Alex Chu
@alexechu.bsky.social
Deep learning & protein design. Currently designing stuff at Google DeepMind, previously at Stanford with Possu Huang. alexechu.github.io
Reposted by Alex Chu
Bluetorial: Adventures with tenure-Part 1
a cartoon says hey everybody an old man 's talking while bart simpson looks on
ALT: a cartoon says hey everybody an old man 's talking while bart simpson looks on
media.tenor.com
December 18, 2024 at 12:25 PM
Bluetorial: Adventures with tenure-Part 1
Reposted by Alex Chu
Many industrially-important reactions (e.g. lipase-catalyzed biofuel production) involve substrates poorly soluble in water. How can we screen enzymes for these reactions? Samuel Thompson invented a new 'triple emulsion' platform for biphasic screening (1/n):
onlinelibrary.wiley.com/doi/full/10....
onlinelibrary.wiley.com/doi/full/10....
FACS‐Sortable Triple Emulsion Picoreactors for Screening Reactions in Biphasic Environments
Biphasic reactions can enhance reactions where the catalyst and substrate have different solvent preferences. This study optimizes triple emulsion picoreactors that encapsulate a biphasic solvent env...
onlinelibrary.wiley.com
December 13, 2024 at 1:54 AM
Many industrially-important reactions (e.g. lipase-catalyzed biofuel production) involve substrates poorly soluble in water. How can we screen enzymes for these reactions? Samuel Thompson invented a new 'triple emulsion' platform for biphasic screening (1/n):
onlinelibrary.wiley.com/doi/full/10....
onlinelibrary.wiley.com/doi/full/10....
At neurips this week - hmu if you’re around, want to catch up, try out some food, explore, etc!
December 9, 2024 at 10:32 PM
At neurips this week - hmu if you’re around, want to catch up, try out some food, explore, etc!
Latent diffusion ftw!
1/🧬 Excited to share PLAID, our new approach for co-generating sequence and all-atom protein structures by sampling from the latent space of ESMFold. This requires only sequences during training, which unlocks more data and annotations:
bit.ly/plaid-proteins
🧵
bit.ly/plaid-proteins
🧵
December 6, 2024 at 5:48 PM
Latent diffusion ftw!
Reposted by Alex Chu
Super excited to preprint our work on developing a Biomolecular Emulator (BioEmu): Scalable emulation of protein equilibrium ensembles with generative deep learning from @msftresearch.bsky.social ch AI for Science.
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
December 6, 2024 at 8:39 AM
Super excited to preprint our work on developing a Biomolecular Emulator (BioEmu): Scalable emulation of protein equilibrium ensembles with generative deep learning from @msftresearch.bsky.social ch AI for Science.
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
Reposted by Alex Chu
Evolution is non-linear, the next step in the evolutionary lineage of the ESM series of models is a sequence only protein language model that sets a new state of the art in representation learning.
Check it out! The 300M and 600M models are open weights, 300M available for commercial usage.
Check it out! The 300M and 600M models are open weights, 300M available for commercial usage.
Introducing ESM Cambrian, a new family of protein language models, focused on creating representations of the underlying biology of proteins.
December 4, 2024 at 5:50 PM
Evolution is non-linear, the next step in the evolutionary lineage of the ESM series of models is a sequence only protein language model that sets a new state of the art in representation learning.
Check it out! The 300M and 600M models are open weights, 300M available for commercial usage.
Check it out! The 300M and 600M models are open weights, 300M available for commercial usage.
Reposted by Alex Chu
AI Proteins is excited to partner with @bms-news.bsky.social to develop novel miniprotein-based therapeutics. This collaboration will leverage our cutting-edge AI-driven platform to design and optimize miniproteins with the potential to transform patient outcomes
www.businesswire.com/news/home/20...
www.businesswire.com/news/home/20...
AI Proteins Announces Research Collaboration and Option Agreement with Bristol Myers Squibb for Miniprotein-Based Therapeutics Valued up to $400M
AI Proteins, Inc., a biotechnology company that utilizes computational de novo protein design to create therapeutic miniproteins, today announced that
www.businesswire.com
December 3, 2024 at 5:30 PM
AI Proteins is excited to partner with @bms-news.bsky.social to develop novel miniprotein-based therapeutics. This collaboration will leverage our cutting-edge AI-driven platform to design and optimize miniproteins with the potential to transform patient outcomes
www.businesswire.com/news/home/20...
www.businesswire.com/news/home/20...
Reposted by Alex Chu
“On a log-log plot, my grandmother fits on a straight line.”
-Physicist Fritz Houtermans
There's a lot of truth to this. log-log plots are often abused and can be very misleading
1/5
-Physicist Fritz Houtermans
There's a lot of truth to this. log-log plots are often abused and can be very misleading
1/5
December 3, 2024 at 4:41 AM
“On a log-log plot, my grandmother fits on a straight line.”
