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Large Language Models (LLMs) have demonstrated remarkable capabilities on general text; however, their proficiency in specialized scientific domains that require deep, interconnected knowledge remains largely uncharacterized. Metabolomics presents unique challenges with its complex biochemical pathways, heterogeneous identifier systems, and fragmented databases. To systematically evaluate LLM capabilities in this domain, we introduce MetaBench, the first benchmark for metabolomics assessment. Curated from authoritative public resources, MetaBench evaluates five capabilities essential for metabolomics research: \emph{knowledge}, understanding, grounding, reasoning, and research. Our evaluation of 25 open- and closed-source LLMs reveals distinct performance patterns across metabolomics tasks: while models perform well on text generation tasks, cross-database identifier grounding remains challenging even with retrieval augmentation. Model performance also decreases on long-tail metabolites with sparse annotations. With MetaBench, we provide essential infrastructure for developing and evaluating metabolomics AI systems, enabling systematic progress toward reliable computational tools for metabolomics research.

ACL 2026

MetaBench: A Multi-task Benchmark for Assessing LLMs in Metabolomics

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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. <br>
[Full Message from General Chair Philipp Koehn](https://drive.google.com/file/d/1QiJFOmMjvDgsDo3i1XzlQnImxe3RU_Cy/view?usp=sharing) <br><br><br>
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The 64th Annual Meeting of the Association for Computational Linguistics (ACL 2026) will take place in San Diego, California, from July 2 - 7, 2026.

Large Reasoning Models (LRMs) have recently demonstrated significant improvements in complex reasoning. While quantifying generation uncertainty in LRMs is crucial, traditional methods are often insufficient because they do not provide finite-sample guarantees for reasoning-answer generation. Conformal prediction (CP) stands out as a model-agnostic methodology that constructs statistically rigorous uncertainty sets. However, existing CP methods ignore the logical connection between the reasoning trace and the final answer. Additionally, prior studies fail to interpret the origins of uncertainty coverage for LRMs as they typically overlook the specific training factors driving valid reasoning. Notably, it is challenging to disentangle reasoning quality from answer correctness, while simultaneously establishing theoretical guarantees for computationally efficient explanation methods. To address these challenges, we first propose a novel methodology that provides the uncertainty of the reasoning-answer structure with statistical guarantees. Subsequently, we develop a unified example-to-step explanation framework using Shapley values that identifies a provably sufficient subset of training data and their specific reasoning steps sufficient to achieve coverage. We also provide the theoretical analysis for our proposed methods. Extensive experiments on challenging reasoning datasets verify the effectiveness of the proposed methods.

Quantifying and Understanding Uncertainty in Large Reasoning Models

AI Clones aim to simulate an individual’s thoughts and behaviors to enable long-term, personalized interaction, placing stringent demands on memory systems to model experiences, emotions, and opinions over time. Existing memory benchmarks primarily rely on user–agent conversational histories, which are temporally fragmented and insufficient for capturing continuous life trajectories. We introduce CloneMem, a benchmark for evaluating long-term memory in AI Clone scenarios grounded in non-conversational digital traces, including diaries, social media posts, and emails, spanning one to three years. CloneMem} adopts a top-down data construction framework to ensure longitudinal coherence and defines tasks that assess an agent’s ability to track evolving personal states. Experiments show that current memory mechanisms struggle in this setting, highlighting open challenges for life-grounded personalized AI. Code and dataset are available at https://github.com/AvatarMemory/CloneMemBench

CloneMem: Benchmarking Long-Term Memory for AI Clones

Large Language Models (LLMs) have been reported to “leak” Personally Identifiable Information (PII), with successful PII reconstruction often interpreted as evidence of memorization. We propose a principled revision of memorization evaluation for LLMs, arguing that PII leakage should be evaluated under low lexical cue conditions, where target PII cannot be reconstructed through prompt-induced generalization or pattern completion. We formalize Cue-Resistant Memorization (CRM) as a cue-controlled evaluation framework and a necessary condition for valid memorization evaluation, explicitly conditioning on prompt-target overlap cues. Using CRM, we conduct a large-scale multilingual re-evaluation of PII leakage across 32 languages and multiple memorization paradigms. Revisiting reconstruction-based settings, including verbatim prefix-suffix completion and associative reconstruction, we find that their apparent effectiveness is driven primarily by direct surface-form cues rather than by true memorization. When such cues are controlled for, reconstruction success diminishes substantially. We further examine cue-free generation and membership inference, both of which exhibit extremely low true positive rates. Overall, our results suggest that previously reported PII leakage is better explained by cue-driven behavior than by genuine memorization, highlighting the importance of cue-controlled evaluation for reliably quantifying privacy-relevant memorization in LLMs.

