Patrick Martin

Okay buddy.

You could also rake it yourself.

Technological and scientific progress needs to move at the same pace as social progress.

Society is like a big ball of pizza dough. You pull too hard in one direction, you end up with holes in your dough, sauce all over, and a shitty pizza.

Nice and even is how you make the perfect pizza.

I would add: they make your mess someone else's problem.

Along these lines, I believe that, sometimes, it's worth slowing down. It's worth remembering that it is simply not feasible to follow through with all your ideas.

www.oliverburkeman.com/river

I'm just going to say it:

Faster iterations and increased productivity with the use of AI means you should make your "product" of much higher quality. Not producing half baked ideas at a faster rate.

Don't ship more garbage. Ship the same amount but better.

#AI #VibeCoding

I can totally see it as some sort of russian roulette of traps. This was a simple spike coming out of the wall? Now it's snakes. You could use some custom wild magic tables.

I'm adding that to my next dnd game. Shuffle doors. Shuffle cards. Shuffle traps. Endless fun

I have been playing around with the
@chanzuckerberg.bsky.social CellXGene census for mouse data. There are a couple of interesting cell types in there.

One of them is just called "cell". It's a cell and its identity is none of your business.

I have seen a few of these bands live. Welcome to the strange world of metal.

We live in the decade of generative models and biology is no exception.

Genome language models can now generate functional bacteriophages!

Read more in my new sub-stack post where I explore the @arcinstitute.org latest pre-print.

We live in the decade of generative models and biology is no exception.

Genome language models can now generate functional bacteriophages!

Read more in my new sub-stack post where I explore the @arcinstitute.org latest pre-print.

FedscGen: privacy-preserving federated batch effect correction of single-cell RNA sequencing data - Genome Biology Single-cell RNA-seq data from clinical samples often suffer from batch effects, but data sharing is limited due to genomic privacy concerns. We present FedscGen, a privacy-preserving communication-eff...

Federated Integration of single cell data!

Now this is an amazing initiative. No need to share the data.

But, and maybe more importantly, demonstrates that complex tasks such as integration can be done using distributed compute power.

genomebiology.biomedcentral.com/articles/10....

spCorr: flexible and scalable inference of spatially varying correlation in spatial transcriptomics Spatial transcriptomics has transformed our ability to explore gene expression within its tissue context, enabling us to dissect subtle yet biologically significant variations in situ . While numerous...

This is actually a pretty neat idea. Spatially correlated genes.

www.biorxiv.org/content/10.1...

Well. I'm not going to say I am surprised by these results. Come on people. We can do better than this.

www.nature.com/articles/s41...

#AI #Honesty

Often working at the intersection of AI and Biology, I have developed a love-hate relationship with AI.

In this essay, I share some thoughts on the modern AI ecosystem. It’s not all doom and gloom but there is room for improvement.

pcnmartin.substack.com/p/a-love-hat...

Multi-scale and multi-context interpretable mapping of cell states across heterogeneous spatial samples - Nature Communications The alignment of heterogeneous spatial samples has become a growing challenge. Here, authors present a multi-scale, multi-context, and interpretable mapping strategy to map cells across space, time, a...

Vesalius 2.0 is in ‪‪@natcomms.nature.com‬ !

We show how using spatial context improves cell-to-cell mapping across heterogenous spatial samples.

Thanks to the reviewers, editors, and collaborators for making this possible.

GitHub: github.com/WonLab-CS/Ve...
Paper: www.nature.com/articles/s41...

It has been quite fun and interesting trying to run scRNA analysis using only distributed/parallelized packages. Finding approximations to non-parallelizable algorithms is quite the challenge.

It also makes you appreciate the amazing work behind Scanpy from the @scverse.bsky.social and Seurat.

Thank you @qchengx1e3.bsky.social for handling this manuscript! Great to see it out.

Multi-scale and multi-context interpretable mapping of cell states across heterogeneous spatial samples - Nature Communications The alignment of heterogeneous spatial samples has become a growing challenge. Here, authors present a multi-scale, multi-context, and interpretable mapping strategy to map cells across space, time, a...

Vesalius 2.0 is in ‪‪@natcomms.nature.com‬ !

We show how using spatial context improves cell-to-cell mapping across heterogenous spatial samples.

Thanks to the reviewers, editors, and collaborators for making this possible.

GitHub: github.com/WonLab-CS/Ve...
Paper: www.nature.com/articles/s41...

Does this plot look ugly? Yes it does.

Am I happy with because of what it represents? Yes I am.

Simulated Gene Pulse

Want to read an article but the article is behind a paywall? I have a trick to get around that.

It is a bit convoluted but hear me out:

1. Open your email.
2. Get the email of the corresponding authors
3. Send them a polite email that you wrote yourself asking for a pdf of the paper.
4. Profit

I am not sure any of those questions would require a token greedy language bot to answer.

A rude awakening Just breathe.

My first "officially" published #scifi story in @naturefutures.bsky.social, a venue which has published stories by the likes of Arthur C Clark and Kim Stanley Robinson!

The story is entitled: A rude awakening. Just breath.

www.nature.com/articles/d41...

A rude awakening Just breathe.

My first "officially" published #scifi story in @naturefutures.bsky.social, a venue which has published stories by the likes of Arthur C Clark and Kim Stanley Robinson!

The story is entitled: A rude awakening. Just breath.

www.nature.com/articles/d41...

A rude awakening Just breathe.

The voyage was over. After 300 years in stasis, the crew had reached their new home. It was time to wake up. To start living again. Only … something wasn’t right. They felt different. What had happened while they slept??

#scifi by @pcnmartin.bsky.social www.nature.com/articles/d41...

Being a researcher requires a certain level of masochism. You have to like to humiliate yourself by feeling stupid everyday.

You read some paper and you think: "Wow this actually makes sense to some people. The equations look cool I guess."

You know how ChatGPT became a bit of a sycophant, validating everyone thoughts, and finding ways to justify them?

How do we know that Agentic AI systems performing a task will not do the same thing? Will they start p-hacking? Cherry picking data?

#LLM #AgenticAI #AI

I have a suggestion but it comes with a serious caveat: I am not sure it was ever translated to english. If it ever does get translated, I would highly recommend:

The Horde of The Counterwind by Alain Damasio

Let me tell you a story Taking lessons from fiction to elevate scientific presentations and story telling.

I love attending conferences but I often struggle to stay attentive during scientific presentations. The main reason: these talks are dryer than Arrakis ever was.

Here, I share some thoughts on scientific story telling through the lens of fiction.

open.substack.com/pub/pcnmarti...