RNA is still waiting for its AlphaFold moment.
ATLAS, a graph motif library for RNA, and ChironRNA, a diffusion model that repairs incomplete and clashing structures.
OPEN THE DISSERTATION ↗READING DESKPAPERS · BOOKS · QUESTIONS
Things I read slowly,
then rebuild for the web.
Not summaries. Each entry starts with something worth understanding, follows the evidence back to its source, and turns the difficult part into something you can see or touch.
Start with the dissertation ↓ papers books open questions
10finished readings
04papers and dissertation
05evidence-led book readings
中 / ENtwo working languages
THE LIBRARY / UPDATED WHEN SOMETHING STICKS
Begin anywhere.
The collection moves between molecular structure, machine learning, attention, fatigue, and the evolutionary stories hiding underneath ordinary behavior.
AlphaFold 3
One model for the molecular world.
A bilingual, interactive reading of the architecture, diffusion process, benchmark results, and limits of AlphaFold 3.
YuelPocket
Where does the drug go?
A graph neural network finds small-molecule binding sites by giving the protein a virtual joint node.
YuelDesign
The pocket was never supposed to hold still.
A diffusion model generates the ligand and its protein pocket together, allowing both sides of molecular recognition to move.
脑力精力：消耗、上限与恢复
你的脑子不是一块会耗尽的电池。
疲劳究竟是什么、精力总量能否提高，以及十分钟休息、小睡、睡眠和运动分别改变了什么。
Deep Work
“看一眼消息”从来不是看一眼。
对 Cal Newport《Deep Work》的交互式细读：注意力残留、组织度量，以及这本书自己没有承认的事。
Exercised
我们从没被演化设计成喜欢运动。
Daniel Lieberman 对运动神话的拆解：不想动不是意志力问题，而这个事实的用法和直觉相反。
The Anxious Generation
争的不是手机有没有害，是问得有多细。
同一批数据，混着算得出 β 约负 0.02，按性别和活动拆开算得出负 0.11 到负 0.24。把这场对骂还原成一个建模粒度问题。
Why Zebras Don't Get Ulcers
结果活下来了，机制被改写了。
Sapolsky 那本书的一次复核：感冒、伤口愈合、心梗这些结果站得住，但「皮质醇长期居高」这条机制，在人类文献的元分析里并不成立。
The Hungry Brain
一本书下的注，两年后被人做成了实验。
环境每天多给你 508 千卡，减重六年后身体每天少烧 499 千卡。这两个数字来自完全不相干的两项研究，而它们几乎一样大。