Guy Wolf

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Core Academic Member
Guy Wolf
Associate Professor, Université de Montréal
Guy Wolf

Guy Wolf is an Associate Professor in the Department of Mathematics and Statistics at the Université de Montréal. His research interests lie at the intersection of machine learning, data science and applied mathematics. He is particularly interested in data mining methods that use manifold learning and deep geometric learning, as well as applications for exploratory analysis of biomedical data.

His research focuses on exploratory data analysis, with applications in bioinformatics. His approaches are multidisciplinary and combine together machine learning, signal processing, and applied math tools. In particular, his recent works use a combination of diffusion geometries and deep learning to find emergent patterns, dynamics, and structure in big high dimensional data (e.g., in single-cell genomics and proteomics).

PhD and MSc students who are interested in doing research at the intersection applied math, machine learning, and data science, are welcome to contact me by email.

Publications

2021-07

Embedding Signals on Knowledge Graphs with Unbalanced Diffusion Earth Mover's Distance.
Alexander Tong, Guillaume Huguet, Dennis L. Shung, Amine Natik, Manik Kuchroo, Guillaume Lajoie, Guy Wolf and Smita Krishnaswamy
arXiv preprint arXiv:2107.12334
(2021-07-26)
ui.adsabs.harvard.eduPDF
Diffusion Earth Mover's Distance and Distribution Embeddings
Alexander Tong, Guillaume Huguet, Amine Natik, Kincaid Macdonald, Manik Kuchroo, Ronald Coifman, Guy Wolf and Smita Krishnaswamy

2021-06

Geometric Scattering Attention Networks
Yimeng Min, Frederik Wenkel and Guy Wolf
Genomic epidemiology and associated clinical outcomes of a SARS-CoV-2 outbreak in a general adult hospital in Quebec
Pare B, Rozendaal M, Morin S, Poujol R, Mostefai F, Grenier J, Kaufmann L, Xing H, Sanchez M, Yechouron A, Racette R, Hussin J, Wolf G, Pavlov I and Smith Ma
medRxiv
(2021-06-01)
europepmc.orgPDF

2021-05

Decoupled Greedy Learning of Graph Neural Networks
Yewen Wang, Jian Tang, Yizhou Sun and Guy Wolf
(venue unknown)
(2021-05-04)
openreview.netPDF
Visualizing High-Dimensional Trajectories on the Loss-Landscape of ANNs
Stefan Horoi, Jessie Huang, Guy Wolf and Smita Krishnaswamy
arXiv e-prints
(2021-05-04)
ui.adsabs.harvard.eduPDF
Data-driven Learning of Geometric Scattering Networks
Alexander Tong, Frederik Wenkel, Kincaid Macdonald, Smita Krishnaswamy and Guy Wolf
arXiv e-prints
(2021-05-04)
ui.adsabs.harvard.eduPDF

2021-02

Structural and developmental principles of neuropil assembly in C. elegans
Mark W. Moyle, Kristopher M. Barnes, Manik Kuchroo, Alex Gonopolskiy, Leighton H. Duncan, Titas Sengupta, Lin Shao, Min Guo, Anthony Santella, Ryan Christensen, Abhishek Kumar, Yicong Wu, Kevin R. Moon, Guy Wolf, Smita Krishnaswamy, Zhirong Bao, Hari Shroff, William A. Mohler and Daniel A. Colón-Ramos
Multimodal data visualization, denoising and clustering with integrated diffusion.
Manik Kuchroo, Abhinav Godavarthi, Guy Wolf and Smita Krishnaswamy
arXiv preprint arXiv:2102.06757
(2021-02-12)
ui.adsabs.harvard.eduPDF
Quantifying the effect of experimental perturbations at single-cell resolution.
Daniel B. Burkhardt, Jay S. Stanley, Alexander Tong, Ana Luisa Perdigoto, Scott A. Gigante, Kevan C. Herold, Guy Wolf, Antonio J. Giraldez, David van Dijk and Smita Krishnaswamy
Nature Biotechnology
(2021-02-08)
europepmc.org[Also on bioRxiv (2020-12-02)]

2021-01

Topological analysis of single-cell data reveals shared glial landscape of macular degeneration and neurodegenerative diseases
Manik Kuchroo, Marcello DiStasio, Eda Calapkulu, Maryam Ige, Le Zhang, Amar H. Sheth, Madhvi Menon, Yu Xing, Scott Gigante, Jessie Huang, Rahul M. Dhodapkar, Bastian Rieck, Guy Wolf, Smita Krishnaswamy and Brian P. Hafler
bioRxiv
(2021-01-20)
www.biorxiv.orgPDF

