Posts Tagged ‘tutorial0mg’

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 .”}}

Heritability 101: What is “heritability”? — Neale lab

December 26, 2025

https://www.nealelab.is/blog/2017/9/13/heritability-101-what-is-heritability

Heritability 201: Types of heritability and how we estimate it — Neale lab

December 26, 2025

https://www.nealelab.is/blog/2017/9/13/heritability-201-types-of-heritability-and-how-we-estimate-it QT:{{” “}}

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!!!)

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)

The Algorithmic Foundations of Differential Privacy

July 14, 2025

https://www.cis.upenn.edu/~aaroth/Papers/privacybook.pdf

The Algorithmic Foundations of Differential Privacy
Cynthia Dwork
Microsoft Research, USA
Aaron Roth
University of Pennsylvania, USA

Foundations and Trends in Theoretical Computer Science, NOW Publishers. 2014.

a few documents from our meeting

July 12, 2025

Gilbert, J. A., & Hartmann, E. M. (2024). The indoors microbiome and human health. Nature Reviews Microbiology, 22(12), 742–755.
https://doi.org/10.1038/s41579-024-01077-3

An updated 2024 indoor microbiome and human health review from Nature Reviews Microbiology.

Practical guide to SHAP analysis: Explaining supervised machine learning model predictions in drug development – PMC

June 10, 2025

https://pmc.ncbi.nlm.nih.gov/articles/PMC11513550/

Ponce‐Bobadilla, A. V., Schmitt, V., Maier, C. S., Mensing, S., & Stodtmann, S. (2024). Practical guide to SHAP analysis: Explaining supervised machine learning model predictions in drug development. Clinical and Translational Science, 17(11).
https://doi.org/10.1111/cts.70056

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/

lecture note on mixed state and density matrix

May 11, 2025

https://www.henryyuen.net/classes/spring2022/
https://www.henryyuen.net/spring2022/lec2-mixed-states.pdf

lecture notes on mixed states and density matrix.

QT:{{”
Frontiers of Quantum Complexity and Cryptography Lecture 2 – Mixed States and Density Matrices
Lecturer: Henry Yuen Spring 2022
Scribes: Melody Hsu

In the third lecture, we wrapped up a review of the foundational concepts we will need to tackle
later topics, and then started our first quantum complexity topic, state tomography. We briefly
discussed several ways to analyze probabilistic mixtures of quantum states; after the conclusion of
the review, we explored lower bounds on complexity of a classic tomography protocol.
“}}