The dumbest programmer I have ever met was me 10 years ago. That code makes no sense...
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/
Something that amuses me with small LLMs is how literally they can take things from a human perspective. I asked qwen2.5 9B model to change the spelling on a word and it simply appended the term "change_spelling". Yes that is indeed a different spelling.
A new story on my substack. The walls, they live. But Craig doesn't get it. open.substack.com/pub/pcnmarti...
Feed the floors
Craig, you oaf...
open.substack.com
Today, I found out that Glenn Baxter died a month ago. Mr Baxter was a surrealist/absurdist visual artist. I discovered his art in a small art gallery somewhere in the middle of the french country side of all places. I thought I would share a few some of his pieces.
CellNeighborEX 2.0 is out on @biorxivpreprint.bsky.social ! This new version allows you to get cell communication expression profiles beyond ligand-receptor pairs and in low resolution spatial transcriptomics such as Visium! #SingleCell #Spatial #10X www.biorxiv.org/content/10.6...
Identifying Context-Specific Cell-Cell Interaction Genes Without Ligand-Receptor Databases from Spatial Transcriptomics
Current approaches to inferring cell-cell interactions (CCIs) are largely constrained by predefined ligand-receptor databases, particularly for low-resolution spatial transcriptomics (ST) platforms such as Visium. Due to the difficulties in accurately resolving interacting cells at coarse spatial resolution, other modes of interaction are often overlooked. Low-resolution ST data, however, can serve as an alternative to high-resolution ST, which suffers from low sensitivity, and to image-based ST, which is limited by restricted gene panels. Here, we present CellNeighborEX v2, a database-free framework that directly infers CCI-associated genes from ST data by detecting deviations between observed and expected gene expression at the spot-population level. These deviations are rigorously evaluated through a hybrid statistical framework involving permutation testing and are further refined by considering the abundance of interacting cell-type pairs. Compared with other conventional approaches relying on ligand-receptor databases, CellNeighborEX v2 can capture CCI genes from a broad spectrum of interactions, including both paracrine signaling and contact-dependent communication. Across datasets from hippocampus, liver cancer, colorectal cancer, ovarian cancer, and lymph node infection, CellNeighborEX v2 accurately recapitulated previously identified CCIs. Notably, it uniquely detected interactions absent from existing ligand-receptor databases, enabling detection of context-specific CCIs from Visium data. CellNeighborEX v2 is a tool that expands the analytical spectrum of Visium data and deepens our understanding of the molecular language of intercellular communication. ### Competing Interest Statement The authors have filed a patent application related to the algorithms described in this work.
biorxiv.org
I think the term you are looking for in fact the "Powerhouse of the Cell".
I don't think the real issue is if we can achieve PhD level intelligence with AI. The issue is who and how AI is being used. I will just leave this video here... youtu.be/snB8u_G3jVI?...
The distinction between Moral Competence and Moral Performance is key: even if we cannot distinguish them in a model's output, Moral Performance is a function of who own's the LLM. www.nature.com/articles/s41...
A roadmap for evaluating moral competence in large language models - Nature
This Perspective offers a roadmap for tackling the challenges of the facsimile problem, moral multidimensionality and moral pluralism in large language models.
nature.com
So... Data Crystals? Sci-fi is just becoming science at this point. www.nature.com/articles/s41...
Laser writing in glass for dense, fast and efficient archival data storage - Nature
An optical archival storage technology based on femtosecond laser direct writing in glass addresses the practical demands of archival storage.
nature.com
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.
nature.com
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...
biorxiv.org
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
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/...
advanced.onlinelibrary.wiley.com
Don't let anyone tell you reading sci-fi is "not work". www.nature.com/articles/d41...
Science in 2050: the future breakthroughs that will shape our world — and beyond
Nuclear fusion. People on Mars. Artificial general intelligence. These are just some of the advances that could come by the mid-century mark.
nature.com
D&D Coding edition 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.
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
Treat your to-read pile like a river | Oliver Burkeman
oliverburkeman.com
Patrick Martin@pcnmartin.bsky.social · 9mo agoI'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'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 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.
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.
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....
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
This is actually a pretty neat idea. Spatially correlated genes. www.biorxiv.org/content/10.1...
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...
biorxiv.org
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...
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...
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...
nature.com
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.
Qian Cheng@qchengx1e3.bsky.social · 12mo agoA 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...
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...
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...
nature.com