Ali Madani (@thisismadani) / X

Ali Madani

467 posts

Ali Madani

@thisismadani

founder / ceo of profluent. build frontier ai models for protein design, create cures.

San Francisco, CA

Joined July 2014

Pinned
Ali Madani
@thisismadani
Apr 28
AI has two modes in drug discovery. Accelerate: moving faster through the existing playbook. Unlock: opening frontiers that weren't possible before. Excited to announce Profluent is partnering with Eli Lilly, the global pharma powerhouse, to unlock breakthrough medicines for
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Ali Madani
@thisismadani
Apr 22, 2024
Can AI rewrite our human genome? ⌨️🧬 Today, we announce the successful editing of DNA in human cells with gene editors fully designed with AI. Not only that, we've decided to freely release the molecules under the @ProfluentBio OpenCRISPR initiative. Lots to unpack👇
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Ali Madani
@thisismadani
Jan 26, 2023
ChatGPT for biology? Excited to share our work on LLMs for protein design out today @NatureBiotech nature.com/articles/s4158… + Proud to publicly announce @ProfluentBio with a $9M seed round to tackle meaningful challenges in biology with AI. Join us!
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Ali Madani
@thisismadani
Jul 19, 2021
This twirling work of science is special ✨ AFAIK, it's the first crystal structure of a functional #protein fully designed by #AI A milestone in our quest to use language models to generate proteins that are unseen in nature & can function well in the real-world. Read below👇
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Ali Madani
@thisismadani
Nov 30, 2020
#Alphafold by #deepmind used solid interdisciplinary intuitions for algorithm/model design. It wasn't just a rinse-and-repeat machine learning exercise. Details on methods are limited, but here's my best interpretation (+some predictions) so far: [1/n]
Ali Madani
@thisismadani
Jun 29, 2022
📢Excited to share our exploration of billion-scale model and dataset sizes to examine the boundaries of protein language models with ProGen2 Paper: arxiv.org/abs/2206.13517 Code: github.com/salesforce/pro… >6B params & >1B seqs from genomic, metagenomic, immune repertoire studies
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Ali Madani
@thisismadani
Feb 15, 2024
Published in @NatureBiotech today: @jeffruffolo and I demystify how to design proteins with LMs. Reach out if you have any Qs on how to apply the power of LMs for your protein design goals-- which we do routinely at @ProfluentBio
Designing proteins with language models
From nature.com
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Ali Madani
@thisismadani
Apr 22, 2024
Replying to @thisismadani
Our LLMs were trained on massive scale sequence and biological context to generate millions of diverse CRISPR-like proteins that do not occur in nature, thereby exponentially expanding virtually all known CRISPR families at-will.
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Ali Madani
@thisismadani
Apr 22, 2024
Replying to @thisismadani
The results point to a future where AI precisely designs what is needed to create a range of bespoke cures for disease. There is still much to build to achieve this vision. To spur innovation and democratization, we are freely releasing OpenCRISPR-1. Try it out!
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Ali Madani
@thisismadani
Aug 5, 2024
LLMs *seem* powerful for biology but how do we best steer them for design? Introducing proseLM: atomic-level control with additional biological context. Lots of cool experimental results! Blog: profluent.bio/blog/generatin… GEN: genengnews.com/topics/artific… Paper: biorxiv.org/content/10.110…
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Ali Madani
@thisismadani
Apr 22, 2024
Replying to @thisismadani
Paper: biorxiv.org/content/10.110… Blog: profluent.bio/blog/editing-t… NYTimes: nytimes.com/2024/04/22/tec… Press Release: businesswire.com/news/home/2024… Access OpenCRISPR-1: forms.gle/zzPFYuesZXZGT5…
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Ali Madani
@thisismadani
Apr 22, 2024
Replying to @thisismadani
We then focus on type II effector complexes, generating cas9-like proteins and gRNAs. These proteins are hundreds of mutations away from anything in nature.
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Ali Madani
@thisismadani
Apr 22, 2024
Replying to @thisismadani
AI has become increasingly pervasive in our daily lives from how we sift through information, produce content, and interact with the world. This marks a new chapter where AI is used to alter the fundamental blueprint of who we are - our DNA.
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Ali Madani
@thisismadani
Apr 22, 2024
Replying to @thisismadani
We then characterized our generations in the wet lab and found that the AI-designed gene editors show comparable or improved activity and specificity relative to SpCas9, the prototypical gene editing effector. More characterization is underway but we're already impressed.
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