TrajectoryNet: A Dynamic Optimal Transport Network for Modeling Cellular Dynamics

9 February 2020

Alexander Tong

Jessie Huang

Guy Wolf

David van Dijk

Smita Krishnaswamy

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Papers citing "TrajectoryNet: A Dynamic Optimal Transport Network for Modeling Cellular Dynamics"

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Title
Efficient Flow Matching using Latent Variables Anirban Samaddar Yixuan Sun Viktor Nilsson Sandeep Madireddy 46 0 0 07 May 2025
Towards scientific machine learning for granular material simulations -- challenges and opportunities Marc Fransen Andreas Fürst D. Tunuguntla Daniel N. Wilke Benedikt Alkin ... Takayuki Shuku WaiChing Sun T. Weinhart Dongwei Ye Hongyang Cheng AI4CE 31 0 0 01 Apr 2025
A scalable gene network model of regulatory dynamics in single cells Paul Bertin J. Viviano Alejandro Tejada-Lapuerta Weixu Wang Stefan Bauer Fabian J. Theis Yoshua Bengio 38 0 0 25 Mar 2025
Trajectory Inference with Smooth Schrödinger Bridges Wanli Hong Yuliang Shi Jonathan Niles-Weed 38 0 0 01 Mar 2025
Optimal Stochastic Trace Estimation in Generative Modeling Xinyang Liu Hengrong Du Wei Deng Ruqi Zhang AI4TS 52 0 0 26 Feb 2025
A Fokker-Planck-Based Loss Function that Bridges Dynamics with Density Estimation Zhixin Lu Łukasz Kuśmierz Stefan Mihalas 70 0 0 24 Feb 2025
Using Linearized Optimal Transport to Predict the Evolution of Stochastic Particle Systems Nicholas Karris Evangelos A. Nikitopoulos Ioannis G. Kevrekidis Seungjoon Lee Alexander Cloninger OT 45 0 0 10 Jan 2025
ImageFlowNet: Forecasting Multiscale Image-Level Trajectories of Disease Progression with Irregularly-Sampled Longitudinal Medical Images Chen Liu Ke Xu Liangbo L. Shen Guillaume Huguet Zilong Wang ... Danilo Bzdok Jay Stewart Jay C. Wang L. V. Priore Smita Krishnaswamy 72 4 0 08 Jan 2025
Governing equation discovery of a complex system from snapshots Qunxi Zhu Bolin Zhao Jingdong Zhang Peiyang Li Wei Lin 26 1 0 22 Oct 2024
Geometry-Aware Generative Autoencoders for Warped Riemannian Metric Learning and Generative Modeling on Data Manifolds Xingzhi Sun Danqi Liao Kincaid MacDonald Yanlei Zhang Chen Liu Guillaume Huguet Guy Wolf Ian M. Adelstein Tim G. J. Rudner Smita Krishnaswamy 46 3 0 16 Oct 2024
Parametric model reduction of mean-field and stochastic systems via higher-order action matching Jules Berman Tobias Blickhan Benjamin Peherstorfer 37 0 0 15 Oct 2024
Learning stochastic dynamics from snapshots through regularized unbalanced optimal transport Zhenyi Zhang Tiejun Li Peijie Zhou OT 143 5 0 01 Oct 2024
Implicit Dynamical Flow Fusion (IDFF) for Generative Modeling Mohammad R. Rezaei Rahul G. Krishnan Milos R. Popovic M. Lankarany DiffM 24 0 0 22 Sep 2024
Meta Flow Matching: Integrating Vector Fields on the Wasserstein Manifold Lazar Atanackovic Xi Zhang Brandon Amos Mathieu Blanchette Leo J. Lee Yoshua Bengio Alexander Tong Kirill Neklyudov 36 5 0 26 Aug 2024
Learning Diffusion at Lightspeed Antonio Terpin Nicolas Lanzetti Florian Dorfler DiffM 43 6 0 18 Jun 2024
Partially Observed Trajectory Inference using Optimal Transport and a Dynamics Prior Anming Gu Edward Chien Kristjan Greenewald 46 4 0 11 Jun 2024
Learning to Approximate Particle Smoothing Trajectories via Diffusion Generative Models Ella Tamir Arno Solin DiffM 31 0 0 01 Jun 2024
Neural Optimal Transport with Lagrangian Costs Aram-Alexandre Pooladian Carles Domingo-Enrich Ricky T. Q. Chen Brandon Amos OT 40 15 0 01 Jun 2024
Efficient Trajectory Inference in Wasserstein Space Using Consecutive Averaging Amartya Banerjee Harlin Lee Nir Sharon Caroline Moosmüller 42 1 0 30 May 2024
Metric Flow Matching for Smooth Interpolations on the Data Manifold Kacper Kapusniak Peter Potaptchik Teodora Reu Leo Zhang Alexander Tong Michael M. Bronstein A. Bose Francesco Di Giovanni 41 12 0 23 May 2024
Dynamic Conditional Optimal Transport through Simulation-Free Flows Gavin Kerrigan Giosue Migliorini Padhraic Smyth OT 38 10 0 05 Apr 2024
Propensity Score Alignment of Unpaired Multimodal Data Johnny Xi Jason S. Hartford 24 2 0 02 Apr 2024
