Histoboard - Pathology Foundation Model Benchmarks

Patho-Bench
pathology
H&E

Comprehensive benchmark from Mahmood Lab with 95 tasks across 33 datasets covering mutation prediction, TME characterization, survival, grading, and treatment response.

5 models evaluated

53 tasks

Organs:

breast

kidney

colon

brain

head-neck

lung

pancreas

cervix

ovary

Detailed Results

Model	Average rank	Average metric	BC Therapy ER AUROC	BC Therapy Grade Kappa	BC Therapy HER2 AUROC	BC Therapy RCB Balanced accuracy	BRCA Immune Balanced accuracy	BRCA PIK3CA AUROC	BRCA TP53 AUROC	CCRCC BAP1 AUROC	CCRCC Immune Balanced accuracy	CCRCC PBRM1 AUROC	CCRCC Survival C-Index	CCRCC VHL AUROC	Cervix Subtype AUROC	COAD ACVR2A AUROC	COAD APC AUROC	COAD ARID1A AUROC	COAD Immune Balanced accuracy	COAD KRAS AUROC	COAD MSI-H AUROC	COAD PIK3CA AUROC	COAD SETD1B AUROC	COAD TP53 AUROC	GBM EGFR AUROC	GBM Immune Balanced accuracy	GBM TP53 AUROC	Hancock Grade Ker Kappa	Hancock Grade NonKer Kappa	Hancock LVI AUROC	Hancock PNI AUROC	Hancock Primary vs Met AUROC	Hancock Survival C-Index	Hancock Tumor Site Balanced accuracy	Hancock VI AUROC	HNSC CASP8 AUROC	HNSC Grade Kappa	HNSC Immune Balanced accuracy	HNSC Survival C-Index	LSCC ARID1A AUROC	LSCC Grade Kappa	LSCC Immune Balanced accuracy	LSCC KEAP1 AUROC	LUAD EGFR AUROC	LUAD Immune Balanced accuracy	LUAD KRAS AUROC	LUAD STK11 AUROC	LUAD Survival C-Index	LUAD TP53 AUROC	MBC RECIST Kappa	MBC Survival C-Index	Ovary Survival C-Index	PDA Immune Balanced accuracy	PDA SMAD4 AUROC	PDA Survival C-Index
1Atlas 2	1.77	0.603	0.764	0.395	0.699	0.337	0.593	0.596	0.836	0.704	0.383	0.524	0.556	0.529	0.947	0.845	0.778	0.758	0.458	0.653	0.939	0.622	0.823	0.725	0.692	0.577	0.855	0.332	0.237	0.699	0.740	0.658	0.570	0.775	0.676	0.658	0.361	0.546	0.511	0.469	0.227	0.578	0.574	0.810	0.566	0.704	0.885	0.522	0.767	0.103	0.490	0.517	0.417	0.476	0.520
2Virchow2	3.19	0.574	0.661	0.324	0.643	0.290	0.558	0.582	0.787	0.674	0.331	0.494	0.582	0.528	0.951	0.782	0.729	0.711	0.421	0.643	0.859	0.637	0.753	0.661	0.621	0.469	0.748	0.280	0.204	0.648	0.723	0.650	0.564	0.746	0.630	0.566	0.360	0.515	0.508	0.419	0.221	0.572	0.631	0.817	0.502	0.739	0.824	0.571	0.773	0.085	0.518	0.508	0.430	0.446	0.507
3UNI2	3.28	0.570	0.700	0.349	0.636	0.312	0.538	0.611	0.777	0.669	0.321	0.416	0.638	0.482	0.954	0.757	0.738	0.697	0.384	0.664	0.890	0.591	0.799	0.673	0.575	0.512	0.819	0.291	0.210	0.654	0.685	0.652	0.539	0.739	0.682	0.601	0.366	0.469	0.567	0.434	0.267	0.507	0.650	0.771	0.473	0.654	0.888	0.481	0.760	0.102	0.510	0.509	0.392	0.370	0.499
4Atlas	3.32	0.570	0.692	0.298	0.609	0.295	0.517	0.594	0.782	0.705	0.357	0.488	0.654	0.487	0.950	0.769	0.747	0.740	0.391	0.617	0.846	0.571	0.760	0.623	0.591	0.520	0.837	0.247	0.206	0.693	0.718	0.619	0.565	0.741	0.669	0.576	0.298	0.486	0.483	0.426	0.238	0.542	0.634	0.811	0.503	0.669	0.856	0.525	0.696	0.161	0.542	0.495	0.408	0.451	0.507
5H-optimus-0	3.43	0.569	0.605	0.278	0.612	0.274	0.522	0.599	0.760	0.653	0.347	0.440	0.552	0.497	0.955	0.795	0.715	0.756	0.360	0.604	0.871	0.639	0.818	0.671	0.580	0.509	0.818	0.309	0.181	0.680	0.725	0.626	0.567	0.744	0.704	0.549	0.336	0.486	0.602	0.418	0.251	0.537	0.626	0.778	0.468	0.721	0.884	0.542	0.714	0.121	0.530	0.492	0.392	0.414	0.513

Patho-BenchpathologyH&E

Detailed Results

Patho-Bench
pathology
H&E