HEST-Benchmark LYMPH_IDC: Gene expression prediction from histology, Lymph node metastasis of invasive ductal carcinoma
Gene expression prediction from histology, Lymph node metastasis of invasive ductal carcinoma. Scored with Pearson correlation on HEST-Benchmark LYMPH_IDC. Random Forest regression with 70 trees over frozen patch features, averaged over folds or patients.
Overview
Gene expression prediction from histology, Lymph node metastasis of invasive ductal carcinoma. Scored with Pearson correlation on HEST-Benchmark LYMPH_IDC. 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.
Evaluation design
Benchmarks bring together tasks and protocols. A task describes the biological question; a protocol defines a particular test.
Benchmarks
These source-backed links do not make different protocols or scores interchangeable.
Recorded evaluations
Each evaluation records what was tested and under which conditions.
- Ciga on HEST-Benchmark LYMPH_IDC: Gene expression prediction from histology, Lymph node metastasis of invasive ductal carcinoma
- CONCH on HEST-Benchmark LYMPH_IDC: Gene expression prediction from histology, Lymph node metastasis of invasive ductal carcinoma
- CTransPath on HEST-Benchmark LYMPH_IDC: Gene expression prediction from histology, Lymph node metastasis of invasive ductal carcinoma
- GigaPath on HEST-Benchmark LYMPH_IDC: Gene expression prediction from histology, Lymph node metastasis of invasive ductal carcinoma
- KimiaNet on HEST-Benchmark LYMPH_IDC: Gene expression prediction from histology, Lymph node metastasis of invasive ductal carcinoma
- Phikon on HEST-Benchmark LYMPH_IDC: Gene expression prediction from histology, Lymph node metastasis of invasive ductal carcinoma
- PLIP on HEST-Benchmark LYMPH_IDC: Gene expression prediction from histology, Lymph node metastasis of invasive ductal carcinoma
- Remedis on HEST-Benchmark LYMPH_IDC: Gene expression prediction from histology, Lymph node metastasis of invasive ductal carcinoma
- ResNet50 on HEST-Benchmark LYMPH_IDC: Gene expression prediction from histology, Lymph node metastasis of invasive ductal carcinoma
- UNI on HEST-Benchmark LYMPH_IDC: Gene expression prediction from histology, Lymph node metastasis of invasive ductal carcinoma
Run instructions
No runnable recipe has been reviewed for this task. Dataset access, model requirements, licences and compute requirements must be checked against its sources before execution.
A task describes a biological question. Choose a linked protocol to obtain concrete split and scoring instructions.
Published comparisons
Explore the results reported under one evaluation protocol. Each figure keeps its source, dataset and metric together; it is not a ranking across studies. The pooled view gathers every source table that reports the same metric and names what it does not hold constant.
HEST-Benchmark LYMPH_IDC: Gene expression prediction from histology, Lymph node metastasis of invasive ductal carcinoma
pearson_r (correlation) · Higher values are better for this metric.
Every method HEST-Benchmark reports on Gene expression prediction from histology, Lymph node metastasis of invasive ductal carcinoma, scored with Pearson correlation on HEST-Benchmark LYMPH_IDC.
Evaluation protocol · HEST-Benchmark LYMPH_IDC (HEST-Benchmark split)
- ResNet50 · Configuration · Author-reported evaluation0.205 ±0.05
- KimiaNet · Configuration · Author-reported evaluation0.206 ±0.06
- Ciga · Configuration · Author-reported evaluation0.218 ±0.07
- CTransPath · Configuration · Author-reported evaluation0.238 ±0.06
- Remedis · Configuration · Author-reported evaluation0.243 ±0.06
- Phikon · Configuration · Author-reported evaluation0.243 ±0.06
- PLIP · Configuration · Author-reported evaluation0.229 ±0.06
- UNI · Configuration · Author-reported evaluation0.234 ±0.05
- CONCH · Configuration · Author-reported evaluation0.249 ±0.06
- GigaPath · Configuration · Author-reported evaluation0.248 ±0.05
Source order is preserved. Plotted marks show point estimates; uncertainty, where reported, is retained in the printed values and table. Differences do not establish statistical significance.
