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New preprint! So excited to present CHOIR, a new clustering method for single-cell data that evaluates whether clusters represent statistically distinct cell populations. CHOIR works with both single- and multi-omic data of any type. Check it out!

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Cathrine Sant

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73,996 görüntüleme • 2 yıl önce •via X (Twitter)

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Cathrine Sant (Petersen) profil fotoğrafı
Cathrine Sant (Petersen)2 yıl önce

CHOIR is available as an R package and is compatible with Seurat, SingleCellExperiment, and ArchR input objects. You can find documentation and a detailed tutorial on our website:

Cathrine Sant (Petersen) profil fotoğrafı
Cathrine Sant (Petersen)2 yıl önce

I've absolutely loved working on this tool and am so thankful for the mentorship of @doctorcorces, and for everyone who provided early suggestions and beta-testing. The code for CHOIR is open source and we welcome feedback!

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@cathrinepet Congrats, awesome work!

Ming "Tommy" Tang profil fotoğrafı
Ming "Tommy" Tang2 yıl önce

@cathrinepet Congratulations! How scalable the tool is?

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Thanks! It scales approx. linearly with the number of cells. CHOIR can be run on a normal laptop but it's highly parallelized, so efficiency improves a lot with more cores. I've found that data up to 500K cells runs in a few hours, and our goal is for 1M+ cells to run overnight!

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Rudi Gunawan2 yıl önce

@cathrinepet Any plan for Python?

Cathrine Sant (Petersen) profil fotoğrafı
Cathrine Sant (Petersen)2 yıl önce

Not at the moment!

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Ashraf Saad, bridging Glycobiology and Oncology!2 yıl önce

@cathrinepet Congratulations 🎊

Mikhael Dito Manurung profil fotoğrafı
Mikhael Dito Manurung2 yıl önce

@cathrinepet Looks like a great package! Is it possible to get marker genes out of the RF models as well?

Cathrine Sant (Petersen) profil fotoğrafı
Cathrine Sant (Petersen)2 yıl önce

Yes! CHOIR can collect the feature importances from the RFs in each pairwise cluster comparison, and we show in the preprint that these correlate well with the log fold change (absolute value) of gene expression between the clusters. The most "important" features are the top DEGs

Benzer Videolar

CHOIR is now online Nature Genetics! CHOIR is a new clustering method for single-cell data that evaluates whether clusters represent statistically distinct cell populations. CHOIR scales to millions of cells and works with single-/multi-omic data of any type!
1:42

CHOIR is now online Nature Genetics! CHOIR is a new clustering method for single-cell data that evaluates whether clusters represent statistically distinct cell populations. CHOIR scales to millions of cells and works with single-/multi-omic data of any type!

Cathrine Sant

55,094 görüntüleme • 1 yıl önce

🚨New Cell cover! We’ve been working with the great Chris Tape again, visualising the Tape lab’s single cell colorectal cancer signalling data in two new papers out today. But wait! There’s a lot more to this story than just the cover… 🧵
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🚨New Cell cover! We’ve been working with the great Chris Tape again, visualising the Tape lab’s single cell colorectal cancer signalling data in two new papers out today. But wait! There’s a lot more to this story than just the cover… 🧵

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1/ The biggest blocker to effective AI-in-bio is lack of quality data, but Vevo Therapeutics is open-sourcing their gigantic #Tahoe100M single cell dataset (on Arc Institute's new Virtual Cell Atlas)! I talk w/Vevo's founders and Arc CEO/CTO about "Virtual Cell Models" and significance
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1/ The biggest blocker to effective AI-in-bio is lack of quality data, but Vevo Therapeutics is open-sourcing their gigantic #Tahoe100M single cell dataset (on Arc Institute's new Virtual Cell Atlas)! I talk w/Vevo's founders and Arc CEO/CTO about "Virtual Cell Models" and significance

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44,512 görüntüleme • 1 yıl önce

