HEST-Benchmark SKCM: Gene expression prediction from histology, Skin cutaneous melanoma
Gene expression prediction from histology, Skin cutaneous melanoma. Scored with Pearson correlation on HEST-Benchmark SKCM. Random Forest regression with 70 trees over frozen patch features, averaged over folds or patients.
Overview
Gene expression prediction from histology, Skin cutaneous melanoma. Scored with Pearson correlation on HEST-Benchmark SKCM. Random Forest regression with 70 trees over frozen patch features, averaged over folds or patients.
Consult the linked sources for architecture or protocol details. Missing evidence is not evidence of a missing capability.
Results
Each comparison retains its reviewed evaluation scope, dataset and metric. Results are shown without a pooled ranking.
HEST-Benchmark SKCM: Gene expression prediction from histology, Skin cutaneous melanoma
pearson_r (correlation) · Higher values are better.
HEST-Benchmark SKCM: Gene expression prediction from histology, Skin cutaneous melanoma · HEST-Benchmark SKCM (HEST-Benchmark split)
Evidence origin: Author-reported evaluation.
HEST-1k: A Dataset for Spatial Transcriptomics and Histology Image Analysis · Table 1, row(SKCM)- Every figure comes from the same Random Forest head over frozen features, so it measures the encoder, not a full prediction pipeline.
- Cohorts differ in size and difficulty, so a figure in one cohort is not comparable to a figure in another.
Comparison details and limitations
Every method HEST-Benchmark reports on Gene expression prediction from histology, Skin cutaneous melanoma, scored with Pearson correlation on HEST-Benchmark SKCM.
- Author-reported numbers, source checked but not independently reproduced.
Automated source review: 2026-09-18. Numerical source review does not establish independent reproduction.
Dots show point estimates. Whiskers show only explicitly defined uncertainty (standard deviation, standard error or a labelled interval); their definitions remain in Table. Unresolved uncertainty is not plotted. Differences do not establish statistical significance.
Showing 10 of 10 matching rows.
Methods and evaluation design
Procedure, tasks and evaluated configurations
Evaluation design
Benchmarks bring together tasks and protocols. A task describes the biological question; a protocol defines a particular test.
Benchmarks
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Recorded evaluations
Each evaluation records what was tested and under which conditions.
- SimCLR histology encoder + random forest (HEST; Ciga et al.) on HEST-Benchmark SKCM: Gene expression prediction from histology, Skin cutaneous melanoma
- CONCH on HEST-Benchmark SKCM: Gene expression prediction from histology, Skin cutaneous melanoma
- CTransPath on HEST-Benchmark SKCM: Gene expression prediction from histology, Skin cutaneous melanoma
- GigaPath on HEST-Benchmark SKCM: Gene expression prediction from histology, Skin cutaneous melanoma
- KimiaNet on HEST-Benchmark SKCM: Gene expression prediction from histology, Skin cutaneous melanoma
- Phikon on HEST-Benchmark SKCM: Gene expression prediction from histology, Skin cutaneous melanoma
- PLIP on HEST-Benchmark SKCM: Gene expression prediction from histology, Skin cutaneous melanoma
- Remedis on HEST-Benchmark SKCM: Gene expression prediction from histology, Skin cutaneous melanoma
- ResNet50 on HEST-Benchmark SKCM: Gene expression prediction from histology, Skin cutaneous melanoma
- UNI on HEST-Benchmark SKCM: Gene expression prediction from histology, Skin cutaneous melanoma
Run instructions
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Strengths, limitations and unresolved questions
Evidence
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Evidence table
Inspect claims, sources and review details
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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 |
|---|---|---|
| Relationship: part of discovery-benchmark-hest-benchmark Individual claims | HEST-1k: A Dataset for Spatial Transcriptomics and Histology Image Analysis Table 1, row(SKCM) Version: Version pinned by URL and artifact SHA256 when available | source checked automated source review · 2026-09-18 Audit detailsPrimary-source transcription with no human sign-off and no independent reproduction. Field: Claim: hest-association-skcm Source artifact SHA-256: Hash scope: Exact retrieved primary paper artifact bytes. |
Sources and history
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Release 2026-09-29-06401fd5b220 · 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-task-skcm
- areas
- cells-tissues
- tasks
- Gene expression prediction from histology, Skin cutaneous melanoma
- metric
- Pearson correlation
- metric direction
- higher
- dataset
- HEST-Benchmark SKCM
- protocol
- Random Forest regression with 70 trees over frozen patch features, averaged over folds or patients.
- source locator
- Table 1, row(SKCM)
- comparison panels
- id: hest-panel-skcm; title: HEST-Benchmark SKCM: Gene expression prediction from histology, Skin cutaneous melanoma; protocol id: hest-task-skcm; dataset id: hest-dataset-hest-benchmark-skcm; metric: pearson_r; unit: correlation; direction: higher; result ids: hest-result-resnet50-skcm-pearson-r; hest-result-kimianet-skcm-pearson-r; hest-result-ciga-skcm-pearson-r; hest-result-ctranspath-skcm-pearson-r; hest-result-remedis-skcm-pearson-r; hest-result-phikon-skcm-pearson-r; hest-result-plip-skcm-pearson-r; hest-result-uni-skcm-pearson-r; hest-result-conch-skcm-pearson-r; hest-result-gigapath-skcm-pearson-r; source ids: evidence-expansion-p2-hest-cached-636099a73dee; source locator: Table 1, row(SKCM); context: Every method HEST-Benchmark reports on Gene expression prediction from histology, Skin cutaneous melanoma, scored with Pearson correlation on HEST-Benchmark SKCM.; caveats: Author-reported numbers, source checked but not independently reproduced.; Every figure comes from the same Random Forest head over frozen features, so it measures the encoder, not a full prediction pipeline.; Cohorts differ in size and difficulty, so a figure in one cohort is not comparable to a figure in another.; review: method: automated_source_review; date: 2026-09-18
Related records
- part of: HEST-Benchmark
- subject: HEST-Benchmark SKCM: part of discovery-benchmark-hest-benchmark
- benchmark: SimCLR histology encoder + random forest (HEST; Ciga et al.) on HEST-Benchmark SKCM: Gene expression prediction from histology, Skin cutaneous melanoma
- benchmark: CONCH on HEST-Benchmark SKCM: Gene expression prediction from histology, Skin cutaneous melanoma
- benchmark: CTransPath on HEST-Benchmark SKCM: Gene expression prediction from histology, Skin cutaneous melanoma
- benchmark: GigaPath on HEST-Benchmark SKCM: Gene expression prediction from histology, Skin cutaneous melanoma
- benchmark: KimiaNet on HEST-Benchmark SKCM: Gene expression prediction from histology, Skin cutaneous melanoma
- benchmark: Phikon on HEST-Benchmark SKCM: Gene expression prediction from histology, Skin cutaneous melanoma
- benchmark: PLIP on HEST-Benchmark SKCM: Gene expression prediction from histology, Skin cutaneous melanoma
- benchmark: Remedis on HEST-Benchmark SKCM: Gene expression prediction from histology, Skin cutaneous melanoma
- benchmark: ResNet50 on HEST-Benchmark SKCM: Gene expression prediction from histology, Skin cutaneous melanoma
- benchmark: UNI on HEST-Benchmark SKCM: Gene expression prediction from histology, Skin cutaneous melanoma