# Plato-Bio: verification-first biological novelty screening with temporal rediscovery and structural benchmarks

arXiv: https://arxiv.org/abs/2607.23975 · HTML: https://mlsanity.com/paper/2607.23975/

## Key facts

- No citing papers in the map yet (data through 14 Oct 2026).
- Placed in Medical and scientific domain agents, one of 16 directions in LLM agents and tool use.
- Builds on 6 of its 18 references that are in the map.
- First posted on arXiv 27 Jul 2026.

## Placed in

- LLM agents and tool use / [Medical and scientific domain agents](https://mlsanity.com/agents/medical-and-scientific-domain-agents/)

## Builds on (most cited first, 6 of 6)

- [The AI Scientist: Towards Fully Automated Open-Ended Scientific Discovery](https://mlsanity.com/paper/2408.06292/) (2024)
- [Agent Laboratory: Using LLM Agents as Research Assistants](https://mlsanity.com/paper/2501.04227/) (2025)
- [ScienceAgentBench: Toward Rigorous Assessment of Language Agents for Data-Driven Scientific Discovery](https://mlsanity.com/paper/2410.05080/) (2024)
- [BixBench: a Comprehensive Benchmark for LLM-based Agents in Computational Biology](https://mlsanity.com/paper/2503.00096/) (2025)
- [The Denario project: Deep knowledge AI agents for scientific discovery](https://mlsanity.com/paper/2510.26887/) (2025)
- [BioDSA-1K: Benchmarking Data Science Agents for Biomedical Research](https://mlsanity.com/paper/2505.16100/) (2025)

## Abstract (arXiv)

Large language model research agents can connect literature retrieval, analysis code, and manuscript preparation, but coherent output does not establish scientific validity. We developed Plato-Bio, a biology-routed extension of the open Plato/Denario architecture that couples explicit workflow states with provenance records, citation checks, claim-to-evidence links, scoped file writes, and publication gates. A source audit identified and repaired three defects that could distort evaluation: loss of task domain in the default factory, omission of declared method signals from scoring, and evidence sidecars that lacked the drafted-claim denominator. On the current clean revision, the full Python suite completed with 931 passes, six skips, and no failures or errors; targeted biology, genomics, evidence/citation, and adversarial-safety suites likewise completed without failure. We evaluated two narrow use cases. In a frozen historical rediscovery task, independent pre-1986 literature bridges ranked the later-studied relation between fish oil and Raynaud phenomenon first; TF-IDF ranked it second and corpus frequency third. This single curated task measures retrospective ranking, not prospective discovery. In a separate comparison of AlphaFold models with experimental structures for 15 human proteins, 11 targets had high-confidence-core C-alpha RMSD below 1 Angstrom (median 0.501 Angstrom). Four targets exceeded 2 Angstrom, and confidence masking reduced the SUMO1 discrepancy from 16.61 to 2.58 Angstrom over 74 residues. The workflow emitted 27 traceable discrepancy regions, all retained as unvalidated hypotheses. Plato-Bio therefore provides reproducible software contracts and auditable screening baselines; broader claims of agent efficacy or biological novelty require preregistered evaluation, independent review, and prospective validation.