HEST-1k: A Dataset for Spatial Transcriptomics and Histology Image Analysis · Table 1, row(LYMPH_IDC)Values, uncertainty and evidence
| Tested entity | Printed value | Uncertainty | Evidence |
|---|---|---|---|
| ResNet50 · Configuration | 0.205 ±0.05 correlation | type: standard_deviation; value: 0.05 | Author-reported evaluation · source checkedHEST-1k: A Dataset for Spatial Transcriptomics and Histology Image Analysis · Table 1, row(LYMPH_IDC), column(ResNet50) |
| KimiaNet · Configuration | 0.206 ±0.06 correlation | type: standard_deviation; value: 0.06 | Author-reported evaluation · source checkedHEST-1k: A Dataset for Spatial Transcriptomics and Histology Image Analysis · Table 1, row(LYMPH_IDC), column(KimiaNet) |
| Ciga · Configuration | 0.218 ±0.07 correlation | type: standard_deviation; value: 0.07 | Author-reported evaluation · source checkedHEST-1k: A Dataset for Spatial Transcriptomics and Histology Image Analysis · Table 1, row(LYMPH_IDC), column(Ciga) |
| CTransPath · Configuration | 0.238 ±0.06 correlation | type: standard_deviation; value: 0.06 | Author-reported evaluation · source checkedHEST-1k: A Dataset for Spatial Transcriptomics and Histology Image Analysis · Table 1, row(LYMPH_IDC), column(CTransPath) |
| Remedis · Configuration | 0.243 ±0.06 correlation | type: standard_deviation; value: 0.06 | Author-reported evaluation · source checkedHEST-1k: A Dataset for Spatial Transcriptomics and Histology Image Analysis · Table 1, row(LYMPH_IDC), column(Remedis) |
| Phikon · Configuration | 0.243 ±0.06 correlation | type: standard_deviation; value: 0.06 | Author-reported evaluation · source checkedHEST-1k: A Dataset for Spatial Transcriptomics and Histology Image Analysis · Table 1, row(LYMPH_IDC), column(Phikon) |
| PLIP · Configuration | 0.229 ±0.06 correlation | type: standard_deviation; value: 0.06 | Author-reported evaluation · source checkedHEST-1k: A Dataset for Spatial Transcriptomics and Histology Image Analysis · Table 1, row(LYMPH_IDC), column(PLIP) |
| UNI · Configuration | 0.234 ±0.05 correlation | type: standard_deviation; value: 0.05 | Author-reported evaluation · source checkedHEST-1k: A Dataset for Spatial Transcriptomics and Histology Image Analysis · Table 1, row(LYMPH_IDC), column(UNI) |
| CONCH · Configuration | 0.249 ±0.06 correlation | type: standard_deviation; value: 0.06 | Author-reported evaluation · source checkedHEST-1k: A Dataset for Spatial Transcriptomics and Histology Image Analysis · Table 1, row(LYMPH_IDC), column(CONCH) |
| GigaPath · Configuration | 0.248 ±0.05 correlation | type: standard_deviation; value: 0.05 | Author-reported evaluation · source checkedHEST-1k: A Dataset for Spatial Transcriptomics and Histology Image Analysis · Table 1, row(LYMPH_IDC), column(GigaPath) |
Scope and limitations
- 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.
Source transcription and grouping reviewed by automated source review on 2026-09-18. These experiments were not independently reproduced by rewire.
Tested entities and results
Release 2026-09-17-134cd1815de8 · 10 evaluations · 10 metric rows. 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 |
|---|---|---|
| Ciga on HEST-Benchmark LYMPH_IDC: Gene expression prediction from histology, Lymph node metastasis of invasive ductal carcinoma Configuration: CigaTask: HEST-Benchmark LYMPH_IDC: Gene expression prediction from histology, Lymph node metastasis of invasive ductal carcinomaDataset subset: HEST-Benchmark LYMPH_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 | ||
| 0.218 ±0.07 pearson_r Unit: correlation · Direction: higher | Uncertainty: type: standard deviation; value: 0.07 Scored: Not reported · Eligible: Not reported | source checkedHEST-1k: A Dataset for Spatial Transcriptomics and Histology Image Analysis · Table 1, row(LYMPH_IDC), column(Ciga) Source checking is not independent reproduction. |
| CONCH on HEST-Benchmark LYMPH_IDC: Gene expression prediction from histology, Lymph node metastasis of invasive ductal carcinoma Configuration: CONCHTask: HEST-Benchmark LYMPH_IDC: Gene expression prediction from histology, Lymph node metastasis of invasive ductal carcinomaDataset subset: HEST-Benchmark LYMPH_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 | ||
| 0.249 ±0.06 pearson_r Unit: correlation · Direction: higher | Uncertainty: type: standard deviation; value: 0.06 Scored: Not reported · Eligible: Not reported | source checkedHEST-1k: A Dataset for Spatial Transcriptomics and Histology Image Analysis · Table 1, row(LYMPH_IDC), column(CONCH) Source checking is not independent reproduction. |
| CTransPath on HEST-Benchmark LYMPH_IDC: Gene expression prediction from histology, Lymph node metastasis of invasive ductal carcinoma Configuration: CTransPathTask: HEST-Benchmark LYMPH_IDC: Gene expression prediction from histology, Lymph node metastasis of invasive ductal carcinomaDataset subset: HEST-Benchmark LYMPH_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 | ||
