Blogs

• JAX-in-the-Box: Unboxing Stateful Training with Flax NNX and Orbax March 2026

  An end-to-end walkthrough of training and checkpointing an MLP with Flax NNX and Orbax, plus how JAX's XLA backend delivers zero-code hardware portability from CPU to TPU.

  • JAX
  • Flax NNX
  • Deep Learning
• Which Statistical Test Should You Actually Use? December 2025

  A practical guide to picking the right statistical test based on group count, distribution shape, and sample size, with Python snippets for each.

  • Statistics
  • Hypothesis Testing
  • Python
• PyTorch Implementation of Skip-gram with Negative Sampling November 2025

  A from-scratch PyTorch walkthrough of Skip-gram Word2Vec with negative sampling, from dataset construction to trained embeddings.

  • PyTorch
  • NLP
  • Deep Learning
• A Practical Guide to K-Means and Hierarchical Clustering June 2025

  A hands-on comparison of K-means and hierarchical clustering for high-dimensional biological data, covering distance metrics, linkage criteria, and cluster validation in both Python and R.

  • Bioinformatics
  • Unsupervised Machine Learning
  • Clustering
• A Short Note on Principal Component Analysis (PCA) in Bulk RNA-seq June 2025

  A concise walkthrough of the linear algebra behind PCA for bulk RNA-seq, from variance-stabilizing transforms through SVD to interpreting loadings and variance explained, with parallel Python and R implementations.

  • Bioinformatics
  • Unsupervised Machine Learning
  • RNA-seq
• Addressing Heteroscedasticity in RNAseq data May 2025

  How mean-variance dependence in RNA-seq counts distorts PCA and clustering, and how DESeq2's variance-stabilizing transformation (VST) fixes it.

  • Bioinformatics
  • Bulk RNA-seq
• Going Offline: Installing EPI2ME Workflows by Hand on WSL2 March 2025

  A step-by-step guide to manually installing and configuring EPI2ME workflows for fully offline execution on WSL2.

  • Bioinformatics
  • WSL2
  • Nextflow
• Beyond the Monolith: Mastering Nested Repositories with Git Submodules February 2025

  A concise guide to managing complex project structures and dependencies efficiently using Git submodules.

  • Git
  • DevOps
• Welcome to My Blog January 2025

  An introduction to this site and what I plan to write about.

  • AIxBio
  • Computational Biology