Austria

Entity linking involves normalizing a mention in medical text to a unique identifier in a knowledge base, such as UMLS or MeSH. Most entity linkers follow a two-stage process: first, a candidate generation step selects high-quality candidates, and then a named entity disambiguation phase determines the best candidate for final linking. This study demonstrates that leveraging a large language model (LLM) as an entity disambiguator significantly enhances entity linking models&#39; accuracy and recall. Specifically, the LLM disambiguator achieves remarkable improvements when applied to alias-matching entity linking methods. Without any fine-tuning, our approach establishes a new state-of-the-art (SOTA), surpassing previous methods on multiple prevalent biomedical datasets by up to 16 points in accuracy. We released our code on GitHub at https://github.com/ChristopheYe/llm_disambiguator

ACL 2025

LLM as Entity Disambiguator for Biomedical Entity-Linking

biomedical entity linking

llms

entity disambiguation

**Welcome to EMNLP 2023!**

On behalf of the EMNLP 2023 Organizing Committee, I extend a warm and heartfelt welcome to all of you to the 2023 Conference on Empirical Methods in Natural Language Processing (EMNLP). It is with immense pleasure and excitement that we gather here in Singapore, a vibrant hub of innovation and technological advancement.

The conference program is packed with insightful presentations, thought-provoking workshops, and engaging networking opportunities. In addition to the technical sessions, we have also planned several social events that will provide you with the opportunity to connect with your colleagues.

The conference is held in person at the Resorts World Convention Centre in Singapore, and available on-line with the help of Underline.

For those in Singapore, I hope that you will find time to explore the exciting Sentosa Island, Gardens by the Bay, Singapore Botanic Gardens and the many other attractions unique to Singapore.

Of course, we are grateful to our sponsors and partners for their generous support of EMNLP 2023, whose contributions make it possible for us to host this world-class event.

Yuji Matsumoto (RIKEN AIP) 
EMNLP 2023 General Chair

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EMNLP 2023

EMNLP 2023 took place in Singapore from Dec 6th to Dec 10th, 2023.

Entity linking involves normalizing a mention in medical text to a unique identifier in a knowledge base, such as UMLS or MeSH. Most entity linkers follow a two-stage process: first, a candidate generation step selects high-quality candidates, and then a named entity disambiguation phase determines the best candidate for final linking. This study demonstrates that leveraging a large language model (LLM) as an entity disambiguator significantly enhances entity linking models' accuracy and recall. Specifically, the LLM disambiguator achieves remarkable improvements when applied to alias-matching entity linking methods. Without any fine-tuning, our approach establishes a new state-of-the-art (SOTA), surpassing previous methods on multiple prevalent biomedical datasets by up to 16 points in accuracy. We released our code on GitHub at https://github.com/ChristopheYe/llm_disambiguator

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)

Large language models (LLMs) play a crucial role in modern applications but face vulnerabilities related to the extraction of sensitive information. This includes unauthorized accesses to internal prompts and retrieval of personally identifiable information (PII) (e.g., in Retrieval-Augmented Generation based agentic applications). We examine these vulnerabilities in a question-answering (QA) setting where LLMs use retrieved documents or training knowledge as few-shot prompts. Although these documents remain confidential under normal use, adversaries can manipulate input queries to extract private content. In this paper, we propose a novel attack method by exploiting the model’s lower-ranked output tokens to leak sensitive information. We systematically evaluate our method, demonstrating its effectiveness in both the agentic application privacy extraction setting and the direct training data extraction. These findings reveal critical privacy risks in LLMs and emphasize the urgent need for enhanced safeguards against information leakage.

Exploiting the Shadows: Unveiling Privacy Leaks through Lower-Ranked Tokens in Large Language Models

Existing evaluation frameworks for retrieval-augmented generation (RAG) systems focus on answerable queries, but they overlook the importance of appropriately rejecting unanswerable requests. In this paper, we introduce UAEval4RAG, a comprehensive evaluation framework designed to evaluate whether RAG systems effectively handle unanswerable queries specific to a given knowledge base. We first define a taxonomy with six unanswerable categories, and UAEval4RAG automatically synthesizes diverse and challenging queries for any given knowledge base and evaluate the RAG systems with unanswered ratio and acceptable ratio metrics. We also conduct experiments with various RAG components and prompting strategies across four datasets, which reveals that due to varying knowledge distribution across datasets, no single configuration consistently delivers optimal performance on both answerable and unanswerable requests across different knowledge bases. Our findings highlight the critical role of component selection and prompt design in optimizing RAG systems to balance the accuracy of answerable queries with high rejection rates of unanswerable ones. UAEval4RAG provides valuable insights and tools for developing more robust and reliable RAG systems.

