Plato 科学研究自主智能体

Plato

Plato is a multi-agent research workflow that turns a data specification into research ideas, methods, executable analyses, and manuscript drafts. Its verification gates are designed to make evidence and limitations inspectable; human authors remain responsible for scientific validity and publication.

Abstract

Large language model research agents can connect literature retrieval, analysis code, and manuscript preparation, but coherent output does not establish scientific validity. Plato-Bio extends the open Plato/Denario architecture with explicit workflow states, provenance records, citation checks, claim-to-evidence links, scoped file writes, and publication gates. A source audit found and repaired three measurement defects: loss of task domain in the default evaluation factory, omission of declared method signals from scoring, and evidence sidecars that lacked the drafted-claim denominator.

The study then evaluated two deliberately limited use cases. In one frozen historical task, independent pre-1986 literature bridges ranked the later-studied fish-oil/Raynaud relation first. In a separate comparison of AlphaFold models with experimental structures for 15 human proteins, 11 targets had high-confidence-core Cα RMSD below 1 Å (median 0.501 Å), while 27 traceable discrepancy regions were retained as unvalidated hypotheses. These results support reproducible software contracts and auditable screening baselines—not autonomous discovery, general agent efficacy, or established biological novelty.

Overview

Plato represents research as explicit state machines rather than one monolithic prompt. The biology profile routes retrieval and analysis toward biomedical sources and tools; downstream controls emit citation reports, claim/evidence matrices, consistency checks, run manifests, analysis outputs, and manuscript artifacts. Human authors remain responsible for source review, scientific interpretation, authorship, and publication.

The study separates three evidence lanes:

1. Software-contract validation tests whether implemented controls behave as declared. 2. Temporal rediscovery tests whether pre-cutoff literature can recover a relation studied later. 3. Structural hypothesis triage compares declared AlphaFold and experimental structures while preserving confidence and experimental context.

The lanes are complementary but not interchangeable. Passing software tests does not measure biological accuracy, and a retrospective or descriptive benchmark does not establish prospective novelty.

What's new in 1.0.1

Phase 5 hardening landed alongside the dashboard's 13-stream feature push:

- Multi-source retrieval — scholarly-source adapters behind a domain-aware orchestrator with rate-limit backoff, ETag caching, and per-host circuit breakers. - Citation validation — every reference is resolved against Crossref + Retraction Watch + arXiv before the paper finalizes. The run dir gets a validation_report.json with per-reference pass/fail. - Claim → Evidence Matrix — the literature pass extracts atomic claims with quote spans and links them to source records. Persisted as evidence_matrix.jsonl per run. - Reviewer-role revision loop — methodology / statistics / novelty / writing axes feed an aggregator that drives a bounded redraft loop. These roles currently use the drafting client and are self-critique, not independent peer review. - Research-loop scaffold — plato loop --hours 8 --max-cost-usd 50 provides wall-clock/cost budgeting and git keep/discard checkpoints. The default adapters score existing artifacts; they do not yet execute a complete research cycle. - Reproducibility manifest primitives — the manifest schema and recorder can capture git/project hashes, models, prompts, seeds, sources, tokens, and cost when supplied by the calling workflow; public-path coverage is not yet complete. - Observability — opt in by setting LANGFUSE_* env vars; LangFuse callbacks are wired into every LangGraph invocation. - Pluggable domains — DomainProfile registry exposes retrieval, keyword extractor, journal preset, executor, and novelty corpus as swap points. Astro is the default; biology ships out-of-the-box. - Multi-tenant dashboard — set PLATO_DASHBOARD_AUTH_REQUIRED=1 and the dashboard reads X-Plato-User from the upstream proxy to scope every project, key store, and run artifact per tenant.

See docs/adr/ for the design decisions behind these changes and dashboard/CHANGELOG.md for the full list.