction

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.

How Does Cognitive Bias Affect Large Language Models? A Case Study on the Anchoring Effect in Price Negotiation Simulations

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.

Backdoor-Powered Prompt Injection Attacks Nullify Defense Methods

Recent advancements in large language models (LLMs) have shown promise in feature engineering for tabular data, but concerns about their reliability persist, especially due to variability in generated outputs. We introduce a multi-level diagnosis and evaluation framework to assess the robustness of LLMs in feature engineering, focusing on identifying key variables, relationships, and decision boundaries for predicting target classes across diverse domains. We demonstrate that the robustness of LLMs varies significantly over different datasets, and that high-quality LLM-generated features can improve prediction performance by up to 10.52%. This work opens a new direction for assessing and enhancing the reliability of LLM-driven feature engineering.

Multi-level Diagnosis and Evaluation for Robust Tabular Feature Engineering with Large Language Models

World models have been widely utilized in robotics, gaming, and auto-driving. However, their applications on natural language tasks are relatively limited. In this paper, we construct the dialogue world model, which could predict the user's emotion, sentiment, and intention, and future utterances. By defining a POMDP, we argue emotion, sentiment and intention can be modeled as the user belief and solved by maximizing the information bottleneck. By this user belief modeling, we apply the model-based reinforcement learning framework to the dialogue system, and propose a framework called DreamCUB. Experiments show that the pretrained dialogue world model can achieve state-of-the-art performances on emotion classification and sentiment identification, while dialogue quality is also enhanced by joint training of the policy, critic and dialogue world model. Further analysis shows that this manner holds a reasonable exploration-exploitation balance and also transfers well to out-of-domain scenarios such as empathetic dialogues.

Dream to Chat: Model-based Reinforcement Learning on Dialogues with User Belief Modeling

Large Language Models (LLMs) exhibit strong reasoning capabilities and are widely applied in event forecasting. However, studies have demonstrated that LLMs exhibit human-like cognitive biases, systematic patterns of deviation from rationality in decision-making. To explore the cognitive biases in event forecasting, we introduce CogForecast, a human-curated dataset comprising six topics. Experimental results on three LLMs reveal significant cognitive biases in LLM-based event forecasting methods. To address this issue, we propose MCA, a Multi-Cognition Agentic framework. Specifically, MCA leverages LLMs to act as multi-cognition event participants, performing perspective-taking based on the cognitive patterns of event participants to alleviate the inherent cognitive biases in LLMs and offer diverse analytical perspectives. Then, MCA clusters agents according to their predictions and derives a final answer through a group-level reliability scoring method. Experimental results on a dataset including eight event categories demonstrate the effectiveness of MCA. Using Llama-3.1-70B, MCA achieves an accuracy of 82.3% (79.5% for the human crowd). Additionally, we demonstrate that MCA can alleviate the cognitive biases in LLMs and investigate three influencing factors. Our code and dataset will be publicly released.

Beyond Inherent Cognition Biases in LLM-Based Event Forecasting: A Multi-Cognition Agentic Framework

Peer review is essential for maintaining academic quality, but the increasing volume of submissions places a significant burden on reviewers. Large language models (LLMs) offer potential assistance in this process, yet their susceptibility to textual adversarial attacks raises reliability concerns. This paper investigates the robustness of LLMs used as automated reviewers in the presence of such attacks. We focus on three key questions: (1) The effectiveness of LLMs in generating reviews compared to human reviewers. (2) The impact of adversarial attacks on the reliability of LLM-generated reviews. (3) Challenges and potential mitigation strategies for LLM-based review. Our evaluation reveals significant vulnerabilities, as text manipulations can distort LLM assessments. We offer a comprehensive evaluation of LLM performance in automated peer reviewing and analyze its robustness against adversarial attacks. Our findings emphasize the importance of addressing adversarial risks to ensure AI strengthens, rather than compromises, the integrity of scholarly communication.

Breaking the Reviewer: Assessing the Vulnerability of Large Language Models in Automated Peer Review Under Textual Adversarial Attacks

Texts generated by large language models (LLMs) are increasingly widespread online. Due to the lack of effective attribution mechanisms, the enforcement of copyright and the prevention of misuse remain significant challenges in the context of LLM-generated content. LLMs watermark emerges as a crucial technology to trace the source of AI-generated content. However, most existing watermarking methods reduce the fidelity of semantics. To address this issue, this paper introduces a novel watermarking framework. To enhance the fidelity of semantics, we propose low-entropy POS-guided token partitioning mechanism and z-score-driven dynamic bias mechanism. Moreover, to enhance the robustness against potential bias sparsity exploitation attack, we propose a relative position encoding (RPE) mechanism, which can uniformly distribute bias in the generated text. Evaluated across 6 baselines, 4 tasks, and 5 LLMs under 8 attacks, compared to the KGW, our watermark improves semantic fidelity by 24.53% (RC-PPL) and robustness by 3.75% (F1). Our code is publicly available, facilitating reproducibility in LLM watermarking research.

Watermarking with Low-Entropy POS-Guided Token Partitioning and Z-Score-Driven Dynamic Bias for Large Language Models

Watermarking is a key technique for detecting AI-generated text. In this work, we study its vulnerabilities and introduce the Smoothing Attack, a novel watermark removal method. By leveraging the relationship between the model's confidence and watermark detectability, our attack selectively smoothes the watermarked content, erasing watermark traces while preserving text quality. We validate our attack on open-source models ranging from 1.3 B to 30B parameters on 10 different watermarks, demonstrating its effectiveness. Our findings expose critical weaknesses in existing watermarking schemes and highlight the need for stronger defenses.

Watermark Smoothing Attacks against Language Models

Few-shot multi-intent spoken language understanding (SLU) aims to identify users' multiple intents and key slots using a tiny amount of annotated data. Recent advances in large language models (LLMs) have utilized instruction learning frameworks to model intent-slot interdependencies, typically requiring abundant data for effective training. However, in few-shot scenarios, these frameworks face challenges such as mismatches between the number of generated slots and input lengths, relational confusion in multi-intent scenarios and neglect of task-specific variations in intent counts across utterances. To overcome the challenges, we propose PICD-Instruct, a novel generative framework based on Basic Instructions (BI), Pairwise Interaction Instructions (PII) and Contrastive Distinct Instructions (CDI). Specifically, BI directs LLMs to generate entities along with associated words, thereby mitigating mismatches in quantitative correspondences. PII explicitly captures dual-task interdependencies by guiding LLMs to pair each intent with its related entities. CDI enhances understanding of utterances by guiding LLMs to determine whether two utterances share the same intent count. Experimental results on public datasets indicate that PICD-Instruct achieves state-of-the-art performance.

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Next from EMNLP 2025

FusionDTI: Fine-grained Binding Discovery with Token-level Fusion for Drug-Target Interaction