11 papers
A homotopy-type-theoretic generalization of neurosymbolic inference
Fernando Zhapa-Camacho, Robert Hoehndorf
A wide range of neurosymbolic (NeSy) systems compute one functional: a belief-weighted sum of a logical quantity over a space of -structures, of which weighted model counting,…
LAFA: A Framework for Reproducible Longitudinal Assessment of Protein Function Annotation Models
An Phan, Yanli Wang, Frimpong Boadu +3
Motivation: Protein function prediction is a challenging task and an open problem in computational biology. The Critical Assessment of protein Function Annotation (CAFA) is a trien…
GRAFT: Decoupling Ranking and Calibration for Survival Analysis
Mohammad Ashhad, Robert Hoehndorf, Ricardo Henao
Survival analysis is complicated by censored data, high-dimensional features, and non-linear interactions. Classical models offer interpretability and superior calibration but are…
SIDEKICK: A Semantically Integrated Resource for Drug Effects, Indications, and Contraindications
Mohammad Ashhad, Olga Mashkova, Ricardo Henao +1
Pharmacovigilance and clinical decision support systems utilize structured drug safety data to guide medical practice. However, existing datasets frequently depend on terminologies…
DELE: Deductive Embeddings for Knowledge Base Completion
Olga Mashkova, Fernando Zhapa-Camacho, Robert Hoehndorf
Ontology embeddings map classes, roles, and individuals in ontologies into , and within similarity between entities can be computed or new axioms infer…
Causal knowledge graph analysis identifies adverse drug effects
Sumyyah Toonsi, Paul Schofield, Robert Hoehndorf
Knowledge graphs and structural causal models have each proven valuable for organizing biomedical knowledge and estimating causal effects, but remain largely disconnected: knowledg…