6/
Another example: SingleCellExperiment.
This object has:
assays (like raw counts)
rowData (gene info)
colData (cell metadata)
reducedDims (PCA, UMAP)
Everything you need to do single-cell analysis—organized.
Another example: SingleCellExperiment.
This object has:
assays (like raw counts)
rowData (gene info)
colData (cell metadata)
reducedDims (PCA, UMAP)
Everything you need to do single-cell analysis—organized.
November 19, 2025 at 2:45 PM
6/
Another example: SingleCellExperiment.
This object has:
assays (like raw counts)
rowData (gene info)
colData (cell metadata)
reducedDims (PCA, UMAP)
Everything you need to do single-cell analysis—organized.
Another example: SingleCellExperiment.
This object has:
assays (like raw counts)
rowData (gene info)
colData (cell metadata)
reducedDims (PCA, UMAP)
Everything you need to do single-cell analysis—organized.
5/
In bioinformatics, meet the Seurat object.
It holds:
gene expression matrix
cell metadata
PCA results
clustering info
UMAP coordinates
All in one place. Just like a phone holds apps, contacts, and photos.
In bioinformatics, meet the Seurat object.
It holds:
gene expression matrix
cell metadata
PCA results
clustering info
UMAP coordinates
All in one place. Just like a phone holds apps, contacts, and photos.
November 19, 2025 at 2:45 PM
5/
In bioinformatics, meet the Seurat object.
It holds:
gene expression matrix
cell metadata
PCA results
clustering info
UMAP coordinates
All in one place. Just like a phone holds apps, contacts, and photos.
In bioinformatics, meet the Seurat object.
It holds:
gene expression matrix
cell metadata
PCA results
clustering info
UMAP coordinates
All in one place. Just like a phone holds apps, contacts, and photos.
Feeling a little unprepared for the rain at #SfN25? Come by booth 2801 tomorrow morning to grab the last of our free umbrellas!
Each umbrella features either a UMAP from the Allen Brain Cell Atlas or an ExA-SPIM visualization.
Each umbrella features either a UMAP from the Allen Brain Cell Atlas or an ExA-SPIM visualization.
November 16, 2025 at 9:27 PM
Feeling a little unprepared for the rain at #SfN25? Come by booth 2801 tomorrow morning to grab the last of our free umbrellas!
Each umbrella features either a UMAP from the Allen Brain Cell Atlas or an ExA-SPIM visualization.
Each umbrella features either a UMAP from the Allen Brain Cell Atlas or an ExA-SPIM visualization.
I think it'd be pretty doable to update embedding + umap as you add a new entry.
Personalized 'related articles' across all your feeds seems very doable with embeddings.
Personalized 'related articles' across all your feeds seems very doable with embeddings.
November 16, 2025 at 12:03 AM
I think it'd be pretty doable to update embedding + umap as you add a new entry.
Personalized 'related articles' across all your feeds seems very doable with embeddings.
Personalized 'related articles' across all your feeds seems very doable with embeddings.
Extended the technical and conceptual proofs of concept, we used our transgene-based barcoding and denoising methods. pubmed.ncbi.nlm.nih.gov/33411784/ to profile whole embryos obtained every hour from 5 to 14 hours post-fertilization in one shot, and recovered evidence for transcriptome maturation
November 15, 2025 at 9:19 AM
Extended the technical and conceptual proofs of concept, we used our transgene-based barcoding and denoising methods. pubmed.ncbi.nlm.nih.gov/33411784/ to profile whole embryos obtained every hour from 5 to 14 hours post-fertilization in one shot, and recovered evidence for transcriptome maturation
This worked nicely to recover known trajectories and cell types.
November 15, 2025 at 8:51 AM
This worked nicely to recover known trajectories and cell types.
We developed a transgene-based sample barcoding approach to profile 10 time points in one shot with scRNA-seq, taking advantage of cell-to-cell variability to capture higher resolution (pseudo)temporal dynamics.
November 15, 2025 at 8:50 AM
We developed a transgene-based sample barcoding approach to profile 10 time points in one shot with scRNA-seq, taking advantage of cell-to-cell variability to capture higher resolution (pseudo)temporal dynamics.
