cs.LGSep 20, 2026

Tool-Augmented On-Policy Distillation for LLM Domain Adaptation in Sequence-Based Omics Tasks

Authors: Jie Ying, Zhefan Wang, Zihong Chen, Zhengqing Li, Jinzhe Li, Gang Li, Jian Liu, Fang Hu, +6 more

Abstract

Multi-omics sequences contain complex biological patterns, yet deciphering their mechanisms for automated scientific discovery remains challenging. As large language models (LLMs) interpret these sequences, evaluating both predictions and scientific reasoning is critical. However, existing benchmarks for multi-omics sequence tasks rely on classification and regression metrics, neglecting whether models grasp the underlying biological evidence. We introduce OmicsBench, the first reasoning benchmark for multi-omics sequences, comprising 1,160 expert-validated questions across six tasks spanning DNA regulation, RNA processing, and protein function. OmicsBench requires traceable evidence chains, evaluated using instance-specific rubrics developed with domain experts. Evaluating 17 LLMs reveals an inverse relationship: while scientific LLMs outperform general-purpose LLMs in sequence classification accuracy, they fail to provide valid evidence to support their predictions. One plausible interpretation is shortcut learning: specialized models may rely on statistical patterns rather than the biological mechanisms needed for scientific discovery. Motivated by this finding, we introduce tool-augmented on-policy distillation (TA-OPD), a post-training method to align sequence prediction with evidence-grounded biological reasoning. Across five Qwen3.5 models spanning 0.8B to 27B parameters, TA-OPD consistently strengthens biological evidence grounding while improving predictive performance on most tasks. These gains persist across model scales, indicating that stronger sequence reasoning does not arise solely from increased model capacity, but can be improved through evidence-aware training. Together, OmicsBench and TA-OPD provide a framework for diagnosing reasoning failures in multi-omics LLMs and a path toward models whose predictions are better grounded in biologically meaningful evidence.

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May 7, 2026q-bio.GN

OmicsLM: A Multimodal Large Language Model for Multi-Sample Omics Reasoning

Interpreting transcriptomic data is one of the most common analytical tasks in modern biology. Yet most current models either consume expression profiles without producing natural-language biological explanations, or reason in language without direct access to quantitative omics measurements. We introduce OmicsLM, a multimodal LLM that connects quantitative omics profiles with natural-language biological tasks. OmicsLM represents each transcriptomic profile as a compact continuous representation within the LLM context. This interface preserves quantitative expression signal while allowing natural-language instructions, explicit gene mentions, and multiple interleaved biological samples to be processed together in one model context. We train OmicsLM on more than 5.5 million instruction-following examples spanning over 70 task types, combining continuous transcriptomic inputs, experimental data rendered through diverse language templates, and free-text biological knowledge and question-answering data. This mixture covers cell type annotation, perturbation prediction, clinical prediction, pathway reasoning, and open-ended biological question answering. Existing benchmarks evaluate either profile-level prediction or text-only biological QA, leaving language-guided, multi-sample reasoning over real expression profiles unmeasured. To close this gap, we introduce GEO-OmicsQA, a benchmark for multi-sample biological question answering built from real Gene Expression Omnibus (GEO) studies. We demonstrate that OmicsLM can use expression profiles directly and perform comparably to specialized omics models on profile-level tasks, while outperforming both omics-specialized models and general LLMs on language-guided biological reasoning over expression data.
Maciej Sypetkowski, Joanna Krawczyk, Łukasz Smoliński +4
Multi-Omic FrameworkSpatial Transcriptomics
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Jul 17, 2026cs.AI

S1-Omni: A Unified Multimodal Reasoning Model for Scientific Understanding, Prediction, and Generation

We present S1-Omni, a unified multimodal reasoning model for scientific understanding, prediction, and generation. AI for Science (AI4S) has advanced significantly through domain-specific models, tool-augmented LLMs, and scientific language models. However, model capabilities remain highly fragmented, limiting the joint modeling of heterogeneous data, scientific laws, and expert knowledge. S1-Omni addresses this gap by consolidating these capabilities into a single, coherent scientific reasoning model. The architecture of S1-Omni is built upon three core components: unified representation of scientific data, natural-world knowledge alignment, and decoding for domain-specific tasks. First, S1-Omni maps natural-language instructions and scientific objects, including CIF, SMILES, protein sequences, spectra, and scientific images, into a shared representation space. Second, it incorporates scientific laws and expert knowledge into data construction and training, enabling the model to reason from scientific evidence. Third, it performs task-specific decoding to support a broad range of applications, including property prediction, spectrum-to-molecular generation, protein site and structure prediction, and scientific image generation and editing. S1-Omni is trained on S1-Omni-Corpus, which covers 200 scientific tasks and contains millions of reasoning samples, and is evaluated on over 60 scientific benchmarks. It outperforms GPT-5.5 and Gemini-3.1-Pro on most benchmarks and matches or surpasses domain-specific models on several benchmarks. Overall, S1-Omni provides a practical path toward unified scientific modeling.
Jiahao Zhao, Junyi Liu, Lifeng Xu +19
Scientific DiscoveryMultimodal ReasoningOmni
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Apr 22, 2026cs.CV

OMIBench: Benchmarking Olympiad-Level Multi-Image Reasoning in Large Vision-Language Model

Large vision-language models (LVLMs) have made substantial advances in reasoning tasks at the Olympiad level. Nevertheless, current Olympiad-level multimodal reasoning benchmarks for these models often emphasize single-image analysis and fail to exploit contextual information across multiple images. We present OMIBench, a benchmark designed to evaluate Olympiad-level reasoning when the required evidence is distributed over multiple images. It contains problems from biology, chemistry, mathematics, and physics Olympiads, together with manually annotated rationales and evaluation protocols for both exact and semantic answer matching. Across extensive experiments on OMIBench, we observe meaningful performance gaps in existing models. Even the strongest LVLMs, such as Gemini-3-Pro, attain only about 50% on the benchmark. These results position OMIBench as a focused resources for studying and improving multi-image reasoning in LVLMs.
Qiguang Chen, Chengyu Luan, Jiajun Wu +7
Multimodal Reasoning BenchmarksLarge Vision Language ModelsOlympiad-Level Problem
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