#UMAP
Why not just do something that gives a tree and can be done
fast? This seems to roughly be the reasoning of the authors of MILK. So we checked how it does on our synthetic datasets. Here's an example.

It's clearly not just about using a tree, because MILK performs worse than UMAP. 10/n
October 1, 2026 at 1:03 PM
across cells. This show that, while Bonsai's distances correlate very well with the ground truth distances, those in PCA and UMAP are far worse.

Ok. But was it really necessary to work so hard? Maybe you just need to put things on a tree. And there are many fast ad hoc ways to get a tree. 9/n
October 1, 2026 at 1:03 PM
Hey, I heard about Bonsai, but now I heard there is another method called MILK that also visualizes scRNA-seq on trees. And it is much faster! Should I just use that then? A tree is a tree, right?
TLDR: No. #methodsmatter

Not even close. On realistic synthetic data MILK performs worse than UMAP.
October 1, 2026 at 1:03 PM
Prefibrotic bone marrow microenvironment is a hallmark of clonal hematopoiesis
a, UMAP of hematopoietic progenitor and mature immune cells. Cells are colored by targeted enrichment strategy (left); non-CHIP (top-right; n = 53,382) and CHIP (bottom-right; n = 35,431). b, Heatmap representing column-scaled expression of selected markers used for cell type annotation. c, Box plots showing frequency of populations in the hematopoietic progenitor (left) and mature immune (right) libraries in non-CHIP (n = 9) and CHIP (n = 6). Boxes span the 25th to 75th percentile, with the horizontal bar in the center representing the 50th percentile, and whiskers spanning 1.5 x IQR. Hypothesis testing was performed using two-sided Wilcoxon rank-sum test, and p-values were FDR adjusted. d, Heatmap representing column-scaled frequencies per sample of hematopoietic progenitor libraries mapped to ‘Level3R’ annotations published by Zhang et al. (2024). e-f, Bar plots representing colony forming units (CFU) per total BM fraction mononuclear cells (MNC; e) in non-CHIP (n = 15) and CHIP (n = 13) and CD34+ cells (f) in non-CHIP (n = 5) and CHIP (n = 4). Data is shown as mean value +/- SEM. Hypothesis testing was performed using two-sided Student’s t-test and p-values were FDR adjusted. g, Heatmap of top 2 population-defining regulons derived from SCENIC in progenitor...
www.nature.com
September 30, 2026 at 11:31 PM
Listening for behavior: Identifying common behavior-associated call types to improve acoustic monitoring of cryptic sound-producing species
https://doi.org/10.1121/10.0046655
September 30, 2026 at 7:00 PM
September 30, 2026 at 2:18 PM
#DBfeature #LatestResearch 🧠

Neural crest marker FOXD3 regulates ventralising SHH expression in the floorplate and is required for proper neural tube morphogenesis.

By Jenaid Rees, Laura Kerosuo, et al.

doi.org/10.1016/j.ydbio.2026.07.001
September 30, 2026 at 12:45 PM
Demander à Claude Opus 4.5 d'optimiser du code Rust en boucle, peut donner des gains de 2x à 20x face à des libs comme UMAP, à condition d'interdire le code unsafe et de cadrer chaque itération. ⬇️
https://news.humancoders.com/t/rust/items/66917-optimiser-du-code-rust-en-demandant-a-des-agents-l
September 30, 2026 at 9:10 AM
Demander à Claude Opus 4.5 d'optimiser du code Rust en boucle, peut donner des gains de 2x à 20x face à des libs comme UMAP, à condition d'interdire le code unsafe et de cadrer chaque itération. ⬇️
https://news.humancoders.com/t/rust/items/66917-optimiser-du-code-rust-en-demandant-a-des-agents-l
September 30, 2026 at 9:10 AM
d\M`6sz{NTD06K]u]?Jq`UmAP~*3n-tp
September 28, 2026 at 7:20 AM
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.
September 27, 2026 at 1:45 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.
September 27, 2026 at 1:45 PM
Écrire du Rust rapide en demandant à l'agent de rendre le code plus rapide. Un UMAP réécrit de zéro, sans unsafe, avec des benchmarks criterion à chaque itération et la consigne de continuer tant que ça progresse. De 2 à 20 fois plus rapide, prompt...
https://minimaxir.com/2026/09/agentic-iteration/
September 27, 2026 at 12:00 PM
How it works 🧵

Each story gets a semantic embedding, then UMAP projects it onto a 2D map. Meaning, not tags, decides where a star lands.

