Paul A. Stewart

Asim Waqas, Aakash Tripathi, Paul Stewart et al.

Cancer clinics capture disease data at various scales, from genetic to organ level. Current bioinformatic methods struggle to handle the heterogeneous nature of this data, especially with missing modalities. We propose PARADIGM, a Graph Neural Network (GNN) framework that learns from multimodal, heterogeneous datasets to improve clinical outcome prediction. PARADIGM generates embeddings from multi-resolution data using foundation models, aggregates them into patient-level representations, fuses them into a unified graph, and enhances performance for tasks like survival analysis. We train GNNs on pan-Squamous Cell Carcinomas and validate our approach on Moffitt Cancer Center lung SCC data. Multimodal GNN outperforms other models in patient survival prediction. Converging individual data modalities across varying scales provides a more insightful disease view. Our solution aims to understand the patient's circumstances comprehensively, offering insights on heterogeneous data integration and the benefits of converging maximum data views.

Benjamin D. Lee, Anthony Gitter, Casey S. Greene et al.

Machine learning is a modern approach to problem-solving and task automation. In particular, machine learning is concerned with the development and applications of algorithms that can recognize patterns in data and use them for predictive modeling. Artificial neural networks are a particular class of machine learning algorithms and models that evolved into what is now described as deep learning. Given the computational advances made in the last decade, deep learning can now be applied to massive data sets and in innumerable contexts. Therefore, deep learning has become its own subfield of machine learning. In the context of biological research, it has been increasingly used to derive novel insights from high-dimensional biological data. To make the biological applications of deep learning more accessible to scientists who have some experience with machine learning, we solicited input from a community of researchers with varied biological and deep learning interests. These individuals collaboratively contributed to this manuscript's writing using the GitHub version control platform and the Manubot manuscript generation toolset. The goal was to articulate a practical, accessible, and concise set of guidelines and suggestions to follow when using deep learning. In the course of our discussions, several themes became clear: the importance of understanding and applying machine learning fundamentals as a baseline for utilizing deep learning, the necessity for extensive model comparisons with careful evaluation, and the need for critical thought in interpreting results generated by deep learning, among others.