My research is focused on the generation and application of biological knowledge graphs in drug discovery and precision medicine. Recently, I’ve had a specific focus on knowledge graph embedding methodologies and downstream application of link prediction.

Research Workflow

Creating Knowledge Graphs

While there are several useful public terminologies useful for curation of biomedical relations, there is often the need to develop new controlled vocabularies, thesauri, taxonomies, and ontologies to support new biological phenomena. I lead the team that created the Curation of Neurodegeneration Supporting Ontology (CONSO).

After identifying named entities within scholarly articles, their relations can be extracted and encoded in a knowledge graph. I lead the team that created the knowledge graph Curation of Neurodegeneration in BEL (CONIB) and later the knowledge graph TauBase.

I also lead the same team to re-curate the knowledge graphs curated and published during the AETIONOMY project. In order to check the syntax and semantics of these knowledge graphs, I developed PyBEL. To interactively explore these graphs in a web-based environment and identify biological contractions, I developed BEL Commons.

Because of curation’s time and cost, prioritization of articles is crucial. I’ve developed semi-automated curation workflows based on a new metric for information density in regions of knowledge graphs.

Finally, to integrate all of the rich biological data sources available to the public, I developed Bio2BEL.

Knowledge Graph Embeddings

Knowledge graph embedding methods learn latent representations for the nodes and edges in a graph to support clustering, link prediction, entity disambiguation, and other downstream machine learning tasks.

I’ve worked on PyKEEN, a PyTorch reimplementation of several recent knowledge graph embedding models with a focus on reproducibility. I’ve also developed BioKEEN, which connects biological knowledge graphs in BEL (notably from Bio2BEL) directly to the PyKEEN pipeline.

Predictions

The link prediction task in knowledge graphs is isomorphic to several tasks in drug discovery and precision medicine.

Predicting links between genes/proteins and diseases accomplishes target identification/prioritization. I’ve worked on GuiltyTargets, which embedded proteins from protein-protein interaction networks annotated with disease-specific differential gene expression patterns. These embeddings were used for positive-unlabeled learning using disease-specific gene lists. While this method works well, it was only single-task (only working on one disease at a time).

Predicting links between chemicals and diseases accomplishes drug repositioning (in the case when the chemical is a known drug) or otherwise novel drug discovery. I’ve worked on DrugReLink, which uses hetionet to make these predictions for a given chemical or disease.

Because many compounds fail in the clinic due to undesirable side effects, predicting them during early-stage drug discovery could drastically improve the efficiency. I’ve worked on SEffNet, which uses a network composed of drug-disease, drug-side effect, drug-target, and drug-drug links to predict compounds’ side effects and give insight into the targets mediating those side effects.

Some of my ongoing work is to apply these methods in precision medicine. I’m doing it by annotating patients as nodes in networks, and creating edges to biological entities based on clinical measurements (e.g., gene expression) then embedding those nodes for downstream machine learning tasks such as subgroup identification and survival analysis.