ML for bio and drug discovery. Recovering chemoinf. Occassionally FulhamFC and London. Views my own. Now @drjoshuabox.bsky.social
London
Joined April 2011
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Excited to share our short review of De novo molecular design and generative models published in Drug Discovery Today! sciencedirect.com/science/ar… #pharmatech #drugdiscovery #ArtificialIntelligence #ML #RealTimeChem
Joshua Box retweeted
Structure or sequence – how should we represent proteins? This question has long challenged SOTA protein property prediction. Read our new post to get our take and meet Boltz-2-PPI, a minimal adaptation of Boltz for predicting protein–protein affinity 🧬👇
open.substack.com/pub/synten…
Off to #NeurIPS2024 next week where we are presenting our approach to diffusion sampling for generalised protein inpainting problems such as floating motif scaffolding and sequence editing. Drop by the AIDrugX Workshop or drop me a message if you're interested! @syntenyAI
Joshua Box retweeted
Big congrats to @aaron_lou, @chenlin_meng & @StefanoErmon on winning an #ICML2024 Best Paper Award for:
Discrete Diffusion Modeling by Estimating the Ratios of the Data Distribution
Exciting work improving diffusion models for symbolic data like text.
arxiv.org/abs/2310.16834
ICML 2024: Best Paper Awards:
Florian Tramèr; Gautam Kamath; Nicholas Carlini. Position: Considerations for Differentially Private Learning with Large-Scale Public Pretraining
Akbir Khan; John Hughes; Dan Valentine; Laura Ruis; Kshitij Sachan; Ansh Radhakrishnan; Edward Grefenstette; Samuel R. Bowman; Tim Rocktäschel; Ethan Perez. Debating with More Persuasive LLMs Leads to More Truthful Answers
Jake Bruce; Michael D Dennis; Ashley Edwards; Jack Parker-Holder; Yuge Shi; Edward Hughes; Matthew Lai; Aditi Mavalankar; Richie Steigerwald; Chris Apps; Yusuf Aytar; Sarah Maria Elisabeth Bechtle; Feryal Behbahani; Stephanie C.Y. Chan; Nicolas Heess; Lucy Gonzalez; Simon Osindero; Sherjil Ozair; Scott Reed; Jingwei Zhang; Konrad Zolna; Jeff Clune; Nando de Freitas; Satinder Singh; Tim Rocktäschel. Genie: Generative Interactive Environments
Dan Kondratyuk; Lijun Yu; Xiuye Gu; Jose Lezama; Jonathan Huang; Grant Schindler; Rachel Hornung; Vighnesh Birodkar; Jimmy Yan; Ming-Chang Chiu; Krishna Somandepalli; Hassan Akbari; Yair Alon; Yong Cheng; Joshua V. Dillon; Agrim Gupta; Meera Hahn; Anja Hauth; David Hendon; Alonso Martinez; David Minnen; Mikhail Sirotenko; Kihyuk Sohn; Xuan Yang; Hartwig Adam; Ming-Hsuan Yang; Irfan Essa; Huisheng Wang; David A Ross; Bryan Seybold; Lu Jiang. VideoPoet: A Large Language Model for Zero-Shot Video Generation
Aaron Lou; Chenlin Meng; Stefano Ermon. Discrete Diffusion Modeling by Estimating the Ratios of the Data Distribution
Patrick Esser; Sumith Kulal; Andreas Blattmann; Rahim Entezari; Jonas Müller; Harry Saini; Yam Levi; Dominik Lorenz; Axel Sauer; Frederic Boesel; Dustin Podell; Tim Dockhorn; Zion English; Robin Rombach. Scaling Rectified Flow Transformers for High-Resolution Image Synthesis
Stephen Zhao; Rob Brekelmans; Alireza Makhzani; Roger Baker Grosse. Probabilistic Inference in Language Models via Twisted Sequential Monte Carlo
Dora Zhao; Jerone Andrews; Orestis Papakyriakopoulos; Alice Xiang. Measure Dataset Diversity, Don’t Just Claim It.
