TraitGym official metrics: AUPRC by chromosome, weighted average (Hugging Face dataset songlab/TraitGym)
Hugging Face dataset revision 1fde19555fe8c0a55b1382bdf4c6f7082209f566 (last modified 2025-03-25); 156 metric CSVs under {dataset}/AUPRC_by_chrom_weighted_average/all/ · Project source
What this source contributed
Records in this release that cite this source. A record can cite several sources.
Results
Values as the source printed them. Compare results only under compatible protocols, datasets and metrics.
Claims
Statements this source supports, each with where in the source it was checked.
- GPN-MSA_absLLR.plus.score (TraitGym): configuration of GPN-MSA: Configuration of GPN-MSA (Configuration name as printed in its source (GPN-MSA_absLLR.plus.score); GPN-MSA identity from gfm-guides-20261014-gpnmsa-source-biorxiv-v2 (Abstract) and gfm-guides-20261014-gpnmsa-source-gpn-msa-doc)
- GPN-MSA_Embeddings.minus.inner_product (TraitGym): configuration of GPN-MSA: Configuration of GPN-MSA (Configuration name as printed in its source (GPN-MSA_Embeddings.minus.inner_product); GPN-MSA identity from gfm-guides-20261014-gpnmsa-source-biorxiv-v2 (Abstract) and gfm-guides-20261014-gpnmsa-source-gpn-msa-doc)
- GPN-MSA_Embeddings.plus.cosine_distance (TraitGym): configuration of GPN-MSA: Configuration of GPN-MSA (Configuration name as printed in its source (GPN-MSA_Embeddings.plus.cosine_distance); GPN-MSA identity from gfm-guides-20261014-gpnmsa-source-biorxiv-v2 (Abstract) and gfm-guides-20261014-gpnmsa-source-gpn-msa-doc)
- GPN-MSA_Embeddings.plus.euclidean_distance (TraitGym): configuration of GPN-MSA: Configuration of GPN-MSA (Configuration name as printed in its source (GPN-MSA_Embeddings.plus.euclidean_distance); GPN-MSA identity from gfm-guides-20261014-gpnmsa-source-biorxiv-v2 (Abstract) and gfm-guides-20261014-gpnmsa-source-gpn-msa-doc)
- GPN-MSA_InnerProduct.minus.score (TraitGym): configuration of GPN-MSA: Configuration of GPN-MSA (Configuration name as printed in its source (GPN-MSA_InnerProduct.minus.score); GPN-MSA identity from gfm-guides-20261014-gpnmsa-source-biorxiv-v2 (Abstract) and gfm-guides-20261014-gpnmsa-source-gpn-msa-doc)
- GPN-MSA_LLR.minus.score (TraitGym): configuration of GPN-MSA: Configuration of GPN-MSA (Configuration name as printed in its source (GPN-MSA_LLR.minus.score); GPN-MSA identity from gfm-guides-20261014-gpnmsa-source-biorxiv-v2 (Abstract) and gfm-guides-20261014-gpnmsa-source-gpn-msa-doc)
- GPN-MSA.LogisticRegression.chrom (TraitGym): configuration of GPN-MSA: Configuration of GPN-MSA (Configuration name as printed in its source (GPN-MSA.LogisticRegression.chrom); GPN-MSA identity from gfm-guides-20261014-gpnmsa-source-biorxiv-v2 (Abstract) and gfm-guides-20261014-gpnmsa-source-gpn-msa-doc)
- Relevance of TraitGym Complex traits, linear-probing, AUPRC by chromosome weighted average to "Select regulatory variants and genes for functional follow-up": Assessed by TraitGym Complex traits, linear-probing, AUPRC by chromosome weighted average (lit-genomics-20261011-traitgym-source-hf-metrics: complex_traits_matched_9/AUPRC_by_chrom_weighted_average/all/)
- Relevance of TraitGym Complex traits, zero-shot, AUPRC by chromosome weighted average to "Select regulatory variants and genes for functional follow-up": Assessed by TraitGym Complex traits, zero-shot, AUPRC by chromosome weighted average (lit-genomics-20261011-traitgym-source-hf-metrics: complex_traits_matched_9/AUPRC_by_chrom_weighted_average/all/)
- Relevance of TraitGym Mendelian traits, linear-probing, AUPRC by chromosome weighted average to "Select regulatory variants and genes for functional follow-up": Assessed by TraitGym Mendelian traits, linear-probing, AUPRC by chromosome weighted average (lit-genomics-20261011-traitgym-source-hf-metrics: mendelian_traits_matched_9/AUPRC_by_chrom_weighted_average/all/)
