GOLDMARK: Governed Outcome-Linked Diagnostic Model Assessment Reference Kit
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| Natura: | Preprint |
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2026
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| author | Vanderbilt, Chad Campanella, Gabriele Singi, Siddharth Nanda, Swaraj Chen, Jie-Fu Kamali, Ali Boroujeni, Amir Momeni Kim, David Yakoub, Mohamed Benhamida, Jamal Hameed, Meera Kumar, Neeraj Goldgof, Gregory |
| author_facet | Vanderbilt, Chad Campanella, Gabriele Singi, Siddharth Nanda, Swaraj Chen, Jie-Fu Kamali, Ali Boroujeni, Amir Momeni Kim, David Yakoub, Mohamed Benhamida, Jamal Hameed, Meera Kumar, Neeraj Goldgof, Gregory |
| contents | Computational biomarkers (CBs) are histopathology-derived patterns extracted from hematoxylin-eosin (H&E) whole-slide images (WSIs) using artificial intelligence (AI) to predict therapeutic response or prognosis. Recently, slide-level multiple-instance learning (MIL) with pathology foundation models (PFMs) has become the standard baseline for CB development. While these methods have improved predictive performance, computational pathology lacks standardized intermediate data formats, provenance tracking, checkpointing conventions, and reproducible evaluation metrics required for clinical-grade deployment.
We introduce GOLDMARK (https://artificialintelligencepathology.org), a standardized benchmarking framework built on a curated TCGA cohort with clinically actionable OncoKB level 1-3 biomarker labels. GOLDMARK releases structured intermediate representations, including tile coordinate maps, per-slide feature embeddings from canonical PFMs, quality-control metadata, predefined patient-level splits, trained slide-level models, and evaluation outputs. Models are trained on TCGA and evaluated on an independent MSKCC cohort with reciprocal testing.
Across 33 tumor-biomarker tasks, mean AUROC was 0.689 (TCGA) and 0.630 (MSKCC). Restricting to the eight highest-performing tasks yielded mean AUROCs of 0.831 and 0.801, respectively. These tasks correspond to established morphologic-genomic associations (e.g., LGG IDH1, COAD MSI/BRAF, THCA BRAF/NRAS, BLCA FGFR3, UCEC PTEN) and showed the most stable cross-site performance. Differences between canonical encoders were modest relative to task-specific variability.
GOLDMARK establishes a shared experimental substrate for computational pathology, enabling reproducible benchmarking and direct comparison of methods across datasets and models. |
| format | Preprint |
| id |
arxiv_https___arxiv_org_abs_2603_20848 |
| institution | arXiv |
| publishDate | 2026 |
| record_format | arxiv |
| spellingShingle | GOLDMARK: Governed Outcome-Linked Diagnostic Model Assessment Reference Kit Vanderbilt, Chad Campanella, Gabriele Singi, Siddharth Nanda, Swaraj Chen, Jie-Fu Kamali, Ali Boroujeni, Amir Momeni Kim, David Yakoub, Mohamed Benhamida, Jamal Hameed, Meera Kumar, Neeraj Goldgof, Gregory Computer Vision and Pattern Recognition Computational Engineering, Finance, and Science Tissues and Organs Computational biomarkers (CBs) are histopathology-derived patterns extracted from hematoxylin-eosin (H&E) whole-slide images (WSIs) using artificial intelligence (AI) to predict therapeutic response or prognosis. Recently, slide-level multiple-instance learning (MIL) with pathology foundation models (PFMs) has become the standard baseline for CB development. While these methods have improved predictive performance, computational pathology lacks standardized intermediate data formats, provenance tracking, checkpointing conventions, and reproducible evaluation metrics required for clinical-grade deployment. We introduce GOLDMARK (https://artificialintelligencepathology.org), a standardized benchmarking framework built on a curated TCGA cohort with clinically actionable OncoKB level 1-3 biomarker labels. GOLDMARK releases structured intermediate representations, including tile coordinate maps, per-slide feature embeddings from canonical PFMs, quality-control metadata, predefined patient-level splits, trained slide-level models, and evaluation outputs. Models are trained on TCGA and evaluated on an independent MSKCC cohort with reciprocal testing. Across 33 tumor-biomarker tasks, mean AUROC was 0.689 (TCGA) and 0.630 (MSKCC). Restricting to the eight highest-performing tasks yielded mean AUROCs of 0.831 and 0.801, respectively. These tasks correspond to established morphologic-genomic associations (e.g., LGG IDH1, COAD MSI/BRAF, THCA BRAF/NRAS, BLCA FGFR3, UCEC PTEN) and showed the most stable cross-site performance. Differences between canonical encoders were modest relative to task-specific variability. GOLDMARK establishes a shared experimental substrate for computational pathology, enabling reproducible benchmarking and direct comparison of methods across datasets and models. |
| title | GOLDMARK: Governed Outcome-Linked Diagnostic Model Assessment Reference Kit |
| topic | Computer Vision and Pattern Recognition Computational Engineering, Finance, and Science Tissues and Organs |
| url | https://arxiv.org/abs/2603.20848 |