All Posts - My Computational Genomic Playground

All Posts

2024

SwiGLU 07-29

RoPE: Rotary Positional Embeddings 07-29

Markov Chain Mento Carlo (MCMC) 2 06-18

2023

Convert Seurat to Scanpy h5ad 02-21

2022

Rust: Advanced Trait 02-10

Bayesian Data Analysis: Basics 02-10

2021

Graph: Train, valid, and test dataset split for link prediction 08-12

Graph: Mini-batch sampling in large-scale graphs 08-11

Graph: Implement a MessagePassing layer in Pytorch Geometric 08-07

Graph: Concepts 04-19

2020

Graph: GraphRNN 12-12

Graph: GCN and GAT 12-11

Graph: Semi-supervised Node Classification 12-10

Graph: Node2Vec 12-06

NLP: Word2Vec 12-05

Probabilistic Graphical Model 11-20

Deploy IGV webapp on linux server 11-16

Canonical Correlation Analysis (CCA) 11-02

Complex number for biologist 10-01

Deploy snakemake pipeline on HPC 08-19

NLP: Parse trees 08-01

Fourier transform for biologist 08-01

NLP: RNN and Transformers 07-31

Graph: GNN review 07-26

Graph: GNN basics 07-25

C++ Notes: CUDA 07-11

C++ Notes: Concurrency 07-10

ANOVA 06-30

Survival Analysis 06-22

NLP: Start point for biologist 06-20

Quantile normalization 06-14

Power, Effect size, Sample size 06-14

Multilevel (Hierachical) Models 06-13

Singular Value Decomposition (SVD) 06-06

Markov Chain Mento Carlo (MCMC) 06-06

Swift Cheat Sheet 05-30

Pointer in UnSafe Swift 05-30

Hidden Markov Model (HMM) 05-03

Latent semantic analysis (LSA) 04-30

Probability, P-value, Likelihood 04-29

Conditional random field (CRF) 04-29

GATK for inbred mouse 03-10

Prim 02-11

How to do deep learning using custom Jupyter kernels on Sherlock 02-10

C++ Notes: Return Pointer or Reference 02-10

C++ Notes: Basics 02-10

C++ Notes: STL 02-10

Priority Queque 02-09

Graph 02-09

Sort 02-08

Binary tree 02-08

What is Big O 02-01

Statistical Modeling and Inference 01-30

Loss function for multi-label classification 01-29

Expectation Maximization 01-26

Derivative, Gradient, Jacobian, Hessian, Laplacian 01-26

SuperFast RNA-seq 01-20

Shortcut to ChIP-seq analysis 01-20

Shortcut to bulk RNA-seq analysis 01-20

Cheatsheet for command line 01-20