Mila > Team > Guy Wolf

# Guy Wolf

Core Academic Member
guy.wolf@umontreal.ca
http://guywolf.org/
Spectral Learning
Manifold Learning
Computational Biology
Data-Mining
Deep Learning
Dynamical Systems
Learning on Graphs
Graph Neural Networks
Medical Machine Learning (ML)
Multimodal Learning
Core Academic Member
Associate Professor, Université de Montréal, Canada CIFAR AI Chair

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).

#### Joining Prof. Wolf’s team (aka RAFALES):

- UdeM students are welcome to take Prof. Wolf’s classes, and then discuss supervision (summer internship and/or graduate research) with him, which will depend on project interests and performance in class.
- Candidates applying to graduate programs through Mila and/or UdeM (DMS or DIRO) are welcome to mark him as requested/preferred supervisor.
- PhD and MSc students who are interested in doing research at the intersection applied math, machine learning, and data science, are welcome to contact Prof. Wolf by email. However, please notice he will likely not respond unless your profile is of interest, and even then it might take a while for him to respond.

## Publications

### 2021-11

Fixing Bias in Reconstruction-based Anomaly Detection with Lipschitz Discriminators
Alexander Tong, Guy Wolf and Smita Krishnaswamy
Journal of Signal Processing Systems
(2021-11-28)
PDF
MURAL: An Unsupervised Random Forest-Based Embedding for Electronic Health Record Data.
Michal Gerasimiuk, Dennis L. Shung, Alexander Tong, Adrian J. Stanley, Michael Schultz, Jeffrey Ngu, Loren Laine, Guy Wolf and Smita Krishnaswamy
arXiv preprint arXiv:2111.10452
(2021-11-19)
dblp.uni-trier.de PDF

### 2021-10

Towards a Taxonomy of Graph Learning Datasets.
Renming Liu, Semih Cantürk, Frederik Wenkel, Dylan Sandfelder, Devin Kreuzer, Anna Little, Sarah McGuire, Leslie O'Bray, Michael Perlmutter, Bastian Rieck, Matthew Hirn, Guy Wolf and Ladislav Rampásek
arXiv preprint arXiv:2110.14809
(2021-10-27)
dblp.uni-trier.de PDF
Data-Driven Learning of Geometric Scattering Modules for GNNs
Alexander Tong, Frederick Wenkel, Kincaid Macdonald, Smita Krishnaswamy and Guy Wolf
MLSP 2021
(2021-10-25)
dblp.uni-trier.de
Multimodal Data Visualization and Denoising with Integrated Diffusion
Manik Kuchroo, Abhinav Godavarthi, Alexander Tong, Guy Wolf and Smita Krishnaswamy
MLSP 2021
(2021-10-25)
dblp.uni-trier.de
Hierarchical Graph Neural Nets can Capture Long-Range Interactions
Ladislav Rampasek and Guy Wolf
MLSP 2021
(2021-10-25)
dblp.uni-trier.de[Also on arXiv preprint arXiv:2107.07432 (2021-07-15)]

### 2021-09

Data-driven approaches for genetic characterization of SARS-CoV-2 lineages
Fatima Mostefai, Isabel Gamache, Jessie Huang, Arnaud N’Guessan, Justin Pelletier, Ahmad Pesaranghader, David Hamelin, Carmen Lia Murall, Raphaël Poujol, Jean-Christophe Grenier, Martin Smith, Etienne Caron, Morgan Craig, Jesse Shapiro, Guy Wolf, Smita Krishnaswamy and Julie G. Hussin
bioRxiv
(2021-09-29)
www.biorxiv.org
Topological Analysis of Single-Cell Hierarchy Reveals Inflammatory Glial Landscape of Macular Degeneration
Manik Kuchroo, Marcello DiStasio, Eric Song, Eda Calapkulu, Le Zhang, Maryam Ige, Amar H. Sheth, Madhvi Menon, Alexander Tong, Abhinav Godavarthi, Yu Xing, Scott Gigante, Holly Steach, Jessie Huang, Guillaume Huguet, Janhavi Narain, George Mourgkos, Rahul M. Dhodapkar, Matthew J. Hirn, Bastian Rieck... (3 more)
Social Science Research Network
(2021-09-29)
papers.ssrn.com

