China

Scientific databases aggregate vast amounts of quantitative data alongside descriptive text. In biochemistry, chemical screening assays evaluate the functional responses of candidate compounds against disease targets. Unstructured text that describes the biological mechanisms through which these targets operate, experimental screening protocols, and other attributes of assays offer rich information for new drug discovery campaigns, but has been untapped because of that unstructured format. We present Assay2Mol, a large language model-based workflow that can capitalize on the vast existing biochemical screening assays for early-stage drug discovery. Assay2Mol retrieves existing assay records involving targets similar to the new target and generates candidate compounds using in-context learning with the retrieved assay screening data. Assay2Mol outperforms recent machine learning approaches that generate candidate ligand compounds for target protein structures, while also promoting more synthesizable molecule generation.

EMNLP 2025

Assay2Mol: Large Language Model-based Drug Design Using BioAssay Context

drug design

large language model

retrieval-augmented generation

### **Precision Diagnostics for Precision Medicine** 
 
Our work continues in [Diagnostics North East](https://diagnosticsnortheast.org.uk/) to provide a unique and integrated diagnostics infrastructure for industry and academia.


Learn more about the resources and expertise available to support researchers, clinicians, and industry in developing and deploying new and innovative diagnostic technologies across the discovery, development, evaluation and adoption pathway.

Speakers are: 

* Dr Michael Wright, Clinical Geneticist, Deputy Medical Director for Newcastle upon Tyne Hospitals
* Professor Sir John Burn, Chair of Newcastle upon Tyne Hospitals
* Professor Nick Reynolds, Consultant Dermatologist and Stratified Medicine Lead for the NIHR Newcastle MIC
* Professor Alastair Burt, Professor of Precision Medicine and Director of NovoPath
* Dr Seamus O'Neill, CEO of Northern Health Science Alliance

Registration for this event is free. 
Please register for the Diagnostics North East Conference 2021 to be able to access the content. [Registration here](https://dxneregistration.paperform.co/)

If you have already registered, please login with the same email you used to registered for the Conference.

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Diagnostics North East

Join us in October to learn more about the resources and expertise available to support researchers, clinicians, and industry in developing and deploying new and innovative diagnostic technologies across the discovery, development, evaluation and adoption pathway.


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." 

*Message from the General Chair, Dirk Hovy*

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

Social and behavioral determinants of health (SBDH) play a crucial role in health outcomes and are frequently documented in clinical text. Automatically extracting SBDH information from clinical text relies on publicly available good-quality datasets. However, existing SBDH datasets exhibit substantial limitations in their availability and coverage. In this study, we introduce Synth-SBDH, a novel synthetic dataset with detailed SBDH annotations, encompassing status, temporal information, and rationale across 15 SBDH categories. We showcase the utility of Synth-SBDH on three tasks using real-world clinical datasets from two distinct hospital settings, highlighting its versatility, generalizability, and distillation capabilities. Models trained on Synth-SBDH consistently outperform counterparts with no Synth-SBDH training, achieving up to 63.75% macro-F improvements. Additionally, Synth-SBDH proves effective for rare SBDH categories and under-resource constraints while being substantially cheaper than expert-annotated real-world data. Human evaluation reveals a 71.06% Human-LLM alignment and uncovers areas for future refinements.

Synth-SBDH: A Synthetic Dataset of Social and Behavioral Determinants of Health for Clinical Text

Large Language Models (LLMs) offer natural language explanations as an alternative to feature attribution methods for model interpretability. However, despite their plausibility, they may not reflect the model's internal reasoning faithfully, which is crucial for understanding the model's true decision-making processes. Although several faithfulness metrics have been proposed, a unified evaluation framework remains absent. Here, we present Causal Diagnosticity, a framework to evaluate faithfulness metrics for natural language explanations. Our framework employs the concept of diagnosticity, and uses model-editing methods to generate faithful-unfaithful explanation pairs. Our benchmark includes four tasks: fact-checking, analogy, object counting, and multi-hop reasoning. We evaluate a prominent faithfulness metrics, including post-hoc explanation and chain-of-thought-based methods. We find that diagnostic performance varies across tasks and models, with Filler Tokens performing best overall. Additionally, continuous metrics are generally more diagnostic than binary ones but can be sensitive to noise and model choice. Our results highlight the need for more robust faithfulness metrics.