2020-12

Uncovering the Folding Landscape of RNA Secondary Structure Using Deep Graph Embeddings
Egbert Castro, Andrew Benz, Alexander Tong, Guy Wolf and Smita Krishnaswamy
BIG DATA 2020
(2020-12-10)
dblp.uni-trier.dePDF
Extendable and invertible manifold learning with geometry regularized autoencoders
Andres F. Duque, Sacha Morin, Guy Wolf and Kevin Moon
BIG DATA 2020
(2020-12-10)
doi.orgPDF
Extendable and invertible manifold learning with geometry regularized autoencoders
Andres F. Duque, Sacha Morin, Guy Wolf and Kevin Moon
BIG DATA 2020
(2020-12-10)
doi.orgPDF

2020-11

Multiscale PHATE Exploration of SARS-CoV-2 Data Reveals Multimodal Signatures of Disease
Manik Kuchroo, Jessie Huang, Patrick Wong, Jean-Christophe Grenier, Dennis Shung, Alexander Tong, Carolina Lucas, Jon Klein, Daniel Burkhardt, Scott Gigante, Abhinav Godavarthi, Benjamin Goldman-Israelow, Tianyang Mao, Ji Eun Oh, Julio Silva, Takehiro Takahashi, Camila Odio, Arnau Casanovas-Massana, John Fournier, Yale Impact Team... (8 more)
Social Science Research Network
(2020-11-23)
papers.ssrn.com
Multiscale PHATE Exploration of SARS-CoV-2 Data Reveals Multimodal Signatures of Disease
Manik Kuchroo, Jessie Huang, Patrick Wong, Jean-Christophe Grenier, Dennis Shung, Alexander Tong, Carolina Lucas, Jon Klein, Daniel Burkhardt, Scott Gigante, Abhinav Godavarthi, Ben Israelow, Tianyang Mao, Ji Eun Oh, Julio Silva, Takehiro Takahashi, Camila Odio, Arnau Casanovas-Massana, John Fournier, Shelli Farhadian... (8 more)
bioRxiv
(2020-11-17)
europepmc.orgPDF

2020-09

Fixing Bias in Reconstruction-Based Anomaly Detection with Lipschitz Discriminators
Alexander Tong, Guy Wolf and Smita Krishnaswamyt
MLSP 2020
(2020-09-01)
dblp.uni-trier.de
Learning General Transformations of Data for Out-of-Sample Extensions
Matthew Amodio, David van Dijk, Guy Wolf and Smita Krishnaswamy
MLSP 2020
(2020-09-01)
dblp.uni-trier.de

2020-07

TrajectoryNet: A Dynamic Optimal Transport Network for Modeling Cellular Dynamics
Alexander Tong, Jessie Huang, Guy Wolf, David van Dijk and Smita Krishnaswamy
Geometric Wavelet Scattering Networks on Compact Riemannian Manifolds.
Michael Perlmutter, Feng Gao, Guy Wolf and Matthew J. Hirn
Proceedings of machine learning research
(2020-07-01)
dblp.uni-trier.dePDF

2020-06

Advantages of biologically-inspired adaptive neural activation in RNNs during learning.
Victor Geadah, Giancarlo Kerg, Stefan Horoi, Guy Wolf and Guillaume Lajoie
arXiv preprint arXiv:2006.12253
(2020-06-22)
dblp.uni-trier.dePDF
Supervised Visualization for Data Exploration
Jake S. Rhodes, Adele Cutler, Guy Wolf and Kevin R. Moon
arXiv preprint arXiv:2006.08701
(2020-06-15)
ui.adsabs.harvard.eduPDF
Uncovering the Folding Landscape of RNA Secondary Structure with Deep Graph Embeddings
Egbert Castro, Andrew Benz, Alexander Tong, Guy Wolf and Smita Krishnaswamy
arXiv preprint arXiv:2006.06885
(2020-06-12)
export.arxiv.orgPDF

2020-05

Low-Dimensional Dynamics of Encoding and Learning in Recurrent Neural Networks
Stefan Horoi, Victor Geadah, Guy Wolf and Guillaume Lajoie
AI 2020
(2020-05-13)
link.springer.com