Do LLMs Really Memorize Personally Identifiable Information? Revisiting PII Leakage with a Cue-Controlled Memorization Framework

Prevailing safety alignment methods still leave Large Language Models (LLMs) vulnerable to sophisticated jailbreak attacks. To bolster defenses, explicit reasoning mechanisms like Safety-oriented Chain-of-Thought (SCoT) have emerged, significantly enhancing robustness. However, this transparency introduces a critical trade-off: the exposed reasoning process itself becomes a new attack surface, risking the leakage of harmful information and revealing the model's safety logic to adversaries. This paper directly confronts this dilemma, asking: Can we achieve the full benefits of deliberative safety without the costs of explicit reasoning generation? We propose Safety Reasoning Internalization to make the deliberative process in SCoT "available but not visible". This approach is grounded in a key theoretical insight: the corrective influence of an SCoT can be effectively approximated by a targeted, low-rank update to the model's Feed-Forward Network (FFN) layers. We operationalize this through Hierarchical Internalization of Adversarially-Guided Reasoning (HIAR), a layer-wise safety alignment framework that internalizes safety reasoning into an implicit computational pathway using Low-Rank Adaptation (LoRA). HIAR enables the model to reach a safe conclusion within a single forward pass, entirely eliminating the need to generate vulnerable SCoT text. Extensive experiments on various LLMs demonstrate that HIAR achieves a 43\% lower Attack Success Rate (ASR) against distinct jailbreak attacks compared to strong baselines.

More Thinking, Less Talking: Internalizing Deliberative Safety into LLM Parameters

Scientific feasibility assessment asks whether a claim is consistent with established knowledge and whether experimental evidence could support or refute it. We frame feasibility assessment as a diagnostic reasoning task in which, given a hypothesis, a model predicts feasible or infeasible and justifies its decision. We evaluate large language models (LLMs) under controlled knowledge conditions (hypothesis-only, with experiments, with outcomes, or both) and probe robustness by progressively removing portions of the experimental and/or outcome context. Across multiple LLMs and two datasets, providing outcome evidence is generally more reliable than providing experiment descriptions. Outcomes tend to improve accuracy beyond what internal knowledge alone provides, whereas experimental text can be brittle and may degrade performance when the context is incomplete. These findings clarify when experimental evidence benefits LLM-based feasibility assessment and when it introduces fragility.

Experiments or Outcomes? Probing Scientific Feasibility in Large Language Models

To address toxic content on social media, we introduce SMARTER, a data-efficient 2-stage framework for explainable content moderation using Large Language Models (LLMs). In Stage 1, we leverage LLMs' own outputs to generate synthetic explanations for correct and incorrect labels, enabling preference optimization with minimal supervision. In Stage 2, we refine explanation quality through cross-model training, allowing weaker models to align with stronger ones. Experiments on 3 benchmarks (HateXplain, Latent Hate, Implicit Hate) show SMARTER achieves up to 13% macro-F1 improvement over few-shot baselines using only 6-57% of training data. Our framework offers a scalable strategy for low-data settings by harnessing LLMs' self-improvement for explainable moderation.

SMARTER: A Data-efficient Framework to Improve Toxicity Detection with Explanation via Self-augmenting Large Language Models

Deciphering ancient Chinese Oracle Bone Script (OBS) is a challenging task that offers insights into the beliefs, systems, and culture of the ancient era. Existing approaches treat decipherment as a closed-set image recognition problem, which fails to bridge the ``interpretation gap'': while individual characters are often unique and rare, they are composed of a limited set of recurring, pictographic components that carry transferable semantic meanings. To leverage this structural logic, we propose an agent-driven Vision-Language Model (VLM) framework that integrates a VLM for precise visual grounding with an LLM-based agent to automate a reasoning chain of component identification, graph-based knowledge retrieval, and relationship inference for linguistically accurate interpretation. To support this, we also introduce OB-Radix, an expert-annotated dataset providing structural and semantic data absent from prior corpora, comprising 1,022 character images (934 unique characters) and 1,853 fine-grained component images across 478 distinct components with verified explanations. By evaluating our system across three benchmarks of different tasks, we demonstrate that our framework yields more detailed and precise decipherments compared to baseline methods.

