John Parkhill
@johnparkhill.bsky.social
Senior director of machine learning @ Terray Therapeutics (https://www.terraytx.com/). Father. NSF CAREER award giver-upper. Gibe and gambol enjoyer. Refugee from https://x.com/j0hnparkhill. http://bbgky.net
This is the way arxiv.org/abs/2506.044...
Multiscale guidance of AlphaFold3 with heterogeneous cryo-EM data
Protein structure prediction models are now capable of generating accurate 3D structural hypotheses from sequence alone. However, they routinely fail to capture the conformational diversity of dynamic...
arxiv.org
June 6, 2025 at 12:55 PM
This is the way arxiv.org/abs/2506.044...
Beautiful. arxiv.org/abs/2505.13447
Mean Flows for One-step Generative Modeling
We propose a principled and effective framework for one-step generative modeling. We introduce the notion of average velocity to characterize flow fields, in contrast to instantaneous velocity modeled...
arxiv.org
May 21, 2025 at 3:55 PM
Beautiful. arxiv.org/abs/2505.13447
I can't decide how I feel about someone vibecoding what is asked for in the job description. It shows initiative? But probably should have added "oh, don't put vibecode emoji's everywhere" to the system prompt.
May 7, 2025 at 9:46 PM
I can't decide how I feel about someone vibecoding what is asked for in the job description. It shows initiative? But probably should have added "oh, don't put vibecode emoji's everywhere" to the system prompt.
The persistence of docking in drug design has been explained. :P www.nature.com/articles/s41...
Using an algorithmic approach to shape human decision-making through attraction to patterns - Nature Communications
Here, using data from a competition between academic teams to influence decision-making, the authors show that people, intending to maximize their profit, prefer options delivering rewards in a discov...
www.nature.com
May 5, 2025 at 12:55 PM
The persistence of docking in drug design has been explained. :P www.nature.com/articles/s41...
gemini is pretty good at making manim animations with a little help, but boy without UV, manim would be impossible to install.
May 1, 2025 at 2:02 PM
gemini is pretty good at making manim animations with a little help, but boy without UV, manim would be impossible to install.
If you think we can avoid Thalidomide like outcomes without animal models today, you're an idiot. If you think you're merely marketing, you should appreciate that idiots will listen to you, and the consequences will be real. I will bet anyone 1000$ if this happens it ends poorly.
April 28, 2025 at 5:07 PM
If you think we can avoid Thalidomide like outcomes without animal models today, you're an idiot. If you think you're merely marketing, you should appreciate that idiots will listen to you, and the consequences will be real. I will bet anyone 1000$ if this happens it ends poorly.
The transition between "wins nobel prize" and "says vitamin C cures mortality" or "HIV doesn't cause AIDS" or "lobotomies for everyone" or "eugenics is cool" - or "disease is over because I interpolated crystal structures" is crazy short. (all utterances of nobel prize winners)
April 25, 2025 at 8:40 PM
The transition between "wins nobel prize" and "says vitamin C cures mortality" or "HIV doesn't cause AIDS" or "lobotomies for everyone" or "eugenics is cool" - or "disease is over because I interpolated crystal structures" is crazy short. (all utterances of nobel prize winners)
Only someone who can't think at 2nd order would ever take virtual cell models seriously without many unrelated breakthroughs. There are obvious, indisputable reasons they are stupid, and no one needs them more than me.
genomebiology.biomedcentral.com/articles/10....
Quite an indictment of some of the current single cell "virtual cell" foundation models. Even for the relatively mundane applications, cell labeling, batch correction etc, they are poor compared to much simpler & cheaper methods.
Quite an indictment of some of the current single cell "virtual cell" foundation models. Even for the relatively mundane applications, cell labeling, batch correction etc, they are poor compared to much simpler & cheaper methods.
Zero-shot evaluation reveals limitations of single-cell foundation models - Genome Biology
Foundation models such as scGPT and Geneformer have not been rigorously evaluated in a setting where they are used without any further training (i.e., zero-shot). Understanding the performance of mode...
genomebiology.biomedcentral.com
April 20, 2025 at 9:30 PM
Only someone who can't think at 2nd order would ever take virtual cell models seriously without many unrelated breakthroughs. There are obvious, indisputable reasons they are stupid, and no one needs them more than me.
If your field is getting more "perspectives" papers or "position" papers, you're going to get feudalism and dreck. I'd hop :)
April 18, 2025 at 5:53 PM
If your field is getting more "perspectives" papers or "position" papers, you're going to get feudalism and dreck. I'd hop :)
"give it to god"-- god of course being the transformer.
April 18, 2025 at 5:25 PM
"give it to god"-- god of course being the transformer.
