China

RNA-binding proteins (RBPs) play essential roles in post-translational gene regulation via recognizing specific RNA molecules as well as modulating several key physiological processes \textit{in cellulo}, represented by alternative splicing and RNA degradation. Despite extensive research, most existing approaches still rely on superficial sequence features or coarse structural representations, limiting their ability to capture the intricate nature of RBP-RNA interactions. The recent surge in large language models (LLMs), combined with advances in geometric deep learning for extracting three-dimensional representations, enables the integration of multi-modal, multi-scale biological data for precise modeling and biologically informed de novo RNA design. In this work, we curate and extend RPI15223 into a multi-resolution, structure-level RBP-RNA dataset, and introduce RBPtool, a multi-task, multi-resolution framework which combines a geometric vector perception (GVP) module together with a deep language model encoder to fuse sequence and structural information. Our tool achieves state-of-the-art performance on public benchmarks and RPI15223 dataset, while also supporting fine-grained residue- and atom-level predictions, and enabling de novo RNA design through a generative module conditioned on protein, cell-type, and specified species. RBPtool provides a fast and versatile platform for both fundamental RBP-RNA research and practical RNA drug design, delivering enhanced predictive accuracy and fine-grained structural insights.

EMNLP 2025

RBPtool: A Deep Language Model Framework for Multi-Resolution RBP-RNA Binding Prediction and RNA Molecule Design

rna design

binding site prediction

rna-binding protein

framework

The purpose of the AAAI conference is to promote research in artificial intelligence (AI) and scientific exchange among AI researchers, practitioners, scientists, and engineers in affiliated disciplines. 

AAAI 2021

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*





<br>

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

Existing research in multi-hop questions has identified two reasoning modes: latent reasoning and factual shortcuts, but has not deeply investigated how these modes differ during inference. This impacts both model generalization ability and downstream reasoning tasks. In this work, we systematically examine these distinctions and propose a simple and efficient classification metric, Attribute Rate Ratio (ARR). First, we construct specialized datasets corresponding to the two reasoning modes based on our proposed criteria. Then, using reverse engineering methods, including attention knockout and logit lens techniques, we reveal that subject representations differ significantly across modes: latent reasoning encodes bridge-related information for final answer extraction, while factual shortcuts bypass intermediate reasoning and resemble single-hop factual queries. Finally, our proposed ARR achieves around 90% accuracy on our datasets and demonstrates effectiveness in RAG conflict scenarios, showing that model behavior under conflicting prompts is closely tied to its underlying reasoning mode. Our findings and proposed metric have significant potential for advancing LLM development and applications.

Unveiling Internal Reasoning Modes in LLMs: A Deep Dive into Latent Reasoning vs. Factual Shortcuts with Attribute Rate Ratio

Softmax self-attention often assigns disproportionate weight to semantically uninformative tokens such as punctuation and special tokens, a phenomenon known as attention noise. While recent methods like Cog Attention and the Differential Transformer have addressed this by introducing negative attention scores, they risk discarding useful information. In this paper, we propose the Integral Transformer, a novel self-attention mechanism that denoises attention by integrating signals sampled from the logit distribution. This approach mitigates noise while preserving the contributions of special tokens critical for model performance. Extensive experiments demonstrate that our model outperforms vanilla, Cog, and Differential attention variants on rigorous knowledge and reasoning benchmarks. Moreover, our analysis reveals that employing vanilla self-attention in the lower Transformer layers enhances performance and that the Integral Transformer more effectively balances attention distributions and reduces rank collapse in upper layers.

Integral Transformer: Denoising Attention, Not Too Much Not Too Little

Multi-label classification is prevalent in real-world settings, but the behavior of Large Language Models (LLMs) in this setting is understudied. We investigate how autoregressive LLMs perform multi-label classification, with a focus on subjective tasks, by analyzing the output distributions of the models in each generation step. We find that their predictive behavior reflects the multiple steps in the underlying language modeling required to generate all relevant labels as they tend to suppress all but one label at each step. We further observe that as model scale increases, their token distributions exhibit lower entropy, yet the internal ranking of the labels improves. Finetuning methods such as supervised finetuning and reinforcement learning amplify this phenomenon. To further study this issue, we introduce the task of distribution alignment for multi-label settings: aligning LLM-derived label distributions with empirical distributions estimated from annotator responses in subjective tasks. We propose both zero-shot and supervised methods which improve both alignment and predictive performance over existing approaches.

Large Language Models Do Multi-Label Classification Differently

This study investigates the feasibility of automating clinical coding in Russian, a language with limited biomedical resources. We present a new dataset for ICD coding, which includes diagnosis fields from electronic health records (EHRs) annotated with over 10,000 entities and more than 1,500 unique ICD codes. This dataset serves as a benchmark for several state-of-the-art models, including BERT, LLaMA with LoRA, and RAG, with additional experiments examining transfer learning across domains (from PubMed abstracts to medical diagnosis) and terminologies (from UMLS concepts to ICD codes). We then apply the best-performing model to label an in-house EHR dataset containing patient histories from 2017 to 2021. Our experiments, conducted on a carefully curated test set, demonstrate that training with the automated predicted codes leads to a significant improvement in accuracy compared to manually annotated data from physicians. We believe our findings offer valuable insights into the potential for automating clinical coding in resource-limited languages like Russian, which could enhance clinical efficiency and data accuracy in these contexts.

