GigaPath on HEST-Benchmark IDC: Gene expression prediction from histology, Invasive ductal carcinoma
HEST-Benchmark evaluation of GigaPath on Gene expression prediction from histology, Invasive ductal carcinoma, scored with Pearson correlation.
Methods and reproduction
HEST-Benchmark evaluation of GigaPath on Gene expression prediction from histology, Invasive ductal carcinoma, scored with Pearson correlation.
- task
- HEST-Benchmark IDC: Gene expression prediction from histology, Invasive ductal carcinoma
- configuration
- GigaPath
- dataset subset
- HEST-Benchmark IDC (HEST-Benchmark split)
- Split
- Not reported
- Adaptation
- Not reported
- Scoring implementation
- Pearson correlation
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.
Evaluation procedure
Random Forest regression with 70 trees over frozen patch features, averaged over folds or patients.
- Configuration
- GigaPath
- Task
- HEST-Benchmark IDC: Gene expression prediction from histology, Invasive ductal carcinoma
- Dataset subset
- HEST-Benchmark IDC (HEST-Benchmark split)
- origin
- Author-reported evaluation
- configuration
- Not reported
- protocol id
- hest-task-idc
- metric implementation
- Pearson correlation
Metadata review: source checked. Unreported conditions prevent automatic comparisons.
Evaluation results
Release 2026-09-17-134cd1815de8 · 1 evaluation · 1 metric row. Different protocols are not a single leaderboard. Where several source tables report the same metric, the published comparisons above offer a pooled view that names what it does not hold constant.
| Metric and finding | Coverage and uncertainty | Evidence |
|---|---|---|
| GigaPath on HEST-Benchmark IDC: Gene expression prediction from histology, Invasive ductal carcinoma Configuration: GigaPathTask: HEST-Benchmark IDC: Gene expression prediction from histology, Invasive ductal carcinomaDataset subset: HEST-Benchmark IDC (HEST-Benchmark split) Random Forest regression with 70 trees over frozen patch features, averaged over folds or patients. Author-reported evaluation · Evaluation metadata: source checked | ||
| 0.492 ±0.05 pearson_r Unit: correlation · Direction: higher | Uncertainty: type: standard deviation; value: 0.05 Scored: Not reported · Eligible: Not reported | source checkedHEST-1k: A Dataset for Spatial Transcriptomics and Histology Image Analysis · Table 1, row(IDC), column(GigaPath) Source checking is not 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.
10 evidence rows matching the loaded filters
| Property and statement | Original source and location | Review and provenance |
|---|---|---|
| attributes.comparison.metric_implementation Pearson correlation Context-only references | HEST-1k: A Dataset for Spatial Transcriptomics and Histology Image Analysis Table 1, row(IDC), column(GigaPath) Version: Version pinned by URL and artifact SHA256 when available | not individually reviewed No individual claim review recorded author reported Audit detailsField: Source artifact SHA-256: Hash scope: Exact retrieved primary paper artifact bytes. |
| attributes.comparison.protocol_id hest-task-idc Context-only references | HEST-1k: A Dataset for Spatial Transcriptomics and Histology Image Analysis Table 1, row(IDC), column(GigaPath) Version: Version pinned by URL and artifact SHA256 when available | not individually reviewed No individual claim review recorded author reported Audit detailsField: Source artifact SHA-256: Hash scope: Exact retrieved primary paper artifact bytes. |
| attributes.origin author_reported Context-only references | HEST-1k: A Dataset for Spatial Transcriptomics and Histology Image Analysis Table 1, row(IDC), column(GigaPath) Version: Version pinned by URL and artifact SHA256 when available | not individually reviewed No individual claim review recorded author reported Audit detailsField: Source artifact SHA-256: Hash scope: Exact retrieved primary paper artifact bytes. |