🔬 Exciting News! Our manuscript, "scGPT: toward building a foundation model for single-cell multi-omics using generative AI" is now finally published in Nature Methods (Nature Methods) 🎉 !!! (Re-)Introducing scGPT: A transformative foundation model engineered for single-cell omics analysis. Developed through the analysis of over 33 million human cells, scGPT sets a new benchmark for application versatility, offering both fine-tuning and zero-shot capabilities. Since its preprint in May 2023, scGPT has significantly impacted the field, evidenced by 13K+ installations, 600+ GitHub stars 🌟, and 40+ citations before its official publication! scGPT has been validated by numerous benchmark studies as a leading foundation model in single-cell analysis. Its pre-trained embeddings extend its utility beyond single-cell studies, enhancing a variety of downstream tasks including protein enrichment and genetic perturbation predictions. Some key updates lately: ---Expanded zero-shot applications for efficient reference mapping and integration, now with CellXGene census integration. ---Advanced perturbation analysis capabilities, including genome-scale perturb-seq data analysis and bulk sequencing data generalization. ---Upgraded scGPT package, offering versatile model loading compatible with PyTorch and flash-attn, for both GPU and CPU. ---Cloud-based scGPT applications for reference mapping, cell annotation, and gene regulatory network inference are available on ---Integration with Hugging Face for easier model training. Limitations: scGPT is an early foray into foundation models for single-cell omics, facing challenges like limited zero-shot learning in some tasks, pretraining constraints, data quality issues, and evaluation limitations. See our Supplementary Notes for details. 🚀 Future Work? Short-Term Goals: 1. Releasing a Mouse Model for broader analysis. 2. Developing a comprehensive evaluation suite for foundation models in single-cell analysis. 3. Creating a foundation model for single-cell spatial omics. 4. Enhancing zero-shot capacity by integrating scGPT with RAG (e.g., knowledge graphs). Long-Term Goals: 1. Expanding scGPT for comprehensive single-cell multi-omics analysis. 2. Developing an in-silico perturbation model for predicting genetic perturbation effects. 3. Merging scGPT with multi-modal genomic sequence models for a deeper understanding of cell biology. 📚 Access the paper on Nature Methods: 🔬Preprint in Bioarixv: 💻 All our codes/data/weights are open source: Wholehearted congratulations to all the authors, especially the two co-first authors, Haotian (Haotian Cui ) and Chloe (ChloeXWang), who are really the emerging superstars in AI and biology! Vector Institute Peter Munk Cardiac Centre AI U of T Department of Computer Science Department of Laboratory Medicine & Pathobiology University Health Network University of Toronto #scGPT #GenerativeAI #AI4Science #Combio #opensource
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🔬 Exciting News! Our manuscript, "scGPT: toward building a foundation model for single-cell multi-omics using generative AI" is now finally published in Nature Methods (Nature Methods) 🎉 !!! (Re-)Introducing scGPT: A transformative foundation model engineered for single-cell omics analysis. Developed through the analysis of over 33 million human cells, scGPT sets a new benchmark for application versatility, offering both fine-tuning and zero-shot capabilities. Since its preprint in May 2023, scGPT has significantly impacted the field, evidenced by 13K+ installations, 600+ GitHub stars 🌟, and 40+ citations before its official publication! scGPT has been validated by numerous benchmark studies as a leading foundation model in single-cell analysis. Its pre-trained embeddings extend its utility beyond single-cell studies, enhancing a variety of downstream tasks including protein enrichment and genetic perturbation predictions. Some key updates lately: ---Expanded zero-shot applications for efficient reference mapping and integration, now with CellXGene census integration. ---Advanced perturbation analysis capabilities, including genome-scale perturb-seq data analysis and bulk sequencing data generalization. ---Upgraded scGPT package, offering versatile model loading compatible with PyTorch and flash-attn, for both GPU and CPU. ---Cloud-based scGPT applications for reference mapping, cell annotation, and gene regulatory network inference are available on ---Integration with Hugging Face for easier model training. Limitations: scGPT is an early foray into foundation models for single-cell omics, facing challenges like limited zero-shot learning in some tasks, pretraining constraints, data quality issues, and evaluation limitations. See our Supplementary Notes for details. 🚀 Future Work? Short-Term Goals: 1. Releasing a Mouse Model for broader analysis. 2. Developing a comprehensive evaluation suite for foundation models in single-cell analysis. 3. Creating a foundation model for single-cell spatial omics. 4. Enhancing zero-shot capacity by integrating scGPT with RAG (e.g., knowledge graphs). Long-Term Goals: 1. Expanding scGPT for comprehensive single-cell multi-omics analysis. 2. Developing an in-silico perturbation model for predicting genetic perturbation effects. 3. Merging scGPT with multi-modal genomic sequence models for a deeper understanding of cell biology. 📚 Access the paper on Nature Methods: 🔬Preprint in Bioarixv: 💻 All our codes/data/weights are open source: Wholehearted congratulations to all the authors, especially the two co-first authors, Haotian (Haotian Cui ) and Chloe (ChloeXWang), who are really the emerging superstars in AI and biology! Vector Institute Peter Munk Cardiac Centre AI U of T Department of Computer Science Department of Laboratory Medicine & Pathobiology University Health Network University of Toronto #scGPT #GenerativeAI #AI4Science #Combio #opensource

