Learning latent progression states from spatial heterogeneity in uterine histopathology

Tumor progression is accompanied by changes in architecture, morphology and microenvironmental organization, yet progression-associated heterogeneity is usually compressed into static diagnostic categories in histopathology. Here we present SpaTIE, a uterus-specific computational pathology framework that learns morphology-aware representations and organizes spatial histopathological heterogeneity into progression-associated tumor states. SpaTIE was developed using 10,426 uterine hematoxylin and eosin whole-slide images and evaluated in TCGA-UCEC and TCGA-UCS cohorts. The learned representations formed morphology manifolds, supported diagnostic, molecular and survival-related prediction tasks, and localized attention to informative tumor regions. Beyond supervised prediction, SpaTIE inferred tumor-state axes from cross-sectional morphology without temporal or molecular supervision. These morphology-derived states were spatially coherent and showed associations with clinicopathological variables and survival outcomes, while not simply recapitulating staging or diagnostic labels. Integrative multi-omics analyses linked the inferred states to DNA methylation, somatic copy-number variation, mutation, RNA-seq and RPPA profiles, highlighting molecular programs related to chromatin regulation, copy-number-associated structural variation, receptor tyrosine kinase signaling, cell adhesion, extracellular-matrix remodeling and metabolic adaptation. Progression-guided virtual perturbation further prioritized molecular features coupled to the morphology-derived state organization. Together, these findings suggest that uterine histopathology contains recoverable progression-associated tumor-state information and establish SpaTIE as a framework for connecting spatial morphology with multi-omics-informed tumor-state discovery.

TorchBench: Benchmarking PyTorch with High API Surface Coverage

Deep learning (DL) has been a revolutionary technique in various domains. To facilitate the model development and deployment, many deep learning frameworks are proposed, among which PyTorch is one of the most popular solutions. The performance of ecosystem around PyTorch is critically important, which saves the costs of training models and reduces the response time of model inferences. In this paper, we propose TorchBench, a novel benchmark suite to study the performance of PyTorch software stack. Unlike existing benchmark suites, TorchBench encloses many representative models, covering a large PyTorch API surface. TorchBench is able to comprehensively characterize the performance of the PyTorch software stack, guiding the performance optimization across models, PyTorch framework, and GPU libraries. We show two practical use cases of TorchBench. (1) We profile TorchBench to identify GPU performance inefficiencies in PyTorch. We are able to optimize many performance bugs and upstream patches to the official PyTorch repository. (2) We integrate TorchBench into PyTorch continuous integration system. We are able to identify performance regression in multiple daily code checkins to prevent PyTorch repository from introducing performance bugs. TorchBench is open source and keeps evolving.