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Alex Tong
Alex Tong
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ALEX TONG


POSTDOCTORAL FELLOW


MILA - QUEBEC AI INSTITUTE


UNIVERSITÉ DE MONTRÉAL

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ABOUT ME

I am a postdoc with Yoshua Bengio studying the causal discovery of cell dynamics
at Mila in Montreal. This work is in collaboration with Bernhard Schölkopf and
Fabian Theis through the newly formed Helmholtz International Lab, a
German-Canadian collaboration.

I recently completed my PhD in the computer science department at Yale
University in 2021 where I was advised by Smita Krishnaswamy. My dissertation
can be found here. My current research interests are in causal machine learning,
deep learning, and optimal transport. I’m working on applying ideas from
causality, optimal transport, graph signal processing, and deep learning towards
biological, and particularly single-cell, questions. 

I grew up in Seattle, Washington, USA, and graduated from Tufts University in
2017 with a B.S. and M.S. in computer science. Outside of work I love sailing
and running.


INTERESTS

 * Causal Inference
 * Optimal Transport
 * Single Cell Transcriptomics
 * Graph Signal Processing
 * Anomaly Detection


EDUCATION

 * PhD in Computer Science, 2021
   
   Yale University

 * MPhil in Computer Science, 2020
   
   Yale University

 * MS in Computer Science, 2017
   
   Tufts University

 * BS in Computer Science, 2017
   
   Tufts University


FEATURED PUBLICATIONS


DIFFUSION EARTH MOVER'S DISTANCE AND DISTRIBUTION EMBEDDINGS

A fast diffusion-based earth mover’s distance
Alexander Tong, Guillaume Huguet, Amine Natik, Kincaid MacDonald, Manik Kuchroo,
Ronald Coifman, Guy Wolf, Smita Krishnaswamy
PDF Cite Code Poster Slides Video Arxiv ICML Page Tweetorial



FIXING BIAS IN RECONSTRUCTION-BASED ANOMALY DETECTION WITH LIPSCHITZ
DISCRIMINATORS

We fix unwanted biases in standard deep anomaly detection with a new
architecture.
Alexander Tong, Guy Wolf, Smita Krishnaswamy
PDF Cite Code Slides Video Yale Daily Article Best Paper Award



TRAJECTORYNET: A DYNAMIC OPTIMAL TRANSPORT NETWORK FOR MODELING CELLULAR
DYNAMICS

A Combination of Continuous Normalizing Flows and Dynamic Optimal Transport to
model the dynamics of cells.
Alexander Tong, Jessie Huang, Guy Wolf, David van Dijk, Smita Krishnaswamy
PDF Cite Code Slides Video Arxiv ICML Page Introductory Talk

See all publications


PREPRINTS

Guillaume Huguet, Alexander Tong, Bastian Rieck, Jessie Huang, Manik Kuchroo,
Matthew Hirn, Guy Wolf, Smita Krishnaswamy (2022). Time-Inhomogeneous Diffusion
Geometry and Topology. arXiv.

Cite arXiv

Alexander Tong, Guillaume Huguet, Dennis Shung, Amine Natik, Manik Kuchroo,
Guillaume Lajoie, Guy Wolf, Smita Krishnaswamy (2021). Embedding Signals on
Knowledge Graphs with Unbalanced Diffusion Earth Mover's Distance. to appear
ICASSP 2022.

PDF Cite Code Arxiv


PUBLICATIONS

Michal Gerasimiuk, Dennis L. Shung, Alexander Tong, Adrian J. Stanley, Machael
Shultz, Jeffrey Ngu, Loren Laine, Guy Wolf, Smita Krishnaswamy (2021). MURAL: An
Unsupervised Random Forest-Based Embedding for Electronic Health Record Data. In
IEEE Big Data.

Cite Code Arxiv Tweetorial

Malte D Luecken, Daniel B Burkhardt, Robrecht Cannoodt, Christopher Lance, Aditi
Agrawal, Hananeh Aliee, Ann T Chen, Louise Deconinck, Angela M Detweiler,
Alejandro Granados, Shelly Huynh, Laura Isacco, Yang Joon Kim, Sunil Kuppasani,
Heiko Lickert, Aaron McGeever, Honey Mekonen, Joaquin Caceres, Maurizio Morri,
Michaela Mueller, Norma F Neff, Sheryl Paul, Kaylie Schneider, Scott Steelman,
Michael Sterr, Dan J Treacy, Alexander Tong, Alexandra-Chloé Villani, Guilin
Wang, Jia Yan, Ce Zhang, Angela O Pisco, Smita Krishnaswamy, Fabian J Theis,
Jonathan M Bloom (2021). A sandbox for prediction and integration of DNA, RNA,
and protein data in single cells. NeurIPS.

PDF Cite Code Competition Dataset

Alexander Tong, Guy Wolf, Smita Krishnaswamy (2021). Fixing Bias in
Reconstruction-based Anomaly Detection with Lipschitz Discriminators. In J Sign
Process Syst.

PDF Cite Code Slides Video

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, Shelli Farhadian, Charles S. Dela Cruz, Albert I.
Ko, F. Perry Wilson, Julie Hussin, Guy Wolf, Akiko Iwasaki, Smita Krishnaswamy
(2021). Multiscale PHATE Exploration of SARS-CoV-2 Data Reveals Multimodal
Signatures of Disease. To Appear Nature Biotechnology.

