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HEST-Benchmark

HEST-Benchmark tests gene-expression prediction from matched histology.

0 evaluations · 0 metric rows

At a glance

Explanatory profile: source reviewed · Automated source review, 2026-09-16. This does not change the review status of its results.

Data, procedure and scoring
PropertyDescription and evidence
Record typeSpatial transcriptomics benchmarkmahmoodlab/HEST official source · README: What does this repository provide?; HEST-Benchmark; Benchmarking your own model
InputsHistology regions paired with spatial gene-expression measurementsmahmoodlab/HEST official source · README: What does this repository provide?; HEST-Benchmark; Benchmarking your own model
Outputs and assessmentPrediction of selected gene-expression targetsmahmoodlab/HEST official source · README: What does this repository provide?; HEST-Benchmark; Benchmarking your own model
DatasetsNot extracted or verified for this record.
OrganismsNot extracted or verified for this record.
AssaysNot extracted or verified for this record.
SplitsNot extracted or verified for this record.
AdaptationNot extracted or verified for this record.
BaselinesNot extracted or verified for this record.

How it works

Procedure overview

Conceptual overview of the cited procedure; consult the pinned source for executable settings.

Procedure overviewMatched histology regions. Then: Image representation. Then: Expression prediction. Then: Compare spatial measurementsMatched histology regionsImage representationExpression predictionCompare spatial measurements
Read the diagram as text
  1. Matched histology regions
  2. Image representation
  3. Expression prediction
  4. Compare spatial measurements
mahmoodlab/HEST official source · README: What does this repository provide?; HEST-Benchmark; Benchmarking your own model

Procedure

Encode spatially matched image regions and use the benchmark procedure to predict measured gene expression. This molecular prediction task is distinct from generic medical-image classification.

mahmoodlab/HEST official source · README: What does this repository provide?; HEST-Benchmark; Benchmarking your own model

Tested models and results

Release 2026-09-16-d74d282221a9 · 0 evaluations · 0 metric rows. Different protocols are not a single leaderboard.

No evaluations linked in this release.

Strengths and limitations

Strengths supported by sources

  • Paired morphology and transcriptomics provide a measurable molecular endpoint.mahmoodlab/HEST official source · README: What does this repository provide?; HEST-Benchmark; Benchmarking your own model

Limitations and conditions

  • A correlation with expression does not establish causal regulation; tissue, assay and split definitions remain essential.mahmoodlab/HEST official source · README: What does this repository provide?; HEST-Benchmark; Benchmarking your own model
Profile review details

Primary-source description checked by an automated research assistant. This is a profile review, not an independent execution or numerical reproduction.

Stable record: discovery-benchmark-hest-benchmark

Applicable tests and references

Applicability is distinct from a completed evaluation.

Sources and history

Release 2026-09-16-d74d282221a9 · Record review: discovered

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Technical metadata and extraction receipts

Stable ID: discovery-benchmark-hest-benchmark

areas
spatial-omics
entity level
suite
missing metadata
dataset release: unextracted; metric implementation: unextracted; split manifest: unextracted; version: unextracted
scope note
Specialist molecular or omics evaluation; protocol details require review before numerical comparison.
task
Gene expression prediction from matched histology
version
Not reported
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