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199,657 görüntüleme • 2 yıl önce

Announcing /extract beta 🔥 Extract structured data from single URLs, multiple URLs, or even entire websites! This new endpoint crawls entire websites for you and then extracts data based on a prompt. Check it out:
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Announcing /extract beta 🔥 Extract structured data from single URLs, multiple URLs, or even entire websites! This new endpoint crawls entire websites for you and then extracts data based on a prompt. Check it out:

Firecrawl

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We are thrilled to share that our first paper from my new lab, Spateo ( for spatiotemporal modeling of molecular holograms, is now online in Cell: Spateo is a comprehensive analytical framework for 3D whole-embryo spatiotemporal modeling. Its advanced features include: • 3D alignment and reconstruction at the whole-mouse-embryo scale (see the animation). • 3D spatial domain digitization and cell-cell communication analysis to understand spatial gene expression gradients and both inter- and intracellular communication. • 3D morphometric and volumetric analyses along with 3D morphogenesis vector field modeling to quantify dynamics such as surface area, volume, and cell density across organs, and to dissect the interplay between morphogenesis factors and cell migration. • A “Google Earth”-like browser, Spateo-viewer ( and for interactive and intuitive exploration of 3D spatial data. • Additional features, such as RNA signal-based single-cell segmentation. We are also honored that Nature “News and Views” has highlighted this work as well: This is really an amazing outcome after two years' heroic revision process that rewrite the entire paper using a new data ( for whole mouse embryos.
1:24

We are thrilled to share that our first paper from my new lab, Spateo ( for spatiotemporal modeling of molecular holograms, is now online in Cell: Spateo is a comprehensive analytical framework for 3D whole-embryo spatiotemporal modeling. Its advanced features include: • 3D alignment and reconstruction at the whole-mouse-embryo scale (see the animation). • 3D spatial domain digitization and cell-cell communication analysis to understand spatial gene expression gradients and both inter- and intracellular communication. • 3D morphometric and volumetric analyses along with 3D morphogenesis vector field modeling to quantify dynamics such as surface area, volume, and cell density across organs, and to dissect the interplay between morphogenesis factors and cell migration. • A “Google Earth”-like browser, Spateo-viewer ( and for interactive and intuitive exploration of 3D spatial data. • Additional features, such as RNA signal-based single-cell segmentation. We are also honored that Nature “News and Views” has highlighted this work as well: This is really an amazing outcome after two years' heroic revision process that rewrite the entire paper using a new data ( for whole mouse embryos.

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Ever wondered how we come up with combos with new characters and new moves? It’s all in the frame data! Frame data opens up a new perspective to the game. This is one of the most basic levels of frame data 101. Check it out! #streetfighter #streetfighter6 #kimberly #sf6

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I’m so excited to team up with NBC Olympics & Paralympics for the official music video of my new single “We Are The Champions/We Will Rock You.” Check it out and mark your calendars for Paris 2024! 🏅
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I’m so excited to team up with NBC Olympics & Paralympics for the official music video of my new single “We Are The Champions/We Will Rock You.” Check it out and mark your calendars for Paris 2024! 🏅

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What’s insane about AI is how good it is at getting structure out of unstructured data. Here’s Box AI using OpenAI’s new GPT-4.1 to comb through a long earnings document to pull out data fields. Now you can query, synthesize, analyze, and summarize any data type at scale.