- Relevance of TraitGym Mendelian traits, zero-shot, AUPRC by chromosome weighted average to "Select regulatory variants and genes for functional follow-up": Assessed by TraitGym Mendelian traits, zero-shot, AUPRC by chromosome weighted average (lit-genomics-20261011-traitgym-source-hf-metrics: mendelian_traits_matched_9/AUPRC_by_chrom_weighted_average/all/)
Models, benchmarks and other records
Models (1)
Methods (5)
Configurations (81)
- AIDO.DNA_absLLR.plus.score (TraitGym)
- AIDO.DNA_Embeddings.minus.inner_product (TraitGym)
- AIDO.DNA_Embeddings.plus.cosine_distance (TraitGym)
- AIDO.DNA_Embeddings.plus.euclidean_distance (TraitGym)
- AIDO.DNA_LLR.minus.score (TraitGym)
- AIDO.DNA.LogisticRegression.chrom (TraitGym)
- Borzoi_L2_L2.plus.all (TraitGym)
- Borzoi.LogisticRegression.chrom (TraitGym)
- CADD.LogisticRegression.chrom (TraitGym)
- CADD.plus.RawScore (TraitGym)
- CADD+Borzoi.LogisticRegression.chrom (TraitGym)
- CADD+GPN-MSA.LogisticRegression.chrom (TraitGym)
- CADD+GPN-MSA+Borzoi.LogisticRegression.chrom (TraitGym)
- Caduceus_absLLR.plus.score (TraitGym)
- Caduceus_Embeddings.minus.inner_product (TraitGym)
- Caduceus_Embeddings.plus.cosine_distance (TraitGym)
- Caduceus_Embeddings.plus.euclidean_distance (TraitGym)
- Caduceus_InnerProduct.minus.score (TraitGym)
- Caduceus_LLR.minus.score (TraitGym)
- Caduceus.LogisticRegression.chrom (TraitGym)
- Enformer_L2_L2.plus.all (TraitGym)
- Enformer.LogisticRegression.chrom (TraitGym)
- evo2_1b_base_absLLR.plus.score (TraitGym)
- evo2_1b_base_Embeddings.minus.inner_product (TraitGym)
- evo2_1b_base_Embeddings.plus.cosine_distance (TraitGym)
Benchmarks (1)
Protocols (4)
- TraitGym Complex traits, linear-probing, AUPRC by chromosome weighted average
- TraitGym Complex traits, zero-shot, AUPRC by chromosome weighted average
- TraitGym Mendelian traits, linear-probing, AUPRC by chromosome weighted average
- TraitGym Mendelian traits, zero-shot, AUPRC by chromosome weighted average
Datasets (2)
Evaluations (156)
- AIDO.DNA_absLLR.plus.score on TraitGym complex_traits_matched_9
- AIDO.DNA_absLLR.plus.score on TraitGym mendelian_traits_matched_9
- AIDO.DNA_Embeddings.minus.inner_product on TraitGym complex_traits_matched_9
- AIDO.DNA_Embeddings.minus.inner_product on TraitGym mendelian_traits_matched_9
- AIDO.DNA_Embeddings.plus.cosine_distance on TraitGym complex_traits_matched_9
- AIDO.DNA_Embeddings.plus.cosine_distance on TraitGym mendelian_traits_matched_9
- AIDO.DNA_Embeddings.plus.euclidean_distance on TraitGym complex_traits_matched_9
- AIDO.DNA_Embeddings.plus.euclidean_distance on TraitGym mendelian_traits_matched_9
- AIDO.DNA_LLR.minus.score on TraitGym complex_traits_matched_9
- AIDO.DNA_LLR.minus.score on TraitGym mendelian_traits_matched_9
- AIDO.DNA.LogisticRegression.chrom on TraitGym complex_traits_matched_9
- AIDO.DNA.LogisticRegression.chrom on TraitGym mendelian_traits_matched_9
- Borzoi_L2_L2.plus.all on TraitGym complex_traits_matched_9
- Borzoi_L2_L2.plus.all on TraitGym mendelian_traits_matched_9
- Borzoi.LogisticRegression.chrom on TraitGym complex_traits_matched_9
- Borzoi.LogisticRegression.chrom on TraitGym mendelian_traits_matched_9
- CADD.LogisticRegression.chrom on TraitGym complex_traits_matched_9
- CADD.LogisticRegression.chrom on TraitGym mendelian_traits_matched_9
- CADD.plus.RawScore on TraitGym complex_traits_matched_9
- CADD.plus.RawScore on TraitGym mendelian_traits_matched_9
- CADD+Borzoi.LogisticRegression.chrom on TraitGym complex_traits_matched_9
- CADD+Borzoi.LogisticRegression.chrom on TraitGym mendelian_traits_matched_9
- CADD+GPN-MSA.LogisticRegression.chrom on TraitGym complex_traits_matched_9
- CADD+GPN-MSA.LogisticRegression.chrom on TraitGym mendelian_traits_matched_9
- CADD+GPN-MSA+Borzoi.LogisticRegression.chrom on TraitGym complex_traits_matched_9
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.
