Portrait of Matthew Scicluna

Matthew Scicluna

PhD - Université de Montréal
Supervisor
Julie Hussin
Co-supervisor
Guy Wolf
Research Topics
Computational Biology
Deep Learning
Google Scholar
GitHub

Publications

Measure Before You Look: Grounding Embeddings Through Manifold Metrics
César Miguel Valdez Cordova
Matthew Scicluna
Shuang Ni
Smita Krishnaswamy
Simon Gravel
Guy Wolf
2025-09-22
NeurIPS.cc/2025/Workshop/UniReps (published)
openreview.net
openreview.net
A Transparent and Generalizable Deep Learning Framework for Genomic Ancestry Prediction
Camille Rochefort-Boulanger
Matthew Scicluna
Raphaël Poujol
Jean-Christophe Grenier
Pierre Luc Carrier
Sébastien Lemieux
Julie G Hussin
1 Accurately capturing genetic ancestry is critical for ensuring reproducibility and fairness in genomic st… (see more)udies and downstream health research. This study aims to address the prediction of ancestry from genetic data using deep learning, with a focus on generalizability across datasets with diverse populations and on explainability to improve model transparency. We adapt the Diet Network, a deep learning architecture proven effective in handling high-dimensional data, to learn population ancestry from single nucleotide polymorphisms (SNPs) data using the populational Thousand Genomes Project dataset. Our results highlight the model’s ability to generalize to diverse populations in the CARTaGENE and Montreal Heart Institute biobanks and that predictions remain robust to high levels of missing SNPs. We show that, despite the lack of North African populations in the training dataset, the model learns latent representations that reflect meaningful population structure for North African individuals in the biobanks. To improve model transparency, we apply Saliency Maps, DeepLift, GradientShap and Integrated Gradients attribution techniques and evaluate their performance in identifying SNPs leveraged by the model. Using DeepLift, we show that model’s predictions are driven by population-specific signals consistent with those identified by traditional population genetics metrics. This work presents a generalizable and interpretable deep learning framework for genetic ancestry inference in large-scale biobanks with genetic data. By enabling more widespread genomic ancestry characterization in these cohorts, this study contributes practical tools for integrating genetic data into downstream biomedical applications, supporting more inclusive and equitable healthcare solutions.
2025-08-29
bioRxiv (preprint)
doi.org
Toward computing attributions for dimensionality reduction techniques
Matthew Scicluna
Jean-Christophe Grenier
Raphaël Poujol
Sébastien Lemieux
Julie G. Hussin
We describe the problem of computing local feature attributions for dimensionality reduction methods. We use one such method that is well es… (see more)tablished within the context of supervised classification—using the gradients of target outputs with respect to the inputs—on the popular dimensionality reduction technique t-SNE, widely used in analyses of biological data. We provide an efficient implementation for the gradient computation for this dimensionality reduction technique. We show that our explanations identify significant features using novel validation methodology; using synthetic datasets and the popular MNIST benchmark dataset. We then demonstrate the practical utility of our algorithm by showing that it can produce explanations that agree with domain knowledge on a SARS-CoV-2 sequence dataset. Throughout, we provide a road map so that similar explanation methods could be applied to other dimensionality reduction techniques to rigorously analyze biological datasets. We have created a Python package that can be installed using the following command: pip install interpretable_tsne. All code used can be found at github.com/MattScicluna/interpretable_tsne.
2022-12-31
Bioinformatics Advances (published)
doi.org