About Me

I’m a PhD Candidate in computer science at Yale University advised by Dr. Smita Krishnaswamy. My current research interests are in machine learning and optimal transport. I’m working on applying ideas from optimal transport and graph signal processing to understand and adapt deep learning models. 

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

Interests

  • Machine Learning
  • Optimal Transport
  • Anomaly Detection
  • Graph Signal Processing
  • Single Cell Transcriptomics

Education

  • PhD in Computer Science focus on Machine Learning, 2017-Present

    Yale University

  • MS in Computer Science, 2017

    Tufts University

  • BS in Computer Science, 2017

    Tufts University

Preprints

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. Preprint.

Code Arxiv

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, Shelli Farhadian, Charles S. Dela Cruz, Albert I. Ko, F. Perry Wilson, Julie Hussin, Guy Wolf, Akiko Iwasaki, Smita Krishnaswamy (2020). Multiscale PHATE Exploration of SARS-CoV-2 Data Reveals Multimodal Signatures of Disease. bioRxiv.

PDF DOI

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

Arxiv

Publications

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.

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.

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.

PDF DOI

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 (0001). Quantifying the effect of experimental perturbations in single-cell RNA-sequencing data using graph signal processing. In Nature Biotechnology.

Code DOI BiorXiv

Workshops

without proceedings

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