William Gibson owes it to the world to do another neuromancer, but where it's just descriptions of how lame the real person or prompt is behind every high follower X shitpost account. Instead of the real sexual content, dms with e-girls. Coin swindles making 5k instead of heists
April 18, 2025 at 3:16 PM
William Gibson owes it to the world to do another neuromancer, but where it's just descriptions of how lame the real person or prompt is behind every high follower X shitpost account. Instead of the real sexual content, dms with e-girls. Coin swindles making 5k instead of heists
If universities don't stand up to the "dark enlightenment" they will lose all their relevance.
Breaking News: Harvard rejected the Trump administration’s demands, including that it submit to monitoring and reduce the power of faculty and students.
Harvard Will Not Comply With a List of Trump Administration Demands
Federal officials said Harvard must enact “merit-based reform” in hiring and admissions, among other things. Harvard called the demands unlawful.
www.nytimes.com
April 14, 2025 at 6:36 PM
If universities don't stand up to the "dark enlightenment" they will lose all their relevance.
We're Hiring. ats.rippling.com/terraytx/job...
Machine Learning Engineer | Current Openings at Terray
Position Summary: Terray Therapeutics is seeking a Machine Learning Engineer to lead the development of cutting-edge models and tools...
ats.rippling.com
April 10, 2025 at 3:05 PM
We're Hiring. ats.rippling.com/terraytx/job...
The amount of disrespect one has for other people's thoughts, is often crazily proportional to how desperately one craves approval and validation. It's a joke embedded in humanity.
April 3, 2025 at 4:59 AM
The amount of disrespect one has for other people's thoughts, is often crazily proportional to how desperately one craves approval and validation. It's a joke embedded in humanity.
Imagine getting ratio'd by a guy with half your rizz on your own crappy propaganda platform 😂
April 1, 2025 at 1:03 AM
Imagine getting ratio'd by a guy with half your rizz on your own crappy propaganda platform 😂
Beautiful work. So beautiful I think it must be viewed as a suggestion. Still pretty. biorxiv.org/content/10.1...
Enthalpy-entropy trade-offs in the evolution of ligand specificity in a superfamily of transcription factors
Proteins operate through ligand and solvent interactions governed by thermodynamics, yet the enthalpy-entropy trade-offs that guide their functional evolution remain poorly understood. The LacI/GalR f...
biorxiv.org
March 28, 2025 at 3:16 PM
Beautiful work. So beautiful I think it must be viewed as a suggestion. Still pretty. biorxiv.org/content/10.1...
Reposted by John Parkhill
Harvard Medical School, are you OK with this outcome? Who will speak up for her?
Kseniia Petrova, a Russian scientist at Harvard Medical School, was detained at Logan Airport after returning from France and sent to an ICE detention in Louisiana, The Insider reports.
A big critic of Putin and the war in Ukraine, she may now be deported to Russia.
A big critic of Putin and the war in Ukraine, she may now be deported to Russia.
March 27, 2025 at 10:05 PM
Harvard Medical School, are you OK with this outcome? Who will speak up for her?
One of the most powerful ideas unused by the average person is to optimize baskets of decisions rather than individual decisions. The reason for this is: even if you have no MEAN signal on the individual decisions, you can optimize the basket.
March 27, 2025 at 3:27 PM
One of the most powerful ideas unused by the average person is to optimize baskets of decisions rather than individual decisions. The reason for this is: even if you have no MEAN signal on the individual decisions, you can optimize the basket.
Is medicinal chemistry semi-martingale? 😀
March 26, 2025 at 4:03 PM
Is medicinal chemistry semi-martingale? 😀
DEI hires never texted war plans. thehill.com/homenews/hou...
thehill.com
March 24, 2025 at 9:07 PM
DEI hires never texted war plans. thehill.com/homenews/hou...
Reposted by John Parkhill
All you need to know about Twitter
March 23, 2025 at 7:07 PM
All you need to know about Twitter
Literature is as close as it gets to a cure for the human condition, and a boox air 4 is a really good way to read.
March 22, 2025 at 10:52 PM
Literature is as close as it gets to a cure for the human condition, and a boox air 4 is a really good way to read.
Reposted by John Parkhill
The Department of Education, among other things, is what funds special education for children with disabilities.
Trump’s executive order will hurt kids and parents in virtually every school district in the country.
Trump’s executive order will hurt kids and parents in virtually every school district in the country.
March 21, 2025 at 10:38 PM
The Department of Education, among other things, is what funds special education for children with disabilities.
Trump’s executive order will hurt kids and parents in virtually every school district in the country.
Trump’s executive order will hurt kids and parents in virtually every school district in the country.