Guy Wolf

Biographie

Guy Wolf est professeur agrégé au Département de mathématiques et de statistique de l'Université de Montréal. Ses intérêts de recherche se situent au carrefour de l'apprentissage automatique, de la science des données et des mathématiques appliquées. Il s'intéresse particulièrement aux méthodes d'exploration de données qui utilisent l'apprentissage multiple et l'apprentissage géométrique profond, ainsi qu'aux applications pour l'analyse exploratoire des données biomédicales.

Ses recherches portent sur l'analyse exploratoire des données, avec des applications en bio-informatique. Ses approches sont multidisciplinaires et combinent l'apprentissage automatique, le traitement du signal et les outils mathématiques appliqués. En particulier, ses travaux récents utilisent une combinaison de géométries de diffusion et d'apprentissage profond pour trouver des modèles émergents, des dynamiques et des structures dans les mégadonnées à grande dimension (par exemple, dans la génomique et la protéomique de la cellule unique).

Étudiants actuels

Ria Arora

Maîtrise recherche - UdeM

Co-superviseur⋅e :

Doctorat - UdeM

Doctorat - UdeM

semihcanturk00@gmail.com

Collaborateur·rice alumni

Enrique Fita Sanmartin

Collaborateur·rice alumni - UdeM

Kameron Harris

Collaborateur·rice de recherche - Western Washington University (faculty; assistant prof))

Co-superviseur⋅e :

Doctorat - UdeM

Will Hua

Collaborateur·rice alumni - McGill

Xiaolong Huang

Maîtrise recherche - Concordia

Superviseur⋅e principal⋅e :

Doctorat - UdeM

Paul Janson

Doctorat - Concordia

Superviseur⋅e principal⋅e :

Charles-Etienne Joseph

Maîtrise recherche - UdeM

Superviseur⋅e principal⋅e :

M. Elyes Kanoun

Stagiaire de recherche - UdeM

Vincent Létourneau

Postdoctorat - UdeM

Myriam Lizotte

Doctorat - UdeM

Philippe Martin

Doctorat - UdeM

Co-superviseur⋅e :

Paul François

Paria Mehrbod

Maîtrise recherche - Concordia

Superviseur⋅e principal⋅e :

Lydia Mezrag

Doctorat - UdeM

Sacha Morin

Doctorat - UdeM

Co-superviseur⋅e :

Postdoctorat - Concordia

Superviseur⋅e principal⋅e :

geraldin.nanfack@mila.quebec

Amine Natik

Doctorat - UdeM

Superviseur⋅e principal⋅e :

Guillaume Lajoie

Shuang Ni

Doctorat - UdeM

stephanie.zandee@mcgill.ca

Albert Orozco Camacho

Doctorat - Concordia

Superviseur⋅e principal⋅e :

Maîtrise recherche - UdeM

Matthew Scicluna

Doctorat - UdeM

Superviseur⋅e principal⋅e :

Collaborateur·rice de recherche - UdeM

Co-superviseur⋅e :

Doctorat - UdeM

Stagiaire de recherche - Western Washington University

Superviseur⋅e principal⋅e :

Postdoctorat - UdeM

Collaborateur·rice de recherche - McGill (assistant professor)

Analyser le paradoxe des interférons inhérent à la COVID-19 au moyen de la réduction de la dimensionnalité et du regroupement

Billets de blogue

Graph and representation of working methodology, and graph of data on deaths 60 days after onset of symptoms.

19 février 2025

par

Sacha Morin

Elsa Brunet-Ratnasingham

Guy Wolf

Lire l'article

Publications

Channel Selection for Test-Time Adaptation Under Distribution Shift

Pedro Vianna

Muawiz Sajjad Chaudhary

An Tang

Guy Cloutier

Michael Eickenberg

To ensure robustness and generalization to real-world scenarios, test-time adaptation has been recently studied as an approach to adjust mod… (voir plus)els to a new data distribution during inference. Test-time batch normalization is a simple and popular method that achieved compelling performance on domain shift benchmarks by recalculating batch normalization statistics on test batches. However, in many practical applications this technique is vulnerable to label distribution shifts. We propose to tackle this challenge by only selectively adapting channels in a deep network, minimizing drastic adaptation that is sensitive to label shifts. We find that adapted models significantly improve the performance compared to the baseline models and counteract unknown label shifts.

2023-10-27

NeurIPS.cc/2023/Workshop/DistShift (poster)

Understanding Graph Neural Networks with Generalized Geometric Scattering Transforms

Michael Perlmutter

Alexander Tong

Feng Gao

Matthew Hirn

The scattering transform is a multilayered wavelet-based deep learning architecture that acts as a model of convolutional neural networks. R… (voir plus)ecently, several works have introduced generalizations of the scattering transform for non-Euclidean settings such as graphs. Our work builds upon these constructions by introducing windowed and non-windowed geometric scattering transforms for graphs based upon a very general class of asymmetric wavelets. We show that these asymmetric graph scattering transforms have many of the same theoretical guarantees as their symmetric counterparts. As a result, the proposed construction unifies and extends known theoretical results for many of the existing graph scattering architectures. In doing so, this work helps bridge the gap between geometric scattering and other graph neural networks by introducing a large family of networks with provable stability and invariance guarantees. These results lay the groundwork for future deep learning architectures for graph-structured data that have learned filters and also provably have desirable theoretical properties.

