My heart goes to out to the ordinary people of Iran and Israel for what seems to me, as an outsider, a completely pointless war. I hope this insanity comes to an end quickly. My hear goes out to the civilians in these countries who really didn't want or deserve this.

Today’s home loss to Arsenal makes it even more obvious.

Ancelotti needs to be fired. Real Madrid have just been uninspiring and at times terrible this season.

As more and more tech companies claim that LLMs will make certain classes of jobs unnecessary in a few years, it amazes me that there is little to no discussion on the effects on the labor force/economy and other societal impacts.

After 3.5 wonderful years at @insitro.bsky.social where I got to work on many interesting problems at the intersection of genetics and ML, I will be joining Oracle Health on Monday as a Senior Applied Science Manager to work on clinical LLMs. (1/)

South Asian friends living in the US - is it me or is Indian food just way more spicy in the US than it is in India (on average)? If y'all agree with me, why do you think this is? Even dishes that were sweet-ish in India, are somehow spicy here.

Happy Nowruz to all my Iranian friends and whoever else celebrates it. Hope y'all have a wonderful day.

We have a new method, HypotheSAEs, for identifying *interpretable text features that predict a target variable* (aka hypothesis generation). What features of a headline predict engagement? What features of a clinical note predict whether a patient will develop cancer? 1/

I'm deeply honored to be elected as an ISCB Fellow this year!🏅 Following last year’s ISCB Innovator Award, this recognition strengthens my commitment to advancing computational biology.🧬 Grateful to my students, mentors, and colleagues for their support! www.iscb.org/iscb-news-it...

Imma be honest, I didn't really see a Gavin Newsom and Charlie Kirk colab coming: www.youtube.com/watch?v=9XJ6...? But then again, there are many things about our political climate in 2025 that I didn't see coming. Might be a me thing.

It's shameful that we have billionaires now feeling empowered to go on highly visible podcasts and say Social Security is a 'ponzi scheme' without explaining a clear alternative that doesn't involve kicking seniors to the curb. Truly shameful!

Jesus Christ, is this true: www.cbsnews.com/news/elon-mu...? Seems like twitter acquisition all over again. And we all saw how well that went.

Happy valentine's day to my science fam!! Hope y'all keep doing all the great science!! :)

There's still time to submit an abstract to the legendary Biology of Genomes meeting! Come and present your work alongside the stellar lineup of invited speakers and keynotes. #BOG25

Awesome new paper led by @zmccaw.bsky.social and my amazing colleagues at @insitro.bsky.social !! Great explainer thread below 👇🧪💻🧬

This is the most relevant article to NIH and research cuts I’ve seen. Imagine if this was today , how many people would be saying “Why are we studying Gila Monsters and their impact on diabetes ? That’s wasted money !” globalnews.ca/news/9793403...

I really enjoyed reading this paper. Very interesting and innovative approach to characterize biomarkers and subtypes of MASLD.

Very cool paper 👇🏼

Very interesting 👇🏼

0/ Essential reading for anyone training or using sequence-function models trained on genomic sequences! 🚨 In our new preprint, we explore the ways homology within genomes can cause leakage when training sequence-based models and ways to prevent it

The success of LLMs has inspired their extension to genomics data. A preprints reports that such models lack understanding of genomics and provide minimal utility, even for basic tasks such as sequence classification. www.biorxiv.org/content/10.1...

I was recently trying out this tool from google called NotebookLM that converts PDFs to a podcast format. It's pretty cool. I used it to summarize this paper and found the description pretty accurate: notebooklm.google.com/notebook/7ab.... Check it out. 🧪💻🧬

My thread on the genomic SEM paper (www.nature.com/articles/s41...). I forgot to add 🧪💻🧬 #StatisticalGenetics

Okay, I am back with another thread on multivariate phenotypes. This will be focused on summarizing this paper: www.nature.com/articles/s41.... This paper introduces a SEM based approach to estimate latent factors underlying multiple relevant traits and using them to improve the power of GWASs. (1/)

Hilarious but true!!

Okay, what is the point of making 6yo's take standardized tests (talking about iReady) in school and then sending them home with the results. My kid did well and I am proud of him. However, it seems to be making him competitive and I'm not sure how I feel about that.