That's why a story on AI chips can sit right next to one on power grids and data centers. The whole map is rendered in WebGL, right in the browser.
September 27, 2026 at 10:59 AM
I am going to be in Boston for the IEEE VIS conference Nov 9 -13 this year! I am keen to talk dimension reduction, clustering, and data maps (UMAP, HDBSCAN, DataMapPlot). If you are going to be at VIS, or are just in Boston, and want to grab a coffee, please reach out. DMs open.
September 25, 2026 at 2:14 AM
SUPeR Viewer stands for scRNA-seq UMAP/pseudospatial eFP Browser Viewer, and it shows not only scRNA-seq UMAPs but eFP pictographs showing expression across inferred cell types in a pseudospatial manner, inspired by collaborators Victoria Mironova and Jian Xu's Root Cell Atlas at Raboud University.
September 24, 2026 at 7:32 PM
Les propriétariens de gauche ont déjà leurs tribunaux, juges, flics et matons pour punir celleux qui respectent pas la Sainte Propriété. Ptet qu'ils ont des projets de camps de travail style UMAP (c'est pas #Mélenchon qui admire Castro ? - Si.) pour la rééducation morale par le travail et par le
September 24, 2026 at 6:51 PM
🎓 The #UMAP2027 Doctoral Consortium is now accepting submissions!

An opportunity for PhD students to present their research, receive feedback and mentorship, and connect with the UMAP community.

📅 Submission deadline: Feb 6, 2027
📍 June 9, 2027 - Chicago

🔗 um.org/umap2027/cal...
September 24, 2026 at 5:15 PM
У мене для вас чудові новини, я відкриваю код власного інструменту UELT!
github.com/hikarosato/U...
А також приготував для вас цікаву статтю про так званих «колег» серед нас, перекладачів! Приємного читання!
medium.com/@hikaro/%D1%...
GitHub - hikarosato/UELT: locres, uasset, umap localization tool. Ukrainian language only. Create forks and translate it for yourself.
locres, uasset, umap localization tool. Ukrainian language only. Create forks and translate it for yourself. - hikarosato/UELT
github.com
September 24, 2026 at 4:48 PM
September 24, 2026 at 2:11 PM
-> l'utilisateur peut se débrouiller du logiciel/de l'appli avec un niveau technique plutôt faible
-> l'appli est gratuite, au moins côté équipe
Qfield est trop compliqué, Organic Maps/OsmAnd n'affichent que des signets kml sans légende différenciée, ni étiquettes, Umap n'a pas d'appli associée..
September 24, 2026 at 1:42 PM
Single-cell RNA sequencing study of PBMCs from patients with myositis ± myocarditis showed a potential role of B cell/antibody-mediated responses and NK cell activation in patients with IIM who develop myocarditis

ACR Open Rheumatology
doi.org/10.1002/acr2...
September 23, 2026 at 8:55 PM
That old image revealed an opportunity hiding in plain sight: an accessible route to developing mesoderm.

We used it to deliver lentiviral reporters and barcodes at E7.5: a scalable, Cre-independent method to manipulate and lineage-trace mammalian mesoderm in utero.
September 23, 2026 at 5:00 PM
Guy who doesn’t know what UMAP is: They are very close together on UMAP
September 23, 2026 at 12:18 PM
🐟 Zebrahub: a zebrafish single-cell UMAP with RNA-velocity streamlines, cells as points and flow as lines in one scene. #SingleCell

Demo: demos.luxarviewer.dev/d/zebrahub_...
September 23, 2026 at 8:49 AM