AutoZyme Lab

Frozen optimization challenges for community speedups

Lab tasks turn slow bioinformatics methods into reproducible optimization challenges. Download the frozen task card, run the public gate locally, and upload an evidence bundle. Public results move a patch into review; verified speedups are produced later by AutoZyme maintainers on hidden OOD data and credited to accepted contributors.

1Download frozen card

2Run public gate

3Upload evidence bundle

4Hidden OOD review

How a submission becomes a new round

Uploaded bundles enter a review queue first. AutoZyme checks the public evidence, reruns the candidate on a maintainer machine, and then evaluates a private held-out suite. Only submissions that improve verified speed while passing every frozen gate are appended to the trajectory as a new credited round and considered for packaging or upstream contribution.

Frozen task Inputs, metrics, and thresholds do not move during a challenge version.

Public evidence Bundles must include machine-readable runtime, memory, and concordance outputs.

Hidden validation Final acceptance depends on private OOD datasets, not self-reported numbers.

Seurat · Ropen for submissions

seurat_findallmarkers_v1

Seurat FindAllMarkers v1

Optimize Seurat's differential marker discovery while preserving marker sets, log-fold-change ranking, adjusted p-values, and output schema.

TargetFindAllMarkers

UpstreamSeurat 5.4.0

Entry symboloptimized_FindAllMarkers

Hidden OODPrivate held-out suite

Speed≥ 1.2×

Gene Jaccard≥ 0.95

Top-20 overlap≥ 0.90

LogFC Spearman≥ 0.98

Adj. p Spearman≥ 0.98

Memory ratio≤ 1.2×

Downloads

Task bundle zip ↓Task card YAML ↓Smoke dataset ↓Solution template ↓

Challenge freeze

Task idseurat_findallmarkers_v1

Versionv1

Smoke SHA-25686c567dedab1...6a796ee3

Public smoke test

PBMC small smoke test · 80 cells · 230 genes

Rscript run_public.R --data public_smoke_pbmc_small.rds --impl solution_template.R --out run_public

Bundle contract

Include run_public/results.json, source changes, environment notes, and any risk notes needed for review.

Public dev status

PBMC68k public dev dataset · external mirror pending

Hidden OOD

Held-out single-cell datasets with larger scale, different tissue context, different sparsity, and different cluster structure. Exact datasets and reference outputs are not disclosed.

Optimization trajectory

FindAllMarkers public development history. Hover each round for the mechanism and submitter.

accepteddiscarded

Submit a bundle

Frozen task evidence, not self-reported leaderboard numbers

Submission contract

The upload API performs a public sanity check and stores your evidence bundle. Verified leaderboard numbers come only from maintainer reruns against the frozen task and hidden OOD suite.

Expected bundle path: run_public/results.json.
Include source changes, dependency changes, environment notes, and any approximation risks.
Do not upload large intermediate outputs; include hashes or reproducible scripts instead.
Accepted submissions are credited in the trajectory and may be packaged or proposed upstream.

Recent submissions

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