Aaron Levie

101,892 görüntüleme • 1 yıl önce

🚀 Introducing scGPT-spatial! 🧬🌍 A game-changing spatial-omic foundation model, built on the powerful scGPT framework with MoE (mixture of experts) and continually pretrained on a massive 30 million spatial single-cell profiles! 🧠 What’s the challenge? Spatial transcriptomics is next-level complex—not only must we model single-cell/spot profiles, but we also need to capture intricate spatial relationships while handling diverse sequencing protocols (imaging-based vs. sequencing-based). 🔥 Why scGPT-spatial? ✨ A Spatial-omic Foundation Model with Continual Pretraining – Built on scGPT’s robust initialization, it unlocks spatial context in tissues. ✨ SpatialHuman30M Dataset – The largest curated dataset: 30M profiles from Visium, Visium HD, Xenium, and MERFISH across 821 slides. ✨ Revolutionary MoE Decoders – A cutting-edge Mixture of Experts (MoE) architecture for protocol-aware gene expression decoding. ✨ Spatially-Aware Training Strategy – A neighborhood-based masked reconstruction approach to capture complex cell-type colocalization. ✨ Multi-Modal & Multi-Slide Integration – Seamless clustering & spatial domain identification across slides and modalities. ✨ Cell-Type Deconvolution & Gene Imputation – Unlocks cross-resolution & cross-modality harmonization with fine-tuned embeddings. 📄 Read the preprint: 💻 Explore the code/weights: #SpatialTranscriptomics #SingleCell #AIResearch #MachineLearning #SpatialData Huge shoutout to the incredible PHD students Chloe (ChloeXWang) and Haotian (Haotian Cui) for leading this groundbreaking project! 🎉 Massive thanks to our amazing co-authors Andrew, Ronald, and Hani (Hani Goodarzi) from Arc Institute—this work wouldn't have been possible without you! 👏
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🚀 Introducing scGPT-spatial! 🧬🌍 A game-changing spatial-omic foundation model, built on the powerful scGPT framework with MoE (mixture of experts) and continually pretrained on a massive 30 million spatial single-cell profiles! 🧠 What’s the challenge? Spatial transcriptomics is next-level complex—not only must we model single-cell/spot profiles, but we also need to capture intricate spatial relationships while handling diverse sequencing protocols (imaging-based vs. sequencing-based). 🔥 Why scGPT-spatial? ✨ A Spatial-omic Foundation Model with Continual Pretraining – Built on scGPT’s robust initialization, it unlocks spatial context in tissues. ✨ SpatialHuman30M Dataset – The largest curated dataset: 30M profiles from Visium, Visium HD, Xenium, and MERFISH across 821 slides. ✨ Revolutionary MoE Decoders – A cutting-edge Mixture of Experts (MoE) architecture for protocol-aware gene expression decoding. ✨ Spatially-Aware Training Strategy – A neighborhood-based masked reconstruction approach to capture complex cell-type colocalization. ✨ Multi-Modal & Multi-Slide Integration – Seamless clustering & spatial domain identification across slides and modalities. ✨ Cell-Type Deconvolution & Gene Imputation – Unlocks cross-resolution & cross-modality harmonization with fine-tuned embeddings. 📄 Read the preprint: 💻 Explore the code/weights: #SpatialTranscriptomics #SingleCell #AIResearch #MachineLearning #SpatialData Huge shoutout to the incredible PHD students Chloe (ChloeXWang) and Haotian (Haotian Cui) for leading this groundbreaking project! 🎉 Massive thanks to our amazing co-authors Andrew, Ronald, and Hani (Hani Goodarzi) from Arc Institute—this work wouldn't have been possible without you! 👏

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We're excited to announce a partnership with Laika AI to make blockchain-specific data accessible through Nuklai's technology and ecosystem! This collaboration introduces a new way to repurpose and monetize that data, making it more accessible for everyone, powered by $NAI 📊
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We're excited to announce a partnership with Laika AI to make blockchain-specific data accessible through Nuklai's technology and ecosystem! This collaboration introduces a new way to repurpose and monetize that data, making it more accessible for everyone, powered by $NAI 📊

