data-protein-engineering-tasks: attributes.limitations[0]
Limitations[0] of BioML-bench v0.1-alpha protein engineering tasks (6 tasks)
The paper's Table 3 and the repository task list disagree on two protein engineering assays (SPA_STAAU versus SBI_STAAM; PSAE_PICP2 indels versus substitutions); see the source limitations.
Two, not three, protein engineering assays conflict; the CBX4 label difference is the same assay.
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.
14 evidence rows matching the loaded filters
| Property and statement | Original source and location | Review and provenance |
|---|---|---|
| Claimed field attributes.limitations[0] Context-only references | BioML-bench: Evaluation of AI Agents for End-to-End Biomedical ML Table 3; repository experiments/biomlbench_v0.1a.txt at commit 673f3d8 Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: bioRxiv 2025.09.01.673319 version 3, posted 2025-09-28 (versions 1 and 2 posted 2025-09-04 and 2025-09-07) | not individually reviewed No individual claim review recorded Audit detailsField: 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. |
| Claimed field attributes.limitations[0] Context-only references | science-machine/biomlbench repository at commit 673f3d8 Table 3; repository experiments/biomlbench_v0.1a.txt at commit 673f3d8 Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: Git commit 673f3d8d3462fc6cdcbbd9695fba612b9332ca65 (2025-09-14, head of main at retrieval); README title 'BioML-bench (v0.1-alpha)' | not individually reviewed No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: SHA-256 of the codeload tar.gz archive for the commit; two downloads gave identical bytes. Per-file hashes of the files cited are in sources.md. |
| Previous value The paper's Table 3 and the repository task list disagree on three protein engineering assays; see the source limitations. Context-only references | BioML-bench: Evaluation of AI Agents for End-to-End Biomedical ML Table 3; repository experiments/biomlbench_v0.1a.txt at commit 673f3d8 Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: bioRxiv 2025.09.01.673319 version 3, posted 2025-09-28 (versions 1 and 2 posted 2025-09-04 and 2025-09-07) | not individually reviewed No individual claim review recorded Audit detailsField: 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. |
| Previous value The paper's Table 3 and the repository task list disagree on three protein engineering assays; see the source limitations. Context-only references | science-machine/biomlbench repository at commit 673f3d8 Table 3; repository experiments/biomlbench_v0.1a.txt at commit 673f3d8 Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: Git commit 673f3d8d3462fc6cdcbbd9695fba612b9332ca65 (2025-09-14, head of main at retrieval); README title 'BioML-bench (v0.1-alpha)' | not individually reviewed No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: SHA-256 of the codeload tar.gz archive for the commit; two downloads gave identical bytes. Per-file hashes of the files cited are in sources.md. |
| Source location Table 3; repository experiments/biomlbench_v0.1a.txt at commit 673f3d8 Context-only references | BioML-bench: Evaluation of AI Agents for End-to-End Biomedical ML Table 3; repository experiments/biomlbench_v0.1a.txt at commit 673f3d8 Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: bioRxiv 2025.09.01.673319 version 3, posted 2025-09-28 (versions 1 and 2 posted 2025-09-04 and 2025-09-07) | not individually reviewed No individual claim review recorded Audit detailsField: 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. |
| Source location Table 3; repository experiments/biomlbench_v0.1a.txt at commit 673f3d8 Context-only references | science-machine/biomlbench repository at commit 673f3d8 Table 3; repository experiments/biomlbench_v0.1a.txt at commit 673f3d8 Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: Git commit 673f3d8d3462fc6cdcbbd9695fba612b9332ca65 (2025-09-14, head of main at retrieval); README title 'BioML-bench (v0.1-alpha)' | not individually reviewed No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: SHA-256 of the codeload tar.gz archive for the commit; two downloads gave identical bytes. Per-file hashes of the files cited are in sources.md. |
| Claimed value The paper's Table 3 and the repository task list disagree on two protein engineering assays (SPA_STAAU versus SBI_STAAM; PSAE_PICP2 indels versus substitutions); see the source limitations. Context-only references | BioML-bench: Evaluation of AI Agents for End-to-End Biomedical ML Table 3; repository experiments/biomlbench_v0.1a.txt at commit 673f3d8 Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: bioRxiv 2025.09.01.673319 version 3, posted 2025-09-28 (versions 1 and 2 posted 2025-09-04 and 2025-09-07) | not individually reviewed No individual claim review recorded Audit detailsField: 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. |
| Claimed value The paper's Table 3 and the repository task list disagree on two protein engineering assays (SPA_STAAU versus SBI_STAAM; PSAE_PICP2 indels versus substitutions); see the source limitations. Context-only references | science-machine/biomlbench repository at commit 673f3d8 Table 3; repository experiments/biomlbench_v0.1a.txt at commit 673f3d8 Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: Git commit 673f3d8d3462fc6cdcbbd9695fba612b9332ca65 (2025-09-14, head of main at retrieval); README title 'BioML-bench (v0.1-alpha)' | not individually reviewed No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: SHA-256 of the codeload tar.gz archive for the commit; two downloads gave identical bytes. Per-file hashes of the files cited are in sources.md. |
| Description Two, not three, protein engineering assays conflict; the CBX4 label difference is the same assay. Context-only references | BioML-bench: Evaluation of AI Agents for End-to-End Biomedical ML Table 3; repository experiments/biomlbench_v0.1a.txt at commit 673f3d8 Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: bioRxiv 2025.09.01.673319 version 3, posted 2025-09-28 (versions 1 and 2 posted 2025-09-04 and 2025-09-07) | not individually reviewed No individual claim review recorded Audit detailsField: 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. |
| Description Two, not three, protein engineering assays conflict; the CBX4 label difference is the same assay. Context-only references | science-machine/biomlbench repository at commit 673f3d8 Table 3; repository experiments/biomlbench_v0.1a.txt at commit 673f3d8 Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: Git commit 673f3d8d3462fc6cdcbbd9695fba612b9332ca65 (2025-09-14, head of main at retrieval); README title 'BioML-bench (v0.1-alpha)' | not individually reviewed No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: SHA-256 of the codeload tar.gz archive for the commit; two downloads gave identical bytes. Per-file hashes of the files cited are in sources.md. |
Sources and history
Release 2026-11-02-a7f03c9e55a5 · Record review: source checked
2 source records 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)
- science-machine/biomlbench repository at commit 673f3d8 · Original source · Git commit 673f3d8d3462fc6cdcbbd9695fba612b9332ca65 (2025-09-14, head of main at retrieval); README title 'BioML-bench (v0.1-alpha)'
Technical metadata and extraction receipts
Stable ID: metadata-correction-biomlbench-20261013-data-protein-engineering-tasks-limitations-0
- field
- attributes.limitations[0]
- previous value
- The paper's Table 3 and the repository task list disagree on three protein engineering assays; see the source limitations.
- value
- The paper's Table 3 and the repository task list disagree on two protein engineering assays (SPA_STAAU versus SBI_STAAM; PSAE_PICP2 indels versus substitutions); see the source limitations.
- source locator
- Table 3; repository experiments/biomlbench_v0.1a.txt at commit 673f3d8
- review
- method: source-hash-verification; independent-cell-check; method note: Compared Table 3 of the pinned v3 PDF with experiments/biomlbench_v0.1a.txt and the description.md of each named task in the repository archive at commit 673f3d8.; 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: Two, not three, protein engineering assays conflict; the CBX4 label difference is the same assay. See docs/reviews/2026-10-13-biomlbench-agents.md.