Verification Debt in Automated Biological Research Workflows: A Proof-of-Concept

Abstract

Recent biological research has shown significant interest and progress towards adoption of agentic AI systems. Domain specific agentic platforms with access to large collections of biological tools with code generation and/or querying capabilities, such as Biomni (illustrative case in point), are representative of the capability to orchestrate automated research workflows. Such platforms enable collaborative AI workspace for drug discovery, genomics, bioinformatics, literature research, and experimental planning for biologists and researchers. When such platforms are used for the aforementioned workflows, individually validating every agentic decision and the research process by which it was reached becomes challenging due to the scale of decisions involved and oftentimes, insufficient disclosure of assumptions and methodological choices, limited traceability of evidence, and interpretive judgments embedded throughout the workflow, giving rise to verification debt. Verification debt in agentic environments could result in unexpected failures and consequences in downstream experiments. This study focuses on empirical qualitative characterization of verification debt in agentic (prompt to outcomes) workflows. Biomni was chosen the testing AI agentic platform in this study mainly due to the descriptive traces it provides to track every agentic step. Verification debt is examined through two complementary angles: the individual agentic decision steps that carry claims and evidence, and the underlying research process by which the agent arrives at and reports them. This study attempts to characterize verification debt with 10 test cases (covering proteomics, genomics and drug discovery) with varying degree of biological nuance across three identical and independent runs. Verification debt is represented through 9 decision-step metrics and 13 research-process metrics, and also propose the VERIFY framework for evaluating scientific verifiability and validity in agentic workflows.