Recent content in Home on Jon Deaton's personal website
Stoic wisdom advocates practice of premeditatio malorum — the continuous visualization of worst-case scenarios. This negative visualization is said to inoculate one’s wellbeing against inevitable misfortune and strengthen gratitude for the everyday. The recommendation rests on the same intuition that derives the famous equality: Happiness = Reality - Expectations . The goal of negative…
Hadamard Conjugation On the wikipedia page for the Hadamard-Walsh Transform, you’ll find a near incomprehensible section the transform’s application in mollecular phylogenetics. It turns out that whats going on here really isn’t that complicated, but is merely being obfuscated by unnecessary jargon (as biologists tend) like “Klein group”. The “Klein group”…
This post is about a technical detail of boundary resetting for Selective State Space Models (S6) like Mamba . I discuss boundary resetting for Selective SSMs, and give an implementaiton that enables resetting at boundaries without sacrificing the associativity of the binary scan operation, thereby maintaining parallelizability. This model architecture was introduced by Albert Gu, Tri Dao in the…
My work in the past few years has focused on translation of methods underlying the remarkable advances in AI and NLP to biological sequence design problems. Many of the most successful algorithms in NLP can be translated with little modification to operate on biological sequences rather than natural language. Take for example the influential Evolutionary Scale Model (ESM) which is basically just…
Originally published on wordpress In my last two blog posts, I discussed how I assembled and configured a distributed computing cluster using some old laptops and Raspberry Pis. In this post I will discuss using this cluster for developing distributed computing tasks in C++ using MPI. The distributed application that I developed is a DNA k-mer counter. Background on DNA Sequence analysis In…
Originally published on wordpress When we left off at part 1, we had ArchLinux installed on each of the computers in the cluster, and each is also running an SSH server so that is can be accessed remotely. The next step is to set up a shared file system that each node has access to. This will be very helpful later when coordinating distributed tasks, if for instance we are processing a bunch of…
Originally published on wordpress My family uses their laptops a lot, and they tend to get them replaced after several years. A year ago, I scrounged around our house and rounded up every old computer that I could find with the hope of putting them together to make some kind of super computer. Five old MacBook Pros in hand (some very old), I did some research and discovered that indeed I could put…
Mentorship Hosted AI resident Kevin Wu at Google X Hosted AI resident Frances Ding at Google X Hosted research intern Wei-Hung Weng at Google Research Honors and Awards 2017 Tau Beta Pi National Engineering Honors Society Member 2015 NCAA First Team Academic All American 2014 NCAA First Team Academic All American 2013 NCAA First Team Academic All American 2013 Lincoln D. Granniss Yale University…
USA Junior National Team Member I was a member of the USA Junior National team from 2008 - 2013. To become a member of the national team I placed within the top seven gymnastics of my age group at national championships. Being on the national team earned me the opportunity to train at week-long training camps at the USA Olympic Training Center in Colorado Springs, CO several times a year.…