| attributes.protocol Random Forest regression with 70 trees over frozen patch features, averaged over folds or patients. Context-only references | HEST-1k: A Dataset for Spatial Transcriptomics and Histology Image Analysis Table 1, row(IDC), column(GigaPath) Version: Version pinned by URL and artifact SHA256 when available | not individually reviewed No individual claim review recorded author reported Audit detailsField: Source artifact SHA-256: Hash scope: Exact retrieved primary paper artifact bytes. |
| attributes.source_locator Table 1, row(IDC), column(GigaPath) Context-only references | HEST-1k: A Dataset for Spatial Transcriptomics and Histology Image Analysis Table 1, row(IDC), column(GigaPath) Version: Version pinned by URL and artifact SHA256 when available | not individually reviewed No individual claim review recorded author reported Audit detailsField: Source artifact SHA-256: Hash scope: Exact retrieved primary paper artifact bytes. |
| description HEST-Benchmark evaluation of GigaPath on Gene expression prediction from histology, Invasive ductal carcinoma, scored with Pearson correlation. Context-only references | HEST-1k: A Dataset for Spatial Transcriptomics and Histology Image Analysis Table 1, row(IDC), column(GigaPath) Version: Version pinned by URL and artifact SHA256 when available | not individually reviewed No individual claim review recorded author reported Audit detailsField: Source artifact SHA-256: Hash scope: Exact retrieved primary paper artifact bytes. |
| Relationship: benchmark hest-task-idc Context-only references | HEST-1k: A Dataset for Spatial Transcriptomics and Histology Image Analysis Table 1, row(IDC), column(GigaPath) Version: Version pinned by URL and artifact SHA256 when available | not individually reviewed No individual claim review recorded author reported Audit detailsField: Source artifact SHA-256: Hash scope: Exact retrieved primary paper artifact bytes. |
| Relationship: dataset hest-dataset-hest-benchmark-idc Context-only references | HEST-1k: A Dataset for Spatial Transcriptomics and Histology Image Analysis Table 1, row(IDC), column(GigaPath) Version: Version pinned by URL and artifact SHA256 when available | not individually reviewed No individual claim review recorded author reported Audit detailsField: Source artifact SHA-256: Hash scope: Exact retrieved primary paper artifact bytes. |
| Relationship: model hest-method-gigapath Context-only references | HEST-1k: A Dataset for Spatial Transcriptomics and Histology Image Analysis Table 1, row(IDC), column(GigaPath) Version: Version pinned by URL and artifact SHA256 when available | not individually reviewed No individual claim review recorded author reported Audit detailsField: Source artifact SHA-256: Hash scope: Exact retrieved primary paper artifact bytes. |
| name GigaPath on HEST-Benchmark IDC: Gene expression prediction from histology, Invasive ductal carcinoma Context-only references | HEST-1k: A Dataset for Spatial Transcriptomics and Histology Image Analysis Table 1, row(IDC), column(GigaPath) Version: Version pinned by URL and artifact SHA256 when available | not individually reviewed No individual claim review recorded author reported Audit detailsField: Source artifact SHA-256: Hash scope: Exact retrieved primary paper artifact bytes. |
Sources and history
Release 2026-09-17-134cd1815de8 · Record review: source checked
1 source records and release history
- HEST-1k: A Dataset for Spatial Transcriptomics and Histology Image Analysis · Original source · Version pinned by URL and artifact SHA256 when available
Technical metadata and extraction receipts
Stable ID: hest-evaluation-gigapath-idc
- areas
- cells-tissues
- tasks
- Gene expression prediction from histology, Invasive ductal carcinoma
- origin
- author_reported
- protocol
- Random Forest regression with 70 trees over frozen patch features, averaged over folds or patients.
- comparison
- protocol id: hest-task-idc; metric implementation: Pearson correlation
- missing metadata
- checkpoint revision: unreported; seeds: unreported; budget: unreported; split manifest: unextracted
- source locator
- Table 1, row(IDC), column(GigaPath)