Posts Tagged ‘email’

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!!!)

NIH-grant statistics

September 13, 2025

https://report.nih.gov/funding/nih-budget-and-spending-data-past-fiscal-years/success-rates
NIH grant statistics for different types of grants.
Form 1 in Research Project Grants and Form 4 in Training and Research career development have the total number of grants reviewed.

A computational pipeline for spatial mechano-transcriptomics | Nature Methods

September 7, 2025

https://www.nature.com/articles/s41592-025-02618-1

Hallou, A., He, R., Simons, B. D., & Dumitrascu, B. (2025). A computational pipeline for spatial mechano-transcriptomics. Nature Methods. https://doi.org/10.1038/s41592-025-02618-1

Reviews:
https://www.nature.com/articles/s41580-023-00583-1#Sec35
(difficult to follow)

Combining with Spatial transcriptomics:
https://www.nature.com/articles/s41592-025-02618-1
(new thing)

AI Agents have, so far, mostly been a dud – by Gary Marcus

September 7, 2025

https://garymarcus.substack.com/p/ai-agents-have-so-far-mostly-been

AbbVie slides

July 3, 2025

https://pages.awscloud.com/rs/112-TZM-766/images/Abbvie_Molecule%20Design%20with%20ESM.pdf?version=1&trk=d8d1d9e7-95be-46b4-9ad0-53e67ac1ea52&sc_channel=el

these slides might be related to the event in this link:

https://aws.amazon.com/blogs/industries/highlights-from-the-2025-aws-life-sciences-symposiums-drug-discovery-track/

Suffix Array and BWT Explaination

May 18, 2025

The book with a nice explanation of suffix array and BWT is
Bioinformatics Algorithms: An Active Learning Approach by Phillip Compeau & Pavel Pevzner. https://www.bioinformaticsalgorithms.org/

2nd “MBB” dept at Yale

March 19, 2025

Didn’t realize we are the 2nd “MBB” dept at Yale.
(See “admin” section in the below:
https://en.wikipedia.org/wiki/Joseph_S._Fruton
)
+
https://mbb.yale.edu/sites/default/files/files/A%20Scandalously%20Short%20History%20of%20MBB%20at%20Yale%20University(2).pdf

The Abstract: 8 Compounds That Target Aging

March 18, 2025

Guarente, L., Sinclair, D. A., & Kroemer, G. (2024). Human trials exploring anti-aging medicines. Cell Metabolism, 36(2), 354–376. https://doi.org/10.1016/j.cmet.2023.12.007

https://www.cell.com/cell-metabolism/fulltext/S1550-4131(23)00458-8

QT:{{”
In a recent issue of Cell Metabolism, Guarente co-authored a review article about human trials exploring compounds that target pathways and mechanisms of aging along with David Sinclair, Ph.D., one of Dr. Guarente’s postdoctoral mentees and now a professor of genetics at Harvard Medical School, and Guido Kroemer, M.D., Ph.D., a professor at the Université Paris Cité. Guarente and his colleagues focus on eight drugs and compounds: metformin, NAD+ precursors, glucagon-like peptide-1 receptor agonists, TORC1 inhibitors, spermidine, senolytics, probiotics, and anti-inflammatories.
These interventions made the list for four reasons: 1) they’re well-represented in ongoing or completed human clinical trials; 2) they’ve been shown to slow aging in preclinical studies; 3) they’re thought to be sufficiently safe for long-term use in humans; and 4) they work by targeting the hallmarks of aging.
“}}

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/