24 evidence rows matching the loaded filters
| Property and statement | Original source and location | Review and provenance |
|---|---|---|
| attributes.artifact_sha256 44dfedc00ac5c7918b188af2a5a200f08da3b641f73d7d5327e26f94a7d0372e Source metadata | TraitGym official metrics: AUPRC by chromosome, weighted average (Hugging Face dataset songlab/TraitGym) No field-specific location recorded Version: Hugging Face dataset revision 1fde19555fe8c0a55b1382bdf4c6f7082209f566 (last modified 2025-03-25); 156 metric CSVs under {dataset}/AUPRC_by_chrom_weighted_average/all/ | catalogued No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: SHA-256 of a JSON bundle listing every retrieved CSV with its path, its own SHA-256 and its bytes (artifacts/traitgym-metrics-bundle.json.gz) |
| Artifact url https://huggingface.co/datasets/songlab/TraitGym/tree/1fde19555fe8c0a55b1382bdf4c6f7082209f566 Source metadata | TraitGym official metrics: AUPRC by chromosome, weighted average (Hugging Face dataset songlab/TraitGym) No field-specific location recorded Version: Hugging Face dataset revision 1fde19555fe8c0a55b1382bdf4c6f7082209f566 (last modified 2025-03-25); 156 metric CSVs under {dataset}/AUPRC_by_chrom_weighted_average/all/ | catalogued No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: SHA-256 of a JSON bundle listing every retrieved CSV with its path, its own SHA-256 and its bytes (artifacts/traitgym-metrics-bundle.json.gz) |
| Hash scope SHA-256 of a JSON bundle listing every retrieved CSV with its path, its own SHA-256 and its bytes (artifacts/traitgym-metrics-bundle.json.gz) Source metadata | TraitGym official metrics: AUPRC by chromosome, weighted average (Hugging Face dataset songlab/TraitGym) No field-specific location recorded Version: Hugging Face dataset revision 1fde19555fe8c0a55b1382bdf4c6f7082209f566 (last modified 2025-03-25); 156 metric CSVs under {dataset}/AUPRC_by_chrom_weighted_average/all/ | catalogued No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: SHA-256 of a JSON bundle listing every retrieved CSV with its path, its own SHA-256 and its bytes (artifacts/traitgym-metrics-bundle.json.gz) |
| Licence MIT Source metadata | TraitGym official metrics: AUPRC by chromosome, weighted average (Hugging Face dataset songlab/TraitGym) No field-specific location recorded Version: Hugging Face dataset revision 1fde19555fe8c0a55b1382bdf4c6f7082209f566 (last modified 2025-03-25); 156 metric CSVs under {dataset}/AUPRC_by_chrom_weighted_average/all/ | catalogued No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: SHA-256 of a JSON bundle listing every retrieved CSV with its path, its own SHA-256 and its bytes (artifacts/traitgym-metrics-bundle.json.gz) |
Limitations3 values
| TraitGym official metrics: AUPRC by chromosome, weighted average (Hugging Face dataset songlab/TraitGym) No field-specific location recorded Version: Hugging Face dataset revision 1fde19555fe8c0a55b1382bdf4c6f7082209f566 (last modified 2025-03-25); 156 metric CSVs under {dataset}/AUPRC_by_chrom_weighted_average/all/ | catalogued No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: SHA-256 of a JSON bundle listing every retrieved CSV with its path, its own SHA-256 and its bytes (artifacts/traitgym-metrics-bundle.json.gz) |
| Media type application/json Source metadata | TraitGym official metrics: AUPRC by chromosome, weighted average (Hugging Face dataset songlab/TraitGym) No field-specific location recorded Version: Hugging Face dataset revision 1fde19555fe8c0a55b1382bdf4c6f7082209f566 (last modified 2025-03-25); 156 metric CSVs under {dataset}/AUPRC_by_chrom_weighted_average/all/ | catalogued No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: SHA-256 of a JSON bundle listing every retrieved CSV with its path, its own SHA-256 and its bytes (artifacts/traitgym-metrics-bundle.json.gz) |