Negative-Binomial Randomized Gamma Markov Processes for Heterogeneous Overdispersed Count Time Series Rui Huang Sikun Yang Heinz Koeppl 37 0 0 29 Feb 2024
Generalized Sobolev Transport for Probability Measures on a Graph Tam Le Truyen V. Nguyen Kenji Fukumizu OT 47 5 0 07 Feb 2024
Correlational Lagrangian Schrödinger Bridge: Learning Dynamics with Population-Level Regularization Yuning You Ruida Zhou Yang Shen 12 0 0 04 Feb 2024
Solution of the Probabilistic Lambert Problem: Connections with Optimal Mass Transport, Schrödinger Bridge and Reaction-Diffusion PDEs Alexis M. H. Teter Iman Nodozi Abhishek Halder 23 4 0 15 Jan 2024
Unbalancedness in Neural Monge Maps Improves Unpaired Domain Translation L. Eyring Dominik Klein Théo Uscidda Giovanni Palla Niki Kilbertus Zeynep Akata Fabian J. Theis OT 30 15 0 25 Nov 2023
Constructing interpretable principal curve using Neural ODEs Guangzheng Zhang Bingxian Xu 11 0 0 15 Nov 2023
Structured Transforms Across Spaces with Cost-Regularized Optimal Transport Othmane Sebbouh Marco Cuturi Gabriel Peyré OT 25 4 0 09 Nov 2023
A Computational Framework for Solving Wasserstein Lagrangian Flows Kirill Neklyudov Rob Brekelmans Alexander Tong Lazar Atanackovic Qiang Liu Alireza Makhzani OT 34 17 0 16 Oct 2023
Entropic (Gromov) Wasserstein Flow Matching with GENOT Dominik Klein Théo Uscidda Fabian J. Theis Marco Cuturi OT 29 2 0 13 Oct 2023
SE(3)-Stochastic Flow Matching for Protein Backbone Generation A. Bose Tara Akhound-Sadegh Guillaume Huguet Kilian Fatras Jarrid Rector-Brooks Cheng-Hao Liu A. Nica Maksym Korablyov Michael M. Bronstein Alexander Tong DiffM 44 73 0 03 Oct 2023
Stochastic force inference via density estimation Victor Chardès S. Maddu Michael J. Shelley DiffM 11 3 0 03 Oct 2023
Light Schrödinger Bridge Alexander Korotin Nikita Gushchin Evgeny Burnaev OT 29 4 0 02 Oct 2023
Flow Factorized Representation Learning Yue Song Thomas Anderson Keller N. Sebe Max Welling DRL OOD 26 3 0 22 Sep 2023
Simulation-free Schrödinger bridges via score and flow matching Alexander Tong Nikolay Malkin Kilian Fatras Lazar Atanackovic Yanlei Zhang G. Huguet Guy Wolf Yoshua Bengio DiffM OT 36 29 0 07 Jul 2023
Equivariant flow matching Leon Klein Andreas Krämer Frank Noé 16 60 0 26 Jun 2023
Learning Elastic Costs to Shape Monge Displacements Michal Klein Aram-Alexandre Pooladian Pierre Ablin Eugène Ndiaye Jonathan Niles-Weed Marco Cuturi 48 3 0 20 Jun 2023
Unbalanced Diffusion Schrödinger Bridge Matteo Pariset Ya-Ping Hsieh Charlotte Bunne Andreas Krause Valentin De Bortoli DiffM OT 25 3 0 15 Jun 2023
Inferring dynamic regulatory interaction graphs from time series data with perturbations Dhananjay Bhaskar Sumner Magruder E. Brouwer Aarthi Venkat Frederik Wenkel Guy Wolf Smita Krishnaswamy 25 3 0 13 Jun 2023
RDA-INR: Riemannian Diffeomorphic Autoencoding via Implicit Neural Representations Sven Dummer N. Strisciuglio Christoph Brune MedIm 26 2 0 22 May 2023
Computing high-dimensional optimal transport by flow neural networks Chen Xu Xiuyuan Cheng Yao Xie OT 35 4 0 19 May 2023
Multisample Flow Matching: Straightening Flows with Minibatch Couplings Aram-Alexandre Pooladian Heli Ben-Hamu Carles Domingo-Enrich Brandon Amos Y. Lipman Ricky T. Q. Chen 60 126 0 28 Apr 2023
Generative modeling of time-dependent densities via optimal transport and projection pursuit Jonah Botvinick-Greenhouse Yunan Yang R. Maulik OT 11 2 0 19 Apr 2023
Biological Factor Regulatory Neural Network Xinnan Dai Caihua Shan Jie Zheng Xiaoxiao Li Dongsheng Li 24 1 0 11 Apr 2023
Geometric constraints improve inference of sparsely observed stochastic dynamics Dimitra Maoutsa AI4CE 17 3 0 02 Apr 2023
Stochastic Interpolants: A Unifying Framework for Flows and Diffusions M. S. Albergo Nicholas M. Boffi Eric Vanden-Eijnden DiffM 251 262 0 15 Mar 2023
Light Unbalanced Optimal Transport Milena Gazdieva Arip Asadulaev Alexander Korotin Evgeny Burnaev OT 23 1 0 14 Mar 2023
Deep Momentum Multi-Marginal Schrödinger Bridge T. Chen Guan-Horng Liu Molei Tao Evangelos A. Theodorou 25 9 0 03 Mar 2023
Aligned Diffusion Schrödinger Bridges Vignesh Ram Somnath Matteo Pariset Ya-Ping Hsieh María Rodríguez Martínez Andreas Krause Charlotte Bunne DiffM 117 30 0 22 Feb 2023