2023-10-25

SIAM Journal on Mathematics of Data Science (publié)

arxiv.org

Comparison of Radiologists and Deep Learning for US Grading of Hepatic Steatosis.

Pedro Vianna

Sara-Ivana Calce

Pamela Boustros

Cassandra Larocque-Rigney

Laurent Patry-Beaudoin

Yi Hui Luo

Emre Aslan

John Marinos

Talal M. Alamri

Kim-Nhien Vu

Jessica Murphy-Lavallée

Jean-Sébastien Billiard

Emmanuel Montagnon

Hongliang Li

Samuel Kadoury

Bich Nguyen

Shanel Gauthier

Benjamin Thérien

Irina Rish

Eugene Belilovsky … (voir 4 de plus)

Michael Chassé

Guy Cloutier

An Tang

Background Screening for nonalcoholic fatty liver disease (NAFLD) is suboptimal due to the subjective interpretation of US images. Purpose T… (voir plus)o evaluate the agreement and diagnostic performance of radiologists and a deep learning model in grading hepatic steatosis in NAFLD at US, with biopsy as the reference standard. Materials and Methods This retrospective study included patients with NAFLD and control patients without hepatic steatosis who underwent abdominal US and contemporaneous liver biopsy from September 2010 to October 2019. Six readers visually graded steatosis on US images twice, 2 weeks apart. Reader agreement was assessed with use of κ statistics. Three deep learning techniques applied to B-mode US images were used to classify dichotomized steatosis grades. Classification performance of human radiologists and the deep learning model for dichotomized steatosis grades (S0, S1, S2, and S3) was assessed with area under the receiver operating characteristic curve (AUC) on a separate test set. Results The study included 199 patients (mean age, 53 years ± 13 [SD]; 101 men). On the test set (n = 52), radiologists had fair interreader agreement (0.34 [95% CI: 0.31, 0.37]) for classifying steatosis grades S0 versus S1 or higher, while AUCs were between 0.49 and 0.84 for radiologists and 0.85 (95% CI: 0.83, 0.87) for the deep learning model. For S0 or S1 versus S2 or S3, radiologists had fair interreader agreement (0.30 [95% CI: 0.27, 0.33]), while AUCs were between 0.57 and 0.76 for radiologists and 0.73 (95% CI: 0.71, 0.75) for the deep learning model. For S2 or lower versus S3, radiologists had fair interreader agreement (0.37 [95% CI: 0.33, 0.40]), while AUCs were between 0.52 and 0.81 for radiologists and 0.67 (95% CI: 0.64, 0.69) for the deep learning model. Conclusion Deep learning approaches applied to B-mode US images provided comparable performance with human readers for detection and grading of hepatic steatosis. Published under a CC BY 4.0 license. Supplemental material is available for this article. See also the editorial by Tuthill in this issue.

2023-10-01

Radiology (publié)

F66. FROM GENE TO COGNITION: MAPPING THE EFFECTS OF GENOMIC DELETIONS AND DUPLICATIONS ON COGNITIVE ABILITY

Sayeh Kazem

Kuldeep Kumar

Guillaume Huguet

Myriam Lizotte

Thomas Renne

Jakub Kopal

Stefan Horoi

Martineau Jean-Louis

Zohra Saci

Laura Almasy

David C. Glahn

Guillaume Dumas

Sébastien Jacquemont

2023-10-01

European Neuropsychopharmacology (publié)

Graph topological property recovery with heat and wave dynamics-based features on graphs

Dhananjay Bhaskar

Yanlei Zhang

Charles Xu

Xingzhi Sun

Oluwadamilola Fasina

Maximilian Nickel

Michael Perlmutter

Smita Krishnaswamy

2023-09-18

ArXiv (prépublication)

arxiv.org

Automated liver segmentation and steatosis grading using deep learning on B-mode ultrasound images

Pedro Vianna

Merve Kulbay

Pamela Boustros

Sara-Ivana Calce

Cassandra Larocque-Rigney

Laurent Patry-Beaudoin

Yi Hui Luo

Muawiz Chaudary

Samuel Kadoury

Bich Nguyen

Emmanuel Montagnon

Michael Chassé

An Tang

Guy Cloutier

Early detection of nonalcoholic fatty liver disease (NAFLD) is crucial to avoid further complications. Ultrasound is often used for screenin… (voir plus)g and monitoring of hepatic steatosis, however it is limited by the subjective interpretation of images. Computer assisted diagnosis could aid radiologists to achieve objective grading, and artificial intelligence approaches have been tested across various medical applications. In this study, we evaluated the performance of a two-stage hepatic steatosis detection deep learning framework, with a first step of liver segmentation and a subsequent step of hepatic steatosis classification. We evaluated the models on internal and external datasets, aiming to understand the generalizability of the framework. In the external dataset, our segmentation model achieved a Dice score of 0.92 (95% CI: 0.78, 1.00), and our classification model achieved an area under the receiver operating characteristic curve of 0.84 (95% CI: 0.79, 0.89). Our findings highlight the potential benefits of applying artificial intelligence models in NAFLD assessment.

