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This looks so much fun!

New preprint on pre-trained models for Bayesian optimization (BO) of sequences! We show LLMs trained on protein seqs can replace Gaussian processes in BO. Examples: BO of peptide inhibitors with AlphaFold and iterative design of proteins. 1/6 biorxiv.org/content/10.110…

Use ensembles of pretrained protein LMs + reparametrization trick for Bayesian optimization of protein sequences. Ziyue Yang 🐣 kat !! Andrew White 🐦‍⬛ biorxiv.org/content/10.110…

I've put our Bayesian Optimization method for protein/peptide sequence design into a Google Colab. Try it out to choose which sequences to try next in your protein design tasks! colab.research.google.com/github/ur-whit…

Packaged our algorithm to design binding peptides into a simple colab. Enter a protein sequence, indicate where you want the peptide to bind, and in a few minutes you'll have a peptide predicted to tightly bind via AlphaFold + Bayesian Optimization. 1/2 colab.research.google.com/github/ur-whit…

This week at M2D2, Ziyue Yang 🐣 will show us how we can improve pre-trained models for novel protein/peptide sequence design with Bayesian Optimization, reducing the amount of experimental data required. Join us tomorrow, Tues Oct 25th at 11am ET!

Happening in 8 mins, welcome to stop by 👏🏽

Some symmetric molecular dynamics to get everyone pumped for my talk Tuesday morning at 8am at AIChE plan.core-apps.com/aiche2022/abst…

Got our new professional head shots at American Institute of Chemical Engineers (AIChE) with Geemi Wellawatte and TheRealAmoo 🤖🧪

hanging out with some dope folks in Phoenix! Andrew White 🐦‍⬛ Ziyue Yang 🐣 TheRealAmoo 🤖🧪 Geemi Wellawatte

Why do molecules smell? We create explanations for why molecules have one of 112 scents. The explanations are distilled into natural language. We're excited about data -> model -> explanation of mols. Work by Aditi (looking for PhD program!), Heta Gandhi, Geemi Wellawatte 1/3

Guess people really like my Twitter profile pic -- Every time they ask me for a photo of myself to put on the cover, no matter which picture I attached to the email, this pic shows up eventually 😓

Feel grateful and lucky for having the chance to watch this amazing Broadway show last night #BeautifulNoise A Beautiful Noise , so magnificent!!👏👏 (Was wandering around TKTS By TDF booth in Times Square and an elegant lady gifted me the ticket🎫)

Here's a picture of Mona Lisa in Paris #midjourney

Preprint alert !! Introducing 🙌XpertAI🙌 - a new framework that combines explainable AI (XAI) methods with large language models (LLMs) to generate natural language explanations of structure-property relationships from raw data. Link to the preprint: arxiv.org/abs/2311.04047

The tweet: 🚨New AI model predicts if you have HIV infection from video of you breathing with 99% accuracy🚨 The model:

Paper from Mayk Caldas and me on building a browser-only deep learning model for molecular property prediction (with uncertainty) is now published in Digital Discovery . You can play with the model here: mol.dev pubs.rsc.org/en/content/art…

How can an introvert get a job?

Minimal AF. A minimal persistent serverless AlphaFold GPU instance thanks to Modal and colabfold. Implemented in 50 lines of code github.com/whitead/minima…

Went back Rochester to see some old mens. Great time! Andrew White 🐦‍⬛ Mayk Caldas Shane Michtavy