Focus on protease: inhibition helps inhibit viral replication; and it is conserved across most coronaviruses; so good point to start working in drug development.

• Take smaller binding fragments covering the binding site, and combine them together
• Try to combine these fragments together into a molecule that fits well with the binding site

protease inhibition is usually achieved with a covalent peptide bond, but this crowd-sourcing effort showed that

machine-learning rapid library synthesis

1. begin with some guess for the model molecule
2. then, use ML to perform modifications to the molecule really quickly by scanning though (“ML-prioritized rapid library synthesis”) a bunch of changes to the molecule
3. pick and repeat

Molecular Transformer

THROW THE FUCKING REACTION INTO AN LLM, as WORDS

https://web.stanford.edu/class/cs205l/

Lectures

• SU-CS205L JAN072025
• SU-CS205L JAN092025
• SU-CS205L JAN142025
• SU-CS205L JAN162025
• SU-CS205L JAN212025
• SU-CS205L JAN232025

Logistics

Let’s say we want to find MLE parameters \(\theta\) for a conditional Gaussian with constant variance. That is:

\begin{equation} p\qty(y_{i} | x_{i}) = \mathcal{N} \qty(y_{i}|f_{\theta } \qty(x_{i}), \sigma^{2}) \end{equation}

and we have a corresponding dataset: \(\qty(x_1, y_1), …, \qty(x_{m}, y_{m})\).

where:

\begin{align} \hat{\theta} &= \arg\max_{\theta} \sum_{i=1}^{m} \log p\qty(y_{i}|x_{i}) \\ &= \arg\max_{\theta} \sum_{i=1}^{m} \log \mathcal{N} \qty(y_{i}| f_{\theta} \qty(x_{i}), \sigma^{2}) \\ &= \arg\max_{\theta } \sum_{i=1}^{m} \log \frac{1}{\sqrt{{2 \pi \sigma^{2}}}} \exp \qty(- \frac{\qty(y_{i}- f_{\theta }\qty(x_{i}))^{2}}{2\sigma^{2}}) \end{align}

MLib is a machine learning library built on top of Spark.

from pyspalk.mllib.clustering import KMeans

KMeans(rdd)

where you pass the MLib a PySpark RDD

Reading notes

Malcom X’s father was an active prechear in the scene

Malcom X and MLK are both made mostly charactures out of context

Malcom X had a belligent upbringing with a belligent father, whereas MLK lived in relative comfort as a son of a successful minister

Malcom was sent into white foster families as his mother became institutionalized

Becasue of his experience in foster system, Malcom tried to pass/be white

King’s nonviolent priciples not understood and became conflicted with ideas of local leaders

Malcom found a father figure in the Nation of Islam, changing his name in prison

MLK had more positive African American role models in life

Malcom X disallusioned with the policy of nonengagement by the nation of islam

Malcom X had support over racial seperatism

Nation of Islam wanted to create a completely seperate Black state, promoting Black Nationalism secret

Malcom X wanted break because of skeptism again Eli Mohammed

Malcom charged MLK with infiltration

Martin believes that the process of voilence is a form of naïve expression

King believes that the “strong demagogic oratory” of Malcom was detrimental and extremist

Martin believes that the personal nature of assults from Malcom maybe result in physical assult

Malcom was suspended during 1963, and became independent—wanted to combine religion and politics like King

Malcom began forging ties with millitan Black movement

Martin regretted that integration has not proceeded, but believed it would have been difficult anyways

Rejected nonviolent and intergrational movement

People saw King and X’s ideas inrecosiliable

But, King and X themselves made a possible shared ending by the end

Believes that suicides were cut short

Racial pride was a centering point: while Malcom saw it as something to be harbored, Martin saw it as inate