A Causal Lens for Evaluating Faithfulness Metrics

Societal stereotypes are at the center of a myriad of responsible AI interventions targeted at reducing the generation and propagation of potentially harmful outcomes. While these efforts are much needed, they tend to be fragmented and often address different parts of the issue without taking in a unified or holistic approach about social stereotypes and how they impact various parts of the machine learning pipeline. As a result, it fails to capitalize on the underlying mechanisms that are common across different types of stereotypes, and to anchor on particular aspects that are relevant in certain cases. In this paper, we draw on social psychological research, and build on NLP data and methods, to propose a unified framework to operationalize stereotypes in generative AI evaluations. Our framework identifies key components of stereotypes that are crucial in AI evaluation, including the target group, associated attribute, relationship characteristics, perceiving group, and relevant context. We also provide considerations and recommendations for its responsible use.

A Comprehensive Framework to Operationalize Social Stereotypes for Responsible AI Evaluations

Large language models (LLMs) are increasingly deployed in domains requiring moral understanding, yet their reasoning often remains shallow and misaligned with human reasoning. Unlike humans, whose moral reasoning integrates contextual trade-offs, value systems, and ethical theories, LLMs often rely on surface patterns, leading to biased decisions in morally and ethically complex scenarios. To address this gap, we present a value-grounded framework for evaluating and distilling structured moral reasoning in LLMs. We benchmark 12 open-source models across four moral datasets using a taxonomy of prompts grounded in value systems, ethical theories, and cognitive reasoning strategies. Our evaluation is guided by four questions: (1) Does reasoning improve LLM decision-making over direct prompting? (2) Which types of value/ethical frameworks most effectively guide LLM reasoning? (3) Which cognitive reasoning strategies lead to better moral performance? (4) Can small-sized LLMs acquire moral competence through distillation? We find that prompting with explicit moral structure consistently improves accuracy and coherence, with first-principles reasoning and Schwartz's + care-ethics scaffolds yielding the strongest gains. Furthermore, our supervised distillation approach transfers moral competence from large to small models without additional inference cost. Together, our results offer a scalable path toward interpretable and value-grounded models.

Structured Moral Reasoning in Language Models: A Value-Grounded Evaluation Framework

We present Cacheback Decoding, a training-free model-agnostic speculative decoding method. Cacheback leverages only a Least Recently Used (LRU) cache of token n-grams to generate draft sequences. Despite its minimalist design, it achieves state-of-the-art performance among comparable methods.

Cacheback: Speculative Decoding With Nothing But Cache

Large language model (LLM) reasoning can be improved by scaling test-time compute with aggregation, i.e., generating multiple samples and aggregating over them. While improving performance, this strategy often reaches a saturation point beyond which additional compute provides no return. Refinement offers an alternative by using model-generated feedback to improve answer quality. However, refinement faces three key challenges: (1) Excessive refinement: Uniformly refining all instances can cause over-correction and reduce overall performance. (2) Inability to localize and address errors: LLMs struggle to identify and correct their own mistakes. (3) Insufficient refinement: Stopping refinement too soon could leave errors unaddressed. To tackle these issues, we propose MAgICoRe, a framework for Multi-Agent Iteration for Coarse-to-fine Refinement. MAgICoRe mitigates excessive refinement by categorizing problems as easy or hard, solving easy problems with coarse-grained aggregation, and solving the hard ones with fine-grained multi-agent refinement. To better localize errors, we incorporate external step-wise reward model scores, and to ensure sufficient refinement, we iteratively refine the solutions using a multi-agent setup. We evaluate MAgICoRe on Llama-3-8B and GPT- 3.5 and show its effectiveness across seven reasoning datasets. One iteration of MAgICoRe beats Self-Consistency by 3.4%, Best-of-k by 3.2%, and Self-Refine by 4.0% even when these baselines use k = 120, and MAgICoRe uses less than 50% of the compute.