Nicholas Carlini; Daniel Paleka; Krishnamurthy Dj Dvijotham; Thomas Steinke; Jonathan Hayase; A. Feder Cooper; Katherine Lee; Matthew Jagielski; Milad Nasr; Arthur Conmy; Eric Wallace; David Rolnick; Florian Tramèr. Stealing Part of a Production Language Model
Idan Attias; Gintare Karolina Dziugaite; Mahdi Haghifam; Roi Livni; Daniel M. Roy. Information Complexity of Stochastic Convex Optimization: Applications to Generalization and Memorization
Joshua Box retweeted
How do healthy tissues evolve to become cancerous? Delighted to share our latest research tracking the somatic evolution that occurs in the decades before AML. 👇Implications for early detection and early interception. biorxiv.org/cgi/content/shor…
Joshua Box retweeted
Not an ML expert, but want to understand AlphaFold3 (AF3)?
I wrote a simple-to-understand AF3 field guide and sprinkled my opinions in along the way.
The full essay is linked at the END of the thread.
Here's a TL;DR 🧵
Joshua Box retweeted
New blog post alert! 🚨
I write about AlphaFold3, how it works, where it works well ✅ (and where we think it might not ❌) and what it means to the TechBio landscape more broadly (if you decide to believe me). 🧬
(1/7) 🧵
open.substack.com/pub/harris…
Nice review of Generative artificial intelligence for de novo protein design sciencedirect.com/science/ar…
Joshua Box retweeted
OpenFold paper is now out in @naturemethods. Timely. I’ll say more about AF3 at the end of this thread, but first I wanted to highlight what’s new since our initial release. (1/9)
Joshua Box retweeted
We’re really happy to share our preprint demonstrating the atomically-accurate design of single-domain antibodies (VHHs) with RFdiffusion!
Our fragment-based molecular generator, FragGT has been published with code. Had a lot of fun with this while on my year out. Thanks to @nathanbroon and @benevolent_ai for supporting open source science #guacamol
chemrxiv.org/engage/chemrxiv…
Raising children on the eve of AI @juliadwise
juliawise.net/raising-childr…
Joshua Box retweeted
here is sora, our video generation model:
openai.com/sora
today we are starting red-teaming and offering access to a limited number of creators.
@_tim_brooks @billpeeb @model_mechanic are really incredible; amazing work by them and the team.
remarkable moment.
Joshua Box retweeted
The first Practical Cheminformatics post of the year is a retrospective of papers published in 2023, “AI in Drug Discovery 2023 - A Highly Opinionated Literature Review”. practicalcheminformatics.blo…
Joshua Box retweeted
Use inverse folding likelihoods as an unsupervised protein sequence optimizer.
@varunrshanker @theobruun @BrianHie Peter Kim
Joshua Box retweeted
some NeurIPS highlights:
LDM tutorial was great. the 1st part is a must-watch, the 2nd part is full of references for recent advancements, and you need to check the 3rd part if you're planning to use LDMs for something other than images/videos.
neurips2023-ldm-tutorial.git…
Joshua Box retweeted
Ever since the invention of the car cities have been changing, and in the 1930s people like Norman Bel Geddes predicted exactly what would come to pass: cities designed for cars rather than people.
A feeling captured rather well by this cartoon...
Joshua Box retweeted
New! We’ve just put up a note evaluating the latest, in-development version of AlphaFold (“AlphaFold-latest”). This is a preview - development is still in progress - but performance across a wide range of tasks is striking.
deepmind.google/discover/blo…
Highlights in the thread.
1/7
Joshua Box retweeted
In 1938, Julian Layton was in Vienna helping to extract Jews from Austria – then the architect of the Final Solution rang.
Here, our writer @JasperRees tells the story of his great uncle.
Read the full article here: telegraph.co.uk/tv/2023/10/2…