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29,711 görüntüleme • 1 yıl önce

PantheonOS allows any biologist to perform complex data analyses of emerging single cell, multi-omics and spatial transcriptomics datasets end to end through AI agent and human collaboration. We are releasing six replays of use cases trajectories. Each "trajectory" is a complete end-to-end run, from prompt to analysis, to figures, and finally to report, and in fully inspectable and reproducible manner. See the six user cases in our PantheonOS Gallery: 1. 3D mouse embryo analysis: Tangram deconvolution and PyVista-based 3D visualization of E6 mouse embryo spatial transcriptomics data 2. 3D human fetal heart analysis: Spatial mapping of heart disease gene patterns using MERFISH data 3. Multi-omics spatial integration: Single cell multi-omics-to-spatial mapping with MOSCOT optimal transport 4. Gene panel design: 1000-plex immune-oncology MERFISH gene panel optimization 5. Cell segmentation benchmarking: Comparative evaluation of Cellpose-SAM, InstanSeg, StarDist, and other tools 6. Spatial disease biology: Ligand–receptor analysis of disease-associated tissue microenvironments We would love to hear how you can use PantheonOS for your research! Got an interesting agent run of your own and want to share? In the Pantheon UI, click Export Bundle (top-right of any chat) to package the full trajectory — chat history, code, figures, report — then submit it here:
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PantheonOS allows any biologist to perform complex data analyses of emerging single cell, multi-omics and spatial transcriptomics datasets end to end through AI agent and human collaboration. We are releasing six replays of use cases trajectories. Each "trajectory" is a complete end-to-end run, from prompt to analysis, to figures, and finally to report, and in fully inspectable and reproducible manner. See the six user cases in our PantheonOS Gallery: 1. 3D mouse embryo analysis: Tangram deconvolution and PyVista-based 3D visualization of E6 mouse embryo spatial transcriptomics data 2. 3D human fetal heart analysis: Spatial mapping of heart disease gene patterns using MERFISH data 3. Multi-omics spatial integration: Single cell multi-omics-to-spatial mapping with MOSCOT optimal transport 4. Gene panel design: 1000-plex immune-oncology MERFISH gene panel optimization 5. Cell segmentation benchmarking: Comparative evaluation of Cellpose-SAM, InstanSeg, StarDist, and other tools 6. Spatial disease biology: Ligand–receptor analysis of disease-associated tissue microenvironments We would love to hear how you can use PantheonOS for your research! Got an interesting agent run of your own and want to share? In the Pantheon UI, click Export Bundle (top-right of any chat) to package the full trajectory — chat history, code, figures, report — then submit it here:

evo-devo

13,151 görüntüleme • 2 ay önce

We’re thrilled to share that our MERFISH+ preprint is now live on bioRxiv!👉 In this work, the Bintu and Zhu labs (UCSD) developed MERFISH+, a next-generation spatial genomics platform that combines genome-wide RNA and epigenetic imaging over a large field of view. By introducing acrydite-modified probes covalently anchored to hydrogels, MERFISH+ achieves remarkable imaging stability and enables >1,800-gene, multi-modal, and multi-month experiments. With this platform, they, together with the Chi lab at UCSD, profiled a whole developing human heart at 12 post-conception week with merely two slides, resulting in a total of 53 slides, 3.1 million single cells and more than 30 cell types. Building upon our previous 3D reconstruction and modeling framework, Spateo ( we reconstruct the 3D human heart that nicely captures the anatomical structure of the heart, including the intricate vasculature network. Sophisticated analyses provide a holistic view of an entire organ and enable systematic characterization of 3D cellular neighborhoods and transcriptional gradients of substructures such as the descending arteries. Furthermore, using a generative integration framework for spatial multimodal data (Spateo-VI), we harmonized these MERFISH+ transcriptomic and chromatin data to reconstruct a 3D spatially-resolved multi-omics atlas of the developing human heart, shared at and MERFISH+ thus sets a new standard for large-format, multi-omic spatial profiling, enabling holistic, 3D characterization of organs at subcellular resolution. Huge congratulations to first authors Colin Kern, qingquan Zhang, Yifan Lu , and Jacqueline Eschbach, and to all collaborators from the Bintu, Zhu, Chi, and Qiu labs for this amazing team effort. Thanks for your diligence, creativity, and hard work on this project. We’re grateful for support from Arc Institute and our generous donors. Our lab is expanding—if you’re excited about building the next generation of single-cell and spatial genomics techniques and predictive single cell and spatial foundation models, we’re hiring! If you are interested, please reach out to me via direct message or email at xiaojie@stanford.edu. We are excited for any potential collaborations along this line of research in Stanford, UCSF and Berkeley and other labs as well.
0:42

