Alex Tong
Alex Tong
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SE(3)-Stochastic Flow Matching for Protein Backbone Generation
We present
FoldFlow
a novel flow matching model for protein design. We present theory and practical tricks for flow models over SE(3)^N. Empirically, we validate these models on protein backbone generation of up to 300 amino acids leading to high-quality designable, diverse, and novel samples.
Avishek Joey Bose
,
Tara Akhound-Sadegh
,
Kilian Fatras
,
Guillaume Huguet
,
Jarrid Rector-Brooks
,
Cheng-Hao Liu
,
Andrei Cristian Nica
,
Maksym Korablyov
,
Michael Bronstein
,
Alex Tong
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Code
MoML Video
Logg Video
VantAI Video
Simulation-Free Schrodinger Bridges via Score and Flow Matching
We present simulation-free score and flow matching ([SF]2M), a simulation-free objective for inferring stochastic dynamics given …
Alex Tong
,
Nikolay Malkin
,
Kilian Fatras
,
Lazar Atanackovic
,
Yanlei Zhang
,
Guillaume Huguet
,
Guy Wolf
,
Yoshua Bengio
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A Heat Diffusion Perspective on Geodesic Preserving Dimensionality Reduction
Guillaume Huguet
,
Alex Tong
,
Edward De Brouwer
,
Yanlei Zhang
,
Guy Wolf
,
Ian Adelstein
,
Smita Krishnaswamy
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Code
DynGFN: Bayesian Dynamic Causal Discovery Using Generative Flow Networks
One of the grand challenges of cell biology is inferring the gene regulatory network (GRN) which describes interactions between genes …
Lazar Atanackovic
,
Alex Tong
,
Jason Hartford
,
Leo J. Lee
,
Bo Wang
,
Yoshua Bengio
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Geodesic Sinkhorn for Fast and Accurate Optimal Transport on Manifolds
Efficient computation of optimal transport distance between distributions is of growing importance in data science. Sinkhorn-based …
Guillaume Huguet
,
Alex Tong
,
María Ramos Zapatero
,
Christpher J. Tape
,
Guy Wolf
,
Smita Krishnaswamy
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Neural FIM for Learning Fisher Information Metrics from Point Cloud Data
Oluwadamilola Fasina
,
Guillaume Huguet
,
Alex Tong
,
Yanlei Zhang
,
Guy Wolf
,
Maximilian Nickel
,
Ian Adelstein
,
Smita Krishnaswamy
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Improving and Generalizing Flow-Based Generative Models with Minibatch Optimal Transport
We present methods for learning simple flows over R^d with optimal transport conditional flow matching (OT-CFM). Training with this objective leads to imprved results on a variety of conditional and unconditional generation tasks, such as inferring single cell dynamics, unsupervised image translation, and Schrodinger bridge inference.
Alex Tong
,
Nikolay Malkin
,
Guillaume Huguet
,
Yanlei Zhang
,
Jarrid Rector-Brooks
,
Kilian Fatras
,
Guy Wolf
,
Yoshua Bengio
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Video
Graph Fourier MMD for signals on data graphs
While numerous methods have been proposed for computing distances between probability distributions in Euclidean space, relatively …
Sam Leone
,
Alex Tong
,
Guillaume Huguet
,
Guy Wolf
,
Smita Krishnaswamy
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Manifold Interpolating Optimal-Transport Flows for Trajectory Inference
We present a method called Manifold Interpolating Optimal-Transport Flow (MIOFlow) that learns stochastic, continuous population …
Guillaume Huguet
,
D. S. Magruder
,
Alex Tong
,
Oluwadamilola Fasina
,
Manik Kuchroo
,
Guy Wolf
,
Smita Krishnaswamy
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NeurIPS
Arxiv
Embedding Signals on Knowledge Graphs with Unbalanced Diffusion Earth Mover's Distance
In modern relational machine learning it is common to encounter large graphs that arise via interactions or similarities between …
Alex Tong
,
Guillaume Huguet
,
Dennis Shung
,
Amine Natik
,
Manik Kuchroo
,
Guillaume Lajoie
,
Guy Wolf
,
Smita Krishnaswamy
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Arxiv
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