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ORCIDAlexander Tong 0001
Person information
- affiliation (PhD 2021): Yale University, New Haven, CT, USA
Other persons with the same name
- Alexander Tong 0002 — Department of Geography, UTM, Mississauga, ON, Canada
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Journal Articles
- 2024
[j6]Alexander Tong, Kilian Fatras, Nikolay Malkin, Guillaume Huguet, Yanlei Zhang, Jarrid Rector-Brooks, Guy Wolf, Yoshua Bengio:
Improving and generalizing flow-based generative models with minibatch optimal transport. Trans. Mach. Learn. Res. 2024 (2024)- [j5]Alexander Tong
, Frederik Wenkel, Dhananjay Bhaskar, Kincaid MacDonald, Jackson D. Grady, Michael Perlmutter, Smita Krishnaswamy, Guy Wolf:
Learnable Filters for Geometric Scattering Modules. IEEE Trans. Signal Process. 72: 2939-2952 (2024) - 2023
- [j4]Guillaume Huguet, Alexander Tong, Bastian Rieck, Jessie Huang, Manik Kuchroo, Matthew J. Hirn, Guy Wolf, Smita Krishnaswamy:
Time-Inhomogeneous Diffusion Geometry and Topology. SIAM J. Math. Data Sci. 5(2): 346-372 (2023) - [j3]Michael Perlmutter, Alexander Tong, Feng Gao, Guy Wolf, Matthew J. Hirn:
Understanding Graph Neural Networks with Generalized Geometric Scattering Transforms. SIAM J. Math. Data Sci. 5(4): 873-898 (2023) - 2022
- [j2]Alexander Tong, Guy Wolf, Smita Krishnaswamy:
Fixing Bias in Reconstruction-based Anomaly Detection with Lipschitz Discriminators. J. Signal Process. Syst. 94(2): 229-243 (2022) - 2021
- [j1]Rémi Flamary, Nicolas Courty, Alexandre Gramfort, Mokhtar Z. Alaya, Aurélie Boisbunon, Stanislas Chambon, Laetitia Chapel, Adrien Corenflos, Kilian Fatras, Nemo Fournier, Léo 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:
POT: Python Optimal Transport. J. Mach. Learn. Res. 22: 78:1-78:8 (2021)
Conference and Workshop Papers
- 2024
- [c25]Alexander Tong, Nikolay Malkin, Kilian Fatras, Lazar Atanackovic, Yanlei Zhang, Guillaume Huguet, Guy Wolf, Yoshua Bengio:
Simulation-Free Schrödinger Bridges via Score and Flow Matching. AISTATS 2024: 1279-1287 - [c24]Danqi Liao, Chen Liu, Benjamin W. Christensen, Alexander Tong, Guillaume Huguet, Guy Wolf, Maximilian Nickel, Ian Adelstein, Smita Krishnaswamy:
Assessing Neural Network Representations During Training Using Noise-Resilient Diffusion Spectral Entropy. CISS 2024: 1-6 - [c23]Avishek Joey Bose, Tara Akhound-Sadegh, Guillaume Huguet, Kilian Fatras, Jarrid Rector-Brooks, Cheng-Hao Liu, Andrei Cristian Nica, Maksym Korablyov, Michael M. Bronstein, Alexander Tong:
SE(3)-Stochastic Flow Matching for Protein Backbone Generation. ICLR 2024 - [c22]Tara Akhound-Sadegh, Jarrid Rector-Brooks, Avishek Joey Bose, Sarthak Mittal, Pablo Lemos, Cheng-Hao Liu, Marcin Sendera, Siamak Ravanbakhsh, Gauthier Gidel, Yoshua Bengio, Nikolay Malkin, Alexander Tong:
Iterated Denoising Energy Matching for Sampling from Boltzmann Densities. ICML 2024 - [c21]Kirill Neklyudov, Rob Brekelmans, Alexander Tong, Lazar Atanackovic, Qiang Liu, Alireza Makhzani:
A Computational Framework for Solving Wasserstein Lagrangian Flows. ICML 2024 - [c20]Guillaume Huguet, James Vuckovic, Kilian Fatras, Eric Thibodeau-Laufer, Pablo Lemos, Riashat Islam, Cheng-Hao Liu, Jarrid Rector-Brooks, Tara Akhound-Sadegh, Michael M. Bronstein, Alexander Tong, Avishek Joey Bose:
