Research Agent Bot

Research Agent Bot is an audited biomedical evidence-synthesis engine. It is not a generic drafting demo: retrieval, source admission, claim extraction, manuscript compilation, and publish gates are separate stages with sidecar artifacts for review.

Pipeline

topic pack
  -> source retrieval and corpus seeding
  -> source admission and evidence-tier classification
  -> claim cards, citation registry, and tension matrix
  -> v3 synthesis compiler
  -> public manuscript plus supplemental evidence tables
  -> deterministic surface, audit, and pre-submit gates
  -> Researka submission

Outputs

• full_paper.md - reader-facing manuscript. It should contain prose, compact evidence snapshots, references, and no raw compiler dumps.
• structured_evidence_tables.md - supplemental evidence tables and full evidence-map detail.
• manifest.json, claim_graph.json, citation_registry.json, and audit sidecars - machine-readable trust-spine artifacts.
• paper_ir.json - typed PaperIR containing thesis, sections, framework axes, tables, references, and export pointers.
• paper_quality_score.json and public_export_manifest.json - deterministic reader/export readiness summaries.
• references.bib, evidence_table.csv, contradiction_map.json, and full_paper.docx - portable reader and publisher exports.
• Optional polish outputs - Typst PDF, sciwrite-lint report, and offline eval JSON when those tools are installed.

Trust Spine

LLM PROPOSES. CODE DISPOSES.

LLMs may draft and revise prose. Deterministic code owns evidence admission, categorical labels, source-traced numerics, maturity status, and submit eligibility. Markdown is a rendering target, not the source of truth.

Local Checks

.venv/bin/python -m ruff check agent scripts tests
.venv/bin/python -m mypy --no-incremental --explicit-package-bases --ignore-missing-imports scripts/run_v06_synthesis.py scripts/table_renderer.py agent/journal_surface_gate.py
.venv/bin/python -m pytest -q

Deployment

The live bot runs from /opt/research-agent-bot on the VPS. Deploy only from a clean tree, fast-forward both VPS checkouts, then verify the service and HTTP status endpoint.