2020-04

Interpretable Neuron Structuring with Graph Spectral Regularization.
Alexander Tong, David van Dijk, Jay S. Stanley, Matthew Amodio, Kristina Yim, Rebecca Muhle, James Noonan, Guy Wolf and Smita Krishnaswamy
IDA 2020
(2020-04-27)
www.ncbi.nlm.nih.govPDF

2020-03

Scattering GCN: Overcoming Oversmoothness in Graph Convolutional Networks
Yimeng Min, Frederik Wenkel and Guy Wolf

2020-02

Identifying Critical Neurons in ANN Architectures using Mixed Integer Programming
Mostafa ElAraby, Guy Wolf and Margarida Carvalho
arXiv preprint arXiv:2002.07259
(2020-02-17)
ui.adsabs.harvard.eduPDF

2020-01

Uncovering axes of variation among single-cell cancer specimens.
William S. Chen, Nevena Zivanovic, David van Dijk, Guy Wolf, Bernd Bodenmiller and Smita Krishnaswamy
Nature Methods
(2020-01-13)
www.nature.comPDF
Internal representation dynamics and geometry in recurrent neural networks.
Stefan Horoi, Guillaume Lajoie and Guy Wolf
arXiv preprint arXiv:2001.03255
(2020-01-09)
ui.adsabs.harvard.eduPDF
Uncovering the Topology of Time-Varying fMRI Data using Cubical Persistence
Bastian Rieck, Tristan Yates, Christian Bock, Karsten M. Borgwardt, Guy Wolf, Nicholas B. Turk-Browne and Smita Krishnaswamy
Author Correction: Visualizing structure and transitions in high-dimensional biological data.
Kevin R. Moon, David van Dijk, Zheng Wang, Scott Gigante, Daniel B. Burkhardt, William S. Chen, Kristina Yim, Antonia van den Elzen, Matthew J. Hirn, Ronald R. Coifman, Natalia B. Ivanova, Guy Wolf and Smita Krishnaswamy
Nature Biotechnology
(2020-01-01)
www.nature.com

2019-12

Finding Archetypal Spaces Using Neural Networks
David van Dijk, Daniel B. Burkhardt, Matthew Amodio, Alexander Tong, Guy Wolf and Smita Krishnaswamy
BIG DATA 2019
(2019-12-01)
doi.org
Visualizing structure and transitions in high-dimensional biological data
Kevin R Moon, David van Dijk, Zheng Wang, Scott Gigante, Daniel B Burkhardt, William S Chen, Kristina Yim, Antonia van den Elzen, Matthew J Hirn, Ronald R Coifman, Natalia B Ivanova, Guy Wolf and Smita Krishnaswamy
Nature Biotechnology
(2019-12-01)
www.nature.com

2019-11

Understanding Graph Neural Networks with Asymmetric Geometric Scattering Transforms
Michael Perlmutter, Feng Gao, Guy Wolf and Matthew J. Hirn
arXiv: Machine Learning
(2019-11-14)
ui.adsabs.harvard.eduPDF

2019-10

Visualizing High Dimensional Dynamical Processes
Andres F. Duque, Guy Wolf and Kevin R. Moon
MLSP 2019
(2019-10-12)
sigport.orgPDF
Exploring single-cell data with deep multitasking neural networks.
Matthew Amodio, David van Dijk, Krishnan Srinivasan, William S Chen, Hussein Mohsen, Kevin R Moon, Allison Campbell, Yujiao Zhao, Xiaomei Wang, Manjunatha Venkataswamy, Anita Desai, V Ravi, Priti Kumar, Ruth Montgomery, Guy Wolf and Smita Krishnaswamy
Nature Methods
(2019-10-07)
www.nature.comPDF

2019-09

Beyond GANs: Transforming without a Target Distribution
Matthew Amodio, David van Dijk, Ruth Montgomery, Guy Wolf and Smita Krishnaswamy
(venue unknown)
(2019-09-25)
openreview.netPDF
Geometric wavelet scattering on graphs and manifolds
Feng Gao, Matthew Hirn, Michael Perlmutter and Guy Wolf
Wavelets and Sparsity XVIII
(2019-09-09)
www.spiedigitallibrary.org
Quantifying the effect of experimental perturbations in single-cell RNA-sequencing data using graph signal processing
Daniel B. Burkhardt, Jay S. Stanley, Alexander Tong, Ana Luisa Perdigoto, Scott A. Gigante, Kevan C. Herold, Guy Wolf, Antonio J. Giraldez, David van Dijk and Smita Krishnaswamy
bioRxiv
(2019-09-06)
www.biorxiv.orgPDF

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