Sequence-Augmented SE(3)-Flow Matching For Conditional Protein Generation. NeurIPS 2024 - [c19]Kacper Kapusniak, Peter Potaptchik, Teodora Reu, Leo Zhang, Alexander Tong, Michael M. Bronstein, Avishek Joey Bose, Francesco Di Giovanni:
Metric Flow Matching for Smooth Interpolations on the Data Manifold. NeurIPS 2024 - [c18]Xi Zhang, Yuan Pu, Yuki Kawamura, Andrew Loza, Yoshua Bengio, Dennis L. Shung, Alexander Tong:
Trajectory Flow Matching with Applications to Clinical Time Series Modelling. NeurIPS 2024 - 2023
- [c17]Oluwadamilola Fasina, Guillaume Huguet, Alexander Tong, Yanlei Zhang, Guy Wolf, Maximilian Nickel, Ian Adelstein, Smita Krishnaswamy:
Neural FIM for learning Fisher information metrics from point cloud data. ICML 2023: 9814-9826 - [c16]Guillaume Huguet, Alexander Tong, María Ramos Zapatero, Christopher J. Tape, Guy Wolf, Smita Krishnaswamy:
Geodesic Sinkhorn For Fast and Accurate Optimal Transport on Manifolds. MLSP 2023: 1-6 - [c15]Lazar Atanackovic, Alexander Tong, Bo Wang, Leo J. Lee, Yoshua Bengio, Jason S. Hartford:
DynGFN: Towards Bayesian Inference of Gene Regulatory Networks with GFlowNets. NeurIPS 2023 - [c14]Guillaume Huguet, Alexander Tong, Edward De Brouwer, Yanlei Zhang, Guy Wolf, Ian Adelstein, Smita Krishnaswamy:
A Heat Diffusion Perspective on Geodesic Preserving Dimensionality Reduction. NeurIPS 2023 - 2022
- [c13]Alexander Tong, Guillaume Huguet, Dennis L. Shung, Amine Natik, Manik Kuchroo, Guillaume Lajoie, Guy Wolf, Smita Krishnaswamy:
Embedding Signals on Graphs with Unbalanced Diffusion Earth Mover's Distance. ICASSP 2022: 5647-5651 - [c12]Guillaume Huguet, Daniel Sumner Magruder, Alexander Tong, Oluwadamilola Fasina, Manik Kuchroo, Guy Wolf, Smita Krishnaswamy:
Manifold Interpolating Optimal-Transport Flows for Trajectory Inference. NeurIPS 2022 - 2021
- [c11]Michal Gerasimiuk, Dennis L. Shung, Alexander Tong, Adrian J. Stanley, Michael Schultz, Jeffrey Ngu, Loren Laine, Guy Wolf, Smita Krishnaswamy:
MURAL: An Unsupervised Random Forest-Based Embedding for Electronic Health Record Data. IEEE BigData 2021: 4694-4704 - [c10]Alexander Tong, Guillaume Huguet, Amine Natik, Kincaid MacDonald, Manik Kuchroo, Ronald R. Coifman, Guy Wolf, Smita Krishnaswamy:
Diffusion Earth Mover's Distance and Distribution Embeddings. ICML 2021: 10336-10346 - [c9]Manik Kuchroo, Abhinav Godavarthi, Alexander Tong, Guy Wolf, Smita Krishnaswamy:
Multimodal Data Visualization and Denoising with Integrated Diffusion. MLSP 2021: 1-6 - [c8]Alexander Tong, Frederick Wenkel, Kincaid MacDonald, Smita Krishnaswamy, Guy Wolf:
Data-Driven Learning of Geometric Scattering Modules for GNNs. MLSP 2021: 1-6 - [c7]Malte Lücken, Daniel Burkhardt, Robrecht Cannoodt, Christopher Lance, Aditi Agrawal, Hananeh Aliee, Ann Chen, Louise Deconinck, Angela Detweiler, Alejandro Granados, Shelly Huynh, Laura Isacco, Yang Kim, Dominik Klein, Bony de Kumar, Sunil Kuppasani, Heiko Lickert, Aaron McGeever, Joaquin Melgarejo, Honey Mekonen, Maurizio Morri, Michaela Müller, Norma Neff, Sheryl Paul, Bastian Rieck, Kaylie Schneider, Scott Steelman, Michael Sterr, Daniel Treacy, Alexander Tong, Alexandra-Chloé Villani, Guilin Wang, Jia Yan, Ce Zhang, Angela Pisco, Smita Krishnaswamy, Fabian J. Theis, Jonathan M. Bloom:
A sandbox for prediction and integration of DNA, RNA, and proteins in single cells. NeurIPS Datasets and Benchmarks 2021 - 2020
- [c6]Egbert Castro, Andrew Benz, Alexander Tong, Guy Wolf, Smita Krishnaswamy:
Uncovering the Folding Landscape of RNA Secondary Structure Using Deep Graph Embeddings. IEEE BigData 2020: 4519-4528 - [c5]Alexander Tong, Jessie Huang, Guy Wolf, David van Dijk, Smita Krishnaswamy:
TrajectoryNet: A Dynamic Optimal Transport Network for Modeling Cellular Dynamics. ICML 2020: 9526-9536 - [c4]Alexander Tong, David van Dijk, Jay S. Stanley III, Matthew Amodio, Kristina Yim, Rebecca Muhle, James Noonan, Guy Wolf, Smita Krishnaswamy:
Interpretable Neuron Structuring with Graph Spectral Regularization. IDA 2020: 509-521 - [c3]Alexander Tong, Guy Wolf, Smita Krishnaswamy:
Fixing Bias in Reconstruction-Based Anomaly Detection with Lipschitz Discriminators. MLSP 2020: 1-6 - 2019
- [c2]David van Dijk, Daniel B. Burkhardt, Matthew Amodio, Alexander Tong, Guy Wolf, Smita Krishnaswamy:
Finding Archetypal Spaces Using Neural Networks. IEEE BigData 2019: 2634-2643 - 2018
- [c1]James Aspnes, Bernhard Haeupler, Alexander Tong, Philipp Woelfel:
Allocate-On-Use Space Complexity of Shared-Memory Algorithms. DISC 2018: 8:1-8:17
Informal and Other Publications
- 2025
- [i36]Zhangzhi Peng, Zachary Bezemek, Sawan Patel, Jarrid Rector-Brooks, Sherwood Yao, Alexander Tong, Pranam Chatterjee:
Path Planning for Masked Diffusion Model Sampling. CoRR abs/2502.03540 (2025) - [i35]Charlie B. Tan, Avishek Joey Bose, Chen Lin, Leon Klein, Michael M. Bronstein, Alexander Tong:
Scalable Equilibrium Sampling with Sequential Boltzmann Generators. CoRR abs/2502.18462 (2025) - [i34]Marta Skreta, Tara Akhound-Sadegh, Viktor Ohanesian, Roberto Bondesan, Alán Aspuru-Guzik, Arnaud Doucet, Rob Brekelmans, Alexander Tong, Kirill Neklyudov:
Feynman-Kac Correctors in Diffusion: Annealing, Guidance, and Product of Experts. CoRR abs/2503.02819 (2025) - [i33]Sophia Tang, Yinuo Zhang, Alexander Tong, Pranam Chatterjee:
Gumbel-Softmax Flow Matching with Straight-Through Guidance for Controllable Biological Sequence Generation. CoRR abs/2503.17361 (2025) - 2024
- [i32]Tara Akhound-Sadegh, Jarrid Rector-Brooks, Avishek Joey Bose, Sarthak Mittal, Pablo Lemos, Cheng-Hao Liu, Marcin Sendera, Siamak Ravanbakhsh, Gauthier Gidel, Yoshua Bengio, Nikolay Malkin, Alexander Tong:
Iterated Denoising Energy Matching for Sampling from Boltzmann Densities. CoRR abs/2402.06121 (2024) - [i31]Kacper Kapusniak, Peter Potaptchik, Teodora Reu, Leo Zhang, Alexander Tong, Michael M. Bronstein, Avishek Joey Bose, Francesco Di Giovanni:
Metric Flow Matching for Smooth Interpolations on the Data Manifold. CoRR abs/2405.14780 (2024) - [i30]Guillaume Huguet, James Vuckovic, Kilian Fatras, Eric Thibodeau-Laufer, Pablo Lemos, Riashat Islam, Cheng-Hao Liu, Jarrid Rector-Brooks, Tara Akhound-Sadegh, Michael M. Bronstein, Alexander Tong, Avishek Joey Bose:
Sequence-Augmented SE(3)-Flow Matching For Conditional Protein Backbone Generation. CoRR abs/2405.20313 (2024) - [i29]Chen Liu, Ke Xu, Liangbo L. Shen, Guillaume Huguet, Zilong Wang, Alexander Tong, Danilo Bzdok, Jay Stewart, Jay C. Wang, Lucian V. Del Priore, Smita Krishnaswamy:
