GenoMAS: Guided Multi-Agent Programming for Scientific Discovery from Genomic Data

The rapid progress of LLM-based multi-agent systems (MAS) has shown that they largely outperform single agents on coding, math, and QA tasks, where executable tests provide a binary success signal. Whether this advantage transfers to real scientific data analysis remains untested. We introduce ST-Bench, a benchmark designed to answer two questions: whether MAS outperform single agents on complex scientific data analysis tasks, and if so, by how much and at what additional cost. ST-Bench contains 100 data science tasks adapted from published Earth science studies across hydrology, agriculture, and wetland methane research, expanded into 2,067 queries grounded in additional published studies and validated by domain experts. Using ST-Bench, we evaluate five recent MAS generation methods under two training protocols, against single-agent baselines on the same GPT-5 backbone. Nine of the ten MAS configurations exceed the cheapest single-agent baseline, with the strongest reaching nearly three times its composite score. This gain is primarily attributable to coverage: trained workflows produce realistic numerical metrics on a larger fraction of queries, while the quality of those metrics, conditional on producing realistic output, is comparable to that of the single-agent baseline. The strongest configuration requires approximately four times the single-agent inference time, whereas a more economical workflow captures the majority of the benefit at less than twice the cost. MAS specialization confers measurable benefit on scientific data analysis, but the benefit is conditional rather than universal.

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.

Designing multi-agent workflows is especially difficult in open-ended scientific settings where tasks lack curated training sets, reliable scalar evaluation metrics, and standardized interfaces between existing tools and agents. We propose AgentCo-op, a retrieval-based synthesis framework that composes reusable skills, tools, and external agents into executable workflows through typed artifact handoffs, then applies bounded self-guided local repair to implicated components when execution evidence indicates failure. In two open-world genomics case studies, AgentCo-op composes independently developed scientific agents and external tool repositories into auditable workflows without redesigning them or running global topology search. It coordinates specialized agents for spatial transcriptomics and gene-set interpretation to enable collaborative discovery from spatial transcriptomics data, and builds a parallel workflow for cross-modality marker analysis on single-cell multiome data. AgentCo-op can also import a searched workflow as a structural prior and improve it by grounding nodes with retrieved components and applying local repair, showing that synthesis and search are complementary. On six coding, math, and question-answering benchmarks, AgentCo-op achieves the best result on four benchmarks and the best average score under a unified backbone setting, while consistently reducing per-task cost relative to multi-agent baselines. Together, these results suggest that retrieval-based synthesis can extend automated agentic workflow design beyond benchmark-optimized agent graphs to open-world workflows built from existing agents, tools, and typed artifacts.