We’re thrilled to share that our MERFISH+ preprint is now live on bioRxiv!👉 In this work, the Bintu and Zhu labs (UCSD) developed MERFISH+, a next-generation spatial genomics platform that combines genome-wide RNA and epigenetic imaging over a large field of view. By introducing acrydite-modified probes covalently anchored to hydrogels, MERFISH+ achieves remarkable imaging stability and enables >1,800-gene, multi-modal, and multi-month experiments. With this platform, they, together with the Chi lab at UCSD, profiled a whole developing human heart at 12 post-conception week with merely two slides, resulting in a total of 53 slides, 3.1 million single cells and more than 30 cell types. Building upon our previous 3D reconstruction and modeling framework, Spateo ( we reconstruct the 3D human heart that nicely captures the anatomical structure of the heart, including the intricate vasculature network. Sophisticated analyses provide a holistic view of an entire organ and enable systematic characterization of 3D cellular neighborhoods and transcriptional gradients of substructures such as the descending arteries. Furthermore, using a generative integration framework for spatial multimodal data (Spateo-VI), we harmonized these MERFISH+ transcriptomic and chromatin data to reconstruct a 3D spatially-resolved multi-omics atlas of the developing human heart, shared at and MERFISH+ thus sets a new standard for large-format, multi-omic spatial profiling, enabling holistic, 3D characterization of organs at subcellular resolution. Huge congratulations to first authors Colin Kern, qingquan Zhang, Yifan Lu , and Jacqueline Eschbach, and to all collaborators from the Bintu, Zhu, Chi, and Qiu labs for this amazing team effort. Thanks for your diligence, creativity, and hard work on this project. We’re grateful for support from Arc Institute and our generous donors. Our lab is expanding—if you’re excited about building the next generation of single-cell and spatial genomics techniques and predictive single cell and spatial foundation models, we’re hiring! If you are interested, please reach out to me via direct message or email at [email protected]. We are excited for any potential collaborations along this line of research in Stanford, UCSF and Berkeley and other labs as well.

evo-devo

42,166 görüntüleme • 8 ay önce

I was super excited to learn from Niko McCarty.'s essay, "How to Scale Proteomics", that there's an FRO working on high-throughput single-cell proteomics (Parallel Squared Technology Institute (PTI)), and even more excited to see the progress they've made in just 2 years via their preprints. So here's a video about it! And some links you should check out⬇️
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I was super excited to learn from Niko McCarty.'s essay, "How to Scale Proteomics", that there's an FRO working on high-throughput single-cell proteomics (Parallel Squared Technology Institute (PTI)), and even more excited to see the progress they've made in just 2 years via their preprints. So here's a video about it! And some links you should check out⬇️

Julia Bauman

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Big News! Meta just released Segment Anything, a new AI model that can "cut out" any object, in any image/video, with a single click. The model is designed and trained to be promptable, so it can transfer zero-shot to new image distributions and tasks.
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Big News! Meta just released Segment Anything, a new AI model that can "cut out" any object, in any image/video, with a single click. The model is designed and trained to be promptable, so it can transfer zero-shot to new image distributions and tasks.

Lior Alexander

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Urban planners spend hours wrangling GIS data for stakeholder presentation, analysis, and reviews. Unify your city planning data in Google Earth with new SHP imports. Securely combine zoning data, environmental constraints, and property boundaries as performant, cloud-native data layers to create a single source of truth for your entire team. Upload your SHP files to Google Earth today.
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Urban planners spend hours wrangling GIS data for stakeholder presentation, analysis, and reviews. Unify your city planning data in Google Earth with new SHP imports. Securely combine zoning data, environmental constraints, and property boundaries as performant, cloud-native data layers to create a single source of truth for your entire team. Upload your SHP files to Google Earth today.