This new executive action on birthright citizenship is so profoundly sad. While it might be struck down by the courts, I think it tells potential immigrants just how little we think of them. Sad.

Increased amounts of fat in skeletal muscle, a marker of inflammation, is associated with higher risk of major cardiovascular events. From an observational study of >600 participants with PET scans, followed for 6 years (a first) academic.oup.com/eurheartj/ad...

Very interesting.

Very interesting 👇🏼

Ok. Folks, I am back from vacation. I am thinking of new topics at the intersection of ML and genetics for my threads. Do people have specific topics or interesting papers that they might want to see explainer threads on? 🧪💻🧬

A new large language of life model (LLLM) for the transcriptome that predicts gene expression within and across human cell types www.nature.com/articles/s41... @nature.com For more on the remarkable surge of LLLMs see erictopol.substack.com/p/learning-t...

Our paper on using generative machine learning to synthesize R2* maps from fat fraction maps derived from 2 point Dixon MRIs is now accepted to #ISBI2025. Check out the preprint here: arxiv.org/abs/2410.11186 (1/)

Our paper on Self-Supervised Learning in Single-Cell Genomics is out in Nature Portfolio Machine Intelligence! 🙌 🧬🤖 Big thank you to my co-authors Mojtaba Bahrami, Yufan Xia, @davidsebfischer.bsky.social, and @fabiantheis.bsky.social . 👏 nature.com/articles/s42...

I am vacationing in Mexico right now and one of the most interesting things is how literally everyone here just assumes I am also Mexican. Meanwhile a group of Iranians assumed I was Iranian because my wife is Iranian American. I feel like I should consider a career as a spy or something.

What a fascinating read. I recommend people read the actual article.

As we ponder ways to use AI to make our lives more efficient, this is an important question to consider. Another one that comes to mind is ‘at what cost?’. As an ML researchers, this are important question to think about so we don’t build pointless things at an unforeseen cost to society.

I wrote about how polygenic heritable conditions present in families and the liability threshold model. This has some counterintuitive implications for considering the risk of a condition in offspring as well as the impact of multi-generational selection. A 🧵:

Happy holidays everyone!!! Hope all of you get to enjoy this time with your family and loved ones. I personally am super excited for the rum soaked fruit cakes I will have over the next few days!!

Spatial omics of human arteries to understand what drives atherosclerosis: highlights role of the microvasculature (vasa vasorum), adventitial inflammation, migration of vascular smooth muscle cells (and more) nature.com/articles/s44...

It seems like I got pneumonia just in time for the holidays. So, it's probably a good time to write that thread on post-prediction inference in the context of GWAS. So what is post-prediction inference? Read on .. 🧬💻🧪 (1/)

MIT researchers introduce Boltz-1, a fully open-source model for predicting biomolecular structures With models like AlphaFold3 limited to academic research, the team built an equivalent alternative, to encourage innovation more broadly www.eurekalert.org/news-release...

Many academics point to bioRxiv as “the one thing improving science publishing”. If so, the one thing you all can do is persuade colleagues to submit and make this a norm. 1/2

This was a period of time where taxpayer funded initiatives funded science at unprecedented rates. These efforts made America a global social, economic, and educational powerhouse. In 1966 at the peak of the Apollo program, we spent 2.5%GDP on science. Now? Now we spend 0.6%GDP on science. 🧪

One thing that is making my bluesky experience less exciting that perhaps the early days of twitter is the lack of engagement. For whatever reason, I don't see a lot of discussions happening. At least not at a level comparable to old twitter. Does this bother others too?

Thought this was an interesting suggestion: AI Liability Standards - Develop standards for AI-related liability to address legal and ethical challenges when AI produces incorrect diagnoses or recommendations. Congress should examine liability laws to protect patients. 🩺🖥️ #MLSky #LawSky

Our new paper on how causal relationships between variables used for imputation and the phenotype being imputed can affect the utility of GWAS using this imputed phenotype. 🧬🧪 🖥️ (1/)

Okay friends, I am back with a new thread and this time about a new pre-print that I co-authored. Today's topic is 'ML assisted GWAS'. What is that, you ask? It's basically estimating missing values in phenotypes of interest using associated measurements (1/)

Interesting thread and very cool paper 👇🏼