United States

The applications of large language models (LLMs) are promising for biomedical and healthcare research. Despite the availability of open-source LLMs trained using a wide range of biomedical data, current research on the applications of LLMs to genomics and proteomics is still limited. To fill this gap, we propose a collection of finetuned LLMs and multimodal LLMs (MLLMs), known as Geneverse, for three novel tasks in genomic and proteomic research. The models in Geneverse are trained and evaluated based on domain-specific datasets, and we use advanced parameter-efficient finetuning techniques to achieve the model adaptation for tasks including the generation of descriptions for gene functions, protein function inference from its structure, and marker gene selection from spatial transcriptomic data. We demonstrate that adapted LLMs and MLLMs perform well for these tasks and may outperform closed-source large-scale models based on our evaluations focusing on both truthfulness and structural correctness. All of the training strategies and base models we used are freely accessible. Our codes can be found at \url{https://github.com/HelloWorldLTY/Geneverse}.

EMNLP 2024

Geneverse: A Collection of Open-source Multimodal Large Language Models for Genomic and Proteomic Research

retrieval-augmented large language models

vector database

data quality

question answering

It is my great pleasure and honor to welcome you to the 64th Annual Meeting of the Association for Computational Linguistics (ACL 2026), held in San Diego, California, USA, July 2–7, 2026. ACL 2026 continues our fields 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.

It is exciting to see the many developments in the field reflected at our conference, such as the advancement of large language models (born out of our community) into many application directions. This is not without challenges, partly due to unsolved problems, and partly due to misuse of the technology. All this is reflected well at ACL 2026. The conference also reflects that the field is not only about advancing technology, but also the science of fundamentally understanding language and how it is use by many different speaker communities. 
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ACL 2026

The 64th Annual Meeting of the Association for Computational Linguistics (ACL 2026) will take place in San Diego, California, from July 2 - 7, 2026.

poster

## Welcome to EMNLP 2024! 
We are excited to welcome you to one of the most prominent conferences in the field of Natural Language Processing. This year, EMNLP 2024 is being held in a hybrid format,
offering both virtual and in-person participation in beautiful Miami. Due to a record-breaking number of submissions, we've expanded the total number of accepted papers to accommodate more cutting-edge research from around the globe.
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EMNLP 2024 will take place in Miami, Florida from Nov 12th to Nov 16th, 2024, at the Hyatt Regency Miami Hote and on Underline for remote participants.

Not everything on the internet is true. This unfortunate fact requires both humans and models to perform complex reasoning about credibility when working with retrieved information. In NLP, this problem has seen little attention. Indeed, retrieval-augmented models are not typically expected to distrust retrieved documents. Human experts overcome the challenge by gathering signals about the context, reliability, and tendency of source documents - that is, they perform *source criticism*. We propose a novel NLP task focused on finding and summarising such signals. We introduce a new dataset of 6,709 "media background checks" derived from Media Bias / Fact Check, a volunteer-run website documenting media bias. We test open-source and closed-source LLM baselines with and without retrieval on this dataset, finding that retrieval greatly improves performance. We furthermore carry out human evaluation, demonstrating that 1) media background checks are helpful for humans, and 2) media background checks are helpful for retrieval-augmented models.

Generating Media Background Checks for Automated Source Critical Reasoning

Large Language Models (LLMs) have made significant progress, becoming more autonomous and capable of handling real-world tasks through their access to tools, various planning strategies, and memory, referred to as LLM agents. One emerging area of focus is customizing these models to cater to individual user preferences, thereby shaping them into personal LLM agents. This work investigates how the user model, which encapsulates user-related information, preferences, and personal concepts, influences an LLM agent's planning and reasoning capabilities. We introduce a personalized version of TravelPlanner, called TravelPlanner+, and establish baselines for personal LLM agents. Our evaluation strategy contains an LLM-as-a-Judge component, which provides further in-depth insights into the decision-making process of a personal LLM agent by comparing generic and personal plans. Our findings reveal that while generic plans perform robustly, personal plans show marked improvement in relevance and suitability, with preference rates up to 74.4% on validation and 87.3% on the test set. These results highlight the potential of personal LLM agents to significantly enhance user satisfaction.

