Compose & reproduce¶
Compose — a pipeline from revived bricks¶
Because every revival speaks the same contract, revived tools compose regardless of domain, language, or era. A pipeline is a small YAML; one command runs it, passing file artifacts between steps on the host you choose.
examples/pipelines/binder_triage.yaml
assembles three methods that were each individually unrunnable a week ago:
structure ─▶ ScanNet ─┐
─▶ dMaSIF ──┼─▶ consensus ─▶ interface residues that also line a druggable pocket
─▶ fpocket ─┘
lazarus run examples/pipelines/binder_triage.yaml \
--input structure=4ZQK.pdb \
--registry examples --registry components \
--docker-host ssh://you@your-x86-gpu-box
Run live on PD-L1, it concluded: 27 interface residues clearly localized, but 0 druggable pockets among them → "a flat protein-protein interface: an antibody / biologic target, not a small-molecule one." That's textbook immuno-oncology (PD-1/PD-L1 is an antibody target), reproduced from dead code.
Reproduce — the trust layer¶
A smoke test proves a method runs; a benchmark proves it's the method. A contract's benchmark
field emits a REPRODUCE.md certificate with a PASS/OFF verdict.
| Method | Paper | Lazarus | Verdict |
|---|---|---|---|
| MaSIF-site transient PPI benchmark | 0.85 | 0.82 | reproduced (±0.05) |
| Basset mean AUROC over 164 cell types | 0.895 | 0.8944 | reproduced |
Basset's reproduction is what exposed a silent bug: the naive run scored mean AUROC 0.675 because half the genome's soft-masked (lowercase) bases fell through the one-hot encoder. Reproducing the paper — not merely executing the code — is what caught it. Full story: the hard problems it solved.
Give back¶
For the genuinely-abandoned repos, Lazarus prepares maintainer-ready PRs — the real fix plus a CI smoke test so the method can't silently rot again: