no code implementations • 30 Jan 2023 • Maciej Wiatrak, Eirini Arvaniti, Angus Brayne, Jonas Vetterle, Aaron Sim
A recent advancement in the domain of biomedical Entity Linking is the development of powerful two-stage algorithms, an initial candidate retrieval stage that generates a shortlist of entities for each mention, followed by a candidate ranking stage.
no code implementations • 2 Dec 2022 • Saee Paliwal, Angus Brayne, Benedek Fabian, Maciej Wiatrak, Aaron Sim
In this paper we generalize single-relation pseudo-Riemannian graph embedding models to multi-relational networks, and show that the typical approach of encoding relations as manifold transformations translates from the Riemannian to the pseudo-Riemannian case.
no code implementations • 16 Jun 2021 • Aaron Sim, Maciej Wiatrak, Angus Brayne, Páidí Creed, Saee Paliwal
The inductive biases of graph representation learning algorithms are often encoded in the background geometry of their embedding space.
1 code implementation • NeurIPS 2021 • Adam Foster, Árpi Vezér, Craig A Glastonbury, Páidí Creed, Sam Abujudeh, Aaron Sim
Learning meaningful representations of data that can address challenges such as batch effect correction and counterfactual inference is a central problem in many domains including computational biology.
no code implementations • 1 Dec 2018 • Daniel Neil, Joss Briody, Alix Lacoste, Aaron Sim, Paidi Creed, Amir Saffari
In this work, we provide a new formulation for Graph Convolutional Neural Networks (GCNNs) for link prediction on graph data that addresses common challenges for biomedical knowledge graphs (KGs).
no code implementations • 24 Sep 2013 • Aaron Sim, Dimosthenis Tsagkrasoulis, Giovanni Montana
We propose a non-parametric regression methodology, Random Forests on Distance Matrices (RFDM), for detecting genetic variants associated to quantitative phenotypes representing the human brain's structure or function, and obtained using neuroimaging techniques.