S2F-agent: Skill-grounded agent for Sequence-to-Function computational genomics workflows

Abstract

Sequence-to-function (S2F) models offer a revolutionary paradigm for genotype-phenotype mapping, yet their broader application is bottlenecked by the need for reliable orchestration and interpretation across a fragmented model ecosystem. While general-purpose language models can automate scientific workflows, they are not inherently grounded in the model-specific execution constraints required for robust S2F analysis. Here, we present S2F-Agent, a human-in-the-loop framework designed for the verifiable orchestration of the heterogeneous S2F ecosystems. The framework employs a contract-based harness to bridge model-specific capabilities (Skills) and model-agnostic biological objectives (Playbooks), seamlessly translating free-form biological requests into reliable execution and rigorous downstream interpretation. Evaluated on a benchmark of 54 query cases derived from published S2F workflows, S2F-Agent systematically outperformed general-purpose LLMs, demonstrating superior reliability accuracy in routing, groundedness, and end-to-end task execution success. We further demonstrate the robustness and scalability of S2F-Agent across model adaptation, variant interpretation, genome-scale functional profiling and personal-genome analysis. First, the agent autonomously adapts a genomic foundation model to quantitative chromatin profiles, resolving sequence features associated with primed and active regulatory states. Second, integrating multi-perspective variant effect predictions prioritized 42 high-priority candidate variants among CAD-associated variants (>16,000), and identified tissue-resolved regulatory mechanisms including the hepatic SORT1 axis. Third, genome-scale profiling of multiple traits GWAS atlas variants (>250,000) revealed pervasive context dependence in molecular consequences and regulatory architecture, highlighting the analytical focus toward fine-grained, tissue-specific regulatory variants. Finally, evidence-gated analysis of personal genomes expanded functional hypothesis generation beyond clinically annotated variants to thousands of prioritized candidates per individual while imposing explicit evidence-dependent boundaries on clinical claims. Collectively, these results establish S2F-Agent as a general framework for converting heterogeneous sequence-to-function capabilities into verifiable, scalable, and evidence-aware genomic analyses. By bridging the chasm between LLMs, specialized S2F ecosystems and rigorous genomic science, this framework democratizes the S2F paradigm for unlocking the full potential of these advanced models in real-world discoveries.