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Atlas 2 -- Foundation models for clinical deployment

arXiv:2601.05148v1 Announce Type: cross Abstract: Pathology foundation models substantially advanced the possibilities in computational pathology -- yet tradeoffs in terms of performance, robustness, and computational requirements remained, which limited their clinical deployment. In this report, we present Atlas 2, Atlas 2-B, and Atlas 2-S, three pathology vision foundation models which bridge these shortcomings by showing state-of-the-art performance in prediction performance, robustness, and resource efficiency in a comprehensive evaluation across eighty public benchmarks. Our models were trained on the largest pathology foundation model dataset to date comprising 5.5 million histopathology whole slide images, collected from three medical institutions Charit\'e - Universt\"atsmedizin Berlin, LMU Munich, and Mayo Clinic.

Benchmarking large language models for personalized, biomarker-based health intervention recommendations

npj Digital Medicine, Published online: 27 October 2025; doi:10.1038/s41746-025-01996-2

Benchmarking large language models for personalized, biomarker-based health intervention recommendations

Cancer biomarkers: Emerging trends and clinical implications for personalized treatment

Cancer biomarkers have transformed oncology, enabling treatments tailored to each tumor’s unique profile. This review highlights the field’s progress due to advancements in understanding cancer biology, testing methods, and understanding of the immune microenvironment to advance precision oncology for improved patient outcomes.

Spatial epigenome–transcriptome co-profiling of mammalian tissues

Nature, Published online: 15 March 2023; doi:10.1038/s41586-023-05795-1

The authors present two technologies for spatially resolved, genome-wide, joint profiling of the epigenome and transcriptome by cosequencing chromatin accessibility and gene expression, or histone modifications and gene expression on the same tissue section at near-single-cell resolution.

Epigenetic aging in patients diagnosed with coronary artery disease: results of the LipidCardio study

People age biologically at different rates. Epigenetic clock-derived DNA methylation age acceleration (DNAmAA) is among the most promising markers proposed to assess the interindividual differences in biologic...

The co-evolution of the genome and epigenome in colorectal cancer

Nature, Published online: 26 October 2022; doi:10.1038/s41586-022-05202-1

A study maps genetic and epigenetic heterogeneity of primary colorectal adenomas and cancers at single-clone resolution through spatial multi-omic profiling of individual glands and adjacent normal tissue.

Phenotypic plasticity and genetic control in colorectal cancer evolution

Nature, Published online: 26 October 2022; doi:10.1038/s41586-022-05311-x

Intratumour genetic ancestry only infrequently affects gene expression traits and subclonal evolution in colorectal cancer, with most genetic intratumour variation having no detected phenotypic consequence and transcriptional plasticity being widespread within a tumour.
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