Google Earth

20,526 görüntüleme • 2 ay önce

How does an embryo reliably "compute" its form - "cell by cell" - using only local interactions and mechanics, yet produce a precise global body plan? I’m excited to share our Nature Methods paper "MultiCell: geometric learning in multicellular development", presenting #AIxBiology research led by Haiqian Yang and the result of a great collaboration with Ming Guo, George Roy, Tomer Stern, Anh Nguyen and Dapeng Bi. A long-standing challenge in developmental biology is to predict how thousands of cells collectively self-organize as tissues fold, divide, and rearrange. In MultiCell, we represent a developing embryo as a dual graph that unifies two complementary views of tissue mechanics with single-cell resolution: cells as moving points (granular) and cells as a connected foam (junction network). This lets the model learn dynamics from both geometry and cell–cell connectivity. On whole-embryo 4D light-sheet movies of Drosophila gastrulation (~5,000 cells), our model predicts key cell behaviors and the timing of events, including junction loss, rearrangements, and divisions with high accuracy, at single-cell resolution. Beyond prediction, the same representation supports robust time alignment across embryos and offers interpretable activation maps that highlight the morphogenetic "drivers" of development. The broader goal is a foundation for cell-by-cell forecasting in more complex tissues, and eventually for detecting subtle dynamical signatures of disease. Kudos to the team for this inspiring collaboration with brilliant researchers to push the boundary of AI for biology! Citation: Yang, H., Roy, G., Nguyen, A.Q., Buehler, M.J., et al. MultiCell: geometric learning in multicellular development. Nature Methods (2025), DOI: 10.1038/s41592-025-02983-x Code/data links are in the manuscript.
0:46

How does an embryo reliably "compute" its form - "cell by cell" - using only local interactions and mechanics, yet produce a precise global body plan? I’m excited to share our Nature Methods paper "MultiCell: geometric learning in multicellular development", presenting #AIxBiology research led by Haiqian Yang and the result of a great collaboration with Ming Guo, George Roy, Tomer Stern, Anh Nguyen and Dapeng Bi. A long-standing challenge in developmental biology is to predict how thousands of cells collectively self-organize as tissues fold, divide, and rearrange. In MultiCell, we represent a developing embryo as a dual graph that unifies two complementary views of tissue mechanics with single-cell resolution: cells as moving points (granular) and cells as a connected foam (junction network). This lets the model learn dynamics from both geometry and cell–cell connectivity. On whole-embryo 4D light-sheet movies of Drosophila gastrulation (~5,000 cells), our model predicts key cell behaviors and the timing of events, including junction loss, rearrangements, and divisions with high accuracy, at single-cell resolution. Beyond prediction, the same representation supports robust time alignment across embryos and offers interpretable activation maps that highlight the morphogenetic "drivers" of development. The broader goal is a foundation for cell-by-cell forecasting in more complex tissues, and eventually for detecting subtle dynamical signatures of disease. Kudos to the team for this inspiring collaboration with brilliant researchers to push the boundary of AI for biology! Citation: Yang, H., Roy, G., Nguyen, A.Q., Buehler, M.J., et al. MultiCell: geometric learning in multicellular development. Nature Methods (2025), DOI: 10.1038/s41592-025-02983-x Code/data links are in the manuscript.

Markus J. Buehler

387,913 görüntüleme • 7 ay önce

Data is the oil of modern biotech. New tools allow us to model living systems too complex for unaided human cognition. Latch is releasing a new capabilities in data curation + delivery: - 30M observational cell atlas across 150 diseases, 200 tissues, 27 technologies - a partnership with two expert labeling teams - an agentic, human-in-the-loop framework for mass scRNA-seq curation
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Data is the oil of modern biotech. New tools allow us to model living systems too complex for unaided human cognition. Latch is releasing a new capabilities in data curation + delivery: - 30M observational cell atlas across 150 diseases, 200 tissues, 27 technologies - a partnership with two expert labeling teams - an agentic, human-in-the-loop framework for mass scRNA-seq curation

Kenny Workman

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