| 0.238 ±0.06 pearson_r Unit: correlation · Direction: higher | Uncertainty: type: standard deviation; value: 0.06 Scored: Not reported · Eligible: Not reported | source checkedHEST-1k: A Dataset for Spatial Transcriptomics and Histology Image Analysis · Table 1, row(LYMPH_IDC), column(CTransPath) Source checking is not independent reproduction. |
| GigaPath on HEST-Benchmark LYMPH_IDC: Gene expression prediction from histology, Lymph node metastasis of invasive ductal carcinoma Configuration: GigaPathTask: HEST-Benchmark LYMPH_IDC: Gene expression prediction from histology, Lymph node metastasis of invasive ductal carcinomaDataset subset: HEST-Benchmark LYMPH_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 | ||
| 0.248 ±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(LYMPH_IDC), column(GigaPath) Source checking is not independent reproduction. |
| KimiaNet on HEST-Benchmark LYMPH_IDC: Gene expression prediction from histology, Lymph node metastasis of invasive ductal carcinoma Configuration: KimiaNetTask: HEST-Benchmark LYMPH_IDC: Gene expression prediction from histology, Lymph node metastasis of invasive ductal carcinomaDataset subset: HEST-Benchmark LYMPH_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 | ||
| 0.206 ±0.06 pearson_r Unit: correlation · Direction: higher | Uncertainty: type: standard deviation; value: 0.06 Scored: Not reported · Eligible: Not reported | source checkedHEST-1k: A Dataset for Spatial Transcriptomics and Histology Image Analysis · Table 1, row(LYMPH_IDC), column(KimiaNet) Source checking is not independent reproduction. |
| Phikon on HEST-Benchmark LYMPH_IDC: Gene expression prediction from histology, Lymph node metastasis of invasive ductal carcinoma Configuration: PhikonTask: HEST-Benchmark LYMPH_IDC: Gene expression prediction from histology, Lymph node metastasis of invasive ductal carcinomaDataset subset: HEST-Benchmark LYMPH_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 | ||
| 0.243 ±0.06 pearson_r Unit: correlation · Direction: higher | Uncertainty: type: standard deviation; value: 0.06 Scored: Not reported · Eligible: Not reported | source checkedHEST-1k: A Dataset for Spatial Transcriptomics and Histology Image Analysis · Table 1, row(LYMPH_IDC), column(Phikon) Source checking is not independent reproduction. |
| PLIP on HEST-Benchmark LYMPH_IDC: Gene expression prediction from histology, Lymph node metastasis of invasive ductal carcinoma Configuration: PLIPTask: HEST-Benchmark LYMPH_IDC: Gene expression prediction from histology, Lymph node metastasis of invasive ductal carcinomaDataset subset: HEST-Benchmark LYMPH_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 | ||
| 0.229 ±0.06 pearson_r Unit: correlation · Direction: higher | Uncertainty: type: standard deviation; value: 0.06 Scored: Not reported · Eligible: Not reported | source checkedHEST-1k: A Dataset for Spatial Transcriptomics and Histology Image Analysis · Table 1, row(LYMPH_IDC), column(PLIP) Source checking is not independent reproduction. |
| Remedis on HEST-Benchmark LYMPH_IDC: Gene expression prediction from histology, Lymph node metastasis of invasive ductal carcinoma Configuration: RemedisTask: HEST-Benchmark LYMPH_IDC: Gene expression prediction from histology, Lymph node metastasis of invasive ductal carcinomaDataset subset: HEST-Benchmark LYMPH_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 | ||
| 0.243 ±0.06 pearson_r Unit: correlation · Direction: higher | Uncertainty: type: standard deviation; value: 0.06 Scored: Not reported · Eligible: Not reported | source checkedHEST-1k: A Dataset for Spatial Transcriptomics and Histology Image Analysis · Table 1, row(LYMPH_IDC), column(Remedis) Source checking is not independent reproduction. |
| ResNet50 on HEST-Benchmark LYMPH_IDC: Gene expression prediction from histology, Lymph node metastasis of invasive ductal carcinoma Configuration: ResNet50Task: HEST-Benchmark LYMPH_IDC: Gene expression prediction from histology, Lymph node metastasis of invasive ductal carcinomaDataset subset: HEST-Benchmark LYMPH_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 | ||
| 0.205 ±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(LYMPH_IDC), column(ResNet50) Source checking is not independent reproduction. |
| UNI on HEST-Benchmark LYMPH_IDC: Gene expression prediction from histology, Lymph node metastasis of invasive ductal carcinoma Configuration: UNITask: HEST-Benchmark LYMPH_IDC: Gene expression prediction from histology, Lymph node metastasis of invasive ductal carcinomaDataset subset: HEST-Benchmark LYMPH_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 | ||
| 0.234 ±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(LYMPH_IDC), column(UNI) 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.
