Abstract: Protein subcellular localization is an important factor in normal cellular processes and dis- ease. While many protein localization resources treat it as static, protein localization is dynamic and heavily influenced by biological context. Biological pathways are graphs that represent a specific biological context and can be inferred from large-scale data. We develop graph algorithms to predict the localization of all interactions in a biological pathway as an edge-labeling task. We compare a variety of models including graph neural networks, probabilistic graphical models, and discriminative classifiers for predicting localization an- notations from curated pathway databases. We also perform a case study where we con- struct biological pathways and predict localizations of human fibroblasts undergoing viral infection.

The diverse metabolic pathways are fundamental to all living organisms, as they harvest energy, synthesize biomass components, produce molecules to interact with the microenvironment, and neutralize toxins. While discovery of new metabolites and pathways continues, the prediction of pathways for new metabolites can be challenging. It can take vast amounts of time to elucidate pathways for new metabolites; thus, according to HMDB only 60% of metabolites get assigned to pathways. Here, we present an approach to identify pathways based on metabolite structure. We extracted 201 features from SMILES annotations, and identified new metabolites from PubMed abstracts and HMDB. After applying clustering algorithms to both groups of features, we quantified correlations between metabolites, and found the clusters accurately linked 92% of known metabolites to their respective pathways. Thus, this approach could be valuable for predicting metabolic pathways for new metabolites.