Related papers: A Comparison of the Pathway Tools Software with th…
Pathway Tools is a bioinformatics software environment with a broad set of capabilities. The software provides genome-informatics tools such as a genome browser, sequence alignments, a genome-variant analyzer, and comparative-genomics…
Metabolomic data sets provide a direct read-out of cellular phenotypes and are increasingly generated to study biological questions. Our previous work revealed the potential of analyzing extracellular metabolomic data in the context of the…
We introduce ProtoPathway, an interpretable-by-design multimodal framework for cancer survival prediction that unifies whole slide imaging and transcriptomics through encoders producing biologically grounded representations on both sides of…
Rapid advances in high-throughput technologies have led to considerable interest in analyzing genome-scale data in the context of biological pathways, with the goal of identifying functional systems that are involved in a given phenotype.…
Despite the promise of computational pathology foundation models, adapting them to specific clinical tasks remains challenging due to the complexity of whole-slide image (WSI) processing, the opacity of learned features, and the wide range…
The emergence of tool-calling-based agent systems introduces a more evidence-driven paradigm for pathology image analysis in contrast to the coarse-grained text-image diagnostic approaches. With the recent large-scale experimental adoption…
Artificial Intelligence (AI) brings advancements to support pathologists in navigating high-resolution tumor images to search for pathology patterns of interest. However, existing AI-assisted tools have not realized this promised potential…
Solving complex reasoning tasks may involve visual understanding, domain knowledge retrieval, numerical calculation, and multi-step reasoning. Existing methods augment large language models (LLMs) with external tools but are restricted to…
We present the design of a new large scale orchestration layer for accelerators. Our system, Pathways, is explicitly designed to enable exploration of new systems and ML research ideas, while retaining state of the art performance for…
A Software Bill of Materials (SBOM) provides transparency by documenting software component metadata and dependencies. However, SBOM adoption depends on tool ecosystems. With two dominant formats: SPDX and CycloneDX - the ecosystems vary…
Computational pathology foundation models (CPathFMs) have emerged as a powerful approach for analyzing histopathological data, leveraging self-supervised learning to extract robust feature representations from unlabeled whole-slide images.…
Purpose: In this work, we present a collaboration to create a validation dataset of pathologist annotations for algorithms that process whole slide images (WSIs). We focus on data collection and evaluation of algorithm performance in the…
Survival outcome assessment is challenging and inherently associated with multiple clinical factors (e.g., imaging and genomics biomarkers) in cancer. Enabling multimodal analytics promises to reveal novel predictive patterns of patient…
Understanding how molecular alterations propagate across biological systems to drive disease remains a central challenge. Although high-throughput profiling enables comprehensive characterization of tumor states, most models neglect…
The identification of metabolites from complex biological samples often involves matching experimental mass spectrometry data to signatures of compounds derived from massive chemical databases. However, misidentifications may result due to…
A prototype for a web application was designed and implemented as a guide to be used by clinicians when designing the best drug therapy for a specific cancer patient, given biological data derived from the patients tumor tissue biopsy. A…
Deciphering tumor microenvironment from Whole Slide Images (WSIs) is intriguing as it is key to cancer diagnosis, prognosis and treatment response. While these gigapixel images on one hand offer a comprehensive portrait of cancer, on the…
Clinical pathways are disseminated as visual flowcharts where spatial topology, arrow direction, colour coding, and font weight encode critical triage logic that remains inaccessible to computational systems. We present PathWISE, a…
Accurate classification of pediatric central nervous system tumors remains challenging due to histological complexity and limited training data. While pathology foundation models have advanced whole-slide image (WSI) analysis, they often…
The emergence of pathology foundation models has revolutionized computational histopathology, enabling highly accurate, generalized whole-slide image analysis for improved cancer diagnosis, and prognosis assessment. While these models show…