Clay Kosonocky
@kosonocky.bsky.social
ML + Biochemistry PhD Candidate at UT Austin. BioML Society Founder. All problems are solvable, so let's solve some
biomlsociety.org
biomlsociety.org
🚨The Bits to Binders Competition has concluded!🧬
One year ago we gathered scientists from around the world to design and submit protein binders that cause immune cells to target and eliminate CD20+ tumors
Spoiler: They work!
One year ago we gathered scientists from around the world to design and submit protein binders that cause immune cells to target and eliminate CD20+ tumors
Spoiler: They work!
September 2, 2025 at 2:45 PM
🚨The Bits to Binders Competition has concluded!🧬
One year ago we gathered scientists from around the world to design and submit protein binders that cause immune cells to target and eliminate CD20+ tumors
Spoiler: They work!
One year ago we gathered scientists from around the world to design and submit protein binders that cause immune cells to target and eliminate CD20+ tumors
Spoiler: They work!
Some recent used bookstore acquisitions of mine
Part of a few themes I'm trying to understand:
- cultures & life via classic lit
- basics of philosophy & history
- modern political climate & trajectory
- how can we make cities better?
- what will the future look like?
Part of a few themes I'm trying to understand:
- cultures & life via classic lit
- basics of philosophy & history
- modern political climate & trajectory
- how can we make cities better?
- what will the future look like?
May 17, 2025 at 2:15 PM
Some recent used bookstore acquisitions of mine
Part of a few themes I'm trying to understand:
- cultures & life via classic lit
- basics of philosophy & history
- modern political climate & trajectory
- how can we make cities better?
- what will the future look like?
Part of a few themes I'm trying to understand:
- cultures & life via classic lit
- basics of philosophy & history
- modern political climate & trajectory
- how can we make cities better?
- what will the future look like?
And we see it more clearly in these plots.
Ideally if there were no effect, the experimental conditions (plots 2 & 3) would be as tight with the y=x as the 1st plot. But we can see that some ligands just don't behave as well
Ideally if there were no effect, the experimental conditions (plots 2 & 3) would be as tight with the y=x as the 1st plot. But we can see that some ligands just don't behave as well
February 12, 2025 at 5:34 PM
And we see it more clearly in these plots.
Ideally if there were no effect, the experimental conditions (plots 2 & 3) would be as tight with the y=x as the 1st plot. But we can see that some ligands just don't behave as well
Ideally if there were no effect, the experimental conditions (plots 2 & 3) would be as tight with the y=x as the 1st plot. But we can see that some ligands just don't behave as well
Then Compute the avg absolute difference between the groups:
- s42 to s43 difference serves as our control
- s42 to oechem, and s43 to oechem serve as our experimental condition
We see from these numbers that there is a larger difference between rdkit and oechem
- s42 to s43 difference serves as our control
- s42 to oechem, and s43 to oechem serve as our experimental condition
We see from these numbers that there is a larger difference between rdkit and oechem
February 12, 2025 at 5:34 PM
Then Compute the avg absolute difference between the groups:
- s42 to s43 difference serves as our control
- s42 to oechem, and s43 to oechem serve as our experimental condition
We see from these numbers that there is a larger difference between rdkit and oechem
- s42 to s43 difference serves as our control
- s42 to oechem, and s43 to oechem serve as our experimental condition
We see from these numbers that there is a larger difference between rdkit and oechem
PSA: Digging into Chai-1 and found out that it gives different protein-ligand structures & confidences depending on the SMILES canonicalization used
May also be the case with AF3 & Boltz-1, but haven't verified
As to what this means... see the rest of the thread 🧵
May also be the case with AF3 & Boltz-1, but haven't verified
As to what this means... see the rest of the thread 🧵
February 4, 2025 at 8:38 PM
PSA: Digging into Chai-1 and found out that it gives different protein-ligand structures & confidences depending on the SMILES canonicalization used
May also be the case with AF3 & Boltz-1, but haven't verified
As to what this means... see the rest of the thread 🧵
May also be the case with AF3 & Boltz-1, but haven't verified
As to what this means... see the rest of the thread 🧵
The DNA for the Bits to Binders competition has just arrived from @twistbio.bsky.social! It is now being handed off to LEAH Labs where they will begin testing the 12,000 binders in a few days 👀
Stay tuned!
Stay tuned!
January 30, 2025 at 5:36 PM
The DNA for the Bits to Binders competition has just arrived from @twistbio.bsky.social! It is now being handed off to LEAH Labs where they will begin testing the 12,000 binders in a few days 👀
Stay tuned!
Stay tuned!
