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

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.

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 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.

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 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 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 DOI

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

PDF 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 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 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 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.

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

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 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 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 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 Code DOI Arxiv

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

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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 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.

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