Posts Tagged ‘YL’

Glucose Manuscripts

September 14, 2025

some tutorials on flow-matching:
https://arxiv.org/pdf/2412.06264
https://arxiv.org/pdf/2506.02070

Lipman, Y., Havasi, M., Holderrieth, P., Shaul, N., Le, M., Karrer, B., Chen, R. T. Q., Lopez-Paz, D., Ben-Hamu, H., & Gat, I. (2024, December 9). Flow matching guide and code. arXiv.org.
https://arxiv.org/abs/2412.06264

(Sometimes difficult to follow formalism)

Holderrieth, P., & Erives, E. (2025). MIT Class 6.S184: Generative AI with Stochastic Differential equations (pp. 1–52).
https://arxiv.org/pdf/2506.02070
OR
Holderrieth, P., & Erives, E. (2025, June 2). An introduction to flow matching and diffusion models. arXiv.org.
https://arxiv.org/abs/2506.02070

(Very intuitive!!!)

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1803.00567 Computational Optimal Transport

March 1, 2025

https://arxiv.org/abs/1803.00567

explains the dual problem well

Peyré, G., & Cuturi, M. (2018, March 1). Computational Optimal transport. arXiv.org. https://arxiv.org/abs/1803.00567

tutorial_on_optimal_transport.pdf

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2312.07511 A Hitchhiker’s Guide to Geometric GNNs for 3D Atomic Systems

March 1, 2025

https://arxiv.org/abs/2312.07511

Duval, A., Mathis, S., V., Joshi, C. K., Schmidt, V., Miret, S., Malliaros, F. D., Cohen, T., Liò, P., Bengio, Y., & Bronstein, M. (2023, December 12). A Hitchhiker’s guide to Geometric GNNs for 3D atomic Systems. arXiv.org. https://arxiv.org/abs/2312.07511

Good intuition on spherical harmonics

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Diffusion Tutorial

March 1, 2025

Some tutorials on diffusion models:

[An Arxiv Tutorial]
https://arxiv.org/pdf/2403.18103
https://arxiv.org/abs/2403.18103

Chan, S. H. (2024, March 26). Tutorial on diffusion models for imaging and vision. arXiv.org. https://arxiv.org/abs/2403.18103

has master equation, forward & back SDE, relationship of SDE to p(x)

[Also, Some Useful Blogs]
https://baincapitalventures.notion.site/Diffusion-Without-Tears-14e1469584c180deb0a9ed9aa6ff7a4c https://yang-song.net/blog/2021/score/
https://lilianweng.github.io/posts/2021-07-11-diffusion-models/

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Diffusion Tutorial

February 17, 2025

some tutorials on diffusion models:

[An Arxiv Tutorial]
https://arxiv.org/pdf/2403.18103

[Some Useful Blogs]
https://baincapitalventures.notion.site/Diffusion-Without-Tears-14e1469584c180deb0a9ed9aa6ff7a4c https://yang-song.net/blog/2021/score/
https://lilianweng.github.io/posts/2021-07-11-diffusion-models/

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2312.07511 A Hitchhiker’s Guide to Geometric GNNs for 3D Atomic Systems

January 18, 2025

https://arxiv.org/abs/2312.07511

Duval, A., Mathis, S., V., Joshi, C. K., Schmidt, V., Miret, S., Malliaros, F. D., Cohen, T., Liò, P., Bengio, Y., & Bronstein, M. (2023, December 12). A Hitchhiker’s guide to Geometric GNNs for 3D atomic Systems. arXiv.org. https://arxiv.org/abs/2312.07511

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Learning single-cell perturbation responses using neural optimal transport | Nature Methods

January 18, 2025

https://www.nature.com/articles/s41592-023-01969-x

Bunne, C., Stark, S. G., Gut, G., Del Castillo, J. S., Levesque, M., Lehmann, K., Pelkmans, L., Krause, A., & Rätsch, G. (2023). Learning single-cell perturbation responses using neural optimal transport. Nature Methods, 20(11), 1759–1768.
https://doi.org/10.1038/s41592-023-01969-x

not so useful for learning OT

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