### 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.edu PDF
Parametric Scattering Networks.
Shanel Gauthier, Benjamin Thérien, Laurent Alsène-Racicot, Irina Rish, Eugene Belilovsky, Michael Eickenberg and Guy Wolf
arXiv preprint arXiv:2107.09539
(2021-07-20)
ui.adsabs.harvard.edu PDF
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
ICML 2021
(2021-07-18)
proceedings.mlr.press PDF[Also on arXiv preprint arXiv:2102.12833 (2021-02-25)]
Random Forest-Based Diffusion Information Geometry for Supervised Visualization and Data Exploration
Jake S. Rhodes, Adele Cutler, Guy Wolf and Kevin R. Moon
SSP 2021
(2021-07-11)
doi.org

### 2021-06

Geometric Scattering Attention Networks
Yimeng Min, Frederik Wenkel and Guy Wolf
ICASSP 2021
(2021-06-06)
ieeexplore.ieee.org[Also on arXiv preprint arXiv:2010.15010 (2020-10-28)]
Genomic epidemiology and associated clinical outcomes of a SARS-CoV-2 outbreak in a general adult hospital in Quebec
Bastien Pare, Marieke Rozendaal, Sacha Morin, Raphael Poujol, Fatima Mostefai, Jean-Christophe Grenier, Lea Kaufmann, Henry Xing, Miguelle Sanchez, Ariane Yechouron, Ronald Racette, Julie Hussin, Guy Wolf, Ivan Pavlov and Martin A Smith
medRxiv
(2021-06-01)
europepmc.org PDF

### 2021-05

Decoupled Greedy Learning of Graph Neural Networks
Yewen Wang, Jian Tang, Yizhou Sun and Guy Wolf
(venue unknown)
(2021-05-04)
openreview.net PDF
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.edu PDF
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.edu PDF

### 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
Nature
(2021-02-24)
econpapers.repec.org[Also on bioRxiv (2020-03-15)]
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.edu PDF
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.org PDF

### 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)
doi.org PDF
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.org PDF
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)
ui.adsabs.harvard.edu PDF

### 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, Benjamin Israelow, Tianyang Mao, Ji Eun Oh, Julio Silva, Takehiro Takahashi, Camila D. Odio, Arnau Casanovas-Massana, John Fournier, Yale Impact Team... (8 more)
bioRxiv
(2020-11-17)
europepmc.org PDF

### 2020-10

Learning General Transformations of Data for Out-of-Sample Extensions
Matthew Amodio, David van Dijk, Guy Wolf and Smita Krishnaswamy
MLSP 2020
(2020-10-20)
www.ncbi.nlm.nih.gov

### 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

### 2020-08

Geometric Wavelet Scattering Networks on Compact Riemannian Manifolds.
Michael Perlmutter, Feng Gao, Guy Wolf and Matthew J. Hirn
Mathematical and Scientific Machine Learning
(2020-08-16)
proceedings.mlr.press PDF

### 2020-07

TrajectoryNet: A Dynamic Optimal Transport Network for Modeling Cellular Dynamics
Alexander Tong, Jessie Huang, Guy Wolf, David van Dijk and Smita Krishnaswamy
ICML 2020
(2020-07-12)
proceedings.mlr.press PDF[Also on arXiv preprint arXiv:2002.04461 (2020-02-09)]
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.de PDF

### 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)
ui.adsabs.harvard.edu PDF
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.edu PDF
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)
ui.adsabs.harvard.edu PDF

### 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)
europepmc.org PDF

### 2020-03

Scattering GCN: Overcoming Oversmoothness in Graph Convolutional Networks
Yimeng Min, Frederik Wenkel and Guy Wolf
NEURIPS 2020
(2020-03-18)
papers.nips.cc PDF[LATEST on arXiv preprint arXiv:2003.08414 (2020-03-18)]

### 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.edu PDF

### 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)
europepmc.org PDF
Internal representation dynamics and geometry in recurrent neural networks.
Stefan Horoi, Guillaume Lajoie and Guy Wolf
arXiv: Learning
(2020-01-09)
ui.adsabs.harvard.edu PDF
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
NEURIPS 2020
(2020-01-01)
papers.nips.cc PDF[LATEST on arXiv preprint arXiv:2006.07882 (2020-06-14)]
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 preprint arXiv:1911.06253
(2019-11-14)
ui.adsabs.harvard.edu PDF

### 2019-10

Visualizing High Dimensional Dynamical Processes
Andres F. Duque, Guy Wolf and Kevin R. Moon
MLSP 2019
(2019-10-12)
doi.org PDF
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.com PDF

### 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.net PDF
Geometric wavelet scattering on graphs and manifolds
Feng Gao, Matthew Hirn, Michael Perlmutter and Guy Wolf
https://doi.org/10.1117/12.2529615
(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.org PDF

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