Machine Learning Projects

Some of my Machine Learning projects. From Neural ODEs to Topological Data Analysis and Graph Neural Networks.

Predicting Disability Progression in Multiple Sclerosis with Machine Learning

Research in Multiple Sclerosis (MS) has recently focused on extracting knowledge from real-world clinical data sources. This type of data is more abundant than data produced during clinical trials and potentially more informative about real-world clinical practice. However, this comes at the cost of less curated and controlled data sets. In this work, we address the task of optimally extracting information from longitudinal patient data in the real-world setting with a special focus on the sporadic sampling problem....

Topological Graph Neural Networks

Graph neural networks (GNNs) are a powerful architecture for tackling graph learning tasks, yet have been shown to be oblivious to eminent substructures such as cycles. We present TOGL, a novel layer that incorporates global topological information of a graph using persistent homology. TOGL can be easily integrated into any type of GNN and is strictly more expressive in terms of the Weisfeiler-Lehman graph isomorphism test. Augmenting GNNs with our layer leads to improved predictive performance for graph and node classification tasks, both on synthetic data sets (which can be classified by humans using their topology but not by ordinary GNNs) and on real-world data....

Latent Convergent Cross Mapping : Causal Directions between Irregular Time Series

Discovering causal structures of temporal processes is a major tool of scientific inquiry because it helps us better understand and explain the mechanisms driving a phenomenon of interest, thereby facilitating analysis, reasoning, and synthesis for such systems. However, accurately inferring causal structures within a phenomenon based on observational data only is still an open problem. Indeed, this type of data usually consists in short time series with missing or noisy values for which causal inference is increasingly difficult....

Continuous modeling of sporadically-observed time series

Modeling real-world multidimensional time series can be particularly challenging when these are sporadically observed (ie, sampling is irregular both in time and across dimensions)—such as in the case of clinical patient data. To address these challenges, we propose (1) a continuous-time version of the Gated Recurrent Unit, building upon the recent Neural Ordinary Differential Equations (Chen et al., 2018), and (2) a Bayesian update network that processes the sporadic observations. We bring these two ideas together in our GRU-ODE-Bayes method....