What Uncle Bob's "I Don't Read Code Anymore" Taught Me About Testing
I've come across a post by Uncle Bob on X ( link ) (the author of Clean Code ) that has a couple thousand reposts. It states that he does not read cod…
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variant-confidence v0.1.0: a calibrated confidence layer for variant-effect pathogenicity scores
variant-confidence v0.1.0: a calibrated confidence layer for variant-effect pathogenicity scores State-of-the-art variant-effect models are accurate i…
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 …
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 …
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…
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,…