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Improving SCVI for low-count cells through self-supervised augmentation

To improve utility of cells with low UMI counts, I wanted to optimize KL weighting in SCVI models.

Mar 2 • Valentine Svensson

January 2026

Serverless GPUs for fast TSNE visualization

TSNE visualization is useful to explore data but is time consuming without access to an Nvidia GPU.

Jan 21 • Valentine Svensson

Training SCVI - Metal acceleration

The single cell analysis package scvi-tools allow you to model data quickly and easily if you have access to a GPU.

Jan 15 • Valentine Svensson

SCVI - Estimating null expression levels

In this post I motivate why I think it would be useful to have clear thresholds for when a gene is not expressed, test a strategy to obtain such…

Jan 6 • Valentine Svensson

November 2025

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, 2025 • 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, 2025 • Valentine Svensson

Causal temperatures

Time is special.

Oct 5, 2025 • 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, 2025 • 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, 2025 • Valentine Svensson

A pre-trained t-test transformer

Generally, neural networks are nonlinear function approximators.

Jul 10, 2025 • 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, 2025 • 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, 2025 • Valentine Svensson