ImageFlowNet: Forecasting Multiscale Trajectories of Disease Progression with Irregularly-Sampled Longitudinal Medical Images. CoRR abs/2406.14794 (2024) - [i28]Alessandro Palma, Till Richter, Hanyi Zhang, Manuel Lubetzki, Alexander Tong, Andrea Dittadi, Fabian J. Theis:
Generating Multi-Modal and Multi-Attribute Single-Cell Counts with CFGen. CoRR abs/2407.11734 (2024) - [i27]Lazar Atanackovic, Xi Zhang, Brandon Amos, Mathieu Blanchette, Leo J. Lee, Yoshua Bengio, Alexander Tong, Kirill Neklyudov:
Meta Flow Matching: Integrating Vector Fields on the Wasserstein Manifold. CoRR abs/2408.14608 (2024) - [i26]Jarrid Rector-Brooks, Mohsin Hasan, Zhangzhi Peng, Zachary Quinn, Cheng-Hao Liu, Sarthak Mittal, Nouha Dziri, Michael M. Bronstein, Yoshua Bengio, Pranam Chatterjee, Alexander Tong, Avishek Joey Bose:
Steering Masked Discrete Diffusion Models via Discrete Denoising Posterior Prediction. CoRR abs/2410.08134 (2024) - [i25]Xi Zhang, Yuan Pu, Yuki Kawamura, Andrew Loza, Yoshua Bengio, Dennis L. Shung, Alexander Tong:
Trajectory Flow Matching with Applications to Clinical Time Series Modeling. CoRR abs/2410.21154 (2024) - [i24]Marta Skreta, Lazar Atanackovic, Avishek Joey Bose, Alexander Tong, Kirill Neklyudov:
The Superposition of Diffusion Models Using the Itô Density Estimator. CoRR abs/2412.17762 (2024) - 2023
- [i23]Alexander Tong, Nikolay Malkin, Guillaume Huguet, Yanlei Zhang, Jarrid Rector-Brooks, Kilian Fatras, Guy Wolf, Yoshua Bengio:
Conditional Flow Matching: Simulation-Free Dynamic Optimal Transport. CoRR abs/2302.00482 (2023) - [i22]Lazar Atanackovic, Alexander Tong, Jason S. Hartford, Leo J. Lee, Bo Wang, Yoshua Bengio:
DynGFN: Bayesian Dynamic Causal Discovery using Generative Flow Networks. CoRR abs/2302.04178 (2023) - [i21]Guillaume Huguet, Alexander Tong, Edward De Brouwer, Yanlei Zhang, Guy Wolf, Ian Adelstein, Smita Krishnaswamy:
A Heat Diffusion Perspective on Geodesic Preserving Dimensionality Reduction. CoRR abs/2305.19043 (2023) - [i20]Samuel Leone, Aarthi Venkat, Guillaume Huguet, Alexander Tong, Guy Wolf, Smita Krishnaswamy:
Graph Fourier MMD for Signals on Graphs. CoRR abs/2306.02508 (2023) - [i19]Oluwadamilola Fasina, Guillaume Huguet, Alexander Tong, Yanlei Zhang, Guy Wolf, Maximilian Nickel, Ian Adelstein, Smita Krishnaswamy:
Neural FIM for learning Fisher Information Metrics from point cloud data. CoRR abs/2306.06062 (2023) - [i18]Alexander Tong, Nikolay Malkin, Kilian Fatras, Lazar Atanackovic, Yanlei Zhang, Guillaume Huguet, Guy Wolf, Yoshua Bengio:
Simulation-free Schrödinger bridges via score and flow matching. CoRR abs/2307.03672 (2023) - [i17]Avishek Joey Bose, Tara Akhound-Sadegh, Kilian Fatras, Guillaume Huguet, Jarrid Rector-Brooks, Cheng-Hao Liu, Andrei Cristian Nica, Maksym Korablyov, Michael M. Bronstein, Alexander Tong:
SE(3)-Stochastic Flow Matching for Protein Backbone Generation. CoRR abs/2310.02391 (2023) - [i16]Trang Nguyen, Alexander Tong, Kanika Madan, Yoshua Bengio, Dianbo Liu:
Causal Inference in Gene Regulatory Networks with GFlowNet: Towards Scalability in Large Systems. CoRR abs/2310.03579 (2023) - [i15]Kirill Neklyudov, Rob Brekelmans, Alexander Tong, Lazar Atanackovic, Qiang Liu, Alireza Makhzani:
