Páidí Creed

Aaron Sim, Maciej Wiatrak, Angus Brayne et al.

The inductive biases of graph representation learning algorithms are often encoded in the background geometry of their embedding space. In this paper, we show that general directed graphs can be effectively represented by an embedding model that combines three components: a pseudo-Riemannian metric structure, a non-trivial global topology, and a unique likelihood function that explicitly incorporates a preferred direction in embedding space. We demonstrate the representational capabilities of this method by applying it to the task of link prediction on a series of synthetic and real directed graphs from natural language applications and biology. In particular, we show that low-dimensional cylindrical Minkowski and anti-de Sitter spacetimes can produce equal or better graph representations than curved Riemannian manifolds of higher dimensions.

Adam Foster, Árpi Vezér, Craig A Glastonbury et al.

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. Adopting a Conditional VAE framework, we show that marginal independence between the representation and a condition variable plays a key role in both of these challenges. We propose the Contrastive Mixture of Posteriors (CoMP) method that uses a novel misalignment penalty defined in terms of mixtures of the variational posteriors to enforce this independence in latent space. We show that CoMP has attractive theoretical properties compared to previous approaches, and we prove counterfactual identifiability of CoMP under additional assumptions. We demonstrate state-of-the-art performance on a set of challenging tasks including aligning human tumour samples with cancer cell-lines, predicting transcriptome-level perturbation responses, and batch correction on single-cell RNA sequencing data. We also find parallels to fair representation learning and demonstrate that CoMP is competitive on a common task in the field.

Daniel Neil, Joss Briody, Alix Lacoste et al.

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). We introduce a regularized attention mechanism to GCNNs that not only improves performance on clean datasets, but also favorably accommodates noise in KGs, a pervasive issue in real-world applications. Further, we explore new visualization methods for interpretable modelling and to illustrate how the learned representation can be exploited to automate dataset denoising. The results are demonstrated on a synthetic dataset, the common benchmark dataset FB15k-237, and a large biomedical knowledge graph derived from a combination of noisy and clean data sources. Using these improvements, we visualize a learned model's representation of the disease cystic fibrosis and demonstrate how to interrogate a neural network to show the potential of PPARG as a candidate therapeutic target for rheumatoid arthritis.