Yihao Yang

📍Altos Labs, San Diego | 🧬 Studying the aging epigenome

[Prof Steve Horvath @prof_horvath]

Important new Nature paper (Alexander Tyshkovskiy, Vadim Gladyshev lab): universal transcriptomic clocks of aging and mortality across mice, rats, macaques and humans, from more than 11,000 transcriptomes. The aging field has long wanted robust multi-species transcriptomic clocks, this seems to fit the bill. I also liked that their chromatin-modification module clock tracks DNA methylation clocks most closely which hints at a transcriptome-epigenome link. https://t.co/oHRf5CA5pc

[Acyn @Acyn]

Aerial view of New York right now.

[Mark Budde 🦕🏆 @markwbudde]

Biologists win again

[Kenny Workman @kenbwork]

Introducing EpiBench, an agentic benchmark for practical epigenomics analysis.

106 evaluations span CUT&Tag/CUT&RUN, ATAC-seq, ChIP-seq, and DNA methylation workflows. The best agent–harness pair passes 45.0% of evaluations.

Evaluations reflect the assay outputs scientists use in practice. A task may depend on alignment files, peak calls, methylation tables, QC metrics, sample metadata, genomic annotations, or downstream summaries. Solving them requires a mix of coding, data analysis, and scientific judgment.

Ground truth is hard to define even for short-horizon scientific tasks. Alternative task interpretations can produce multiple plausible answers. Candidate tasks are hardened through manual quality control. We remove prompts that over-specify the method, answers that can be solved with general literature knowledge, and ground truths that fail to reproduce under peer reproduction.

Short-horizon tasks are the current frontier for scientific agents in epigenomics. Before models can own deeper biological reasoning, they need to become reliable at local assay-specific decisions.

[Anthropic @AnthropicAI]

New Science Blog: Why has AI advanced faster in coding than in biology?

To agents, bio databases are like cities built before cars—maddening to drive in because they're designed for different traffic.

How do we build infrastructure agents can use?
https://t.co/PQaNQ4GRJZ

[Dan Landau @landau_lab]

Exciting breakthrough technology from the lab, now live in @CellCellPress ! Instead of cutting the genome where proteins bind (e.g., Cut&Tag), D&D-seq scars the DNA with a deaminase, allowing single cell genome mapping of TFs and chromatin remodellers!

[Crémieux @cremieuxrecueil]

Oh my god, almost no biomedical AI papers had proper validations.

This feels like field-wide malpractice.

[Andrej Karpathy @karpathy]

Personal update: I've joined Anthropic. I think the next few years at the frontier of LLMs will be especially formative. I am very excited to join the team here and get back to R&D. I remain deeply passionate about education and plan to resume my work on it in time.

[.stuff @vintagestuff4]

"They're having problems with their economy again."
Ron Cobb
1975

[sui generis @sui_generis__]

@YourAnonCentral I sincerely hope that if he dies of a stroke, someone runs this photo next to his obit.

[Skyleigh Uhrich @Sky_Lee_1]

I bookmarked this for a reason….

[Wordita @wordi25]

Three nationalities left out of the list. Possibly coz their high contribution along with the color of their skin doesn’t align with the narrative.

Indian : $1.7 million
Chinese : $800K
Filipino : $600K

[Oded Rechavi @OdedRechavi]

We built an AI that will tell you what will get your grant rejected. It’s a tough critique, but it’s better to know when you can still do something about it 👇 @qedScience

[First To Hear It @firsttohearit]

REPORTER: You mentioned that, staying on as Fed governor, you intend to keep a low profile. Could you give us a little more detail on what that looks like?

JEROME POWELL: *ducks down*

[Yihao Yang @EpiYang]

Unfortunately this is true….. @MicrobiomDigest

[Richard Fuisz @richardfuisz]

This paper got a few million views across various RTs two weeks ago: EMF remote-controlled mice...

Look carefully at the saline & control images from the paper -- can you see how the two images are flipped and re-cropped? h/t @AndrewGYork and friends for the close read

[John F Kennedy @Kennedy35POTUS]

fuck you

[Yann LeCun @ylecun]

Shooting oneself in the foot?
Nope.
Shooting oneself in the prefrontal cortex.

[unusual_whales @unusual_whales]

BREAKING: A Syrian billionaire needed U.S. sanctions lifted so he could cash in on $12 billion in reconstruction contracts, per NYT.

In an attempt to influence American foreign policy, he proposed a Trump-branded golf course, cut Jared Kushner & Ivanka Trump into a multibillion-dollar real estate deal for a resort in Albania, and had someone physically deliver a stone engraved with the Trump family crest to a Republican Member of Congress with instructions to take it to the White House to get the President's attention.

Trump threw his weight behind repealing the sanctions. They were lifted. The contracts are moving, and the Trump family’s deals are expanding.

[antisense. @razoralign]

Benchmarking single-cell foundation models for real-world RNA-seq data integration https://t.co/m0GFyqFRk5

[Alex Strudwick Young @AlexTISYoung]

Frontier models aren't ready for end to end genomics analyses yet.

But I wonder how an average grad student would do on these problems...