Building Flexible, Scalable, and Machine Learning-ready Multimodal Oncology Datasets

The advancements in data acquisition, storage, and processing techniques have resulted in the rapid growth of heterogeneous medical data. Integrating radiological scans, histopathology images, and molecular information with clinical data is essential for developing a holistic understanding of the disease and optimizing treatment. The need for integrating data from multiple sources is further pronounced in complex diseases such as cancer for enabling precision medicine and personalized treatments. This work proposes Multimodal Integration of Oncology Data System (MINDS) - a flexible, scalable, and cost-effective metadata framework for efficiently fusing disparate data from public sources such as the Cancer Research Data Commons (CRDC) into an interconnected, patient-centric framework. MINDS offers an interface for exploring relationships across data types and building cohorts for developing large-scale multimodal machine learning models. By harmonizing multimodal data, MINDS aims to potentially empower researchers with greater analytical ability to uncover diagnostic and prognostic insights and enable evidence-based personalized care. MINDS tracks granular end-to-end data provenance, ensuring reproducibility and transparency. The cloud-native architecture of MINDS can handle exponential data growth in a secure, cost-optimized manner while ensuring substantial storage optimization, replication avoidance, and dynamic access capabilities. Auto-scaling, access controls, and other mechanisms guarantee pipelines' scalability and security. MINDS overcomes the limitations of existing biomedical data silos via an interoperable metadata-driven approach that represents a pivotal step toward the future of oncology data integration.

Multimodal Data Integration for Oncology in the Era of Deep Neural Networks: A Review

Cancer has relational information residing at varying scales, modalities, and resolutions of the acquired data, such as radiology, pathology, genomics, proteomics, and clinical records. Integrating diverse data types can improve the accuracy and reliability of cancer diagnosis and treatment. There can be disease-related information that is too subtle for humans or existing technological tools to discern visually. Traditional methods typically focus on partial or unimodal information about biological systems at individual scales and fail to encapsulate the complete spectrum of the heterogeneous nature of data. Deep neural networks have facilitated the development of sophisticated multimodal data fusion approaches that can extract and integrate relevant information from multiple sources. Recent deep learning frameworks such as Graph Neural Networks (GNNs) and Transformers have shown remarkable success in multimodal learning. This review article provides an in-depth analysis of the state-of-the-art in GNNs and Transformers for multimodal data fusion in oncology settings, highlighting notable research studies and their findings. We also discuss the foundations of multimodal learning, inherent challenges, and opportunities for integrative learning in oncology. By examining the current state and potential future developments of multimodal data integration in oncology, we aim to demonstrate the promising role that multimodal neural networks can play in cancer prevention, early detection, and treatment through informed oncology practices in personalized settings.

Exploring Robustness of Neural Networks through Graph Measures

Motivated by graph theory, artificial neural networks (ANNs) are traditionally structured as layers of neurons (nodes), which learn useful information by the passage of data through interconnections (edges). In the machine learning realm, graph structures (i.e., neurons and connections) of ANNs have recently been explored using various graph-theoretic measures linked to their predictive performance. On the other hand, in network science (NetSci), certain graph measures including entropy and curvature are known to provide insight into the robustness and fragility of real-world networks. In this work, we use these graph measures to explore the robustness of various ANNs to adversarial attacks. To this end, we (1) explore the design space of inter-layer and intra-layers connectivity regimes of ANNs in the graph domain and record their predictive performance after training under different types of adversarial attacks, (2) use graph representations for both inter-layer and intra-layers connectivity regimes to calculate various graph-theoretic measures, including curvature and entropy, and (3) analyze the relationship between these graph measures and the adversarial performance of ANNs. We show that curvature and entropy, while operating in the graph domain, can quantify the robustness of ANNs without having to train these ANNs. Our results suggest that the real-world networks, including brain networks, financial networks, and social networks may provide important clues to the neural architecture search for robust ANNs. We propose a search strategy that efficiently finds robust ANNs amongst a set of well-performing ANNs without having a need to train all of these ANNs.