A tissue-agnostic pipeline that turns weighted gene programs into biological interpretation — where every claim links to a real, verified citation, never a fabricated one.
gene_loading.csv · research/bundle.py · gpi/context_profile.py
One weighted gene list per program — from cNMF / NMF / Perturb-seq — is packaged into a self-contained research brief: its marker genes framed with a structured ContextProfile, the high-leverage context_terms that define normal cell function, and its activating / repressing perturbation regulators. Capturing biological context for real data; this brief is the only thing each research agent sees.
gpi/enrichment.py · gpi/string_api.py
Before any model sees the program, the pipeline gathers conventional STRING evidence: GO & KEGG functional enrichment over the marker genes, and the protein–protein interaction network that links each perturbation regulator to its confidence-scored targets. Bundled into the brief, this evidence anchors the literature search and the final annotation.
research/research_parallel.py · research/literature.py
One isolated Claude Agent-SDK session per program, fanned out under a Python asyncio Semaphore — there is no manager agent. Each session is sandboxed to see only its own brief and queries PubMed, OpenAlex & Crossref through an in-process literature server. The agent decides every search; deterministic code never researches on its own.
research/verify.py
Before anything is shown, every PMID and DOI the agents returned is resolved against CrossRef and NCBI, checked for retraction, and de-duplicated. Identifiers that don't resolve are dropped and the run degrades honestly — the pipeline never invents an identifier to fill a gap.
gpi/evidence_context.py · gpi/anthropic_batch.py
Verified evidence is folded back into a per-program prompt and synthesized through the Anthropic Batch API — functional modules, a lead sentence, and a cross-program label. Research bills the subscription; batch synthesis bills API credit — a clean auth split by executor.
gpi/html_report.py → report.html
A single interactive HTML report. Each functional module carries an evidence-status colour, and every supporting claim is one click from the resolvable paper — PMID, DOI, out to PubMed. Disagreement and gaps are shown, not hidden. Click any citation below.
The pericentral (zone 3) compartment — Wnt/β-catenin zonation, ammonia detoxification via glutamine synthesis, and pericentral xenobiotic metabolism.
An AXIN2⁺ lineage-tracing study argues pericentral hepatocytes contribute little to homeostatic turnover — challenging the pericentral stem-cell hypothesis. Surfaced, not suppressed.
No hepatocyte-specific functional papers were retrieved for Tbx3, Lhpp, Gulo, Lect2 — recorded as open questions.