Proportion (share of tasks where the agent's mean score exceeds the median human leaderboard submission (Section 3.4 definition); non-penalized: runs without a valid submission omitted) of Dummy agent (BioML-bench) on BioML-bench v0.1-alpha protein engineering tasks (6 tasks)
0.0 ± 0.0% Proportion (share of tasks where the agent's mean score exceeds the median human leaderboard submission (Section 3.4 definition); non-penalized: runs without a valid submission omitted)
Methods
- Tested configuration
- Dummy agent (BioML-bench)
- Protocol
- BioML-bench protein engineering domain: agent leaderboard percentile over 6 tasks
- Dataset subset
- BioML-bench v0.1-alpha protein engineering tasks (6 tasks)
- Procedure
- BioML-bench protein engineering domain: agent leaderboard percentile over 6 tasks
- Evaluation
- Dummy on BioML-bench protein engineering (non-penalized)
- Coverage
- Not reported scored / Not reported eligible
- Uncertainty
- ± 0.0 (type not stated). Table 4 caption does not name the spread. Figures 2 and 4 show per-domain leaderboard percentiles as mean ± SEM across tasks; the Table 2 caption refers to the reported SEM.
- Evidence
- Independent external evaluation · source checkedBioML-bench: Evaluation of AI Agents for End-to-End Biomedical ML · Table 4 (page 12), block 'Non-penalized', domain 'Protein Engineering', row 'Dummy', column 'Above Median (%)'
A source-checked result verifies the numerical transcription, not every model or protocol detail. Evaluation metadata: source checked. Source checked does not mean independently reproduced.
Reproduction
- Split
- ProteinGym supervised cross-validation folds (fold_random_5, fold_modulo_5, fold_contiguous_5) per DMS assay
- Adaptation
- Autonomous agent builds and trains its own ML pipeline; LLM backend: none
- Scoring implementation
- Task's original metric mapped to the task's public leaderboard percentile
No execution recipe has been verified for this exact configuration and evaluation. A benchmark's general instructions may use different inputs, splits or model settings.
Reproducing this published result requires matching its model configuration, data, split and scorer. Source checking or a successful smoke test does not establish score reproduction.
Evidence
Source checking verifies the cited claim or transcription. It does not establish independent reproduction.
Evidence table
Inspect claims, sources and review details
Trace each statement to its source and review. A context-only reference supports the record generally; it does not verify an individual field. Source checking does not reproduce an experiment.
One row per statement and cited source. Multiple citations are not independent evaluations. Shared locators are labelled explicitly.
1 evidence row matching the loaded filters
| Property and statement | Original source and location | Review and provenance |
|---|---|---|
| Reported result 0.0 ± 0.0 Individual claims | BioML-bench: Evaluation of AI Agents for End-to-End Biomedical ML Table 4 (page 12), block 'Non-penalized', domain 'Protein Engineering', row 'Dummy', column 'Above Median (%)' Version: bioRxiv 2025.09.01.673319 version 3, posted 2025-09-28 (versions 1 and 2 posted 2025-09-04 and 2025-09-07) | source checked ["source-hash-verification","pdf-text-parse","independent-cell-check","scope-review"] · 2026-10-13 independent paper Audit detailsExtraction: parsed from the pdftotext -layout text of the pinned PDF by extract/extract_biomlbench.py. Independent review 2026-10-13: matched. The spread stays unresolved_spread: the Table 4 caption does not name it, although every cell is arithmetically consistent with the SEM across the domain's tasks (see docs/reviews/2026-10-13-biomlbench-agents.md). Field: Source artifact SHA-256: Hash scope: SHA-256 of the PDF bytes as downloaded 2026-10-13T12:38:42Z. bioRxiv rewrites the XMP dates and document IDs, the Info ModDate and the trailer /ID on download, so a re-download does not reproduce the hash; the review found a fresh copy differing only in those 43 bytes, with an identical text layer. Extraction artifact SHA-256: |
Sources and history
Release 2026-11-02-a7f03c9e55a5 · Record review: source checked
1 source record and release history
- BioML-bench: Evaluation of AI Agents for End-to-End Biomedical ML · Original source · bioRxiv 2025.09.01.673319 version 3, posted 2025-09-28 (versions 1 and 2 posted 2025-09-04 and 2025-09-07)
Technical metadata and extraction receipts
Stable ID: lit-agents-20261013-biomlbench-result-protein-engineering-non-penalized-dummy-above-median
- metric
- proportion
- metric qualifier
- share of tasks where the agent's mean score exceeds the median human leaderboard submission (Section 3.4 definition); non-penalized: runs without a valid submission omitted
- metric direction
- higher
- unit
- percent
- printed value
- 0.0 ± 0.0
- numeric value
- 0.0
- source locator
- Table 4 (page 12), block 'Non-penalized', domain 'Protein Engineering', row 'Dummy', column 'Above Median (%)'
- uncertainty
- type: unresolved_spread; value: 0.0; printed: ± 0.0; note: Table 4 caption does not name the spread. Figures 2 and 4 show per-domain leaderboard percentiles as mean ± SEM across tasks; the Table 2 caption refers to the reported SEM.
- review
- method: source-hash-verification; pdf-text-parse; independent-cell-check; scope-review; method note: Pinned v3 PDF re-checked: the extractor's file hashes to the pinned SHA-256, and a fresh download differs only in bioRxiv's per-download stamps (43 bytes: XMP dates and IDs, Info ModDate, trailer /ID) with an identical pdftotext -layout text layer. An independent parser of Table 4 (rows located by domain and agent labels, 5 cells per row asserted) matched printed_value, numeric_value, spread, locator, metric, unit, direction and evaluation link for all 132 results. Section 3.4 definitions, Table 2 and the bioRxiv v2 Table 4 were read for context.; reviewer: claude; reviewer note: Claude (Opus 5.5) research agent, independent of the extractor; no human review claimed; date: 2026-10-13; artifact sha256: 875cb3519dac9b0ec51c35224e1fc90b107b0676a4cc7c22cecb56eb8ac38b35; retrieval url: https://www.biorxiv.org/content/10.1101/2025.09.01.673319v3.full.pdf; note: Extraction: parsed from the pdftotext -layout text of the pinned PDF by extract/extract_biomlbench.py. Independent review 2026-10-13: matched. The spread stays unresolved_spread: the Table 4 caption does not name it, although every cell is arithmetically consistent with the SEM across the domain's tasks (see docs/reviews/2026-10-13-biomlbench-agents.md).