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Maciej Sypetkowski

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Artificial Intelligence Cell Behavior Computer Vision Genomics Multiagent Systems Quantitative Methods

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preprint2026arXiv

BioResearcher: Scenario-Guided Multi-Agent for Translational Medicine

Translational medicine turns underspecified development goals into evidence synthesis that must combine literature, trials, patents, and quantitative multi-omics analysis while preserving identifiers, uncertainty, and retrievable provenance. General-purpose foundation models and off-the-shelf tool-augmented or multi-agent systems are not built for this: they tend to produce single-shot answers or run open-endedly, and fall short on the auditable, scenario-specific workflows that heterogeneous biomedical sources demand. This paper introduces Ingenix BioResearcher, a scenario-guided multi-agent system that maps queries to versioned research playbooks, delegates to specialized subagents over 30+ tools and machine-learning endpoints, mixes structured database access with sandboxed code for genome-scale analyses, and applies claim-level multi-model reconciliation before editorial assembly. We evaluate BioResearcher across unit-level capabilities, open-ended biomedical reasoning, and end-to-end clinical discovery. It leads evaluated baselines on 109 single-step tests (83.49% pass rate; 0.892 average score), achieves strong biomedical benchmark performance (89.33% on BixBench-Verified-50 and the top 0.758 mean score on BaisBench Scientific Discovery), and leads on a 30-query clinical end-to-end benchmark with the highest positive hit rate (74.7% $\pm$ 3.3%) and negative clear rate (96.8% $\pm$ 0.2%). These results show broad, competitive performance across unit-level, open-ended, and end-to-end clinical evaluations.

preprint2026arXiv

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.

preprint2023arXiv

RxRx1: A Dataset for Evaluating Experimental Batch Correction Methods

High-throughput screening techniques are commonly used to obtain large quantities of data in many fields of biology. It is well known that artifacts arising from variability in the technical execution of different experimental batches within such screens confound these observations and can lead to invalid biological conclusions. It is therefore necessary to account for these batch effects when analyzing outcomes. In this paper we describe RxRx1, a biological dataset designed specifically for the systematic study of batch effect correction methods. The dataset consists of 125,510 high-resolution fluorescence microscopy images of human cells under 1,138 genetic perturbations in 51 experimental batches across 4 cell types. Visual inspection of the images alone clearly demonstrates significant batch effects. We propose a classification task designed to evaluate the effectiveness of experimental batch correction methods on these images and examine the performance of a number of correction methods on this task. Our goal in releasing RxRx1 is to encourage the development of effective experimental batch correction methods that generalize well to unseen experimental batches. The dataset can be downloaded at https://rxrx.ai.