Yossa Dwi Hartono

Yossa Dwi Hartono

Computational Biologist / Structural Bioinformatician

Link roundup: Apr–Jun 2021

1 minute read

Published:

Papers
The Expanding Role of Chemistry in Optimizing Proteins for Human Health Applications
Artificial intelligence in drug discovery: what is realistic, what are illusions? Part 2: a discussion of chemical and biological data
Artificial intelligence in drug discovery: what is realistic, what are illusions? Part 1: Ways to make an impact, and why we are not there yet
Deep Dive into Machine Learning Models for Protein Engineering

Science
Artificial Proteins Never Seen in the Natural World Are Becoming New COVID Vaccines and Medicines
Too hot to live: Millions worldwide will face unbearable temperatures
Scientific Publishing Is a Joke
Previously unknown type of protein crosslink discovered Cys-Lys bridge
After Covid, Your Health May Depend on Living With Germs
In Our Hurry to Conquer Nature and Death, We Have Made a New Religion of Science
Kati Kariko Helped Shield the World From the Coronavirus
Six lessons from the biotech startup world

Others
The project finishing mindset
The pervasive problem of ‘linguistic racism’
What friends are for Sci-fi short story
Prometheus’ Toolbox
The k-Nearest Neighbors (kNN) Algorithm in Python
The Power of Writing by Hand
Scikit-learn Crash Course - Machine Learning Library for Python

Have you ever thought of the perfect quip or comeback after it didn’t matter—a minute, hour, or day after your conversation has ended?
Well, there’s a name for that phenomenon. It’s called l’esprit de l’escalier, or the spirit of the staircase, and refers to the perfect retort that arises at the wrong time.
– The Secret to Being Witty, Revealed

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Link roundup: Jan–Jun 2023

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Link roundup: Apr–Dec 2022

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Science
Wood spirits: How Japan made the world’s first liquor from trees
The price of ‘sugar free’: are sweeteners as harmless as we thought?
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‘The entire protein universe’: AI predicts shape of nearly every known protein
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PNAS | Leveraging nonstructural data to predict structures and affinities of protein–ligand complexes
Breaking into the black box of artificial intelligence

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When a Houseplant Obsession Becomes a Nightmare
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Link roundup: Jan–Mar 2022

2 minute read

Published:

Since these AIs are just giant matrix multiplication machines, “intuition” now has a firm grounding in math - just much bigger, more complicated math than the usual kind that we call “logical”.

This would be a common pattern for sciences: much worse at everyday tasks than people who do them intuitively, until it generates some surprising and powerful new technology. Democritus figured out what matter was made of in 400 BC, and it didn’t help a single person do a single useful thing with matter for the next 2000 years of followup research, and then you got the atomic bomb (I may be skipping over all of chemistry, sorry).
– What Are We Arguing About When We Argue About Rationality?

What he seeks to practice is, in a phrase popularized by the Marxist philosopher Antonio Gramsci, “pessimism of the intellect, optimism of the will.”
– Can Science Fiction Wake Us Up to Our Climate Reality?

Caulfield then introduced two different ways of thinking about how we engage with ideas when we’re on the internet: The web as a garden and the web as a stream. Think of the web as an organically developing garden: a space in which there’s no predetermined order or relationship of things to one another. Caulfield writes, “Every walk through the garden creates new paths, new meanings.” What came first in the garden doesn’t matter either. Each thing in the garden is related to the other things as it exists in the moment.
– The Faithful Gardener

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Dual use of artificial-intelligence-powered drug discovery
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The pandemic’s true death toll: millions more than official counts
5 nutrition goals that are better than weight loss

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https://github.com/csinva/imodels
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Transformative Experience and Pascal’s Wager
Do Good Doorbell Cams Make Good Neighbors?
How to Want Less
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How to be useless
What We Don’t Want to Know
It’s Time for Some Game Theory
Why does woman have ‘man’ in it and female has the word ‘male’ in it?

2021 book list

1 minute read

Published:

Compared to 2020, I slowly regained my reading habit again. One notable book is Camus’ The Plague that I didn’t finish in 2020, but picked it up again. Nothing really stood out for me, but I would recommend the starred ones.