Patrick Martin
@pcnmartin.bsky.social
Aiming to make the Solar Punk Aesthetic a reality. Science, World Building and Story telling. Researcher/Bioinformatician/Data Scientist.
"Always strive to contribute to others."
Contact:
https://patrickcnmartin.github.io/
"Always strive to contribute to others."
Contact:
https://patrickcnmartin.github.io/
Pinned
Patrick Martin
@pcnmartin.bsky.social
· Aug 21
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...
www.nature.com
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...
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...
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.
@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.
October 31, 2025 at 6:46 PM
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.
@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.
Reposted by Patrick Martin
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.
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.
October 22, 2025 at 6:29 PM
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.
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.
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.
October 22, 2025 at 6:29 PM
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.
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.
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....
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....
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...
genomebiology.biomedcentral.com
October 20, 2025 at 10:38 PM
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....
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....
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
www.nature.com/articles/s41...
#AI #Honesty
October 6, 2025 at 9:02 PM
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
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...
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...
September 19, 2025 at 4:08 AM
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...
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...
Reposted by Patrick Martin
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...
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...
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...
www.nature.com
August 21, 2025 at 10:25 PM
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...
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.
It also makes you appreciate the amazing work behind Scanpy from the @scverse.bsky.social and Seurat.
August 22, 2025 at 8:30 PM
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.
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.
A multi-scale, multi-context, and interpretable mapping strategy to map cells across space, time, and disease. @pcnmartin.bsky.social @wonkj.bsky.social
#spatialMapping #spatialOmics #BiotechNatureComms
www.nature.com/articles/s41...
#spatialMapping #spatialOmics #BiotechNatureComms
www.nature.com/articles/s41...
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...
www.nature.com
August 22, 2025 at 2:29 PM
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...
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...
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...
www.nature.com
August 21, 2025 at 10:25 PM
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...
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
Am I happy with because of what it represents? Yes I am.
Simulated Gene Pulse
August 20, 2025 at 10:25 PM
Does this plot look ugly? Yes it does.
Am I happy with because of what it represents? Yes I am.
Simulated Gene Pulse
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
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
August 18, 2025 at 7:08 PM
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
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.
August 11, 2025 at 7:22 PM
I am not sure any of those questions would require a token greedy language bot to answer.
Reposted by Patrick Martin
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 story is entitled: A rude awakening. Just breath.
www.nature.com/articles/d41...
A rude awakening
Just breathe.
www.nature.com
August 8, 2025 at 2:12 PM
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 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 story is entitled: A rude awakening. Just breath.
www.nature.com/articles/d41...
A rude awakening
Just breathe.
www.nature.com
August 8, 2025 at 2:12 PM
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 story is entitled: A rude awakening. Just breath.
www.nature.com/articles/d41...
Reposted by Patrick Martin
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...
#scifi by @pcnmartin.bsky.social www.nature.com/articles/d41...
A rude awakening
Just breathe.
www.nature.com
August 8, 2025 at 10:07 AM
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...
#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 read some paper and you think: "Wow this actually makes sense to some people. The equations look cool I guess."
July 23, 2025 at 6:39 PM
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 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
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
July 11, 2025 at 9:17 PM
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
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
Reposted by Patrick Martin
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...
Here, I share some thoughts on scientific story telling through the lens of fiction.
open.substack.com/pub/pcnmarti...
Let me tell you a story
Taking lessons from fiction to elevate scientific presentations and story telling.
open.substack.com
June 23, 2025 at 8:32 PM
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...
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/...
"Predicting cellular responses to perturbation
across diverse contexts with State"
arcinstitute.org/manuscripts/...
Manuscript | Arc Institute
Arc Institute is a independent nonprofit research organization headquartered in Palo Alto, California.
arcinstitute.org
June 23, 2025 at 9:08 PM
The Arc Institute has just released their pre-print STATE.
"Predicting cellular responses to perturbation
across diverse contexts with State"
arcinstitute.org/manuscripts/...
"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...
Here, I share some thoughts on scientific story telling through the lens of fiction.
open.substack.com/pub/pcnmarti...
Let me tell you a story
Taking lessons from fiction to elevate scientific presentations and story telling.
open.substack.com
June 23, 2025 at 8:32 PM
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...
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...
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...
Oral history interview with R. W. Taylor
Following a brief description of his academic and professional background before joining ARPA, Taylor describes his impression of the IPT Office when he arrived in 1965.
Most of the interview is conc...
conservancy.umn.edu
June 17, 2025 at 4:32 PM
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...
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...
June 3, 2025 at 10:18 PM
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.
"Belgium is like the Monty Python sketch of nations: serious face, absurd punchline."
As a Belgian, I can't say I disagree.
June 2, 2025 at 9:00 PM
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.
"Belgium is like the Monty Python sketch of nations: serious face, absurd punchline."
As a Belgian, I can't say I disagree.