Valentine Svensson
@nxn.se
Molecular cell biology and stats / ML, mostly scRNA-seq.
Principal Scientist at Tahoe Tx.
https://www.nxn.se/archive
Principal Scientist at Tahoe Tx.
https://www.nxn.se/archive
Chance favors the (theoretically) prepared mind - arjunrajlab.substack.com/p/chance-fav...
Chance favors the (theoretically) prepared mind
In defense of the role of theory in innovation
arjunrajlab.substack.com
January 26, 2026 at 2:46 AM
Chance favors the (theoretically) prepared mind - arjunrajlab.substack.com/p/chance-fav...
Reposted by Valentine Svensson
I just thought everyone should see this
January 22, 2026 at 11:02 PM
I just thought everyone should see this
Why we (usually) don't have to worry about multiple comparisons - arxiv.org/abs/0907.2478
Why we (usually) don't have to worry about multiple comparisons
Applied researchers often find themselves making statistical inferences in settings that would seem to require multiple comparisons adjustments. We challenge the Type I error paradigm that underlies t...
arxiv.org
January 22, 2026 at 6:54 AM
Why we (usually) don't have to worry about multiple comparisons - arxiv.org/abs/0907.2478
Serverless GPUs for fast TSNE visualization - www.nxn.se/p/serverless...
January 21, 2026 at 7:18 AM
Serverless GPUs for fast TSNE visualization - www.nxn.se/p/serverless...
Life's most important problems - blog.jck.bio/p/lifes-most...
Life's most important problems
Richard Hamming's question applied to the life sciences
blog.jck.bio
January 21, 2026 at 5:45 AM
Life's most important problems - blog.jck.bio/p/lifes-most...
We predict that the transcript abundance from the gene we are knocking down will (checks notes) decrease - ekernf01.github.io/target_gene_...
We predict that the transcript abundance from the gene we are knocking down will (checks notes) decrease
The problem with gene-wise characterization of genetic interventions
ekernf01.github.io
January 20, 2026 at 6:20 AM
We predict that the transcript abundance from the gene we are knocking down will (checks notes) decrease - ekernf01.github.io/target_gene_...
The spectrum of inflammatory responses - doi.org/10.1126/scie...
The spectrum of inflammatory responses
doi.org
January 19, 2026 at 6:39 AM
The spectrum of inflammatory responses - doi.org/10.1126/scie...
Training SCVI - Metal acceleration - www.nxn.se/p/training-s...
January 15, 2026 at 8:12 AM
Training SCVI - Metal acceleration - www.nxn.se/p/training-s...
Reposted by Valentine Svensson
Pertpy: a one-stop and performant framework for single-cell perturbation analysis. @lukasheumos.bsky.social @fabiantheis.bsky.social
www.nature.com/articles/s41...
www.nature.com/articles/s41...
January 14, 2026 at 4:20 PM
Pertpy: a one-stop and performant framework for single-cell perturbation analysis. @lukasheumos.bsky.social @fabiantheis.bsky.social
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Assessing a Virtual Cell’s utility - blog.turbine.ai/p/assessing-...
Assessing a Virtual Cell’s utility
Hitting 2026 running, I can tell you that the team was asked a lot internally to evaluate and share their opinion on many published approaches on creating virtual cells.
blog.turbine.ai
January 14, 2026 at 6:59 AM
Assessing a Virtual Cell’s utility - blog.turbine.ai/p/assessing-...
Reposted by Valentine Svensson
PCA is one of those techniques that sounds unreasonable (yeah sure we all want to fit a p-dimensional ellipsoid to our data) but turns out to be a reasonable solution to a wide range of problems.
Also: I do hope stackexchange has been archived, because it is my gen's library of alexandria
Also: I do hope stackexchange has been archived, because it is my gen's library of alexandria
still one of the best explanations of principal component analysis (pca), explained at different levels from layman to the more math inclined stats.stackexchange.com/a/140579/132...
Making sense of principal component analysis, eigenvectors & eigenvalues
In today's pattern recognition class my professor talked about PCA, eigenvectors and eigenvalues.
I understood the mathematics of it. If I'm asked to find eigenvalues etc. I'll do it correctly li...
stats.stackexchange.com
January 13, 2026 at 4:13 PM
PCA is one of those techniques that sounds unreasonable (yeah sure we all want to fit a p-dimensional ellipsoid to our data) but turns out to be a reasonable solution to a wide range of problems.
Also: I do hope stackexchange has been archived, because it is my gen's library of alexandria
Also: I do hope stackexchange has been archived, because it is my gen's library of alexandria
Citizen Kane is a good movie in general, but the one thing I can't stop thinking about is how thick and substantial the jigsaw puzzle pieces in it are. I've only experienced thin cardboard jigsaw puzzles; these wood ones must feel very satisfying.
January 10, 2026 at 7:54 PM
Citizen Kane is a good movie in general, but the one thing I can't stop thinking about is how thick and substantial the jigsaw puzzle pieces in it are. I've only experienced thin cardboard jigsaw puzzles; these wood ones must feel very satisfying.
Selective remodelling of the adipose niche in obesity and weight loss - www.nature.com/articles/s41...
Selective remodelling of the adipose niche in obesity and weight loss - Nature
An atlas study of adipose tissue in people with obesity undergoing weight loss and their lean counterparts reveals that weight loss reduces cell senescence but cannot reverse all the metabolic problem...
www.nature.com
January 7, 2026 at 7:43 AM
Selective remodelling of the adipose niche in obesity and weight loss - www.nature.com/articles/s41...
