For 2024 2025, I’m renewing my blog. You can expect me to post at least once this year. Blink and you’ll miss it so subscribe.
Anything worth doing is worth doing poorly — GK Chesterton
No preamble. Just the list this year. Thanks for reading, and send me your list if you’ve got one.
Best Books
Phillip Meyer, The Son
Min Jin Lee, Pachinko
ML Wang, The Sword of Kaigen
Tara Westover, Educated
James Clear, Atomic Habits
I hate that this one made the list. It’s full of meaningless charts and equations like happiness + laugh * love = winning, but nonetheless it is a most potent form of self-propaganda and a great reminder that change is always within reach. And it got me to do core for the first time in my life.
Amor Towles, A Gentleman in Moscow
I gave this one 3 stars after reading it, but it’s continued to grow on me and I’ve recommended it more than any other book this year.
Best Songs
JMSN, Soft Spot
Joey Valence & Brae, PUNK TACTICS
Vona Vella, Thought We Were Falling In Love
Internet Girl, dumb party
The Night Painters, Sirens
Tyler, The Creator, Darling I
Toutant, Rebirth — Original Mix
Miniature Tigers, Like or Like Like
Best Papers
Tomaz Da Silva, Pedro, Alexander Karollus, Johannes Hingerl, Gihanna Galindez, Nils Wagner, Xavier Hernandez-Alias, Danny Incarnato, and Julien Gagneur. 2024. “Nucleotide Dependency Analysis of DNA Language Models Reveals Genomic Functional Elements.” https://doi.org/10.1101/2024.07.27.605418.
Nguyen, Eric, Michael Poli, Matthew G. Durrant, Armin W. Thomas, Brian Kang, Jeremy Sullivan, Madelena Y. Ng, et al. 2024. “Sequence Modeling and Design from Molecular to Genome Scale with Evo.” bioRxiv. https://doi.org/10.1101/2024.02.27.582234.
McNutt, Andrew T., Abhinav K. Adduri, Caleb N. Ellington, Monica T. Dayao, Eric P. Xing, Hosein Mohimani, and David R. Koes. 2024. “SPRINT Enables Interpretable and Ultra-Fast Virtual Screening against Thousands of Proteomes.” arXiv. https://doi.org/10.48550/arXiv.2411.15418.
This project is why I love research. My favorite paper from last year inspired this study. It became a bit of a joke in some circles how much I talked about that paper. The original work touched on something remarkable, but it stopped short. It felt like the authors didn’t realize what they had almost created. Eventually Abhi and I sat down and hacked for a night on this in April. Things looked good so we roped in Drew and Monica, and we spent another 2 nights hacking in May. It was a good enough for a short paper, so we slapped together a manuscript and a poster which Abhi and I took to a conference in Seattle and Drew took to a symposium at MIT. Then people started to get excited. Drew and Abhi really took off with it in Fall, and it recently appeared at the Machine Learning for Structural Biology workshop at NeurIPS (see below). All of this happened while Monica, Abhi, and (soon) Drew defended their theses and went through the post-PhD interview gauntlet, and while I worked on getting GenBio AI to launch. It was a very inconvenient time for everyone, but it’s a good reminder that working with people you enjoy doesn’t feel like work at all, and that some ideas are so captivating that they take on a life of their own.
Best Art
Alexander Archipenko, Egyptian Motif, 1917
Best Quotes
If it's your job to eat a frog, it's best to do it first thing in the morning. And if it's your job to eat two frogs, it's best to eat the biggest one first — Mark Twain
Anything worth doing is worth doing poorly — GK Chesterton
Best Open-Source Software
LightningCLI. Reproducible, hackable, composable ML experiments from the command line. The ModelGenerator package we released from GenBio AI a few weeks ago uses this as its main interface, and I’ve never had so much fun doing research.
Best Games
Wingspan iOS with friends online
Unspottable. I didn’t play many video games this year while we were building GenBio, but this was probably the best $10 I spent all year.
Best Movie
DiDi
Best Places
The Cut, UW Seattle
Dish Osteria, Pittsburgh PA
The Palace, Brooklyn NYC
Cafe Bloc, Montreal QC
Ocean Beach, San Francisco CA
Waimea Bay Beach, Oahu HI
Best Moments
Big year for me. Got my shoulder and wrist surgically fixed, and I’m pain-free for the first time in 2 years. Shaved my head. Ran a half marathon with my best friends. Proposed my thesis and became a PhD candidate. Took an evil landlord to court and won. Was awarded a fellowship after 4 years and 13 rejections. Saw my littlest brother become an Eagle Scout. Saw my friends get married. Took leave from my PhD to build GenBio. And we got kicked out of our own company launch party because twice as many people as we expected showed up.