| Publication status official_project_source Source metadata | TraitGym official metrics: AUPRC by chromosome, weighted average (Hugging Face dataset songlab/TraitGym) No field-specific location recorded Version: Hugging Face dataset revision 1fde19555fe8c0a55b1382bdf4c6f7082209f566 (last modified 2025-03-25); 156 metric CSVs under {dataset}/AUPRC_by_chrom_weighted_average/all/ | catalogued No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: SHA-256 of a JSON bundle listing every retrieved CSV with its path, its own SHA-256 and its bytes (artifacts/traitgym-metrics-bundle.json.gz) |
| Retrieval note 156 CSVs downloaded 01:39-01:40 UTC from the resolve endpoint at the pinned revision; time is the last download Source metadata | TraitGym official metrics: AUPRC by chromosome, weighted average (Hugging Face dataset songlab/TraitGym) No field-specific location recorded Version: Hugging Face dataset revision 1fde19555fe8c0a55b1382bdf4c6f7082209f566 (last modified 2025-03-25); 156 metric CSVs under {dataset}/AUPRC_by_chrom_weighted_average/all/ | catalogued No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: SHA-256 of a JSON bundle listing every retrieved CSV with its path, its own SHA-256 and its bytes (artifacts/traitgym-metrics-bundle.json.gz) |
| Retrieved at 2026-10-11T01:40:33Z Source metadata | TraitGym official metrics: AUPRC by chromosome, weighted average (Hugging Face dataset songlab/TraitGym) No field-specific location recorded Version: Hugging Face dataset revision 1fde19555fe8c0a55b1382bdf4c6f7082209f566 (last modified 2025-03-25); 156 metric CSVs under {dataset}/AUPRC_by_chrom_weighted_average/all/ | catalogued No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: SHA-256 of a JSON bundle listing every retrieved CSV with its path, its own SHA-256 and its bytes (artifacts/traitgym-metrics-bundle.json.gz) |
| Review: date 2026-10-11 Source metadata | TraitGym official metrics: AUPRC by chromosome, weighted average (Hugging Face dataset songlab/TraitGym) No field-specific location recorded Version: Hugging Face dataset revision 1fde19555fe8c0a55b1382bdf4c6f7082209f566 (last modified 2025-03-25); 156 metric CSVs under {dataset}/AUPRC_by_chrom_weighted_average/all/ | catalogued No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: SHA-256 of a JSON bundle listing every retrieved CSV with its path, its own SHA-256 and its bytes (artifacts/traitgym-metrics-bundle.json.gz) |
Sources and history
Release 2026-10-22-1b7cf027e4f6 · Record review: source checked
Primary source retrieved and hashed for the 2026-10-11 genomics literature pass.
Technical metadata and extraction receipts
Stable ID: lit-genomics-20261011-traitgym-source-hf-metrics
- areas
- dna-genomes
- contexts
- research
- url
- https://huggingface.co/datasets/songlab/TraitGym
- artifact url
- https://huggingface.co/datasets/songlab/TraitGym/tree/1fde19555fe8c0a55b1382bdf4c6f7082209f566
- version
- Hugging Face dataset revision 1fde19555fe8c0a55b1382bdf4c6f7082209f566 (last modified 2025-03-25); 156 metric CSVs under {dataset}/AUPRC_by_chrom_weighted_average/all/
- retrieved at
- 2026-10-11T01:40:33Z
- retrieval note
- 156 CSVs downloaded 01:39-01:40 UTC from the resolve endpoint at the pinned revision; time is the last download
- artifact sha256
- 44dfedc00ac5c7918b188af2a5a200f08da3b641f73d7d5327e26f94a7d0372e
- publication status
- official_project_source
- licence
- MIT
- hash scope
- SHA-256 of a JSON bundle listing every retrieved CSV with its path, its own SHA-256 and its bytes (artifacts/traitgym-metrics-bundle.json.gz)
- media type
- application/json
- limitations
- Official benchmark repository by the TraitGym authors, who also developed GPN-MSA and GPN-Promoter; those rows are author_reported.; Benchmark paper: Benegas, Eraslan and Song, bioRxiv 10.1101/2025.02.11.637758 v2 (2025-03-04, CC BY-NC-ND), outside the search window; its Figure 2 plots these metrics. The paper's Table S8 prints rounded zero-shot AUPRCs on a related but unweighted basis and was not extracted.; Hugging Face datasets are mutable; the revision hash pins this retrieval.
- review
- method: source-hash-verification; method note: Artifact re-retrieved or unpacked and SHA-256 matched.; reviewer: claude; reviewer note: Claude review agent reviewer-gen-3, independent of the extractor lit-genomics; no human review claimed; date: 2026-10-11