SCVI - Estimating null expression levels -- www.nxn.se/p/scvi-estim...
January 6, 2026 at 7:57 AM
SCVI - Estimating null expression levels -- www.nxn.se/p/scvi-estim...
Finally watched Contagion. Amazing movie! Especially in retrospect.
January 5, 2026 at 4:47 AM
Finally watched Contagion. Amazing movie! Especially in retrospect.
Hoping the mechnical keyboard community at some points discover the 'matter over thread' smart home world. All the current smart buttons are mushy and unsatisfying.
January 4, 2026 at 2:50 AM
Hoping the mechnical keyboard community at some points discover the 'matter over thread' smart home world. All the current smart buttons are mushy and unsatisfying.
Reposted by Valentine Svensson
Why does anyone use the Wilcoxon test for anything?
It's not even transitive. It's sensitive to things one most likely is not looking for (changes in distribution shape) and relatively insensitive to what one usually is looking for (change in location).
www.sciencedirect.com/science/arti...
It's not even transitive. It's sensitive to things one most likely is not looking for (changes in distribution shape) and relatively insensitive to what one usually is looking for (change in location).
www.sciencedirect.com/science/arti...
December 10, 2025 at 9:36 AM
Why does anyone use the Wilcoxon test for anything?
It's not even transitive. It's sensitive to things one most likely is not looking for (changes in distribution shape) and relatively insensitive to what one usually is looking for (change in location).
www.sciencedirect.com/science/arti...
It's not even transitive. It's sensitive to things one most likely is not looking for (changes in distribution shape) and relatively insensitive to what one usually is looking for (change in location).
www.sciencedirect.com/science/arti...
Virtual Cell Perturbation Metrics Reloaded - giovannipalla.substack.com/p/virtual-ce...
Virtual Cell Perturbation Metrics Reloaded
Thoughts on metrics for perturbation prediction models
giovannipalla.substack.com
December 10, 2025 at 4:13 AM
Virtual Cell Perturbation Metrics Reloaded - giovannipalla.substack.com/p/virtual-ce...
Interpretable Inflammation Landscape of Circulating Immune cells - www.biorxiv.org/content/10.1...
www.biorxiv.org
December 9, 2025 at 4:43 AM
Interpretable Inflammation Landscape of Circulating Immune cells - www.biorxiv.org/content/10.1...
Claude agent skill to infer experimental designs from .h5ad’s - www.nxn.se/p/claude-age...
Claude agent skill to infer experimental designs from .h5ad’s
Anthropic recently launched Claude for Life Sciences, which in practical terms means a marketplace of plugins, MCP’s, and agent skills focused on tasks you encounter in biomedical research.
www.nxn.se
November 14, 2025 at 5:59 AM
Claude agent skill to infer experimental designs from .h5ad’s - www.nxn.se/p/claude-age...
What will it take for AI to change drug discovery? - www.writingruxandrabio.com/p/what-will-...
What will it take for AI to change drug discovery?
Some thoughts on avoiding self delusion.
www.writingruxandrabio.com
November 13, 2025 at 7:11 AM
What will it take for AI to change drug discovery? - www.writingruxandrabio.com/p/what-will-...
We still can’t predict much of anything in biology - blog.genesmindsmachines.com/p/we-still-c...
We still can’t predict much of anything in biology
Biology is hard. Yes, even for AI.
blog.genesmindsmachines.com
November 12, 2025 at 9:10 PM
We still can’t predict much of anything in biology - blog.genesmindsmachines.com/p/we-still-c...
The Truth Is Out There, Part 4: The Downside of Belief - www.filfre.net/2024/10/the-...
» The Truth Is Out There, Part 4: The Downside of Belief The Digital Antiquarian
www.filfre.net
November 12, 2025 at 5:35 PM
The Truth Is Out There, Part 4: The Downside of Belief - www.filfre.net/2024/10/the-...
Hollywood Archaeology: The Super Mario Bros. Movie - grantland.com/features/the...
» Hollywood Archaeology: The Super Mario Bros. Movie
grantland.com
November 11, 2025 at 5:18 AM
Hollywood Archaeology: The Super Mario Bros. Movie - grantland.com/features/the...
Reposted by Valentine Svensson
🧬 Tahoe Workshop at scverse conference 2025 🧬
Disease Biology and Therapeutics in the Age of Frontier Datasets
@tahoetherapeutics.bsky.social
#scverse2025 #ComputationalBiology #DrugDiscovery #TahoeTherapeutics #SingleCell #PerturbationBiology
Disease Biology and Therapeutics in the Age of Frontier Datasets
@tahoetherapeutics.bsky.social
#scverse2025 #ComputationalBiology #DrugDiscovery #TahoeTherapeutics #SingleCell #PerturbationBiology
October 15, 2025 at 2:28 PM
🧬 Tahoe Workshop at scverse conference 2025 🧬
Disease Biology and Therapeutics in the Age of Frontier Datasets
@tahoetherapeutics.bsky.social
#scverse2025 #ComputationalBiology #DrugDiscovery #TahoeTherapeutics #SingleCell #PerturbationBiology
Disease Biology and Therapeutics in the Age of Frontier Datasets
@tahoetherapeutics.bsky.social
#scverse2025 #ComputationalBiology #DrugDiscovery #TahoeTherapeutics #SingleCell #PerturbationBiology