Paul Scherer

Maja Trębacz, Zohreh Shams, Mateja Jamnik et al.

Stratifying cancer patients based on their gene expression levels allows improving diagnosis, survival analysis and treatment planning. However, such data is extremely highly dimensional as it contains expression values for over 20000 genes per patient, and the number of samples in the datasets is low. To deal with such settings, we propose to incorporate prior biological knowledge about genes from ontologies into the machine learning system for the task of patient classification given their gene expression data. We use ontology embeddings that capture the semantic similarities between the genes to direct a Graph Convolutional Network, and therefore sparsify the network connections. We show this approach provides an advantage for predicting clinical targets from high-dimensional low-sample data.

Paul Scherer, Maja Trȩbacz, Nikola Simidjievski et al.

We propose a method for gene expression based analysis of cancer phenotypes incorporating network biology knowledge through unsupervised construction of computational graphs. The structural construction of the computational graphs is driven by the use of topological clustering algorithms on protein-protein networks which incorporate inductive biases stemming from network biology research in protein complex discovery. This structurally constrains the hypothesis space over the possible computational graph factorisation whose parameters can then be learned through supervised or unsupervised task settings. The sparse construction of the computational graph enables the differential protein complex activity analysis whilst also interpreting the individual contributions of genes/proteins involved in each individual protein complex. In our experiments analysing a variety of cancer phenotypes, we show that the proposed methods outperform SVM, Fully-Connected MLP, and Randomly-Connected MLPs in all tasks. Our work introduces a scalable method for incorporating large interaction networks as prior knowledge to drive the construction of powerful computational models amenable to introspective study.

Paul Scherer, Pietro Lio

We present Geo2DR (Geometric to Distributed Representations), a GPU ready Python library for unsupervised learning on graph-structured data using discrete substructure patterns and neural language models. It contains efficient implementations of popular graph decomposition algorithms and neural language models in PyTorch which can be combined to learn representations of graphs using the distributive hypothesis. Furthermore, Geo2DR comes with general data processing and loading methods to bring substantial speed-up in the training of the neural language models. Through this we provide a modular set of tools and methods to quickly construct systems capable of learning distributed representations of graphs. This is useful for replication of existing methods, modification, or development of completely new methods. This paper serves to present the Geo2DR library and perform a comprehensive comparative analysis of existing methods re-implemented using Geo2DR across widely used graph classification benchmarks. Geo2DR displays a high reproducibility of results in published methods and interoperability with other libraries useful for distributive language modelling.

Paul Scherer, Helena Andres-Terre, Pietro Lio et al.

We present two instances, L-GAE and L-VGAE, of the variational graph auto-encoding family (VGAE) based on separating feature propagation operations from graph convolution layers typically found in graph learning methods to a single linear matrix computation made prior to input in standard auto-encoder architectures. This decoupling enables the independent and fixed design of the auto-encoder without requiring additional GCN layers for every desired increase in the size of a node's local receptive field. Fixing the auto-encoder enables a fairer assessment on the size of a nodes receptive field in building representations. Furthermore a by-product of fixing the auto-encoder design often results in substantially smaller networks than their VGAE counterparts especially as we increase the number of feature propagations. A comparative downstream evaluation on link prediction tasks show comparable state of the art performance to similar VGAE arrangements despite considerable simplification. We also show the simple application of our methodology to more challenging representation learning scenarios such as spatio-temporal graph representation learning.