#7 · ML / AI methods
LLM agents ground omics and clinical genomic analysis in executable skills, memory, and…
The dominant thread is coupling LLMs to executable skills, shared laboratory memory, structured query interfaces, or trained predictors so outputs are checkable. ClinGeX composes 105 skills for clinical genomic analysis and reports 71.7% macro-averaged concordance with expert classifications. SMART tests transfer of scRNA-seq cancer findings across six cancer types in 121 studies, while LabWeaver adds laboratory-tier memory and skills on a synovial sarcoma dataset. SPaRTA contributes a 7,500-pair benchmark for text-to-spatial-SQL and analyzes LLM failure modes. SurvXAI layers locally run LLM narratives over Random Survival Forest predictions and SurvSHAP attributions. The Rosalind assessment of GPT-5.2, Claude Sonnet 4.6 and other LLMs against expert and human answers offers a baseline for unaided multi-step reasoning and code writing. The items are not uniform in design: some are agents, others benchmarks or explanation layers.
Published papers
Assessment of LLMs on basic bioinformatics tasks requiring multi-step reasoning and code writing.
Benchmarks GPT-5.2, Claude Sonnet 4.6 and other LLMs on 104 Rosalind bioinformatics questions versus expert and 68,760 human answers.
Narrative-based explainable AI for precision oncology survival prediction.
SurvXAI pairs Random Survival Forest survival prediction with SurvSHAP feature attributions and locally run LLMs to generate narrative explanations for…
Preprints
Advancing Clinical Genomic Analysis with a Skill-Centred Agent
ClinGeX, an LLM agent composing 105 executable skills for clinical genomic analysis, reported 71.7% macro-averaged concordance with expert classifications on…
Agentic Discovery Transfer Enables Cross-Cancer Discovery at Scale
SMART: a multi-agent LLM framework that tests whether scRNA-seq cancer findings transfer across six cancer types, applied to 121 studies.
LabWeaver: reliable agentic data analysis grounded in laboratory knowled
LabWeaver is an agentic data analysis framework with laboratory-tier memory and skills; on a synovial sarcoma scRNA-seq dataset, shared context recovered…
SPaRTA: Spatial Reasoning in Text-to-SQL for Omics Analysis
SPaRTA: a text-to-spatial-SQL interface for spatial-omics data, with a 7,500-pair benchmark and analysis of LLM failure modes across fine-tuning and execution…
Topic history
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