10) Homage to Catalonia (1938) by George Orwell
Orwell's account of fighting for the Republic in the Spanish Civil War. Beyond the historical knowledge, the writing is fantastic
Orwell's account of fighting for the Republic in the Spanish Civil War. Beyond the historical knowledge, the writing is fantastic
December 22, 2024 at 5:13 PM
10) Homage to Catalonia (1938) by George Orwell
Orwell's account of fighting for the Republic in the Spanish Civil War. Beyond the historical knowledge, the writing is fantastic
Orwell's account of fighting for the Republic in the Spanish Civil War. Beyond the historical knowledge, the writing is fantastic
9) The Ancient City (1864) by Numa Denis Fustel de Coulanges
Fairly dense read on the role of religion in ancient Greek & Roman society. E.g., How religion lead to the consolidation of tribes into cities & empires and just how authoritarian their societies were compared to today
Fairly dense read on the role of religion in ancient Greek & Roman society. E.g., How religion lead to the consolidation of tribes into cities & empires and just how authoritarian their societies were compared to today
December 22, 2024 at 5:13 PM
9) The Ancient City (1864) by Numa Denis Fustel de Coulanges
Fairly dense read on the role of religion in ancient Greek & Roman society. E.g., How religion lead to the consolidation of tribes into cities & empires and just how authoritarian their societies were compared to today
Fairly dense read on the role of religion in ancient Greek & Roman society. E.g., How religion lead to the consolidation of tribes into cities & empires and just how authoritarian their societies were compared to today
8) The Managerial Revolution (1941) by James Burnham
Perspective on bourgeois vs managerial capitalism. Don't fully agree with it, but useful nonetheless
Prediction: we will see a return to bourgeois capitalism as AI allows any given individual to do more with less delegation
Perspective on bourgeois vs managerial capitalism. Don't fully agree with it, but useful nonetheless
Prediction: we will see a return to bourgeois capitalism as AI allows any given individual to do more with less delegation
December 22, 2024 at 5:13 PM
8) The Managerial Revolution (1941) by James Burnham
Perspective on bourgeois vs managerial capitalism. Don't fully agree with it, but useful nonetheless
Prediction: we will see a return to bourgeois capitalism as AI allows any given individual to do more with less delegation
Perspective on bourgeois vs managerial capitalism. Don't fully agree with it, but useful nonetheless
Prediction: we will see a return to bourgeois capitalism as AI allows any given individual to do more with less delegation
7) The Cossacks (1863) by Leo Tolstoy
Lesser known Tolstoy acquired from my dad's bookshelf. I didn't expect this one to stay with me as much as it did. Themes include environmental romanticism, purpose of life, and love
Lesser known Tolstoy acquired from my dad's bookshelf. I didn't expect this one to stay with me as much as it did. Themes include environmental romanticism, purpose of life, and love
December 22, 2024 at 5:13 PM
7) The Cossacks (1863) by Leo Tolstoy
Lesser known Tolstoy acquired from my dad's bookshelf. I didn't expect this one to stay with me as much as it did. Themes include environmental romanticism, purpose of life, and love
Lesser known Tolstoy acquired from my dad's bookshelf. I didn't expect this one to stay with me as much as it did. Themes include environmental romanticism, purpose of life, and love
6) Anna Karenina (1873) by Leo Tolstoy
Another long (but great) novel. This book has ~5 different storylines all interweaving throughout. Each character feels like someone I have met in my life
Another long (but great) novel. This book has ~5 different storylines all interweaving throughout. Each character feels like someone I have met in my life
December 22, 2024 at 5:13 PM
6) Anna Karenina (1873) by Leo Tolstoy
Another long (but great) novel. This book has ~5 different storylines all interweaving throughout. Each character feels like someone I have met in my life
Another long (but great) novel. This book has ~5 different storylines all interweaving throughout. Each character feels like someone I have met in my life
5) The True Believer (1951) by Eric Hoffer
If you want insight into why people join mass political movements that ultimately lead to situations like the above book
Endorsed by Dwight D. Eisenhower & Hillary Clinton
If you want insight into why people join mass political movements that ultimately lead to situations like the above book
Endorsed by Dwight D. Eisenhower & Hillary Clinton
December 22, 2024 at 5:13 PM
5) The True Believer (1951) by Eric Hoffer
If you want insight into why people join mass political movements that ultimately lead to situations like the above book
Endorsed by Dwight D. Eisenhower & Hillary Clinton
If you want insight into why people join mass political movements that ultimately lead to situations like the above book
Endorsed by Dwight D. Eisenhower & Hillary Clinton
4) The Diary of Young Girl (1947) by Anne Frank
Required reading if you haven't already read it
Required reading if you haven't already read it
December 22, 2024 at 5:13 PM
4) The Diary of Young Girl (1947) by Anne Frank
Required reading if you haven't already read it
