Jeff Leek

The ITCR Training Network (ITN) www.itcrtraining.org develops training materials for informatics and research.

We have a short survey ~3-9 min about your experience & preferences for learning as a researcher. Previous engagement not required!

xiar7j-itn.shinyapps.io/itn_follow_up/

GitHub - jtleek/scorcher: This is a repo for working on scorcher This is a repo for working on scorcher. Contribute to jtleek/scorcher development by creating an account on GitHub.

You are brave!!! And for deep learning we are trying to separate logic from logistics with scorcher: github.com/jtleek/scorc... (in R! :))

Ad hoc, post hoc and intrinsic-hoc in bioinformatics www.nature.com/articles/s41... (read free: rdcu.be/eNGd3) 🧬🖥️🧪

YouTube video by Madrona The Experiments #Biology Can’t Run — Until Now. #AI #entrepreneur #technology #tech #geneexpression

A cool story that connects the first data I ever analyzed to the work we are doing with Synthesize ! youtube.com/shorts/zN4_m...

Generative genomics predicts future and impossible experiments! Read the new preprint from Synthesize Bio: www.biorxiv.org/content/10.1... and anyone can try our models on the cloud or in R/Python! product.synthesize.bio

Research beyond silos - Cancer AI Alliance The Cancer AI Alliance (CAIA) brings together top cancer centers and tech leaders to break down institutional silos. Using federated learning, they securely train AI models on diverse patient data, ac...

CAIA is breaking down research silos with federated learning. AI models learn from diverse data without moving it.

Read more: www.canceralliance.ai/blog/beyond-...

Congrats to @jtleek.bsky.social + CAIA for advancing secure, equitable cancer research.

#CancerAI #FederatedLearning #Biostatistics

Dude this is like pro-grade!!! I mashed that subscribe button :)

Our pioneering partnership with leading cancer centers and tech companies has been recognized by TIME magazine’s #TIME100AI 2025 for groundbreaking work in artificial intelligence and cancer research!

So amazing to be working with you on this fantastic sprint!

It is my favorite measure of accomplishment that people that work with me have gone on to do amazing things that make them happy and the world better!

Honored to see the Cancer AI Alliance included on TIME's list of the TIME100 AI of 2025! #TIME100AI.

CAIA has been a true team sport based on the shared commitment of all our Alliance members to accelerate cancer research and ultimately improve and save patient’s lives.

time.com/collections/...

How CAIA harnesses federated learning for secure collaboration - Cancer AI Alliance How can we train AI models on the collective knowledge of the nation's top cancer centers without exposing sensitive patient information? CAIA’s solution is an AI training approach called federated ...

Check out this great post explaining our approach to enabling AI model learning and reasoning across multiple-institutions while carefully protecting (and never transferring!) patient data! www.canceralliance.ai/blog/caia-fe...

YouTube video by Madrona The Future of Drug Discovery: AI, Data, and Design

I was recently on a panel talking about Synthesize Bio and the future of AI in biotech! www.youtube.com/watch?v=AR5s...

OpenAI launches reasoning LLM that you can download and tweak One version of the gpt-oss large language model can run on a laptop, and performs nearly as well as the company’s most powerful models.

Fred Hutch data scientists Carrie Wright and Elizabeth Humphries weigh in on OpenAI's first open-weight reasoning #AI, noting its potential for personalization in research applications while emphasizing thoughtful integration. Via @nature.com go.nature.com/4mFSoRb

@fredhutchbiostat.bsky.social

Code from my first live R package demo talk in honor of Hadley at #jsm2025

gist.github.com/jtleek/8c927...

Steve Salerno, Awan Afiaz, and I have been developing the scorcher package to help you more easily fit deep learning models in R !

github.com/jtleek/scorc...

The highlight of my #jsm2025 talk was @hadley.nz roasting the panel with ChatGPT.😂

I also love that he talked about aspiring to kindness!

We are about to be live talking about how cool @hadley.nz is in CC214 at 1030am ! Come hang out if you are at #jsm2025

Jeff Leek Help Fred Hutch Cancer Center advance innovative research. Donate today!

My family and I are going to be running the 5k at Obliteride again this year! (we'll be biking as soon as the boys are old enough :)). We are raising funds for data science and AI efforts to find cancer cures at the Fred Hutch, consider donating if you are able! secure.fredhutch.org/site/TR/Obli...

Wild congratulations to one of the most incredible people I’ve ever worked with. @benlangmead.bsky.social I hope you are celebrating this very well deserved honor!!!

An estimate of the science-wise false discovery rate and application to the top medical literature - PubMed The accuracy of published medical research is critical for scientists, physicians and patients who rely on these results. However, the fundamental belief in the medical literature was called into seri...

Also empirical estimates don't agree with the simulation....

pubmed.ncbi.nlm.nih.gov/24068246/

These are not just grants. This is thousands of people who devoted their lives and careers - taking pay cuts, working long hours, living with uncertainty - all for the chance to try to make people's lives a bit better for you and your loved ones. This breaks my heart.

Damn... I wonder why scientists wouldn't want to come to the US to compete at the highest levels for highly-restricted funding that then gets pulled surreptitiously for some imagined reason or no reason at all, all while being vilified by the federal government for their work? A mystery! 🤔

Industry friends, now is the time for MUCH more speaking out on behalf of academic colleagues under duress. Here are core open source methods that many of your products doubtlessly depend on either directly or indirectly (see en.wikipedia.org/wiki/HMMER) being abruptly defunded. Make noise.

If you are around Seattle, see ya there :)

Bright and early talk by @jtleek.bsky.social at the Princess Margaret Cancer Centre Grand Rounds on building and scaling AI engines in oncology.

NOOOOOOOOOOOOOOOOOOOOOO

Congratulations to the @jxtxfoundation.bsky.social scholarship winners for the 2025 Biology of Genomes conference @cshlnews.bsky.social! Learn more about their research and the scholarship program here: jxtxfoundation.org/news/2025-3-... #bog25

Synthesize Bio's platform is awesome as a teaching tool. In just a couple of minutes you can (a) find a dataset, (b) run a validated workflow like @mikelove.bsky.social's published EDA workflow, and (c) share with your friends:
app.synthesize.bio/notebooks/3a...

This alliance helps solve the key technical challenges that will enable us to securely use both #AI and massive computational power to find these breakthrough insights and save more lives. Congrats to the CAIA team on this well-deserved recognition! #oncsky

An incredible honor and the momentum is building for the Cancer AI Alliance. We have been hard at work behind the scenes - expect more public from us soon! @brianmbot.bsky.social (pictured) and the broader CAIA team are amazing and it is fantastic to see their work rewarded.