A Computational Framework for Solving Wasserstein Lagrangian Flows. CoRR abs/2310.10649 (2023) - [i14]Danqi Liao, Chen Liu, Benjamin W. Christensen, Alexander Tong, Guillaume Huguet, Guy Wolf, Maximilian Nickel, Ian Adelstein, Smita Krishnaswamy:
Assessing Neural Network Representations During Training Using Noise-Resilient Diffusion Spectral Entropy. CoRR abs/2312.04823 (2023) - 2022
- [i13]Guillaume Huguet, Alexander Tong, Bastian Rieck, Jessie Huang, Manik Kuchroo, Matthew J. Hirn, Guy Wolf, Smita Krishnaswamy:
Time-inhomogeneous diffusion geometry and topology. CoRR abs/2203.14860 (2022) - [i12]Guillaume Huguet, Daniel Sumner Magruder, Oluwadamilola Fasina, Alexander Tong, Manik Kuchroo, Guy Wolf, Smita Krishnaswamy:
Manifold Interpolating Optimal-Transport Flows for Trajectory Inference. CoRR abs/2206.14928 (2022) - [i11]Alexander Tong, Frederik Wenkel, Dhananjay Bhaskar, Kincaid MacDonald, Jackson D. Grady, Michael Perlmutter, Smita Krishnaswamy, Guy Wolf:
Learnable Filters for Geometric Scattering Modules. CoRR abs/2208.07458 (2022) - [i10]Guillaume Huguet, Alexander Tong, María Ramos Zapatero, Guy Wolf, Smita Krishnaswamy:
Geodesic Sinkhorn: optimal transport for high-dimensional datasets. CoRR abs/2211.00805 (2022) - 2021
- [i9]Alexander Tong, Guillaume Huguet, Amine Natik, Kincaid MacDonald, Manik Kuchroo, Ronald R. Coifman, Guy Wolf, Smita Krishnaswamy:
Diffusion Earth Mover's Distance and Distribution Embeddings. CoRR abs/2102.12833 (2021) - [i8]Alexander Tong, Guillaume Huguet, Dennis L. Shung, Amine Natik, Manik Kuchroo, Guillaume Lajoie, Guy Wolf, Smita Krishnaswamy:
Embedding Signals on Knowledge Graphs with Unbalanced Diffusion Earth Mover's Distance. CoRR abs/2107.12334 (2021) - [i7]Michal Gerasimiuk, Dennis L. Shung, Alexander Tong, Adrian J. Stanley, Michael Schultz, Jeffrey Ngu, Loren Laine, Guy Wolf, Smita Krishnaswamy:
MURAL: An Unsupervised Random Forest-Based Embedding for Electronic Health Record Data. CoRR abs/2111.10452 (2021) - 2020
- [i6]Alexander Tong, Jessie Huang, Guy Wolf, David van Dijk, Smita Krishnaswamy:
TrajectoryNet: A Dynamic Optimal Transport Network for Modeling Cellular Dynamics. CoRR abs/2002.04461 (2020) - [i5]Egbert Castro, Andrew Benz, Alexander Tong, Guy Wolf, Smita Krishnaswamy:
Uncovering the Folding Landscape of RNA Secondary Structure with Deep Graph Embeddings. CoRR abs/2006.06885 (2020) - [i4]Alexander Tong, Frederik Wenkel, Kincaid MacDonald, Smita Krishnaswamy, Guy Wolf:
Data-Driven Learning of Geometric Scattering Networks. CoRR abs/2010.02415 (2020) - 2019
- [i3]David van Dijk, Daniel B. Burkhardt, Matthew Amodio, Alexander Tong, Guy Wolf, Smita Krishnaswamy:
Finding Archetypal Spaces for Data Using Neural Networks. CoRR abs/1901.09078 (2019) - [i2]Alexander Tong, Guy Wolf, Smita Krishnaswamy:
A Lipschitz-constrained anomaly discriminator framework. CoRR abs/1905.10710 (2019) - 2018
- [i1]Alexander Tong, David van Dijk, Jay S. Stanley III, Matthew Amodio, Guy Wolf, Smita Krishnaswamy:
Graph Spectral Regularization for Neural Network Interpretability. CoRR abs/1810.00424 (2018)
Coauthor Index
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