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(LYMPH_IDC) 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-lymph-idc 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-task-lymph-idc
- areas
- cells-tissues
- tasks
- Gene expression prediction from histology, Lymph node metastasis of invasive ductal carcinoma
- metric
- Pearson correlation
- metric direction
- higher
- dataset
- HEST-Benchmark LYMPH_IDC
- protocol
- Random Forest regression with 70 trees over frozen patch features, averaged over folds or patients.
- source locator
- Table 1, row(LYMPH_IDC)
- comparison panels
- id: hest-panel-lymph-idc; title: HEST-Benchmark LYMPH_IDC: Gene expression prediction from histology, Lymph node metastasis of invasive ductal carcinoma; protocol id: hest-task-lymph-idc; dataset id: hest-dataset-hest-benchmark-lymph-idc; metric: pearson_r; unit: correlation; direction: higher; result ids: hest-result-resnet50-lymph-idc-pearson-r; hest-result-kimianet-lymph-idc-pearson-r; hest-result-ciga-lymph-idc-pearson-r; hest-result-ctranspath-lymph-idc-pearson-r; hest-result-remedis-lymph-idc-pearson-r; hest-result-phikon-lymph-idc-pearson-r; hest-result-plip-lymph-idc-pearson-r; hest-result-uni-lymph-idc-pearson-r; hest-result-conch-lymph-idc-pearson-r; hest-result-gigapath-lymph-idc-pearson-r; source ids: evidence-expansion-p2-hest-cached-636099a73dee; source locator: Table 1, row(LYMPH_IDC); context: Every method HEST-Benchmark reports on Gene expression prediction from histology, Lymph node metastasis of invasive ductal carcinoma, scored with Pearson correlation on HEST-Benchmark LYMPH_IDC.; 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 LYMPH_IDC: part of discovery-benchmark-hest-benchmark
- benchmark: Ciga on HEST-Benchmark LYMPH_IDC: Gene expression prediction from histology, Lymph node metastasis of invasive ductal carcinoma
- benchmark: CONCH on HEST-Benchmark LYMPH_IDC: Gene expression prediction from histology, Lymph node metastasis of invasive ductal carcinoma
- benchmark: CTransPath on HEST-Benchmark LYMPH_IDC: Gene expression prediction from histology, Lymph node metastasis of invasive ductal carcinoma
- benchmark: GigaPath on HEST-Benchmark LYMPH_IDC: Gene expression prediction from histology, Lymph node metastasis of invasive ductal carcinoma
- benchmark: KimiaNet on HEST-Benchmark LYMPH_IDC: Gene expression prediction from histology, Lymph node metastasis of invasive ductal carcinoma
- benchmark: Phikon on HEST-Benchmark LYMPH_IDC: Gene expression prediction from histology, Lymph node metastasis of invasive ductal carcinoma
- benchmark: PLIP on HEST-Benchmark LYMPH_IDC: Gene expression prediction from histology, Lymph node metastasis of invasive ductal carcinoma
- benchmark: Remedis on HEST-Benchmark LYMPH_IDC: Gene expression prediction from histology, Lymph node metastasis of invasive ductal carcinoma
- benchmark: ResNet50 on HEST-Benchmark LYMPH_IDC: Gene expression prediction from histology, Lymph node metastasis of invasive ductal carcinoma
- benchmark: UNI on HEST-Benchmark LYMPH_IDC: Gene expression prediction from histology, Lymph node metastasis of invasive ductal carcinoma