MAgICoRe: Multi-Agent, Iterative, Coarse-to-Fine Refinement for Reasoning

Large language models (LLMs) have improved significantly in their reasoning through extensive training on massive datasets. However, relying solely on additional data for improvement is becoming increasingly impractical, highlighting the need for models to autonomously enhance their reasoning without external supervision. In this paper, we propose textbfDebate, Train, Evolve (DTE), a novel ground truth-free training framework that uses multi-agent debate traces to evolve a single language model. We also introduce a new prompting strategy textbfReflect-Critique-Refine, to improve debate quality by explicitly instructing agents to critique and refine their reasoning. Extensive evaluations on textbffive reasoning benchmarks with textbfsix open-weight models show that our DTE framework achieve substantial improvements, with an average accuracy gain of textbf8.92\% on the challenging GSM-PLUS dataset. Furthermore, we observe strong cross-domain generalization, with an average accuracy gain of textbf5.8\% on all other benchmarks, suggesting that our method captures general reasoning capabilities.

DEBATE, TRAIN, EVOLVE: Self‑Evolution of Language Model Reasoning

Nonverbal vocalizations are an essential component of human communication, conveying rich information without linguistic content. However, the computational analysis of nonverbal vocalization faces significant challenges due to a lack of lexical anchors in the data, compounded by biased distributions of imbalanced multi-label data. While disentangled representation learning has shown promise in isolating specific speech features, its application to nonverbal speech remains unexplored. In this paper, we introduce N-CORE, a novel supervised framework designed to disentangle representations in nonverbal vocalizations by leveraging N views of the audio sample to learn invariance to specific perturbed features. We find that N-CORE achieves competitive performance compared to the baseline methods when tested for emotion and speaker classification tasks on the VIVAE, ReCANVo, and ReCANVo-Balanced datasets. We further propose an emotion perturbation function for audio signals that preserves speaker information, and validate speech transformation functions on nonverbal vocalizations. Our work informs research directions on the application of paralinguistic speech, including privacy-preserving encoding, clinical diagnoses of atypical speech, and longitudinal analysis of communicative development.

N-CORE: N-View Consistency Regularization for Disentangled Representation Learning in Nonverbal Vocalizations

State-of-the-art automatic speech recognition (ASR) models like Whisper, perform poorly on atypical speech, such as that produced by individuals with dysarthria. Past works for atypical speech have mostly investigated fully personalized (or idiosyncratic) models, but modeling strategies that can both generalize and and handle idiosyncracy could be more effective for capturing atypical speech. To investigate this, we compare four strategies: (a) *normative* models trained on typical speech (no personalization), (b) *idiosyncratic* models completely personalized to individuals, (c) *dyarthric-normative* models trained on other dysarthric speakers and (d) *dyarthric-idiosyncratic* models which combine strategies by first modeling normative patterns before adapting to individual speech. We find the dysarthric-idiosyncratic model performs better than idiosyncratic approach while requiring less than half as much personalized data (36.43 WER with 128 train size vs 36.99 with 256). Further, we found that tuning the speech encoder alone (as opposed to the LM decoder) yielded the best results reducing word error rate from 71% to 32% on average. Our findings highlight the value of leveraging both normative (cross-speaker) and idiosyncratic (speaker-specific) patterns to improve ASR for underrepresented speech populations.

Idiosyncratic Versus Normative Modeling of Atypical Speech Recognition: Dysarthric Case Studies

The resurgence of autonomous agents built using large language models (LLMs) to solve complex real-world tasks has brought increased focus on LLMs' fundamental ability of tool or function calling. At the core of these agents, an LLM must plan, execute, and respond using external tools, APIs, and custom functions. Research on tool calling has gathered momentum, but evaluation benchmarks and datasets representing the complexity of the tasks have lagged behind. In this work, we focus on one such complexity, nested sequencing, with the goal of extending existing benchmarks and evaluation. Specifically, we present NESTFUL, a benchmark to evaluate LLMs on nested sequences of API calls, i.e., sequences where the output of one API call is passed as input to a subsequent call. NESTFUL contains 1800+ nested sequences where all the function calls are executable. Experimental results on a variety of models show that the best-performing model (GPT-4o) achieves a full sequence match accuracy of 28% and a win-rate of 60%, necessitating a large scope for improvement in the nested sequencing aspect of function calling. Our analysis of these results provides possible future research directions for the community, in addition to a benchmark to track progress.

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