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...

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.

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.

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...

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...

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 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...

The Arc Institute has just released their pre-print STATE. "Predicting cellular responses to perturbation across diverse contexts with State" arcinstitute.org/manuscripts/...

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...

I have just read the transcript of an interview with Robert Taylor (head of ARPA). He had some interesting things to say about AI and the issue with AI hype. This was in 1989 and still holds wisdom today. conservancy.umn.edu/items/16d6b5...

It was just a matter of time before we saw the rise of AI charlatans. Not sure it is worse than AI generated rage bait though...

Through some conversations with ChatGPT, it said this about Belgium: "Belgium is like the Monty Python sketch of nations: serious face, absurd punchline." As a Belgian, I can't say I disagree.

This is an extremely powerful method! In essence, they can re-create the raw data from embedding space across models. arxiv.org/abs/2505.12540

After a month of developing with #Julia, it is becoming my favorite language! It's crazy how having strict type setting can catch most bugs. Yes, I know python has that as well. And Rust. And C/C++. But R doesn't... New project coming out soon? Any guesses as to what this is?

"ML is the process of learning from data to perform complex tasks for which there is no known deterministic and algorithmic solution, or building such a solution is not practical." Not all problems need ML. Not all questions can be solved without. Choose Wisely. arxiv.org/abs/2312.03120

You know what? Package development in Julia is pretty neat. #Julia #Dev

The Institute Chapter 4: Rock Vocals The single link between geology and singing pcnmartin.substack.com/p/rock-vocals

In that last few weeks, I have been seeing a few posts talking about the caveats of "vibe coding". Unsurprisingly, "vibe coding" only works if you are already an expect programmer who can spot terrible code at a glance. So I ask: What makes us think that PhD level agents are a good idea ?

Well the Evo 2 model from the @arcinstitute.org has been dropped. Looking forward to reading this one. arcinstitute.org/manuscripts/...

Imagine if we have enough spatial omics data to the same thing as this. Well done to whole team. arxiv.org/abs/2502.02673

This paper is finally out! I thought it had gotten stuck at the pre-print stage. Congrats to the authors. In a nutshell: Using deep learning to investigate spatial domains and, more interestingly, spatial gradients of gene expression! www.nature.com/articles/s41...

The antidote for despair is action ❤️ * Dial (202) 224-3121 * Enter zip code * Leave voicemail * Say “My name is ___, I’m a constituent in [town]. (If clinician/scientist, say so) “The NIH freeze harms research and patients and must be lifted immediately.” Be brief. Staffers tally all calls. Go! ✅

This is a great initiative. LLM's are great but not accessible to everyone in biomedical community. www.nature.com/articles/s41...

In need of a bit of a sugar rush, I get myself a zesty beverage from the vending machine on my floor. It was hot. Not room temperature but actually hot...

$500 Billion Dollars invested into AI. "For the benefit of all of humanity" Color me skeptical. Wasn't OpenAI supposed to be a non-profit? openai.com/index/announ...

I would be curious to see how well this works! arxiv.org/abs/2501.06314

In the current publishing climate, how do you deal with the sunken cost fallacy for your papers? As in, you worked on project for years and you realize that it doesn't work or that better alternatives are being published. Do you just scrap it and move on or do you try to salvage it?

I read the first version and it was a great read! This is such an interesting take on the subject!

Just evacuated our home during the LA fires. We are in a hotel for the night. Here's to hoping we won't come back to ruins. The utter devastation throughout out the city is gut wrenching.

Now this could have some interesting applications in biology! www.arxiv.org/abs/2501.01073

This took longer than it should have but I have finally got myself a nice little webpage! A bit bare bones but it will do for now! patrickcnmartin.github.io

Pretty neat concept right here arxiv.org/abs/2412.17799

I look at a computer and sigh a lot.

Would appreciate a RT from the scientists for this one! We have 665 scientists in the spring database and I want to get us to about 1000 before we set the teachers loose on the database for January matches.

One of the reasons I got interested in biology and bioinformatics was to be able to do something like this. arxiv.org/abs/2412.06993

Over the last year, I have started writing sci-fi short stories. The Institute explores real science in a fictional setting. Chapter 1 : pcnmartin.substack.com/p/reorganize... Chapter 2 : pcnmartin.substack.com/p/tipping-po... Chapter 3 : pcnmartin.substack.com/p/just-15-mi...

Over the last year, I have started writing sci-fi short stories. The Institute explores real science in a fictional setting. Chapter 1 : pcnmartin.substack.com/p/reorganize... Chapter 2 : pcnmartin.substack.com/p/tipping-po... Chapter 3 : pcnmartin.substack.com/p/just-15-mi...

The Institute: Chapter III - Just 15 minutes away. A discussion on the concept of chrono-urbanism. open.substack.com/pub/pcnmarti...

The Institute: Chapter III - Just 15 minutes away. A discussion on the concept of chrono-urbanism. open.substack.com/pub/pcnmarti...

The answer to this question will probably depend on which moral philosophy you align yourself with the most.

I had really enjoyed the preprint! Glad to see this out in Cell. www.cell.com/cell/fulltex...

I’m proud to join more than 30 colleagues today in sharing our analysis of potential risks from “mirror life”. We summarize our findings in a @science.org article, and in greater detail in a 300pg technical report: Article: www.science.org/doi/10.1126/... Report: purl.stanford.edu/cv716pj4036

CZI science is providing high quality cell models on top of their high quality curated data sets! On step closer to their goal of the full virtual cell. chanzuckerberg.com/blog/ai-cell...