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...
Reposted by Patrick Martin
Making large language models reliable data science programming copilots for biomedical research www.nature.com/articles/s41... #llms #bioinformatics #datascience #coding
Making large language models reliable data science programming copilots for biomedical research - Nature Biomedical Engineering
AI is a powerful tool for facilitating data science programming in biomedicine. This study benchmarks the performance of existing tools and introduces a reliable AI agent copilot.
www.nature.com
January 26, 2026 at 4:19 PM
Making large language models reliable data science programming copilots for biomedical research www.nature.com/articles/s41... #llms #bioinformatics #datascience #coding
PersonaAI developed by @wonkj.bsky.social lab at Cedars-Sinai!
Human in the loop agentic AI system to accelerate hypothesis testing in aging research. It combines a RAG summary of over 600k papers and uses scRNA atlases to convert ideas into verifiable hypotheses!
www.biorxiv.org/content/10.6...
Human in the loop agentic AI system to accelerate hypothesis testing in aging research. It combines a RAG summary of over 600k papers and uses scRNA atlases to convert ideas into verifiable hypotheses!
www.biorxiv.org/content/10.6...
www.biorxiv.org
January 21, 2026 at 5:00 AM
PersonaAI developed by @wonkj.bsky.social lab at Cedars-Sinai!
Human in the loop agentic AI system to accelerate hypothesis testing in aging research. It combines a RAG summary of over 600k papers and uses scRNA atlases to convert ideas into verifiable hypotheses!
www.biorxiv.org/content/10.6...
Human in the loop agentic AI system to accelerate hypothesis testing in aging research. It combines a RAG summary of over 600k papers and uses scRNA atlases to convert ideas into verifiable hypotheses!
www.biorxiv.org/content/10.6...
A new sci-fi short story on my Substack: Voices.
What happens when AI tries to find its own voice?
#AI #Scifi #ProjectSuncatcher
pcnmartin.substack.com/p/voices
What happens when AI tries to find its own voice?
#AI #Scifi #ProjectSuncatcher
pcnmartin.substack.com/p/voices
January 20, 2026 at 5:57 PM
A new sci-fi short story on my Substack: Voices.
What happens when AI tries to find its own voice?
#AI #Scifi #ProjectSuncatcher
pcnmartin.substack.com/p/voices
What happens when AI tries to find its own voice?
#AI #Scifi #ProjectSuncatcher
pcnmartin.substack.com/p/voices
Another great piece of work by Guangzheng Weng and Kyoung-Jae Won's Lab! Glad to have been part of it.
The model incorporates LLM embeddings and ChIP-seq data in a Transformer-based Graph Neural Network to generate GRN predictions.
advanced.onlinelibrary.wiley.com/doi/10.1002/...
The model incorporates LLM embeddings and ChIP-seq data in a Transformer-based Graph Neural Network to generate GRN predictions.
advanced.onlinelibrary.wiley.com/doi/10.1002/...
advanced.onlinelibrary.wiley.com
January 15, 2026 at 11:18 PM
Another great piece of work by Guangzheng Weng and Kyoung-Jae Won's Lab! Glad to have been part of it.
The model incorporates LLM embeddings and ChIP-seq data in a Transformer-based Graph Neural Network to generate GRN predictions.
advanced.onlinelibrary.wiley.com/doi/10.1002/...
The model incorporates LLM embeddings and ChIP-seq data in a Transformer-based Graph Neural Network to generate GRN predictions.
advanced.onlinelibrary.wiley.com/doi/10.1002/...
D&D Coding edition
Wizard = Backend Dev
Artificer = IOS and Android Only
Bard = Front End Dev
Sorcerer = Leet Coder
Warlock = Vibe Coder
Wizard = Backend Dev
Artificer = IOS and Android Only
Bard = Front End Dev
Sorcerer = Leet Coder
Warlock = Vibe Coder
December 19, 2025 at 4:33 AM
D&D Coding edition
Wizard = Backend Dev
Artificer = IOS and Android Only
Bard = Front End Dev
Sorcerer = Leet Coder
Warlock = Vibe Coder
Wizard = Backend Dev
Artificer = IOS and Android Only
Bard = Front End Dev
Sorcerer = Leet Coder
Warlock = Vibe Coder
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.
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.
December 1, 2025 at 9:47 PM
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.
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.
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
www.oliverburkeman.com/river
November 20, 2025 at 11:19 PM
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
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
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
November 19, 2025 at 7:26 PM
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
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 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...