RuCCoD: Towards Automated ICD Coding in Russian

Automatic survey generation has emerged as a key task in scientific document processing. While large language models (LLMs) have shown promise in generating survey texts, the lack of standardized evaluation datasets critically hampers rigorous assessment of their performance against human-written surveys. In this work, we present SurveyGen, a large-scale dataset comprising over 4,200 human-authored surveys across diverse scientific domains, along with 242,143 cited references and extensive quality-related metadata for both the surveys and the cited papers. Leveraging this resource, we build QUAL-SG, a novel quality-aware framework for survey generation that enhances the standard Retrieval-Augmented Generation (RAG) pipeline by incorporating quality-aware indicators into literature retrieval stage to assess and select higher-quality source papers. Using this dataset and framework, we systematically evaluate state-of-the-art LLMs under varying levels of human involvement—from fully automatic generation to human-guided writing. Experimental results and human evaluations reveal that while semi-automatic pipelines can achieve partially competitive outcomes, fully automatic survey generation still suffers from low citation quality and limited critical analysis. The dataset and code will be publicly available upon paper acceptance to support future research at <URL>.

SurveyGen: Quality-Aware Scientific Survey Generation with Large Language Models

Understanding the prevalence of misinformation in health topics online can inform public health policies and interventions. However, measuring such misinformation at scale remains a challenge, particularly for high-stakes but understudied topics like opioid-use disorder (OUD)—a leading cause of death in the U.S. We present the first large-scale study of OUD-related myths on YouTube, a widely-used platform for health information. With clinical experts, we validate 8 pervasive myths and release an expert-labeled video dataset. To scale labeling, we introduce MythTriage, an efficient triage pipeline that uses a lightweight model for routine cases and defers harder ones to a high-performing, but costlier, large language model (LLM). MythTriage achieves up to 0.86 macro F1-score while estimated to reduce annotation time and financial cost by over 76% compared to experts and full LLM labeling. We analyze 2.9K search results and 343K recommendations, uncovering how myths persist on YouTube and offering actionable insights for public health and platform moderation.

MythTriage: Scalable Detection of Opioid Use Disorder Myths on a Video-Sharing Platform

Modern language models (LMs) are not robust to out-of-distribution inputs. Machine generated (``optimized'') prompts can be used to modulate LM outputs and induce specific behaviors while appearing completely uninterpretable. In this work, we investigate the composition of optimized prompts, as well as the mechanisms by which LMs parse and build predictions from optimized prompts. We find that optimized prompts primarily consist of punctuation and noun tokens which are more rare in the training data. Internally, optimized prompts are clearly distinguishable from natural language counterparts based on sparse subsets of the model's activations. Across various families of instruction-tuned models, optimized prompts follow a similar path in how their representations form through the network.

Demystifying optimized prompts in language models

Efficient simulation is essential for enhancing proactive preparedness for sudden-onset disasters such as earthquakes. Recent advancements in large language models (LLMs) as world models show promise in simulating complex scenarios. This study examines multiple LLMs to proactively estimate perceived earthquake impacts. Leveraging multimodal datasets including geospatial, socioeconomic, building, and street-level imagery data, our framework generates Modified Mercalli Intensity (MMI) predictions at zip code and county scales. Evaluations on the 2014 Napa and 2019 Ridgecrest earthquakes using USGS ``Did You Feel It? (DYFI)'' reports demonstrate significant alignment, as evidenced by high correlation of 0.88 and low RMSE of 0.77 as compared to real reports at the zip code level. Techniques such as RAG and ICL can improve simulation performance, while visual inputs notably enhance accuracy compared to structured numerical data alone. These findings show the promise of LLMs in simulating disaster impacts that can help strengthen pre-event planning.

LLMs as World Models: Data-Driven and Human-Centered Pre-Event Simulation for Disaster Impact Assessment

Quality Estimation (QE) is estimating quality of the model output during inference when the ground truth is not available. Deriving output quality from the models' output probability is the most trivial and low-effort way. However, we show that the output probability of text-generation models can appear underconfident. At each output step, there can be multiple correct options, making the probability distribution spread out more. Thus, lower probability does not necessarily mean lower output quality. Due to this observation, we propose a QE approach called BoostedProb, which boosts the model's confidence in cases where there are multiple viable output options. With no increase in complexity, BoostedProb is notably better than raw model probability in different settings, achieving on average +0.194 improvement in Pearson correlation to ground-truth quality. It also comes close to or outperforms more costly approaches like supervised or ensemble-based QE in certain settings.

Are Generative Models Underconfident? Better Quality Estimation with Boosted Model Probability

Low-bit weight-only quantization significantly reduces the memory footprint of large language models (LLMs), but disproportionately affects certain examples. We analyze diverse 3-4 bit methods on LLMs ranging from 7B-70B in size and find that the quantization errors of 50 pairs of methods are strongly correlated (avg. ρ = 0.82) on FineWeb examples. Moreover, the residual stream magnitudes of full-precision models are indicative of future quantization errors. We further establish a hypothesis that relates the residual stream magnitudes to error amplification and accumulation over layers. Using LLM localization techniques, early exiting, and activation patching, we show that examples with large errors rely on precise residual activations in the late layers, and that the outputs of MLP gates play a crucial role in maintaining the perplexity. Our work reveals why certain examples result in large quantization errors and which model components are most critical for performance preservation.

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Next from EMNLP 2025

Unveiling Internal Reasoning Modes in LLMs: A Deep Dive into Latent Reasoning vs. Factual Shortcuts with Attribute Rate Ratio

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