
@talkgenomesi
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Café Scientifique meets Genomics meets Social Media. Created by @GenomeNathan and @johnpharmd
Joined November 2013
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#TalkGenomes retweeted
Congratulations to our @WCMEnglanderIPM colleague Dr. Dan Landau (@landau_lab) on being named Inaugural Chair of the Department of Systems and Computational Biomedicine @WeillCornell! #ArtificialIntelligence #LiquidBiopsy #genomics #biomedicine #DreamBig
news.weill.cornell.edu/news/…
🤖 Made with AI
#TalkGenomes retweeted
In a new Science study, researchers show that chromatin exists as a hydrogel that undergoes a volume phase transition between condensed and uncondensed states that correspond to regions of gene activity and silence, respectively.
Learn more in a new #SciencePerspective: scim.ag/4x2vkRX
#TalkGenomes retweeted
Thrilled to post thread re: new single-cell lineage of mouse embryo reconstructed w/ DNA Typewriter. One animal, zygote to late organogenesis (E13.5). Tree has 1,340,794 transcriptionally profiled, annotated tips (cells), 1,142,588 dated internal nodes, rooted at zygote
1/n
#TalkGenomes retweeted
Why is the X chromosome rich in L1 mobile elements? @ScienceMagazine X-chromosome inactivation draws L1 mutagenesis to the human X chromosome | Science science.org/doi/10.1126/scie…
#TalkGenomes retweeted
"GPT-5.5 Pro Outperforms 99.9% of Doctors and Predicts AI Superiority in Medicine by Next Year"
An optimistic AI viewpoint since there are no studies in real world medicine; all we have now are simulations, case vignettes, patient actors, etc. Beyond that, performance metrics need work as we've recently open-source published.
Here's what the editors @NatureMedicine wrote: This study cuts through the optimism surrounding medical AI by showing how easily benchmark success can be
mistaken for real readiness. In medical AI, impressive scores are clearly not the same as trustworthy capability.” [link below]
Our results were independently confirmed by @yishan in current frontier models, such as GPT-5.5 Pro, text below
nature.com/articles/s41591-0…
nitter.cf/yishan/status/20707427…"
A big problem with research studies on AI models is that given how long the peer review process is, the results are always out-of-date by the time the paper is published.
This time, we have something better!
The typical reaction to research results like this roughly goes "You're just testing on old models. Today's models are way better and surely can do it now!"
But the best solution is for these papers to also open-source all of their testing framework so that upon publication, others can reproduce their results, as well as run it on the newest models of the day - and into the future. After all, "this is the worst they'll ever be" so what really matters is determining when they DO pass the threshold.
As it turns out, the authors of this paper DID open-source their evaluation framework!
Here:
github.com/aiden-ygu/health-…
So I figured... let's re-run the tests on the latest models!
Summary of our results are here:
github.com/ywong137/health-a…
One drawback is that, unfortunately, the authors didn't (or weren't legally able to) open-source ALL the testing data, since apparently some of it is copyrighted by JAMA/NEJM etc. That's a separate problem with the medical research publishing industry for another time.
However, we were able to reproduce the test on the public datasets they did include!
First, we re-ran the same tests (as closely as we could) on the old models the paper claimed to use, in order to establish a baseline and determine how much "drift" there would be. (Answer: not too much)
Then we ran those tests on the newest frontier models we could find.
The results are: the most capable models today (GPT-5.5 Pro) did outperform the best models from before (79/100 vs 69/100), but did not improve enough to be considered sufficient for reliable medical use.
In fact, the paper's criterion for "fit for reliable medical use" is more stringent, requiring the models to be robust under perturbation and bad data, knowing when to say there's not enough information, give clinically valid reasoning rather than hallucinations, etc. Those sound pretty reasonable to me.
I wasn't able to reproduce that kind of qualitative evaluation, but even on the basic pass/fail test using public datasets of interpreting radiology images, the newest models are better, but not yet quite good enough.
Nevertheless, I would like to praise the paper's authors for at least open-sourcing what they could, enabling me to (fairly quickly) attempt to reproduce their results. This is definitely a step in the right direction!
While my reproduction wasn't able to be comprehensive, it certainly gave me useful directional info and - perhaps more importantly - allowed me (a random dude on the internet) to directly reproduce the results in their paper and validate them.
I would like to encourage ALL authors of research papers on AI models to do similar open-sourcing of their experimental frameworks!
#TalkGenomes retweeted
Social media is an important skill. He nails it. Will the policy work ? Does it really matter ?
#TalkGenomes retweeted
Whenever @lpachter reads a bioinformatics paper nitter.cf/DeebsFLA/status/207023…
#TalkGenomes retweeted
Congrats @KevinADavies & looking forward to reading Curved Air!
A preview of my new book, Curved Air, on this World #sicklecell Day.
The book is out this September.
hup.harvard.edu/books/978067…
#TalkGenomes retweeted
A new technology, developed by @WeillCornell and @nygenome researchers, allows scientists to map the DNA-binding sites of transcription factors and other regulatory proteins that control gene activity. @CellPressNews @WCM_MeyerCancer @WCMEnglanderIPM news.cornell.edu/stories/202…
Jeremy Wang developed rammap, a minimap2 rewrite in Rust. It achieves comparable or better performance than minimap2 and produces identical output to minimap2. During rewrite, Jeremy found two long-existing bugs in minimap2 which are fixed in v2.31. biorxiv.org/content/10.64898…
#TalkGenomes retweeted
Sex-specific gene expression of the human brain, for >3,000 genes (of our ~20,000 total)
@ScienceMagazine
science.org/doi/10.1126/scie…
#TalkGenomes retweeted
Genotype frequency dynamics in finite-sized, partially clonal population with mutation biorxiv.org/content/10.64898… #biorxiv_genetic
#TalkGenomes retweeted
Discovery of a small peptide that activates both APCCdc20 and APCCdh1 in yeast, driving increased lifespan biorxiv.org/content/10.64898… #biorxiv_genetic
#TalkGenomes retweeted
🔥New episode of the Night Science Podcast comes out today! We talk about how science is secretly driven by analogy with Melanie Mitchell, a professor at the Santa Fe Institute and a leading thinker on AI, analogy and abstraction.
open.spotify.com/episode/1hq… @MelMitchell1 @sfiscience
#TalkGenomes retweeted
"We’ve gotten really good at stopping enzymes. But could we make them go faster?"
For decades, scientists have designed drugs to slow down or block enzymes, but @KapoorLab_RU wondered if tackling some diseases requires the opposite approach.
rockefeller.edu/news/38871-s…
#TalkGenomes retweeted
How has AI impacted science? Analysis of >41m papers.
A paradox: Expansion of individual's impact but contraction in breadth of topics researched collectively
nature.com/articles/s41586-0…
nature.com/articles/d41586-0…
#TalkGenomes retweeted
The U.S. House of Representatives unanimously passing the bill to reauthorize @US_FDA’s Priority Review Vouchers awarded for rare pediatric disease approvals is a big win for rare genetic disease patients. 🙏
🚨 BIG WIN FOR THE #RareDisease COMMUNITY! 🚨
Yesterday, the House passed the #GiveKidsAChanceAct – a major step forward for the Rare #Pediatric Disease Priority Review Voucher (#PRV) program, which has helped bring 63 innovative treatments to children.
Our work isn’t done. Contact your Senators and urge them to pass this bill: rarediseases.org/driving-pol…































