petermchale

math105A

Numerical analysis course in Python

tumor

A spatial Markov model of agents making decisions based upon their surroundings. Stochastic optimization via Markov Chain Monte Carlo (Metropolis-Hastings algorithm). Interactive visualization of data using the JavaScript library D3.

denoising_coverage_profiles

Using Convolutional Neural Networks to model an association between a genomic sequence and the number of sequenced reads that align to it

igv-grid

Create thumbnails of igv.js visualizations and view them all simultaneously in an interactive, responsive web app.

llm-powered-applications

Orchestrating the interaction between users and Large Language Models

gnn

A collection of projects using graph neural networks implemented from first principles, and using the PyTorch Geometric library

Math175

Upper-division Combinatorics Class

trfermikit

Discover VNTR-associated DELs that are hard to find using Illumina reads

diffusion

Implementation of a Denoising Diffusion Probabilistic Model with some mathematical background.

fine-tune-llm

Fine-tune open-source LLM on an instruction dataset

nucleotide-transformer

Using an LLM to discover the genetic causes of rare disease

pong_RL

Training a simple AI using the policy-gradient approach to Reinforcement Learning.

visualize-streaming-data

Visualize the geographic location of tweets in real time using Apache Kafka

algorithms_and_data_structures_CPlusPlus

Standard algorithm and data-structure problems in C++

algorithms_and_data_structures_Python

Standard algorithm and data-structure problems in Python

constraint-tools-data

dairy-spread

Create a nice creamy spread(-sheet). Makes me want soda bread, so it does.

docker-ci

GitHub Action CI pipeline with Docker containers

genomics-web-app

vue app with flask REST api to process genomic data

linkedin-learning-open-source-project-python-py3.11

lofTolEnhancers

Code for Xu et al. Loss-of-function tolerance of enhancers in the human genome

LOGO

minDiffusion

Self-contained, minimalistic implementation of diffusion models with Pytorch.

NAHRly

Genomic copy-number variant calling on NAHR-based events

nextflow

Basic examples of nextflow syntax/usage

petermchale.github.io

PySyft

Perform data science on data that remains in someone else's server

QQ-plots

Model decision making ... and the beauty of order statistics.

truvari

Structural variant comparison tool for VCFs

web-app-lambda-api-gateway-dynamodb

How to build a web app on AWS using lambda functions, API gateway, and DynamoDB