Unanswerability Evaluation for Retrieval Augmented Generation

We introduce SciVer, the first benchmark specifically designed to evaluate the ability of foundation models to verify claims within a multimodal scientific context.
SciVer consists of 3,000 expert-annotated examples over 1,113 scientific papers, covering four subsets, each representing a common reasoning type in multimodal scientific claim verification. 
To enable fine-grained evaluation, each example includes expert-annotated supporting evidence.
We assess the performance of 21 state-of-the-art multimodal foundation models, including o4-mini, Gemini-2.5-Flash, Llama-3.2-Vision, and Qwen2.5-VL. 
Our experiment reveals a substantial performance gap between these models and human experts on SciVer.
Through an in-depth analysis of retrieval-augmented generation (RAG), and human-conducted error evaluations, we identify critical limitations in current open-source models, offering key insights to advance models' comprehension and reasoning in multimodal scientific literature tasks.

SciVer: Evaluating Foundation Models for Multimodal Scientific Claim Verification

Large Language Models (LLMs) have shown remarkable capabilities as autonomous agents; yet existing benchmarks either focus on single-agent tasks or are confined to narrow domains, failing to capture the dynamics of multi-agent coordination and competition. In this paper, we introduce MultiAgentBench, a comprehensive benchmark designed to evaluate LLM-based multi-agent systems across diverse, interactive scenarios. Our framework measures not only task completion but also the quality of collaboration and competition using novel, milestone-based key performance indicators. Moreover, we evaluate various coordination protocols (including star, chain, tree, and graph topologies) and innovative strategies such as group discussion and cognitive planning. Notably, cognitive planning improves milestone achievement rates by 3%. Code and dataset will be made publicly available. Code and datasets are publicavailable at 
https://github.com/ulab-uiuc/MARBLE

MultiAgentBench : Evaluating the Collaboration and Competition of LLM agents

The proliferation of large language models (LLMs) has introduced unprecedented challenges in fake news detection due to benchmark data contamination (BDC), where evaluation benchmarks are inadvertently memorized during the pre-training, leading to the inflated performance metrics. Traditional evaluation paradigms, reliant on static datasets and closed-world assumptions, fail to account the BDC risk in large-scale pre-training of current LLMs. This paper introduces TripleFact, a novel evaluation framework for fake news detection task, which designed to mitigate BDC risk while prioritizing real-world applicability. TripleFact integrates three components: (1) Human-Adversarial Preference Testing (HAPT) to assess robustness against human-crafted misinformation, (2) Real-Time Web Agent with Asynchronous Validation (RTW-AV) to evaluate temporal generalization using dynamically sourced claims, and (3) Entity-Controlled Virtual Environment (ECVE) to eliminate entity-specific biases. Through experiments on 17 state-of-the-art LLMs, including GPT, LLaMA, and DeepSeek variants, TripleFact demonstrates superior contamination resistance compared to traditional benchmarks. Results reveal that BDC artificially inflates performance by up to 23\% in conventional evaluations, while TripleFact Score (TFS) remain stable within 4\% absolute error under controlled contamination. The framework's ability to disentangle genuine detection capabilities from memorization artifacts underscores its potential as a fake news detection benchmark for the LLM era.

TripleFact: Defending Data Contamination in the Evaluation of LLM-driven Fake News Detection

We present a hierarchy of natural language understanding abilities and argue for the importance of moving beyond assessments of understanding at the lexical and sentence levels to the discourse level. We propose the task of anaphora accessibility as a diagnostic for assessing discourse understanding, and to this end, present an evaluation dataset inspired by theoretical research in dynamic semantics. We evaluate human and LLM performance on our dataset and find that LLMs and humans align on some tasks and diverge on others. Such divergence can be explained by LLMs' reliance on specific lexical items during language comprehension, in contrast to human sensitivity to structural abstractions.