2023-09-03

IUS (publié)

Neural FIM for learning Fisher information metrics from point cloud data

Oluwadamilola Fasina

Guillaume Huguet

Alexander Tong

Yanlei Zhang

Maximilian Nickel

Ian Adelstein

Smita Krishnaswamy

Although data diffusion embeddings are ubiquitous in unsupervised learning and have proven to be a viable technique for uncovering the under… (voir plus)lying intrinsic geometry of data, diffusion embeddings are inherently limited due to their discrete nature. To this end, we propose neural FIM, a method for computing the Fisher information metric (FIM) from point cloud data - allowing for a continuous manifold model for the data. Neural FIM creates an extensible metric space from discrete point cloud data such that information from the metric can inform us of manifold characteristics such as volume and geodesics. We demonstrate Neural FIM’s utility in selecting parameters for the PHATE visualization method as well as its ability to obtain information pertaining to local volume illuminating branching points and cluster centers embeddings of a toy dataset and two single-cell datasets of IPSC reprogramming and PBMCs (immune cells).

2023-07-03

Proceedings of the 40th International Conference on Machine Learning (publié)

Pretrained Language Models to Solve Graph Tasks in Natural Language

Frederik Wenkel

Boris Knyazev

Pretrained large language models (LLMs) are powerful learners in a variety of language tasks. We explore if LLMs can learn from graph-struct… (voir plus)ured data when the graphs are described using natural language. We explore data augmentation and pretraining specific to the graph domain and show that LLMs such as GPT-2 and GPT-3 are promising alternatives to graph neural networks.

2023-06-19

ICML.cc/2023/Workshop/SPIGM (poster)

Simulation-Free Schrödinger Bridges via Score and Flow Matching

Alexander Tong

Nikolay Malkin

Kilian FATRAS

Lazar Atanackovic

Yanlei Zhang

Guillaume Huguet

Yoshua Bengio

We present simulation-free score and flow matching ([SF]…

2023-06-19

ICML.cc/2023/Workshop/Frontiers4LCD (publié)

Geometry Regularized Autoencoders

Andres F. Duque Correa

Sacha Morin

Kevin R. Moon

A fundamental task in data exploration is to extract low dimensional representations that capture intrinsic geometry in data, especially for… (voir plus) faithfully visualizing data in two or three dimensions. Common approaches use kernel methods for manifold learning. However, these methods typically only provide an embedding of the input data and cannot extend naturally to new data points. Autoencoders have also become popular for representation learning. While they naturally compute feature extractors that are extendable to new data and invertible (i.e., reconstructing original features from latent representation), they often fail at representing the intrinsic data geometry compared to kernel-based manifold learning. We present a new method for integrating both approaches by incorporating a geometric regularization term in the bottleneck of the autoencoder. This regularization encourages the learned latent representation to follow the intrinsic data geometry, similar to manifold learning algorithms, while still enabling faithful extension to new data and preserving invertibility. We compare our approach to autoencoder models for manifold learning to provide qualitative and quantitative evidence of our advantages in preserving intrinsic structure, out of sample extension, and reconstruction. Our method is easily implemented for big-data applications, whereas other methods are limited in this regard.

2023-06-01

IEEE Transactions on Pattern Analysis and Machine Intelligence (publié)

Identifying Critical Neurons in ANN Architectures using Mixed Integer Programming

Mostafa ElAraby

Margarida Carvalho

2023-05-23

Integration of Constraint Programming, Artificial Intelligence, and Operations Research (publié)

arxiv.org

Data Imputation with an Autoencoder and MAGIC

Devin Eddington

Andres Felipe Duque Correa

Kevin R. Moon

Missing data is a common problem in many applications. Imputing missing values is a challenging task, as the imputations need to be accurate… (voir plus) and robust to avoid introducing bias in downstream analysis. In this paper, we propose an ensemble method that combines the strengths of a manifold learning-based imputation method called MAGIC and an autoencoder deep learning model. We call our method Deep MAGIC. Deep MAGIC is trained on a linear combination of the mean squared error of the original data and the mean squared error of the MAGIC-imputed data. Experimental results on three benchmark datasets show that Deep MAGIC outperforms several state-of-the-art imputation methods, demonstrating its effectiveness and robustness in handling large amounts of missing data.

2023-05-21

SampTA/2023/Conference (publié)