Stephen A. Ramsey

Validated Semantic Scoring Improves Filtering of Generic Concepts from Knowledge-Graphs for Drug Repurposing Queries

This paper introduces a semantic precision score to filter generic concepts from biomedical knowledge graphs, outperforming existing methods in drug repurposing queries.

PloverDB: A high-performance platform for serving biomedical knowledge graphs as standards-compliant web APIs

PloverDB provides a platform to serve biomedical knowledge graphs as standards-compliant web APIs, enhancing data accessibility and interoperability.

Comparative Transcriptomes of Canine and Human Prostate Cancers Identify Mediators of Castration Resistance

This study compares transcriptomes of canine and human prostate cancers to identify genes associated with castration resistance, finding shared molecular features in both species.

ARAX: a graph-based modular reasoning tool for translational biomedicine

ARAX is a graph-based reasoning tool that integrates knowledge across sources to answer translational biomedical questions.

RTX-KG2: a system for building a semantically standardized knowledge graph for translational biomedicine

RTX-KG2 integrates 70 biomedical knowledge sources into a standards-compliant knowledge graph with a Biolink schema, providing downloadable and queryable versions via API.

Predicting chemotherapy response using a variational autoencoder approach

This study uses a variational autoencoder to encode tumor transcriptomes and combines it with XGBoost to predict chemotherapy response across five cancer types, achieving better performance than PCA or raw data in four types.

Voting-based integration algorithm improves causal network learning from interventional and observational data: an application to cell signaling network inference

The paper introduces a method called 'Learn and Vote' to improve causal network learning from mixed observational and interventional data, showing it is more accurate than existing methods on larger datasets.