Some Thoughts on a Mysterious Universe: Recent Episodes
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Just over a week ago the long-awaited AlphaFold2 (AF2) method paper and associated code finally came out, putting to rest questions that I and many others raised about public disclosure of AF2. Already, the code is being pushed in all sorts of interesting ways, and three days ago the companion paper and database were published, where … Continue reading →
The past week was a momentous occasion for protein structure prediction, structural biology at large, and in due time, may prove to be so for the whole of life sciences. CASP14, the conference for the biennial competition for the prediction of protein structure from sequence, took place virtually over multiple remote working platforms. DeepMind, Google’s … Continue reading →
But it may well be semi-supervised. For some time now I have thought that building a latent representation of protein sequence space is a really good idea, both because we have far more sequences than any form of labelled data, and because, once built, such a representation can inform a broad range of downstream tasks. … Continue reading →
Update: An updated version of this blogpost was published as a (peer-reviewed) Letter to the Editor at Bioinformatics, sans the “sociology” commentary. I just came back from CASP13, the biennial assessment of protein structure prediction methods (I previously blogged about CASP10.) I participated in a panel on deep learning methods in protein structure prediction, as well … Continue reading →
For over a decade now I have been working, essentially off the grid, on protein folding. I started thinking about the problem during my undergraduate years and actively working on it from the very beginning of grad school. For about four years, during the late 2000s, I pursued a radically different approach (to what was … Continue reading →
Earlier this week I found myself in Rome in the morning with about 20 minutes to spare. Walking around the neighborhood I was staying in (Trastevere), I came across an elderly nun walking along one of the bigger, and more crowded, streets of Rome. As I waited for her to go through a narrow passage … Continue reading →
For two weeks last July, I cocooned myself in a hotel in Portland, OR, living and breathing probabilistic programming as a “student” in the probabilistic programming summer school run by DARPA. The school is part of the broader DARPA program on Probabilistic Programming for Advanced Machine Learning (PPAML), which has resulted in a great infusion … Continue reading →
Yesterday’s news about the horrific massacre in Paris shook me really hard. I spent the day very upset, and the night puzzled by my extreme reaction. Terrorist attacks have become fixtures of the daily news, with yesterday alone seeing over a dozen killed in Iraq. Why did this bother me so much? I think I’m … Continue reading →
I previously blogged on my adventures in self quantification (QS). In that post I wrote about the general system but did not delve into specific projects. Ultimately however the utility of self quantification is in the detailed insights it gives, and so I’m going to dive deeper into a project that passed a major milestone earlier today: publication of a paper. If … Continue reading →
I am pleased to announce that earlier today the embargo was lifted on our most recent paper. This work represents the culmination of over two years of effort by my collaborators and I. You can find the official version on the Nature Genetics website here, and the freely available ReadCube version here. In this post, I … Continue reading →