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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…

Nov 14 • 

Valentine Svensson

October 2025

Training SCVI — Differential expression over epochs

With a trained SCVI model you can perform differential expression analysis to learn which genes are increased and decreased in gene expression as cells…

Oct 14 • 

Valentine Svensson

Causal temperatures

Time is special.

Oct 5 • 

Valentine Svensson

September 2025

Negative binomial regression and inference using a pre-trained transformer

I wanted to speed up negative binomial regression with a novel transformer model, but it actually turns out that a classical method of moments is a…

Sep 23 • 

Valentine Svensson

July 2025

H5AD files in GEO

I’m working on a project where I want to use a lot of well-annotated scRNA-seq data.

Jul 25 • 

Valentine Svensson

A pre-trained t-test transformer

Generally, neural networks are nonlinear function approximators.

Jul 10 • 

Valentine Svensson

Slot machine strategy

In the game Blue Prince , every run of the game have you fill a mansion with different rooms to wander through.

Jul 6 • 

Valentine Svensson

June 2025

SCVI with variational batch encoding

For last couple of months I have been exploring batch integration strategies with SCVI and MRVI, and the possibility to optionally disable integration…

Jun 21 • 

Valentine Svensson

May 2025

Evaluating automatic cell number extraction from single cell papers

For the past ~7 years I have been tracking the scale of scRNA-seq experiments in a spreadsheet which we published as the ‘Single Cell Studies Database…

May 26 • 

Valentine Svensson

Merging SCVI models

There are massive amounts of single-cell RNA-seq data, and data is still being produced.

May 21 • 

Valentine Svensson

April 2025

An attempt at speeding up TSNE using Apple MLX

I’m often encountering situations where I want to do a quick 2D visualization of some data.

Apr 1 • 

Valentine Svensson

March 2025

SCVI — Inference-based optional integration

The batch-integrating SCVI model is a conditional variational autoencoder (cVAE, Sohn et al.

Mar 28 • 

Valentine Svensson