Personal Large Language Model Agents: A Case Study on Tailored Travel Planning

Due to emergent capabilities, large language models (LLMs) have been utilized as language-based agents to perform a variety of tasks and make decisions with an increasing degree of autonomy. These autonomous agents can understand high-level instructions, interact with their environments, and execute complex tasks using a selection of tools available to them. As the capabilities of the agents expand, ensuring their safety and trustworthiness becomes more imperative. In this study, we introduce the Athena framework which leverages the concept of verbal contrastive learning where past safe and unsafe trajectories are used as in-context (contrastive) examples to guide the agent towards safety while fulfilling a given task. The framework also incorporates a critiquing mechanism to guide the agent to prevent risky actions at every step. Furthermore, due to the lack of existing benchmarks on the safety reasoning ability of LLM-based agents, we curate a set of 80 toolkits across 8 categories with 180 scenarios to provide a safety evaluation benchmark. Our experimental evaluation, with both closed- and open-source LLMs, indicates verbal contrastive learning and interaction-level critiquing improve the safety rate significantly.

Athena: Safe Autonomous Agents with Verbal Contrastive Learning

This work focuses on the task of query-based meeting summarization in which the summary of a context (meeting transcript) is generated in response to a specific query. When using Large Language Models (LLMs) for this task, a new call to the LLM inference endpoint/API is required for each new query even if the context stays the same. However, repeated calls to the LLM inference endpoints would significantly increase the costs of using them in production, making LLMs impractical for many real-world use cases. To address this problem, in this paper, we investigate whether combining the queries for the same input context in a single prompt to minimize repeated calls can be successfully used in meeting summarization. In this regard, we conduct extensive experiments by comparing the performance of various popular LLMs: GPT-4, Gemini, Claude-3, LLaMA2, Mistral, Phi-3, and Qwen-2 in single-query and multi-query settings. We observe that the capability to reliably generate the response in the expected format is usually limited to closedsource LLMs, with most open-source LLMs lagging behind (except Mistral). We conclude that multi-query prompting could be useful to optimize the inference costs by significantly reducing calls to the inference endpoints/APIs for the task of meeting summarization.

Query-OPT: Optimizing Inference of Large Language Models via Multi-Query Instructions in Meeting Summarization

Structured generation, the process of producing content in standardized formats like JSON and XML, is widely utilized in real-world applications to extract key output information from large language models (LLMs). This study investigates whether such constraints on generation space impact LLMs’ abilities, including reasoning and domain knowledge comprehension. Specifically, we evaluate LLMs’ performance when restricted to adhere to structured formats versus generating free-form responses across various common tasks. Surprisingly, we observe a significant decline in LLMs’ reasoning abilities under format restrictions. Furthermore, we find that stricter format constraints generally lead to greater performance degradation in reasoning tasks.

Let Me Speak Freely? A Study On The Impact Of Format Restrictions On Large Language Model Performance.

We present a practical distillation approach to fine-tune LLMs for invoking tools in real-time applications. We focus on visual editing tasks; specifically, we modify images and videos by interpreting user stylistic requests, specified in natural language (``golden hour''), using an LLM to select the appropriate tools and their parameters to achieve the desired visual effect. We found that proprietary LLMs such as GPT-3.5-Turbo show potential in this task, but their high cost and latency make them unsuitable for real-time applications. In our approach, we fine-tune a (smaller) student LLM with guidance from a (larger) teacher LLM and behavioral signals. We introduce offline metrics to evaluate student LLMs. Both online and offline experiments show that our student models manage to match the performance of our teacher model (GPT-3.5-Turbo), significantly reducing costs and latency. Lastly, we show that fine-tuning was improved by 25\% in low-data regimes using augmentation.

