VitaGraph: Building a Knowledge Graph for Biologically Relevant Learning Tasks

The intrinsic complexity of human biology presents ongoing challenges to scientific understanding. Researchers collaborate across disciplines to expand our knowledge of the biological interactions that define human life. AI methodologies have emerged as powerful tools across scientific domains, particularly in computational biology, where graph data structures effectively model biological entities such as protein-protein interaction (PPI) networks and gene functional networks. Those networks are used as datasets for paramount network medicine tasks, such as gene-disease association prediction, drug repurposing, and polypharmacy side effect studies. Reliable predictions from machine learning models require high-quality foundational data. In this work, we present a comprehensive multi-purpose biological knowledge graph constructed by integrating and refining multiple publicly available datasets. Building upon the Drug Repurposing Knowledge Graph (DRKG), we define a pipeline tasked with a) cleaning inconsistencies and redundancies present in DRKG, b) coalescing information from the main available public data sources, and c) enriching the graph nodes with expressive feature vectors such as molecular fingerprints and gene ontologies. Biologically and chemically relevant features improve the capacity of machine learning models to generate accurate and well-structured embedding spaces. The resulting resource represents a coherent and reliable biological knowledge graph that serves as a state-of-the-art platform to advance research in computational biology and precision medicine. Moreover, it offers the opportunity to benchmark graph-based machine learning and network medicine models on relevant tasks. We demonstrate the effectiveness of the proposed dataset by benchmarking it against the task of drug repurposing, PPI prediction, and side-effect prediction, modeled as link prediction problems.

Kolmogorov-Arnold Graph Neural Networks

Graph neural networks (GNNs) excel in learning from network-like data but often lack interpretability, making their application challenging in domains requiring transparent decision-making. We propose the Graph Kolmogorov-Arnold Network (GKAN), a novel GNN model leveraging spline-based activation functions on edges to enhance both accuracy and interpretability. Our experiments on five benchmark datasets demonstrate that GKAN outperforms state-of-the-art GNN models in node classification, link prediction, and graph classification tasks. In addition to the improved accuracy, GKAN's design inherently provides clear insights into the model's decision-making process, eliminating the need for post-hoc explainability techniques. This paper discusses the methodology, performance, and interpretability of GKAN, highlighting its potential for applications in domains where interpretability is crucial.