Haudenschild, C. | Search bioRxiv

bioRxiv2021

Configuring a federated network of real-world patient health data for multimodal deep learning prediction of health outcomes.

Vast quantities of electronic patient medical data are currently being collated and processed in large federated data repositories. For instance, TriNetX, Inc., a global health research network, has access to more than 300 million patients, sourced from healthcare organizations, biopharmaceutical companies, and contract research organizations. As such, pipelines that are able to algorithmically extract huge quantities of patient data from multiple modalities present opportunities to leverage machine learning and deep learning approaches with the possibility of generating actionable insight. In this work, we present a modular, semi-automated end-to-end machine and deep learning pipeline designed to interface with a federated network of structured patient data. This proof-of-concept pipeline is disease-agnostic, scalable, and requires little domain expertise and manual feature engineering in order to quickly produce results for the case of a user-defined binary outcome event. We demonstrate the pipelines efficacy with three different disease workflows, with high discriminatory power achieved in all cases.

bioinformatics↗

bioRxiv2020

Topological Feature Extraction and Visualization of Whole Slide Images using Graph Neural Networks

Whole-slide images (WSI) are digitized representations of thin sections of stained tissue from various patient sources (biopsy, resection, exfoliation, fluid) and often exceed 100,000 pixels in any given spatial dimension. Deep learning approaches to digital pathology typically extract information from sub-images (patches) and treat the sub-images as independent entities, ignoring contributing information from vital large-scale architectural relationships. Modeling approaches that can capture higher-order dependencies between neighborhoods of tissue patches have demonstrated the potential to improve predictive accuracy while capturing the most essential slide-level information for prognosis, diagnosis and integration with other omics modalities. Here, we review two promising methods for capturing macro and micro architecture of histology images, Graph Neural Networks, which contextualize patch level information from their neighbors through message passing, and Topological Data Analysis, which distills contextual information into its essential components. We introduce a modeling framework, WSI-GTFE that integrates these two approaches in order to identify and quantify key pathogenic information pathways. To demonstrate a simple use case, we utilize these topological methods to develop a tumor invasion score to stage colon cancer.

pathology↗