Histoboard - Pathology Foundation Model Benchmarks

STAMP Benchmark
pathology
H&E

Nature Biomedical Engineering benchmark evaluating 15 foundation models as feature extractors for weakly supervised computational pathology across morphology, biomarker, and prognosis tasks.

13 models evaluated

31 tasks

Organs:

lung

breast

colorectal

gastric

Detailed Results

Model	Average rank	Average metric	BERN STAD LAUREN AUROC	BERN STAD MSI AUROC	BERN STAD N STATUS AUROC	CPTAC BRCA ERBB2 AUROC	CPTAC BRCA ESR1 AUROC	CPTAC BRCA PGR AUROC	CPTAC BRCA PIK3CA AUROC	CPTAC CRC BRAF AUROC	CPTAC CRC KRAS AUROC	CPTAC CRC MSI AUROC	CPTAC CRC N STATUS AUROC	CPTAC CRC PIK3CA AUROC	CPTAC CRC Sidedness AUROC	CPTAC LUAD EGFR AUROC	CPTAC LUAD KRAS AUROC	CPTAC LUAD STK11 AUROC	CPTAC LUAD TP53 AUROC	DACHS CRC BRAF AUROC	DACHS CRC CIMP AUROC	DACHS CRC KRAS AUROC	DACHS CRC M STATUS AUROC	DACHS CRC MSI AUROC	DACHS CRC N STATUS AUROC	DACHS CRC Sidedness AUROC	IEO BRCA N STATUS AUROC	KIEL STAD EBV AUROC	KIEL STAD LAUREN AUROC	KIEL STAD M STATUS AUROC	KIEL STAD MSI AUROC	KIEL STAD N STATUS AUROC	NSCLC Subtyping AUROC
1CONCH	3.13	0.711	0.721	0.739	0.719	0.688	0.821	0.800	0.675	0.709	0.674	0.917	0.630	0.618	0.613	0.712	0.582	0.728	0.782	0.709	0.671	0.535	0.675	0.829	0.648	0.708	0.575	0.879	0.796	0.544	0.731	0.632	0.993
2Virchow2	3.74	0.709	0.729	0.796	0.599	0.662	0.895	0.796	0.611	0.725	0.613	0.923	0.615	0.637	0.584	0.702	0.523	0.767	0.752	0.725	0.699	0.548	0.697	0.862	0.633	0.723	0.558	0.863	0.795	0.526	0.813	0.617	0.983
3Prov-GigaPath	5.29	0.692	0.645	0.791	0.499	0.563	0.817	0.779	0.626	0.764	0.628	0.888	0.616	0.620	0.572	0.769	0.552	0.749	0.732	0.741	0.693	0.536	0.632	0.816	0.622	0.707	0.549	0.878	0.711	0.534	0.779	0.658	0.987
4Lunit ViT-S/8	5.52	0.690	0.705	0.685	0.628	0.620	0.852	0.807	0.634	0.753	0.637	0.850	0.595	0.603	0.603	0.718	0.540	0.737	0.720	0.649	0.650	0.533	0.662	0.834	0.621	0.737	0.574	0.838	0.806	0.507	0.678	0.633	0.971
5H-optimus-0	6.23	0.685	0.677	0.747	0.570	0.574	0.848	0.782	0.570	0.780	0.568	0.886	0.588	0.605	0.621	0.708	0.529	0.744	0.733	0.710	0.661	0.547	0.680	0.802	0.597	0.698	0.549	0.854	0.755	0.537	0.742	0.578	0.983
6UNI	6.29	0.684	0.675	0.722	0.573	0.588	0.859	0.790	0.648	0.752	0.604	0.901	0.526	0.606	0.622	0.764	0.569	0.744	0.738	0.680	0.631	0.544	0.629	0.819	0.586	0.661	0.557	0.863	0.742	0.504	0.707	0.629	0.976
7Hibou-L	7.87	0.668	0.718	0.738	0.584	0.587	0.898	0.750	0.608	0.702	0.563	0.865	0.574	0.529	0.593	0.714	0.562	0.580	0.739	0.709	0.639	0.517	0.614	0.786	0.574	0.659	0.559	0.804	0.709	0.531	0.733	0.593	0.971
8CTransPath	7.97	0.668	0.656	0.711	0.562	0.593	0.850	0.784	0.656	0.646	0.632	0.879	0.572	0.576	0.569	0.659	0.561	0.642	0.707	0.633	0.627	0.525	0.601	0.820	0.594	0.649	0.568	0.850	0.767	0.511	0.693	0.631	0.982
9Virchow	8.13	0.670	0.680	0.723	0.606	0.529	0.844	0.777	0.571	0.670	0.579	0.860	0.568	0.572	0.548	0.693	0.498	0.700	0.714	0.687	0.683	0.510	0.657	0.855	0.595	0.636	0.574	0.837	0.804	0.513	0.714	0.599	0.982
10Hibou-B	8.35	0.665	0.680	0.718	0.560	0.592	0.874	0.767	0.574	0.655	0.546	0.858	0.542	0.566	0.574	0.702	0.572	0.618	0.718	0.706	0.627	0.519	0.628	0.786	0.596	0.669	0.565	0.859	0.745	0.466	0.739	0.633	0.970
11Kaiko ViT-L/14	9.10	0.656	0.681	0.774	0.583	0.620	0.844	0.793	0.611	0.614	0.540	0.842	0.519	0.567	0.526	0.705	0.540	0.713	0.724	0.635	0.634	0.515	0.564	0.776	0.531	0.661	0.559	0.727	0.697	0.516	0.757	0.609	0.972
12Phikon	9.52	0.654	0.646	0.701	0.574	0.507	0.760	0.727	0.608	0.679	0.575	0.872	0.560	0.587	0.553	0.714	0.542	0.635	0.700	0.642	0.600	0.534	0.616	0.774	0.609	0.636	0.564	0.797	0.705	0.591	0.692	0.614	0.952
13PLIP	9.87	0.640	0.657	0.612	0.588	0.666	0.821	0.783	0.673	0.606	0.625	0.723	0.549	0.551	0.545	0.635	0.559	0.574	0.676	0.668	0.557	0.517	0.563	0.710	0.571	0.614	0.596	0.806	0.702	0.480	0.618	0.626	0.974

STAMP BenchmarkpathologyH&E

Detailed Results

STAMP Benchmark
pathology
H&E