Visual Editing with LLM-based Tool Chaining: An Efficient Distillation Approach for Real-Time Applications

Large language model advancements have enabled the development of multi-agent frameworks to tackle complex, real-world problems such as to automate workflows that require interactions with diverse tools, reasoning, and human collaboration. We present MARCO, a Multi-Agent Real-time Chat Orchestration framework for automating workflows using LLMs. MARCO addresses key challenges in utilizing LLMs for complex, multi-step task execution in a production environment. It incorporates robust guardrails to steer LLM behavior, validate outputs, and recover from errors that stem from inconsistent output formatting, function and parameter hallucination, and lack of domain knowledge. Through extensive experiments we demonstrate MARCO's superior performance with 94.48\% and 92.74\% accuracy on task execution for Digital Restaurant Service Platform conversations and Retail conversations datasets respectively along with 44.91\% improved latency and 33.71\% cost reduction in a production setting. We also report effects of guardrails in performance gain along with comparisons of various LLM models, both open-source and proprietary. The modular and generic design of MARCO allows it to be adapted for automating workflows across domains and to execute complex tasks through multi-turn interactions.

MARCO: Multi-Agent Real-time Chat Orchestration

Citywalk, a recently popular form of urban travel, requires genuine personalization and understanding of fine-grained requests compared to traditional itinerary planning. In this paper, we introduce the novel task of Open-domain Urban Itinerary Planning (OUIP), which generates personalized urban itineraries from user requests in natural language. We then present ItiNera, an OUIP system that integrates spatial optimization with large language models to provide customized urban itineraries based on user needs. This involves decomposing user requests, selecting candidate points of interest (POIs), ordering the POIs based on cluster-aware spatial optimization, and generating the itinerary. Experiments on real-world datasets and the performance of the deployed system demonstrate our system's capacity to deliver personalized and spatially coherent itineraries compared to current solutions.

ItiNera: Integrating Spatial Optimization with Large Language Models for Open-domain Urban Itinerary Planning

Large language models (LLMs) trained on general domain corpora showed remarkable results on natural language processing (NLP) tasks. However, previous research demonstrated (LLMs) trained using domain-focused corpora perform better on specialized tasks. Inspired by this insight, we developed INDUS, a comprehensive suite of LLMs tailored for the closely-related domains of Earth science, biology, physics, heliophysics, planetary sciences and astrophysics and trained using curated scientific corpora drawn from diverse data sources. The suite of models include: (1) an encoder model trained using domain-specific vocabulary and corpora to address NLP tasks, (2) a contrastive-learning-based text embedding model trained using a diverse set of datasets to address information retrieval tasks and (3) smaller versions of these models created using knowledge distillation for applications which have latency or resource constraints. We also created three new scientific benchmark datasets, Climate-Change-NER (entity-recognition), Earth-QA (extractive QA) and Astro-IR (IR) to accelerate research in these multi-disciplinary fields. We show that our models outperform both general-purpose (RoBERTa) and domain-specific (SciBERT) encoders on these new tasks as well as existing tasks in the domains of interest. Furthermore, we demonstrate the use of these models in two industrial settings- as a retrieval model for large-scale vector search applications and in an automatic content tagging system.

INDUS: Effective and Efficient Language Models for Scientific Applications

This study presents a novel learning approach designed to enhance both mathematical reasoning and problem-solving abilities of Large Language Models (LLMs). We focus on integrating the Chain-of-Thought (CoT) and the Program-of-Thought (PoT) learning, hypothesizing that prioritizing the learning of mathematical reasoning ability is helpful for the amplification of problem-solving ability. Thus, the initial learning with CoT is essential for solving challenging mathematical problems. To this end, we propose a sequential learning approach, named SAAS (Solving Ability Amplification Strategy), which strategically transitions from CoT learning to PoT learning. Our empirical study, involving an extensive performance comparison using several benchmarks, demonstrates that our SAAS achieves state-of-the-art (SOTA) performance. The results underscore the effectiveness of our sequential learning approach, marking a significant advancement in the field of mathematical reasoning in LLMs.

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Generating Media Background Checks for Automated Source Critical Reasoning

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