Meaning Beyond Truth Conditions: Evaluating Discourse Level Understanding via Anaphora Accessibility

The advent of 1-bit large language models (LLMs), led by BitNet b1.58, has spurred interest in ternary LLMs. Despite this, research and practical applications focusing on efficient edge inference for ternary LLMs remain scarce. To bridge this gap, we introduce Bitnet.cpp, an inference system optimized for BitNet b1.58 and ternary LLMs. Given that mixed-precision matrix multiplication (mpGEMM) constitutes the bulk of inference time in ternary LLMs, Bitnet.cpp incorporates a novel mpGEMM library to facilitate sub-2-bits-per-weight, efficient and lossless inference. The library features two core solutions: Ternary Lookup Table (TL), which addresses spatial inefficiencies of previous bit-wise methods, and Int2 with a Scale (I2_S), which ensures lossless edge inference, both enabling high-speed inference. Our experiments show that Bitnet.cpp achieves up to a 6.25x increase in speed over full-precision baselines and up to 2.32x over low-bit baselines, setting new benchmarks in the field. Additionally, we expand TL to element-wise lookup table (ELUT) for low-bit LLMs in the appendix, presenting both theoretical and empirical evidence of its considerable potential. Bitnet.cpp is publicly available at https://github.com/microsoft/BitNet/tree/paper, offering a sophisticated solution for the efficient and practical deployment of edge LLMs.

Bitnet.cpp: Efficient Edge Inference for Ternary LLMs

In this paper, we aim to improve the reasoning ability of large language models(LLMs) over knowledge graphs(KGs) to answer complex questions. Inspired by existing methods that design the interaction strategy between LLMs and KG, we propose an autonomous LLM-based agent framework, called \textbf{KG-Agent}, which enables a small LLM to actively make decisions until finishing the reasoning process over KGs. In KG-Agent, we integrate the LLM, multifunctional toolbox, KG-based executor, and knowledge memory, and develop an iteration mechanism that autonomously selects the tool and then updates the memory for reasoning over KG. To guarantee the effectiveness, we leverage program language to formulate the multi-hop reasoning process over the KG and synthesize a code-based instruction dataset to fine-tune the base LLM. Extensive experiments demonstrate that only using 10K samples for tuning LLaMA2-7B can outperform competitive methods using larger LLMs or more data, on both in-domain and out-domain datasets. Our code and data will be publicly released.

KG-Agent: An Efficient Autonomous Agent Framework for Complex Reasoning over Knowledge Graph

Most discussions about Large Language Model (LLM) safety have focused on single-agent settings but multi-agent LLM systems now create novel adversarial risks because their behavior depends on communication between agents and decentralized reasoning. 
In this work, we innovatively focus on attacking pragmatic systems that have constrains such as limited token bandwidth, latency between message delivery, and defense mechanisms. We design a $\textit{permutation-invariant adversarial attack}$ that optimizes prompt distribution across latency and bandwidth-constraint network topologies to bypass distributed safety mechanisms within the system. Formulating the attack path as a problem of $\textit{maximum-flow minimum-cost}$, coupled with the novel $\textit{Permutation-Invariant Evasion Loss (PIEL)}$, we leverage ${graph-based optimization}$ to maximize attack success rate while minimizing detection risk. Evaluating across models including $\texttt{Llama}$, $\texttt{Mistral}$, $\texttt{Gemma}$, $\texttt{DeepSeek}$ and other variants on various datasets like $\texttt{JailBreakBench}$ and $\texttt{AdversarialBench}$, our method outperforms conventional attacks by up to $7\times$, exposing critical vulnerabilities in multi-agent systems. Moreover, we demonstrate that existing defenses, including variants of $\texttt{Llama-Guard}$ and $\texttt{PromptGuard}$, fail to prohibit our attack, emphasizing the urgent need for multi-agent specific safety mechanisms.

Agents Under Siege: Breaking Pragmatic Multi-Agent LLM Systems with Optimized Prompt Attacks

Large Language Models (LLMs) are cutting-edge generative AI models built on transformer architecture, which tend to be highly memory-intensive when performing real-time inference. Various strategies have been developed to enhance the end-to-end inference speed for LLMs, one of which is speculative decoding. This technique involves running a smaller LLM (draft model) for inference over a defined window size, denoted as $\gamma$, while simultaneously being validated by the larger LLM (target model). Choosing the optimal $\gamma$ value and the draft model is essential for unlocking the potential of speculative decoding. But it is difficult to do due to the complicated influence from various factors, including the nature of the task, the hardware in use, and the combination of the large and small models. This paper introduces *on-the-fly adaption of speculative decoding*, a solution that dynamically adapts the choices to maximize the efficiency of speculative decoding for LLM inferences. As a drop-in solution, it needs no offline benchmarking or training. Experiments show that the solution can lead to 3.55-16.48% speed improvement over the standard speculative decoding, and 1.2-3.4$\times$ over the default LLMs.

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Exploiting the Shadows: Unveiling Privacy Leaks through Lower-Ranked Tokens in Large Language Models

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