GOLDMARK: Public Computational Pathology Portal

Stage Summary Pipeline status at a glance Pipeline

Features
Encoders detected: gigapath_ft (484 files), h-optimus-0 (484 files), prov-gigapath (484 files), uni (484 files), virchow (484 files), virchow2 (484 files)
Inference
640 prediction(s) · 35 positive label(s) · dataset tcga
Manifest
485 rows, 12 columns
Tiling
Tiling manifest covers 484 case(s)
Training
80 training run(s)

Case Summary Track cohort coverage by encoder Cohort

Cases Inspect case-level tiles and encoders Cases

Manifest Overview Preview the manifest and target distribution Manifest

485 rows · 11 columns

Target: HRAS_BINARY Target: HRAS Target: PIK3CA_BINARY Target: PIK3CA

slide_id	DMP_ASSAY_ID	split_1	split_2	split_3	split_4	split_5	HRAS	PIK3CA
P-0000227-T01-IM3	P-0000227-T01-IM3	test	train	train	test	train	Negative	Negative
P-0000277-T02-IM6	P-0000277-T02-IM6	test	train	train	test	test	Negative	Negative
P-0000284-T01-IM3	P-0000284-T01-IM3	test	train	train	train	train	Negative	Negative
P-0000319-T01-IM3	P-0000319-T01-IM3	train	train	train	test	train	Negative	Negative
P-0000396-T01-IM3	P-0000396-T01-IM3	train	train	test	test	train	Negative	Negative

Cross-Validation Performance Compare experiments across validation splits Validation

Training Runs Artifacts and metrics for each experiment Experiments

Gene Show archived Expand All

Model	Target	Aggregator	Split	Epoch 200	Macro AUC	Macro BER	Macro FPR	Macro FNR	Artifact
h-optimus-0	PIK3CA	GMA PUB	split_3	120	0.5996240601503761	0.4981203007518797	0.0676691729323308	0.9285714285714286	`cumulative_results.csv`
gigapath_ft	PIK3CA	GMA PUB	split_4	120	0.5603354978354977	0.474025974025974	0.0909090909090909	0.8571428571428571	`cumulative_results.csv`
gigapath_ft	PIK3CA	GMA PUB	split_3	120	0.6660848549946293	0.4492481203007519	0.112781954887218	0.7857142857142857	`cumulative_results.csv`
gigapath_ft	PIK3CA	GMA PUB	split_1	120	0.621969696969697	0.4431818181818182	0.053030303030303	0.8333333333333334	`cumulative_results.csv`
gigapath_ft	PIK3CA	GMA PUB	split_4	120	0.5603354978354977	0.474025974025974	0.0909090909090909	0.8571428571428571	`cumulative_results.csv`
gigapath_ft	PIK3CA	GMA PUB	split_2	120	0.6341991341991342	0.4918831168831169	0.0909090909090909	0.8928571428571429	`cumulative_results.csv`
h-optimus-0	PIK3CA	GMA PUB	split_3	120	0.5996240601503761	0.4981203007518797	0.0676691729323308	0.9285714285714286	`cumulative_results.csv`
h-optimus-0	PIK3CA	GMA PUB	split_5	120	0.5725071225071225	0.4978632478632478	0.1111111111111111	0.8846153846153846	`cumulative_results.csv`
h-optimus-0	PIK3CA	GMA PUB	split_4	120	0.5936147186147186	0.4318181818181818	0.1136363636363636	0.75	`cumulative_results.csv`
h-optimus-0	PIK3CA	GMA PUB	split_5	120	0.5725071225071225	0.4978632478632478	0.1111111111111111	0.8846153846153846	`cumulative_results.csv`
h-optimus-0	PIK3CA	GMA PUB	split_2	120	0.6195887445887445	0.4599567099567099	0.0984848484848484	0.8214285714285714	`cumulative_results.csv`
h-optimus-0	PIK3CA	GMA PUB	split_1	120	0.591540404040404	0.471969696969697	0.1439393939393939	0.8	`cumulative_results.csv`
gigapath_ft	PIK3CA	GMA PUB	split_5	120	0.5427350427350428	0.5089743589743589	0.1333333333333333	0.8846153846153846	`cumulative_results.csv`
gigapath_ft	PIK3CA	GMA PUB	split_3	120	0.6660848549946293	0.4492481203007519	0.112781954887218	0.7857142857142857	`cumulative_results.csv`
h-optimus-0	PIK3CA	GMA PUB	split_2	120	0.6195887445887445	0.4599567099567099	0.0984848484848484	0.8214285714285714	`cumulative_results.csv`
h-optimus-0	PIK3CA	GMA PUB	split_1	120	0.591540404040404	0.471969696969697	0.1439393939393939	0.8	`cumulative_results.csv`
h-optimus-0	PIK3CA	GMA PUB	split_4	120	0.5936147186147186	0.4318181818181818	0.1136363636363636	0.75	`cumulative_results.csv`
gigapath_ft	PIK3CA	GMA PUB	split_2	120	0.6341991341991342	0.4918831168831169	0.0909090909090909	0.8928571428571429	`cumulative_results.csv`
gigapath_ft	PIK3CA	GMA PUB	split_1	120	0.621969696969697	0.4431818181818182	0.053030303030303	0.8333333333333334	`cumulative_results.csv`
gigapath_ft	PIK3CA	GMA PUB	split_5	120	0.5427350427350428	0.5089743589743589	0.1333333333333333	0.8846153846153846	`cumulative_results.csv`

External Inference Diagnostics Interactive ROC/PR curves for each external inference experiment Inference