United States

Drug discovery (DD) has tremendously contributed to maintaining and improving public health. Hypothesizing that inhibiting protein misfolding can slow disease progression, researchers focus on target identification (Target ID) to find protein structures for drug binding. While Large Language Models (LLMs) and Retrieval-Augmented Generation (RAG) frameworks have accelerated drug discovery, integrating models into cohesive workflows remains challenging. We conducted a user study with drug discovery researchers to identify the applicability of LLMs and RAGs in Target ID. We identified two main findings: 1) an LLM should provide multiple Protein-Protein Interactions (PPIs) based on an initial protein and protein candidates that have a therapeutic impact; 2) the model must provide the PPI and relevant explanations for better understanding. Based on these observations, we identified three limitations on previous approaches for Target ID: 1) semantic ambiguity, 2) lack of explainability, and 3) short retrieval units. To address these issues, we propose GraPPI, a large-scale knowledge graph (KG)-based retrieve-divide-solve agent pipeline RAG framework to support large-scale PPI signaling pathway exploration in understanding therapeutic impacts by decomposing the analysis of entire PPI pathways into sub-tasks focused on the analysis of PPI edges.

NAACL 2025

GraPPI: A Retrieve-Divide-Solve GraphRAG Framework for Large-scale Protein-protein Interaction Exploration

nlp4drugdiscovery

retrieval-augmented generation

knowledge graph

### 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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ACL 2025

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

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### Welcome to 2025 Annual Conference of the Nations of the Americas Chapter of the Association for Computational Linguistics

Welcome to the 2025 meeting of the Nations of the Americas Chapter of the Association for Computational Linguistics! I am proud to help organize the first NAACL conference to carry the new name of our organization, one that emphasizes inclusion for all of the Americas. I am also pleased to welcome you to Albuquerque, New Mexico, a state whose unique blend of cultural influences will make for an excellent backdrop for NAACL 2025, especially with this year’s special theme on NLP in a Multicultural World. 
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*- Colin Cherry, Google, NAACL 2025 General Chair* 

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Welcome to 2025 Annual Conference of the Nations of the Americas Chapter of the Association for Computational Linguistics

Resume matching assesses the extent to which candidates qualify for jobs based on the content of resumes. This process increasingly uses natural language processing (NLP) techniques to automate parsing and rating tasks—saving time and effort. Large language models (LLMs) are increasingly used for this purpose—thus, we explore their capabilities for resume matching in an observational study. We compare zero-shot GPT-4 and human ratings for 736 resumes submitted to job openings from diverse fields using real-world evaluation criteria. We also study the effects of prompt engineering techniques on GPT-4 ratings and compare differences in GPT-4 and human ratings across racial and gender groups. Our results show: LLM scores correlate minorly with humans, suggesting they are not interchangeable; prompt engineering such as CoT improves the quality of LLM ratings; and LLM scores do not show larger group differences (i.e., bias) than humans. Our findings provide implications for LLM-based resume rating to promote more fair and NLP-based resume matching in a multicultural world.

Human and LLM-Based Resume Matching: An Observational Study

Large language models (LLMs) are increasingly used as automated judges to evaluate recommendation systems, search engines, and other subjective tasks, where relying on human evaluators can be costly, time-consuming, and unscalable. LLMs offer an efficient solution for continuous, automated evaluation. However, since the systems that are built and improved with these judgments are ultimately designed for human use, it is crucial that LLM judgments align closely with human evaluators to ensure such systems remain human-centered. On the other hand, aligning LLM judgments with human evaluators is challenging due to individual variability and biases in human judgments. We propose a simple yet effective framework to align LLM judgments with individual human evaluators or their aggregated judgments, without retraining or fine-tuning the LLM. Our approach learns a linear mapping between the LLM's outputs and human judgments, achieving over 142% average improvement in agreement across 29 tasks with only a small number of calibration examples used for training. Notably, our method works in zero-shot and few-shot settings, exceeds inter-human agreement on four out of six tasks, and enables smaller LLMs to achieve performance comparable to that of larger models.

