Discover ericmjl/flu-gibson Open Source project by Eric Ma (@ericmjl)

How to do Bayesian statistical modelling using numpy and PyMC3

977

bayesian-stats-modelling-tutorial

A collection of Bayesian data analysis recipes using PyMC3

630

bayesian-analysis-recipes

Visualization Package for NetworkX

544

nxviz

In which I put together my thoughts on the practice of data science.

450

essays-on-data-science

Dockerfile

231

dl-workshop

Crash course to master gradient-based machine learning. Also secretly a JAX course in disguise!

In which I try to demystify the fundamental concepts behind Bayesian deep learning.

200

bayesian-deep-learning-demystified

A short tutorial for data scientists on how to write tests for code + data.

118

data-testing-tutorial

Hive Plots in using Python & matplotlib!

116

hiveplot

Doing Bayesian statistics in Python!

bayesian-stats-talk

Computes a molecular graph for protein structures.

protein-interaction-network

The simplest complex example that I can think of to show main Flask app concepts.

minimal-flask-example

In which I play with the ideas surrounding causality

causality

An experimental deep learning & genotype network-based system for predicting new influenza protein sequences.

flu-sequence-predictor

A minimal example of how to use streamlit on Heroku

minimal-streamlit-example

Helping you manage your data science projects sanely.

pyds-cli

Pythonic class-based interface to LLMs

llamabot

My conda environment YAML files

conda-envs

distributions

Central repository for my distributions figures

Circos

A pedagogical, functional-oriented deep learning library built on top of jax.

fundl

scikit-learn-tutorial

A pedagogical implementation of panel apps served up on a remote machine.

minimal-panel-app

PyCon 2019 talk on Bayesian multi-group testing.

bayesian-generalized-abcde-testing

A utility for flattening nested data structures into an array.

pyflatten

PyCon 2020 Talk on "what probability distributions are"

what-are-probability-distributions

Delivered at PyData Boston on 21 July 2020

principled-ds-workflow

resume

Building a resume using nothing but YAML files and Python. A prototype.

ericmjl.github.io

A talk on what probability distributions are, using Python

probability-distributions-with-python

A package for using convolutional neural nets to learn a graph fingerprint.

graph-fingerprint

Materials for IACS 2017 contest.

iacs2017

Machine learning and phylogenetics on HIV

probabilistic-programming-tutorial

systems-microbiology-hiv

An attempt at demystifying graph deep learning

graph-deep-learning-demystified

In which I learn about score functions and how they can be used to generate data.

score-models

Eric Ma's Personal Website

website

dotfiles

my dotfiles

Slides for my talk on testing for data scientists.

testing-for-data-scientists

A short tutorial on how to make matplotlib plots.

matplotlib-tutorial

In which I try to replicate the main findings of Ferrero, E., Dunham, I., & Sanseau, P. (2017), Journal of Translational Medicine, 15(1), 182.

target-prediction

Deeply learning about normalizing flows.

normalizing-flows

Open source software for worship coordinators and leaders.

czbiohub

TeX

worship-manager

JavaScript

autograd-cupy

Autograd wrapper for CuPy

Software Testing in Open Source and Data Science: A talk delivered at the Data Umbrella speaker series

software-testing-open-source-and-data-science

curve-fitting-talk

"Fret not, it's curve fitting all the way down!

insight-data-challenges

Scripts for running the influenza reassortment detector

influenza-reassortment-detector

A Python module to email myself from Python scripts and the command line.

thesis

PhD thesis!!!!!

TeX

emailme

influenza-reassortment-analysis

dream-respiratory-viral-challenge

In which I try to use ML models to predict HIV resistance phenotypes.

hiv-resistance-prediction

A Streamlit app that monitors internet locally

internet-monitor

A tool for automating my primer design workflow

Primer-Design-Automator

A short website that describes how to create an Amazon AWS GPU instance that runs BEAST + BEAGLE.

beast-gpu-tutorial

Personal Flask app for tracking a habit.

habit-tracker

My academic 'rant' on why n=3 is not sufficient.

bayesian-measurement-paper

Part of my thesis work. Doing convolutional neural nets on protein graphs to make predictions.

protein-convolutional-nets

All our protocols, data, analysis, and papers related to this project are stored here.

protein-systematic-characterization

A command-line utility to continuously pull Git repository locally.

continuous-pull

A short technical piece on how message passing on graphs can be simultaneously made efficient and easy to read.

computational-representations-message-passing

Jupyter notebooks and data - reproducible analysis from reassortment paper

influenza-global-reassortment

My exercises answers from Jeremy Kun's book, Mathematics for Programmers.

math-for-programmers-exercises

Toy project, in which I train a neural network to predict influenza virus host tropism.

nnet-HA

A local web app I built to store information about our Bible Study small group and use it to divide us into smaller groups.

small-group

A small utility for converting between polar and cartesian units.

polcart

Publicly written white paper on genomic surveillance.

genomic-surveillance-whitepaper

A Flask-based UI for the FluGibson package.

flu-gibson-webui

easy-talk-slides-and-notes

My repository of custom scripts and functions.

Personal-Scripts-and-Functions

In which I teach myself TensorFlow.

tensor-flow-tutorial

Influenza-Reassortment-Simulation-and-Identification

Influenza-Network-Transmission-Model

A Python command-line app for displaying photos as a slideshow in a directory.

imgdisplay

mbtools

Molecular Biology Tools

boston-gov-data

something cool happening here

generative-thinking

Dockerfile

pymc3-models

Default models built on top of PyMC3.

Influenza-RNA-Secondary-Structure-Prediction

A personal implementation of the Nord theme + other slide utilities for reveal.js slides.

reveal-nord-theme

Opinionated and personalized cookie-cutter data project template

cookiecutter-data-project

tensor-fun

Minimal tensor operations examples. Playing around with higher-dimensional tensors.

Genotype network software, collaboration with Kyle Yuan.

genotype-network

h9-pb2-global-analysis

Song-Sheet-Transposer

A repository for me to remember how to use d3's force-directed layout API.

d3-graph

My personal blogging assistant, built on top of llamabot and GPT4.

blog-assistant

Dockerfile

epaper-badge

Code for ePaper display badge

Me playing around with autoencoders. For fun.

autoencoders

An interactive guide to ECDFs.

ecdf-guide

In which i futz around with Flask, trying to make a random web app that does something.

flask-sandbox

A curated set of recipes that I've used with pandoc to make all sorts of documents.

pandoc-recipes

In which I play around with PyTorch.

pytorch-playground

flu-assembler

In which I try to implement my own influenza genome assembler. For funzies.

Autograd wrapper for scipy.sparse

autograd-sparse

A repository containing all of the raw data and experiments done on the Raspberry Pi bluetooth tracker.

bluetooth-proximity-tracker-calibration

A repository to bootstrap my writing using Markdown, Pandoc, HTML and Reveal.js

quarto-scipy24-exercises

100

cookiecutter-talk