Posts Tagged ‘YL’

RL Project

January 11, 2026

some reading materials on RL:
https://arxiv.org/pdf/2412.05265
https://arxiv.org/abs/2412.05265

Murphy, K. (2024, December 6). Reinforcement Learning: An Overview. arXiv.org. https://arxiv.org/abs/2412.05265

QT:{{”
Reinforcement learning or RL is a class of methods for solving various kinds of sequential decision making
tasks. In such tasks, we want to design an agent that interacts with an external environment. The agent
maintains an internal state zt, which it passes to its policy π to choose an action at = π(zt). The environment
responds by sending back an observation ot+1, which the agent uses to update its internal state using the
state-update function zt+1 = SU(zt, at, ot+1). See Figure 1.1 for an illustration.
To simplify things, we often assume that the environment is also a Markovian process, which has internal
world state wt, from which the observations ot are derived. (This is called a POMDP — see Section 1.2.1).
We often simplify things even more by assuming that the observation ot reveals the hidden environment state;
in this case, we denote the internal agent state and external environment state by the same letter, namely
st = ot = wt = zt. (This is called an MDP — see Section 1.2.2). We discuss these assumptions in more detail
in Section 1.1.3.
RL is more complicated than supervised learning (e.g., training a classifier) or self-supervised learning
(e.g., training a language model), because this framework is very general: there are many assumptions we can
make about the environment and its observations ot, and many choices we can make about the form the
agent’s internal state zt and policy π, as well the ways to update these objects as we see more data. We
will study many different combinations in the rest of this document. The right choice ultimately depends on
which real-world application you are interested in solving.1 .”}}

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!!!)

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

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

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/

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/

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

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