Aligning Black-box Language Models with Human Judgments

Like most of NLP, models for human-centered NLP tasks—tasks attempting to assess author-level information—predominantly use rep- resentations derived from hidden states of Transformer-based LLMs. However, what component of the LM is used for the representation varies widely. Moreover, there is a need for Human Language Models (HuLMs) that implicitly model the author and provide a user-level hidden state. Here, we systematically evaluate different ways of representing documents and users using different LM and HuLM architectures to predict task outcomes as both dynamically changing states and averaged trait-like user-level attributes of valence, arousal, empathy, and distress. We find that representing documents as an average of the token hidden states performs the best generally. Further, while a user-level hidden state itself is rarely the best representation, we find its inclusion in the model strengthens token or document embeddings used to derive document- and user-level representations resulting in best performances.

Evaluation of LLMs-based Hidden States as Author Representations for Psychological Human-Centered NLP Tasks

Recent advancements in Large Language Models (LLMs) have led to their adaptation in various domains as conversational agents. We wonder: can personality tests be applied to these agents to analyze their behavior, similar to humans? We introduce TRAIT, a new benchmark consisting of 8K multi-choice questions designed to assess the personality of LLMs. TRAIT is built on two psychometrically validated small human questionnaires, Big Five Inventory (BFI) and Short Dark Triad (SD-3), enhanced with the ATOMIC-10X knowledge graph to a variety of real-world scenarios. TRAIT also outperforms existing personality tests for LLMs in terms of reliability and validity, achieving the highest scores across four key metrics: Content Validity, Internal Validity, Refusal Rate, and Reliability. Using TRAIT, we reveal two notable insights into personalities of LLMs: 1) LLMs exhibit distinct and consistent personality, which is highly influenced by their training data (e.g., data used for alignment tuning), and 2) current prompting techniques have limited effectiveness in eliciting certain traits, such as high psychopathy or low conscientiousness, suggesting the need for further research in this direction.

Do LLMs Have Distinct and Consistent Personality? TRAIT: Personality Testset designed for LLMs with Psychometrics

Multiple-Choice Question Answering (MCQA) is a widely used task in the evaluation of Large Language Models (LLMs). In this work, we reveal that current LLMs' performance in MCQA could be heavily influenced by the choice of option symbol sets, due to the option symbol bias. That is, when altering only the option symbols (e.g., A/B/C/D→ i/ii/iii/iv), the results could vary sharply, leading to a margin of approximately 10% in accuracy. To uncover the mechanisms behind this, we investigate the internal components of LLMs from a causal perspective. By measuring the causal effects, we identify a small subset of attention heads responsible for the symbol bias. Subsequently, we interpret these key components in a human-understandable way, showing that attention heads with higher causal effects are more likely to focus on only option symbols, while those with lower causal effects tend to distribute their attention across the content of questions and options. It also motivates us to pursue debiasing based on the causal effects. Specifically, to mitigate such bias, we propose a tuning-free, causal effect driven debiasing method which intervenes the activations of identified components according to their causal effects, with stronger interventions corresponding to higher causal effects. Experimental results demonstrate that the proposed method not only alleviates aforementioned bias, but also improves the MCQA performance of LLMs.

Option Symbol Matters: Investigating and Mitigating Multiple-Choice Option Symbol Bias of Large Language Models

Large language Models (LLMs) have demonstrated remarkable skills across various domains. Understanding the mechanisms behind their abilities and implementing controls over them is becoming increasingly important for developing better models. In this paper, we focus on skill unlearning in LLMs, specifically unlearning a particular skill while retaining their overall capabilities. We introduce two lightweight, training-free machine skill unlearning techniques for LLMs. First, we observe that the pre-activation distribution of neurons in each Feed-Forward Layer (FFL) differs when the model demonstrates different skills. Additionally, we find that queries triggering the same skill cluster within the FFL key space and can be separated from other queries using a hypercube. Based on these observations, we propose two lightweight, training-free skill unlearning methods: `Neuron Adjust` and `Key Space Detection (KSD)`. We evaluate our methods on unlearning math-solving, Python-coding, and comprehension skills across seven different languages. The results demonstrate their strong unlearning capabilities for the designated skills. Specifically, `Key Space Detection` achieves over 80% relative performance drop on the forgetting skill and less than 10% relative performance drop on other skills and the model's general knowledge (MMLU) for most unlearning tasks.