Specializing Large Models for Oracle Bone Script Interpretation via Component-Grounded Multimodal Knowledge Augmentation

The recent explosion of large language models (LLMs), each with its own general or specialized strengths, makes scalable, reliable benchmarking more urgent than ever. Standard practices nowadays face fundamental trade-offs: closed-ended question-based benchmarks (\eg MMLU) struggle with saturation as newer models emerge, while crowd-sourced leaderboards (\eg Chatbot Arena) rely on costly and slow human judges. Recently, automated methods (\eg LLM-as-a-judge) shed light on the scalability, but risk bias by relying on one or a few ``authority'' models. To tackle these issues, we propose Decentralized Arena (\dearena), a fully automated framework leveraging collective intelligence from all LLMs to evaluate each other. It mitigates single-model judge bias by democratic, pairwise evaluation, and remains efficient at scale through two key components: (1) a coarse-to-fine ranking algorithm for fast incremental insertion of new models with sub-quadratic complexity, and (2) an automatic question selection strategy for the construction of new evaluation dimensions. Across extensive experiments across 66 LLMs, \dearena attains up to 97% correlation with human judgements, while significantly reducing the cost.

Decentralized Arena: Towards Democratic and Scalable Automatic Evaluation of Language Models

Large Language Models (LLMs) are increasingly adopted as conversational assistants in genomics, where they are mainly used to reason over biological knowledge, annotations, and analysis outputs through natural language interfaces. However, existing benchmarks either focus on specialized DNA models trained for sequence prediction or evaluate biological knowledge using text-only questions, leaving the behavior of general-purpose LLMs when directly exposed to raw genome sequences underexplored. We introduce GenomeQA, a benchmark designed to provide a controlled evaluation setting for general-purpose LLMs on sequence-based genome inference tasks. GenomeQA comprises 5,200 samples drawn from multiple biological databases, with sequence lengths ranging from 6 to 1,000 base pairs (bp), spanning six task families: Enhancer and Promoter Identification, Splice Site Identification, Taxonomic Classification, Histone Mark Prediction, Transcription Factor Binding Site Prediction, and TF Motif Prediction. Across six frontier LLMs, we find that models often outperform random baselines, particularly on tasks driven by local sequence cues such as GC content and short motifs, while performance degrades on tasks that require more indirect or multi-step inference over sequence patterns. GenomeQA establishes a diagnostic benchmark for studying and improving the use of general-purpose LLMs on raw genomic sequences.

GenomeQA: Benchmarking General Large Language Models for Genome Sequence Understanding

Mixture-of-Experts (MoE) models rely on an external router to assign tokens to experts. This design inherently separates the routing decision from each expert's internal capabilities, leading to suboptimal performance. In this work, we address this limitation with Union-of-Experts (UoE), an MoE variant that performs "expert-autonomous routing''. The core mechanism of UoE is to pre-designate a minute fraction of neurons within each expert as "routing neurons''. Experts autonomously select relevant tokens by comparing the activation intensity of these neurons, aligning routing decisions with each expert’s functional profile. To prevent the waste of activations from unselected experts' routing neurons, we aggregate all routing neuron outputs and sum them into the final layer output. This aggregation acts as a novel virtual shared expert whose parameters are distributed across the individual experts, and improves overall parameter efficiency. We pre-train UoE models with up to 3B parameters, demonstrating that they outperform traditional MoEs with matched efficiency. Furthermore, our analysis of the routing neurons provides valuable insights into expert-autonomous selection and the broader routing mechanisms of MoE models.

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Quantifying and Understanding Uncertainty in Large Reasoning Models

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Quantifying and Understanding Uncertainty in Large Reasoning Models

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Integrating metabolomics and lipidomics approaches to investigate the sensitivity of marine ectotherms from different climatic regimes to marine heatwaves

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