Join the 1-day seminar "Dimensionality Reduction with UMAP and Beyond 2.0" on Nov 25, led by Dr. Nikolay Oskolkov. Learn essential techniques for high-dimensional datasets. Sign up: https://instats.org/seminar/dimensionality-reduction-with-umap-and-b #course #workshop
Dimensionality Reduction with UMAP and Beyond 2.0 - Livestreamed Research Training | Instats
PhD-level seminar on Dimensionality Reduction with UMAP and Beyond 2.0 with Nikolay Oskolkov . Live Q&A plus on‑demand access. Join via your university’s Instats membership or enroll directly.
instats.org
November 13, 2025 at 2:54 PM
Join the 1-day seminar "Dimensionality Reduction with UMAP and Beyond 2.0" on Nov 25, led by Dr. Nikolay Oskolkov. Learn essential techniques for high-dimensional datasets. Sign up: https://instats.org/seminar/dimensionality-reduction-with-umap-and-b #course #workshop
t-SNEか、UMAPか……それとも……
November 13, 2025 at 2:43 PM
t-SNEか、UMAPか……それとも……
Sai Puppala, Ismail Hossain, Md Jahangir Alam, Tanzim Ahad, Sajedul Talukder: LLM-Guided Dynamic-UMAP for Personalized Federated Graph Learning https://arxiv.org/abs/2511.09438 https://arxiv.org/pdf/2511.09438 https://arxiv.org/html/2511.09438
November 13, 2025 at 6:34 AM
Sai Puppala, Ismail Hossain, Md Jahangir Alam, Tanzim Ahad, Sajedul Talukder: LLM-Guided Dynamic-UMAP for Personalized Federated Graph Learning https://arxiv.org/abs/2511.09438 https://arxiv.org/pdf/2511.09438 https://arxiv.org/html/2511.09438
DiverGen Proves AI Models Learn Better with Variety
This section describes DiverGen's comprehensive implementation and visualization techniques. To verify generative diversity, the authors use UMAP visualization and CLIP-based data distribution analysis. While ChatGPT-gen…
#chatgpt #gpt #hackernews
This section describes DiverGen's comprehensive implementation and visualization techniques. To verify generative diversity, the authors use UMAP visualization and CLIP-based data distribution analysis. While ChatGPT-gen…
#chatgpt #gpt #hackernews
DiverGen Proves AI Models Learn Better with Variety
This section describes DiverGen's comprehensive implementation and visualization techniques. To verify generative diversity, the authors use UMAP visualization and CLIP-based data distribution analysis. While ChatGPT-generated prompts increase textual variety and visual richness, they also improve generative model diversity through the use of Stable Diffusion and DeepFloyd-IF. Compared to previous methods like max CLIP or SAM-foreground, the suggested SAM-background (SAM-bg) annotation method generates more precise and comprehensive masks.
hackernoon.com
November 13, 2025 at 1:54 AM
DiverGen Proves AI Models Learn Better with Variety
This section describes DiverGen's comprehensive implementation and visualization techniques. To verify generative diversity, the authors use UMAP visualization and CLIP-based data distribution analysis. While ChatGPT-gen…
#chatgpt #gpt #hackernews
This section describes DiverGen's comprehensive implementation and visualization techniques. To verify generative diversity, the authors use UMAP visualization and CLIP-based data distribution analysis. While ChatGPT-gen…
#chatgpt #gpt #hackernews
UMAPs are useful for dataviz! The problem is that many people (over)interpret due to limited understanding what UMAP is/does.
And yes, Bernhard has retired! There was actually a symposium a few months ago…
And yes, Bernhard has retired! There was actually a symposium a few months ago…
November 12, 2025 at 4:36 PM
UMAPs are useful for dataviz! The problem is that many people (over)interpret due to limited understanding what UMAP is/does.
And yes, Bernhard has retired! There was actually a symposium a few months ago…
And yes, Bernhard has retired! There was actually a symposium a few months ago…
Jesse, this is awesome!! hahah... poor soul. But UMAP with or without cluster that moves have limited usage, no?
PS I head about retirements in Berlin.. is our PI included? will there be a symposium? Would be fun to go :)
PS I head about retirements in Berlin.. is our PI included? will there be a symposium? Would be fun to go :)
November 12, 2025 at 4:31 PM
Jesse, this is awesome!! hahah... poor soul. But UMAP with or without cluster that moves have limited usage, no?
PS I head about retirements in Berlin.. is our PI included? will there be a symposium? Would be fun to go :)
PS I head about retirements in Berlin.. is our PI included? will there be a symposium? Would be fun to go :)
Personalized prehabilitation improved physical and cognitive function, altered immune signaling, and reduced postoperative complications compared to standard programs in elective surgery patients. ja.ma/4p0ny6F
November 12, 2025 at 4:30 PM
Personalized prehabilitation improved physical and cognitive function, altered immune signaling, and reduced postoperative complications compared to standard programs in elective surgery patients. ja.ma/4p0ny6F
Lettering, type, and graphic design folk: a call for help.
