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

arXiv: https://arxiv.org/abs/2605.06728 · HTML: https://mlsanity.com/paper/2605.06728/

## Key facts

- No citing papers in the map yet (data through 14 Oct 2026).
- Placed in Clinical and biomedical applications, one of 17 directions in LLM reasoning.
- Builds on 11 of its 59 references that are in the map.
- First posted on arXiv 7 May 2026.

## Placed in

- LLM reasoning / [Clinical and biomedical applications](https://mlsanity.com/lr/clinical-and-biomedical-applications/)
- Multimodal LLMs / vision-language models / [Medical vision-language models](https://mlsanity.com/mllm/medical-vision-language-models/)

## Builds on (most cited first, 11 of 11)

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- [Qwen-VL: A Versatile Vision-Language Model for Understanding, Localization, Text Reading, and Beyond](https://mlsanity.com/paper/2308.12966/) (2023)
- [TxGemma: Efficient and Agentic LLMs for Therapeutics](https://mlsanity.com/paper/2504.06196/) (2025)
- [BioMaze: Benchmarking and Enhancing Large Language Models for Biological Pathway Reasoning](https://mlsanity.com/paper/2502.16660/) (2025)
- [Cell-o1: Training LLMs to Solve Single-Cell Reasoning Puzzles with Reinforcement Learning](https://mlsanity.com/paper/2506.02911/) (2025)
- [CellVerse: Do Large Language Models Really Understand Cell Biology?](https://mlsanity.com/paper/2505.07865/) (2025)
- [Single-Cell Omics Arena: A Benchmark Study for Large Language Models on Cell Type Annotation Using Single-Cell Data](https://mlsanity.com/paper/2412.02915/) (2024)
- [scBench: Evaluating AI Agents on Single-Cell RNA-seq Analysis](https://mlsanity.com/paper/2602.09063/) (2026)

## Abstract (arXiv)

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.