-Physicist Fritz Houtermans
There's a lot of truth to this. log-log plots are often abused and can be very misleading
1/5
-Physicist Fritz Houtermans
There's a lot of truth to this. log-log plots are often abused and can be very misleading
1/5
Reposted by Alex Chu
AF3 BEST METHOD followed by cluspro but also some conversion errors
December 3, 2024 at 5:07 PM
AF3 BEST METHOD followed by cluspro but also some conversion errors
Reposted by Alex Chu
go.bsky.app/BoXpqQp
Computational protein design starter pack. Let me know if I missed you!
Computational protein design starter pack. Let me know if I missed you!
November 17, 2024 at 11:55 AM
go.bsky.app/BoXpqQp
Computational protein design starter pack. Let me know if I missed you!
Computational protein design starter pack. Let me know if I missed you!
Reposted by Alex Chu
Asking the following earnestly: what is the strongest case for GANs standing the "test of time"? Are they important 10 years later in modern ML research? How have they influenced the way we think about generative models today?
Ironically, while I love GANs, one could argue they did NOT stand the test of time....as they've mostly disappeared from modern ML.
Also fun, I remember being in the room for Ilya's talk of this paper (right after our talk on How transferable are features in deep neural networks?").
Also fun, I remember being in the room for Ilya's talk of this paper (right after our talk on How transferable are features in deep neural networks?").
November 27, 2024 at 9:05 PM
Asking the following earnestly: what is the strongest case for GANs standing the "test of time"? Are they important 10 years later in modern ML research? How have they influenced the way we think about generative models today?
Reposted by Alex Chu
Amazing blog post on flow matching, stunning visuals! It also makes the connection with normalising flows crystal clear. Incredible effort!
Anne Gagneux, Ségolène Martin, @quentinbertrand.bsky.social Remi Emonet and I wrote a tutorial blog post on flow matching: dl.heeere.com/conditional-... with lots of illustrations and intuition!
We got this idea after their cool work on improving Plug and Play with FM: arxiv.org/abs/2410.02423
We got this idea after their cool work on improving Plug and Play with FM: arxiv.org/abs/2410.02423
November 27, 2024 at 6:31 PM
Amazing blog post on flow matching, stunning visuals! It also makes the connection with normalising flows crystal clear. Incredible effort!
Reposted by Alex Chu
A weekend project from a while back -- this little package (with no dependencies) allows you to interact with pymol remotely.
I use it a lot for my protein design workflows together with @biotite.bsky.social.
Just `pip install pymol-remote`
I use it a lot for my protein design workflows together with @biotite.bsky.social.
Just `pip install pymol-remote`
November 25, 2024 at 2:50 PM
A weekend project from a while back -- this little package (with no dependencies) allows you to interact with pymol remotely.
I use it a lot for my protein design workflows together with @biotite.bsky.social.
Just `pip install pymol-remote`
I use it a lot for my protein design workflows together with @biotite.bsky.social.
Just `pip install pymol-remote`
Reposted by Alex Chu
The complete guide for transfer learning with the protein language model ESM-2.
(In brief: Use ESM-2 650M and calculate mean embeddings across sites.)
www.biorxiv.org/content/10.1...
(In brief: Use ESM-2 650M and calculate mean embeddings across sites.)
www.biorxiv.org/content/10.1...
Scaling Down for Efficiency: Medium-Sized Transformer Models for Protein Sequence Transfer Learning
Protein language models such as the transformer-based Evolutionary Scale Modeling 2 (ESM2) can offer deep insights into evolutionary and structural properties of proteins. While larger models, such as...
www.biorxiv.org
November 25, 2024 at 2:50 AM
The complete guide for transfer learning with the protein language model ESM-2.
(In brief: Use ESM-2 650M and calculate mean embeddings across sites.)
www.biorxiv.org/content/10.1...
(In brief: Use ESM-2 650M and calculate mean embeddings across sites.)
www.biorxiv.org/content/10.1...
Reposted by Alex Chu
Experimental kcat and KM measurements for hundreds of naturally variants of adenylate kinase.
- thermophilic enzymes are not slower than mesophilic!
- general kcat/KM predictors are bad and easily beaten by models trained on this specific dataset!
www.biorxiv.org/content/10.1...
- thermophilic enzymes are not slower than mesophilic!
- general kcat/KM predictors are bad and easily beaten by models trained on this specific dataset!
www.biorxiv.org/content/10.1...
November 13, 2024 at 10:30 PM
Experimental kcat and KM measurements for hundreds of naturally variants of adenylate kinase.
- thermophilic enzymes are not slower than mesophilic!
- general kcat/KM predictors are bad and easily beaten by models trained on this specific dataset!
www.biorxiv.org/content/10.1...
- thermophilic enzymes are not slower than mesophilic!
- general kcat/KM predictors are bad and easily beaten by models trained on this specific dataset!
www.biorxiv.org/content/10.1...
Our team at deepmind is hiring! boards.greenhouse.io/deepmind/job...
Laboratory Research Scientist, Protein Design, Science
London, UK
boards.greenhouse.io
November 14, 2024 at 5:53 PM
Our team at deepmind is hiring! boards.greenhouse.io/deepmind/job...