Google inexplicably blocked my 'Lettering Locations' map, so I'm rebuilding it in uMap. (Thank you @InsertUser.)
I've forgotten most of the locations I'd previously pinned — why I had the map in the first place! — so I need your help […]
Google inexplicably blocked my 'Lettering Locations' map, so I'm rebuilding it in uMap. (Thank you @InsertUser.)
I've forgotten most of the locations I'd previously pinned — why I had the map in the first place! — so I need your help […]
Original post on typo.social
typo.social
November 12, 2025 at 9:58 AM
Lettering, type, and graphic design folk: a call for help.
Google inexplicably blocked my 'Lettering Locations' map, so I'm rebuilding it in uMap. (Thank you @InsertUser.)
I've forgotten most of the locations I'd previously pinned — why I had the map in the first place! — so I need your help […]
Google inexplicably blocked my 'Lettering Locations' map, so I'm rebuilding it in uMap. (Thank you @InsertUser.)
I've forgotten most of the locations I'd previously pinned — why I had the map in the first place! — so I need your help […]
As someone who once wasted half a day wondering why this one cell wouldn’t cluster with any other & always stayed in the same position in the UMAP this physically hurts 😅
As someone who looks at a lot of Manhattan plots, I can say that an under-appreciated cause of false positive GWAS hits is stuff stuck to my computer screen.
November 12, 2025 at 6:31 AM
As someone who once wasted half a day wondering why this one cell wouldn’t cluster with any other & always stayed in the same position in the UMAP this physically hurts 😅
I have been playing with the open source "UMap" along with CAWM & DARE Maptiles of the Roman Empire to help people make their own maps for websites, teaching, and books using ancient world data. Is there any interest in learning the basics of DIY maps? umap.openstreetmap.de/en/map/ancie...
November 11, 2025 at 4:51 PM
I have been playing with the open source "UMap" along with CAWM & DARE Maptiles of the Roman Empire to help people make their own maps for websites, teaching, and books using ancient world data. Is there any interest in learning the basics of DIY maps? umap.openstreetmap.de/en/map/ancie...
I use UMAP to visualize a growing set of vectors sometimes, so I always get a different result, but for example, I can always find the cluster about <whatever topic> because they're always off by themselves in a little arc or whatever. So yes, I think there'd be convergence. That's my guess! 🤷♂️
November 11, 2025 at 4:32 PM
I use UMAP to visualize a growing set of vectors sometimes, so I always get a different result, but for example, I can always find the cluster about <whatever topic> because they're always off by themselves in a little arc or whatever. So yes, I think there'd be convergence. That's my guess! 🤷♂️
THIS IS EXTREMELY COOL though I wonder if they computed once and then cached the UMAP embedding, or whether they're building it on the fly. If they cached it, you get the same embedding every time and you can get to know the geography. That could be fun.
November 11, 2025 at 3:06 PM
THIS IS EXTREMELY COOL though I wonder if they computed once and then cached the UMAP embedding, or whether they're building it on the fly. If they cached it, you get the same embedding every time and you can get to know the geography. That could be fun.
Built by Magenta, it maps 300 genres as stars in 3D using UMAP, then blends nearby prompts into realtime audio via Lyria RealTime. Fly, click, anchor—your path becomes a dynamic mashup. Deployed via AI Studio with Cloud Run proxying the Gemini key.
magenta.withgoogle.com/spacedj-anno...
magenta.withgoogle.com/spacedj-anno...
Space DJ: Navigating a Musical Universe
Today, we’re excited to launch Space DJ, a web application from Magenta thatturns music exploration into an interactive journey through a constellation ofsou...
magenta.withgoogle.com
November 11, 2025 at 3:03 PM
Built by Magenta, it maps 300 genres as stars in 3D using UMAP, then blends nearby prompts into realtime audio via Lyria RealTime. Fly, click, anchor—your path becomes a dynamic mashup. Deployed via AI Studio with Cloud Run proxying the Gemini key.
magenta.withgoogle.com/spacedj-anno...
magenta.withgoogle.com/spacedj-anno...
Space DJ turns genre embeddings into a playable galaxy—pilot a ship, the music follows. 🚀
Key stats
768→128 PCA compression; 3D UMAP projection; three.js rendering; autopilot drift; high‑dim neighbors surfacing hidden similarities.
Key stats
768→128 PCA compression; 3D UMAP projection; three.js rendering; autopilot drift; high‑dim neighbors surfacing hidden similarities.
November 11, 2025 at 3:03 PM
Space DJ turns genre embeddings into a playable galaxy—pilot a ship, the music follows. 🚀
Key stats
768→128 PCA compression; 3D UMAP projection; three.js rendering; autopilot drift; high‑dim neighbors surfacing hidden similarities.