Required reading if you haven't already read it
3) The Brothers Karamazov (1880) by Fyodor Dostoevsky
Tried reading this in 2019 but gave up early on. Came back to it this spring. Incredible book, 100% worth the time investment
Tried reading this in 2019 but gave up early on. Came back to it this spring. Incredible book, 100% worth the time investment
December 22, 2024 at 5:13 PM
3) The Brothers Karamazov (1880) by Fyodor Dostoevsky
Tried reading this in 2019 but gave up early on. Came back to it this spring. Incredible book, 100% worth the time investment
Tried reading this in 2019 but gave up early on. Came back to it this spring. Incredible book, 100% worth the time investment
2) Autobiography (1791) by Benjamin Franklin
Franklin spent just 5 pages talking about his discovery of electricity and nearly *9* pages about how better irrigating roads will make them less dusty
Yet it all makes sense. He's not writing for fame but to show how builders think
Franklin spent just 5 pages talking about his discovery of electricity and nearly *9* pages about how better irrigating roads will make them less dusty
Yet it all makes sense. He's not writing for fame but to show how builders think
December 22, 2024 at 5:13 PM
2) Autobiography (1791) by Benjamin Franklin
Franklin spent just 5 pages talking about his discovery of electricity and nearly *9* pages about how better irrigating roads will make them less dusty
Yet it all makes sense. He's not writing for fame but to show how builders think
Franklin spent just 5 pages talking about his discovery of electricity and nearly *9* pages about how better irrigating roads will make them less dusty
Yet it all makes sense. He's not writing for fame but to show how builders think
1.5) Love in the Time of Cholera (1985) by Gabriel Garcia Marquez
Another fantastic novel. Not counting this as one of the 10 but it gets an honorable mention. The writing is just so good!
Another fantastic novel. Not counting this as one of the 10 but it gets an honorable mention. The writing is just so good!
December 22, 2024 at 5:13 PM
1.5) Love in the Time of Cholera (1985) by Gabriel Garcia Marquez
Another fantastic novel. Not counting this as one of the 10 but it gets an honorable mention. The writing is just so good!
Another fantastic novel. Not counting this as one of the 10 but it gets an honorable mention. The writing is just so good!
This year I've read 30 books so far. Here are the ~10 that I found the most valuable 🧵
1) One Hundred Years of Solitude (1967) by Gabriel Garcia Marquez
Fantastic novel that I think everybody should read once. Captures the feeling of human life that feels instinctually correct
1) One Hundred Years of Solitude (1967) by Gabriel Garcia Marquez
Fantastic novel that I think everybody should read once. Captures the feeling of human life that feels instinctually correct
December 22, 2024 at 5:13 PM
This year I've read 30 books so far. Here are the ~10 that I found the most valuable 🧵
1) One Hundred Years of Solitude (1967) by Gabriel Garcia Marquez
Fantastic novel that I think everybody should read once. Captures the feeling of human life that feels instinctually correct
1) One Hundred Years of Solitude (1967) by Gabriel Garcia Marquez
Fantastic novel that I think everybody should read once. Captures the feeling of human life that feels instinctually correct
Unparalleled levels of productivity this week
December 20, 2024 at 7:31 PM
Unparalleled levels of productivity this week
It wasn't idle. They tried to see what it would do if they forced it to be greedy and 'accidentally' showed it info saying it would be shut down
From x.com/simonw/statu...
From x.com/simonw/statu...
December 6, 2024 at 4:20 PM
It wasn't idle. They tried to see what it would do if they forced it to be greedy and 'accidentally' showed it info saying it would be shut down
From x.com/simonw/statu...
From x.com/simonw/statu...
@ddelalamo.bsky.social Just looked at the data. We fine-tuned ProteinMPNN on AlphaFold structures from each class of temperature in the HotProtein dataset. We found no change in performance on FireProtDB ddG or dTM.
Work done w/ Phillip Woolley at UT Austin
Work done w/ Phillip Woolley at UT Austin
December 3, 2024 at 4:23 PM
@ddelalamo.bsky.social Just looked at the data. We fine-tuned ProteinMPNN on AlphaFold structures from each class of temperature in the HotProtein dataset. We found no change in performance on FireProtDB ddG or dTM.
Work done w/ Phillip Woolley at UT Austin
Work done w/ Phillip Woolley at UT Austin
Last year I made an intro Protein + ML project to teach BioML Society members about protein embeddings. Here it is! Hope you all enjoy
Should get you familiar extracting embeddings for proteins, visualizing them, and using them for property prediction
Should get you familiar extracting embeddings for proteins, visualizing them, and using them for property prediction
November 22, 2024 at 6:12 PM
Last year I made an intro Protein + ML project to teach BioML Society members about protein embeddings. Here it is! Hope you all enjoy
Should get you familiar extracting embeddings for proteins, visualizing them, and using them for property prediction
Should get you familiar extracting embeddings for proteins, visualizing them, and using them for property prediction