PDF Cite DOI

Alexander Tong, Frederik Wenkel, Kincaid MacDonald, Smita Krishnaswamy, Guy Wolf
(2021). Data-Driven Learning of Geometric Scattering Networks. In IEEE MLSP.

PDF Cite Code Slides Video ArXiv Tweetorial

Manik Kuchroo, Abhinav Godavarthi, Alexander Tong, Smita Krishnaswamy, Guy Wolf
(2021). Multimodal data visualization and denoising with integrated diffusion.
In IEEE MLSP.

PDF Cite Arxiv

Alexander Tong, Guillaume Huguet, Amine Natik, Kincaid MacDonald, Manik Kuchroo,
Ronald Coifman, Guy Wolf, Smita Krishnaswamy (2021). Diffusion Earth Mover's
Distance and Distribution Embeddings. In ICML.

PDF Cite Code Poster Slides Video Arxiv ICML Page Tweetorial

Remi Flamary, Nicolas Courty, Alexandre Gramfort, Mokhtar Z Alaya, Aurelie
Boisbunon, Stanislas Chambon, Laetitia Chapel, Adrien Corenflos, Kilian Fatras,
Nemo Fournier, Leo Gautheron, Nathalie T H Gayraud, Hicham Janati, Alain
Rakotomamonjy, Ievgen Redko, Antoine Rolet, Antony Schutz, Vivien Seguy, Danica
J Sutherland, Romain Tavenard, Alexander Tong, Titouan Vayer (2021). POT: Python
Optimal Transport. In JMLR.

PDF Cite Code

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,
Smita Krishnaswamy (2021). Quantifying the effect of experimental perturbations
in single-cell RNA-sequencing data using graph signal processing. In Nature
Biotechnology.

Cite Code DOI BiorXiv

Egbert Castro, Andrew Benz, Alexander Tong, Guy Wolf, Smita Krishnaswamy (2020).
Uncovering the Folding Landscape of RNA Secondary Structure with Deep Graph
Embeddings. In IEEE Big Data.

PDF Cite

Alexander Tong, Guy Wolf, Smita Krishnaswamy (2020). Fixing Bias in
Reconstruction-based Anomaly Detection with Lipschitz Discriminators. In IEEE
MLSP. Best Student Paper Award.

PDF Cite Code Slides Video Yale Daily Article Best Paper Award

Alexander Tong, Jessie Huang, Guy Wolf, David van Dijk, Smita Krishnaswamy
(2020). TrajectoryNet: A Dynamic Optimal Transport Network for Modeling Cellular
Dynamics. In ICML.

PDF Cite Code Slides Video Arxiv ICML Page Introductory Talk

Alexander Tong, David van Dijk, Jay S. Stanley III, Matthew Amodio, Kristina
Yim, Rebecca Muhle, James Noonan, Guy Wolf, Smita Krishnaswamy (2020).
Interpretable Neuron Structuring with Graph Spectral Regularization. In IDA.

PDF Cite Code Slides Video DOI

David van Dijk, Daniel B. Burkhardt, Matthew Amodio, Alexander Tong, Guy Wolf,
Smita Krishnaswamy (2019). Finding Archetypal Spaces Using Neural Networks. In
IEEE Big Data.

PDF Cite Code DOI Arxiv

James Aspnes, Bernhard Haeupler, Alexander Tong, Philipp Woelfel (2018).
Allocate-On-Use Space Complexity of Shared-Memory Algorithms. In DISC.

PDF Cite DOI


WORKSHOPS

and presentations without proceedings

Alexander Tong, Beatriz P. San Juan, Brandon Zhu, Christine L. Chaffer, Smita
Krishnaswamy (2021). Abstract 2839: Understanding the mesenchymal-to-epithelial
transition and its drivers in triple-negative breast cancer with continuous
normalizing flows. Cancer Research.

PDF Cite DOI

Alexander Tong, Manik Kuchroo, Guillaume Huguet, Ronald Coifman, Guy Wolf, Smita
Krishnaswamy (2020). Fast Diffusion Optimal Transport for Manifold-of-Manifold
Embeddings. NeurIPS LMRL Workshop.

Poster

Alexander Tong, Frederik Wenkel, Kincaid MacDonald, Smita Krishnaswamy, Guy Wolf
(2020). Scattering Priors for Graph Neural Networks. DeepMath.

Poster Conference

Egbert Castro, Andrew Benz, Alexander Tong, Guy Wolf, Smita Krishnaswamy (2020).
Uncovering the Folding Landscape of RNA Secondary Structure with Deep Graph
Embeddings. ICML 2020 GRLB Workshop.

PDF

Alexander Tong, Frederik Wenkel, Kincaid MacDonald, Smita Krishnaswamy, Guy Wolf
(2020). Data-Driven Learning of Geometric Scattering Networks. NeurIPS ML4M
Workshop.

Cite Arxiv

Alexander Tong, Smita Krishnaswamy (2020). Interpolating Optimal Transport
Barycenters of Patient Manifolds. ISMB.

Poster Slides Video

Alexander Tong, Jessie Huang, Guy Wolf, David van Dijk, Smita Krishnaswamy
(2019). Modeling Cellular Dynamics with Continuous Normalizing Flows. NeurIPS
LMRL Workshop.

Poster

Alexander Tong, David van Dijk, Jay S. Stanley III, Matthew Amodio, Kristina
Yim, Rebecca Muhle, James Noonan, Guy Wolf, Smita Krishnaswamy (2019). Graph
Spectral Regularization for Neural Network Interpretability. ICLR RLGM Workshop.

PDF Workshop

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