Key stats
768→128 PCA compression; 3D UMAP projection; three.js rendering; autopilot drift; high‑dim neighbors surfacing hidden similarities.
🌿 RESEARCH 🌿
Single-nucleus RNAseq reveals bundle sheath cell-specific photorespiration pathways in Moricandia arvensis, incl ammonium assimilation & redox regulation, highlighting metabolic compartmentalization in C3–C4 photosynthesis – Triesch et al.
🔗 doi.org/10.1093/jxb/...
#PlantScience 🧪
Single-nucleus RNAseq reveals bundle sheath cell-specific photorespiration pathways in Moricandia arvensis, incl ammonium assimilation & redox regulation, highlighting metabolic compartmentalization in C3–C4 photosynthesis – Triesch et al.
🔗 doi.org/10.1093/jxb/...
#PlantScience 🧪
November 11, 2025 at 1:00 PM
🌿 RESEARCH 🌿
Single-nucleus RNAseq reveals bundle sheath cell-specific photorespiration pathways in Moricandia arvensis, incl ammonium assimilation & redox regulation, highlighting metabolic compartmentalization in C3–C4 photosynthesis – Triesch et al.
🔗 doi.org/10.1093/jxb/...
#PlantScience 🧪
Single-nucleus RNAseq reveals bundle sheath cell-specific photorespiration pathways in Moricandia arvensis, incl ammonium assimilation & redox regulation, highlighting metabolic compartmentalization in C3–C4 photosynthesis – Triesch et al.
🔗 doi.org/10.1093/jxb/...
#PlantScience 🧪
From Germany:
Transcriptome analysis of classical blood cells reveals down-regulation of proinflammatory genes in the classical monocytes of Long-COVID patients
www.frontiersin.org/journals/imm...
Screenshot from latest Science for ME weekly update
#LongCovid #PASC
Transcriptome analysis of classical blood cells reveals down-regulation of proinflammatory genes in the classical monocytes of Long-COVID patients
www.frontiersin.org/journals/imm...
Screenshot from latest Science for ME weekly update
#LongCovid #PASC
November 11, 2025 at 1:41 AM
From Germany:
Transcriptome analysis of classical blood cells reveals down-regulation of proinflammatory genes in the classical monocytes of Long-COVID patients
www.frontiersin.org/journals/imm...
Screenshot from latest Science for ME weekly update
#LongCovid #PASC
Transcriptome analysis of classical blood cells reveals down-regulation of proinflammatory genes in the classical monocytes of Long-COVID patients
www.frontiersin.org/journals/imm...
Screenshot from latest Science for ME weekly update
#LongCovid #PASC
Something I had Claude Code put together some weeks ago. It came together fast, so I don't remember the details of how we did it! I know we used UMAP in the browser to down-project the high-dimensional points to 3D, then it was just threejs. I art-directed the project. It was my idea to do HDR. 😁
November 10, 2025 at 9:21 PM
Something I had Claude Code put together some weeks ago. It came together fast, so I don't remember the details of how we did it! I know we used UMAP in the browser to down-project the high-dimensional points to 3D, then it was just threejs. I art-directed the project. It was my idea to do HDR. 😁
Yeahhhhh 🥳🥳
The UMAP 2026 call for workshops and tutorials is out!!
Proposal Submission: January 22, 2026
For more information 👇
Workshop Website: www.um.org/umap2026/cal...
Tutorial Website: www.um.org/umap2026/cal...
For questions: umap2026-workshop-tutorial@um.org
The UMAP 2026 call for workshops and tutorials is out!!
Proposal Submission: January 22, 2026
For more information 👇
Workshop Website: www.um.org/umap2026/cal...
Tutorial Website: www.um.org/umap2026/cal...
For questions: umap2026-workshop-tutorial@um.org
Call for Workshop Proposals – ACM UMAP 2026
www.um.org
November 10, 2025 at 12:59 PM
Yeahhhhh 🥳🥳
The UMAP 2026 call for workshops and tutorials is out!!
Proposal Submission: January 22, 2026
For more information 👇
Workshop Website: www.um.org/umap2026/cal...
Tutorial Website: www.um.org/umap2026/cal...
For questions: umap2026-workshop-tutorial@um.org
The UMAP 2026 call for workshops and tutorials is out!!
Proposal Submission: January 22, 2026
For more information 👇
Workshop Website: www.um.org/umap2026/cal...
Tutorial Website: www.um.org/umap2026/cal...
For questions: umap2026-workshop-tutorial@um.org