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John Parkhill @johnparkhill.bsky.social · Jun 6

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

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John Parkhill @johnparkhill.bsky.social · May 21

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

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John Parkhill @johnparkhill.bsky.social · May 8

The problem with healthcare in the US is the lack of a market. Consumers are captive, and there is no price discovery process. Despite this, improved technology continues to arrive because the humans pursuing treatments genuinely care.

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John Parkhill @johnparkhill.bsky.social · May 8

... And yet we live in a time where fairly complex quantitative reasoning is free. Some would say a reckoning is due. Anyone reading resumes and using AI these days is probably genuinely worried... I am.

John Parkhill @johnparkhill.bsky.social · May 7

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.

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John Parkhill @johnparkhill.bsky.social · May 7

When your whole exec team is dumping the stock for the last year, this is implied.

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John Parkhill @johnparkhill.bsky.social · May 5

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

John Parkhill @johnparkhill.bsky.social · May 2

abcnews.go.com/Politics/rfk...

RFK Jr. reports up to $1.2M in credit card debt, $30M net worth

From law firm payouts to endorsements and book deals, nominee for HHS secretary Robert F. Kennedy Jr. raked in at least $12 million in the past two years.

abcnews.go.com

John Parkhill @johnparkhill.bsky.social · May 2

I will fund a study examining either: author preference for outcomes of an LLM based review process over human cartel, or publication impact in an LLM review process vs. human cartel.

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John Parkhill @johnparkhill.bsky.social · May 1

gemini is pretty good at making manim animations with a little help, but boy without UV, manim would be impossible to install.

John Parkhill @johnparkhill.bsky.social · Apr 28

Yes. this type of thing happens constantly in drug discovery, the cereblon binding etc. but that's precisely why models cannot _replace_ experiments. They are based on observations which are themselves often contradictory, or impossible to explain without entire new domains of knowledge.

John Parkhill @johnparkhill.bsky.social · Apr 28

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.

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John Parkhill @johnparkhill.bsky.social · Apr 25

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)

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John Parkhill @johnparkhill.bsky.social · Apr 20

A virtual cell is like trying to emulate a computer with only the rom, no instruction set, and 20 types of registers you don't even know exist and have no hope to simulate because their physics is chaotic and nonlinear.

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John Parkhill @johnparkhill.bsky.social · Apr 20

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.

Anshul Kundaje @anshulkundaje.bsky.social · Apr 20

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.

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

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John Parkhill @johnparkhill.bsky.social · Apr 18

If your field is getting more "perspectives" papers or "position" papers, you're going to get feudalism and dreck. I'd hop :)

John Parkhill @johnparkhill.bsky.social · Apr 18

"give it to god"-- god of course being the transformer.

John Parkhill @johnparkhill.bsky.social · Apr 18

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

John Parkhill @johnparkhill.bsky.social · Apr 16

Honestly these mostly solidified mafias. Certainly not the worst loss within the trashfire of cuts.

John Parkhill @johnparkhill.bsky.social · Apr 15

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John Parkhill @johnparkhill.bsky.social · Apr 15

John Parkhill @johnparkhill.bsky.social · Apr 14

If universities don't stand up to the "dark enlightenment" they will lose all their relevance.

The New York Times @nytimes.com · Apr 14

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

John Parkhill @johnparkhill.bsky.social · Apr 10

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

John Parkhill @johnparkhill.bsky.social · Apr 4

MSAs are precisely the reason this field is stuck...

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John Parkhill @johnparkhill.bsky.social · Apr 3

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.

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