Effective Skill Unlearning through Intervention and Abstention

In this paper, we investigate the overlooked impact of instruction-tuning on memorization in large language models (LLMs), which has largely been studied in base, pre-trained models. We propose a black-box prompt optimization method where an attacker LLM agent uncovers higher levels of memorization in a victim agent, surpassing traditional approaches that prompt the model directly with training data. Using an iterative rejection-sampling process, we design instruction-based prompts that minimize overlap with training data to avoid providing direct solutions while maximizing overlap between the victim's output and the training data to induce memorization. Our method shows 23.7% more overlap with training data compared to state-of-the-art baselines. We explore two attack settings: an analytical approach that determines the empirical upper bound of the attack, both with and without access to responses for prompt initialization, and a practical classifier-based method for assessing memorization without access to memorized data. Our findings reveal that instruction-tuned models can expose pre-training data as much as, or more than, base models; contexts beyond the original training data can lead to leakage; and instructions generated by other LLMs open new avenues for automated attacks, which we believe require further exploration.

ALPACA AGAINST VICUNA: Using LLMs to Uncover Memorization of LLMs

The rapid development of Large Multimodal Models (LMMs) has significantly advanced multimodal understanding by harnessing the language abilities of Large Language Models (LLMs) and integrating modality-specific encoders. However, LMMs are plagued by hallucinations that limit their reliability and adoption. While traditional methods to detect and mitigate these hallucinations often involve costly training or rely heavily on external models, recent approaches utilizing internal model features present a promising alternative. In this paper, we critically assess the limitations of the state-of-the-art training-free technique, the logit lens, in handling generalized visual hallucinations. We introduce *ContextualLens*, a refined method that leverages contextual token embeddings from middle layers of LMMs. This approach significantly improves hallucination detection and grounding across diverse categories, including actions and OCR, while also excelling in tasks requiring contextual understanding, such as spatial relations and attribute comparison. Our novel grounding technique yields highly precise bounding boxes, facilitating a transition from Zero-Shot Object Segmentation to Grounded Visual Question Answering. Our contributions pave the way for more reliable and interpretable multimodal models.

Beyond Logit Lens: Contextual Embeddings for Robust Hallucination Detection & Grounding in VLMs

This paper investigates the knowledge of language models from the perspective of Bayesian epistemology. We explore how language models adjust their confidence and responses when presented with evidence with varying levels of informativeness and reliability. To study these properties, we create a dataset with various types of evidence and analyze language models' responses and confidence using verbalized confidence, token probability, and sampling. We observed that language models do not consistently follow Bayesian epistemology: language models follow the Bayesian confirmation assumption well with true evidence but fail to adhere to other Bayesian assumptions when encountering different evidence types. Also, we demonstrated that language models can exhibit high confidence when given strong evidence, but this does not always guarantee high accuracy. Our analysis also reveals that language models are biased toward golden evidence and show varying performance depending on the degree of irrelevance, helping explain why they deviate from Bayesian assumptions.

From Evidence to Belief: A Bayesian Epistemology Approach to Language Models

Vision-Language Models (VLMs) have gained prominence due to their success in solving complex cross-modal tasks. However, the internal mechanisms of VLMs, particularly the roles of cross-attention and self-attention in multimodal integration, are not fully understood. To address this gap, we introduce NOTICE, a Gaussian-Noise-free Text-Image Corruption and Evaluation pipeline for mechanistic interpretability in VLMs. NOTICE introduces Semantic Image Pairs (SIP) corruption, the first visual counterpart to Symmetric Token Replacement (STR) for text. Through NOTICE, we uncover a set of ``universal attention heads'' in BLIP and LLaVA that consistently contribute across different tasks and modalities. In BLIP, cross-attention heads implement object detection, object suppression, and outlier suppression, whereas important self-attention heads in LLaVA only perform outlier suppression. Notably, our findings reveal that cross-attention heads perform image-grounding, while self-attention in LLaVA heads do not, highlighting key differences in how VLM architectures handle multimodal learning.

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