When SuSiE Says '95% Confident', Is It?
Benchmarking the Honesty of Fine-Mapping Credible Sets Fine-mapping has a promise built into its output, and almost nobody checks whether the promise …
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Your Variant Caller Tells You How Confident It Is. Have You Ever Checked If It's Telling the Truth?
Every variant caller you have ever used attaches a number to each call: QUAL. It is a confidence score, a claim about how likely the call is to be cor…
Your LLM Got the Variant Right. But Did It Get It Right for the Right Reason?
I built a benchmark to find out whether a frontier language model can be trusted to interpret clinical genetic variants. The result surprised me, and …
Spatial Transcriptomics Plus Topological Data Analysis: A Complete End-to-End Tutorial with squidpy and GUDHI
Build a real spatial transcriptomics pipeline on Visium mouse brain, then go one step past every tutorial: use persistent homology to find spatial str…
I Built SeqBench - Free Bioinformatics Tools in the Browser
SeqBench is a free, browser-based bioinformatics toolkit designed for molecular biologists, bioinformaticians, and students working with DNA, RNA, and…
A UMAP With Arrows Is Not a Benchmark. This Is
How I built a three-task evaluation framework for RNA velocity trajectory inference -- measuring global ordering, pairwise rank preservation, and robu…
Engineering CellFateBench: A Reproducible Python Benchmark for Single-Cell Genomics Reasoning
CellFateBench is a scientific software and benchmark-engineering project for evaluating reasoning over single-cell genomics workflows. The project was…
A MOGONET-Style Multi-Omics Biomarker Pipeline: Why a Near-Random Graph Net Still Earns Its Place
TL;DR (Quick Answer) This is an honest engineering write-up of a MOGONET-style multi-omics consensus biomarker pipeline built as an internal R&D p…
Why I built cloudfit
A few months back I was sitting in front of GCP Compute Engine pricing for the hundredth time, trying to pick a machine type for a Nextflow process th…
From Repo Scanner to Audit Architecture: What Changed in STEM BIO-AI Through v1.7.8
Three technical changes that made the scanner less Python-shaped, the warning model more stable, and the reports more inspectable. The last time I wro…
When Control Becomes Authority: Calibration Governance in STEM BIO-AI 1.7.x
Control slowly becomes authority when nobody marks the boundary. That is the calibration problem I kept running into while building STEM BIO-AI. At fi…
From Score to Workflow: Turning STEM BIO-AI Into a Local Audit System
Earlier in this series, I wrote about why bio/medical AI repositories need more than benchmarks, what I learned after auditing 10 public repositories,…