This is an example of a reproducible modelling project

Overview

An example of a reproducible modelling project

What are we doing?

This example was created for the 2021 fall lecture series of Stanford's Center for Open and REproducible Science (CORES).

A video of the talk can be found at: https://youtu.be/JAQot6b1Cng

The goal of this exemplary analysis is to explore the effect of varying different hyper-parameters of the training of a simple classification model on its performance in scikit-learn's handwritten digit dataset.

Specifically, we will study the effect of varying the learning rate, regularisation strength, number of gradient descent steps, and random shuffling of the data on the 3-fold cross-validation performance of scikit-learn's linear support vector machine classifier.

Importantly, each hyper-parameter is varied separately while all other hyper-parameters are set to default values (for details, see scripts/evaluate_hyper_params_effect.py).

Project organization

├── LICENSE            <- MIT License
├── Makefile           <- Makefile with targets to 'load', 'evaluate', and 'plot' ('make all' runs all three analysis steps)
├── poetry.lock        <- Details of used package versions
├── pyproject.toml     <- Lists all dependencies
├── README.md          <- This README file.
├── docs/              
|    └──               <- Slides of the practical tutorial
├── data/
|    └──               <- A copy of the handwritten digit dataset provided by scikit-learn
|
├── results/
|    ├── estimates/
|    │    └──          <- Generated estimates of classifier performance
|    └── figures/
|         └──          <- Generated figures
|
├── scrips/
|    ├── load_data.py                       <- Downloads the dataset to specified 'data-path'
|    ├── evaluate_hyper_params_effect.py    <- Runs cross-validated hyper-parameter evaluation
|    ├── plot_hyper_params_effect.py        <- Summarizes results of evaluation in a figure
|    └── run_analysis.sh                    <- Runs all analysis steps
|
└── src/
    ├── hyper/
    │    ├──  __init__.py                   <- Makes 'hyper' a Python module
    │    ├── grid.py                        <- Functionality to sample hyper-parameter grid
    │    ├── evaluation.py                  <- Functionality to evaluate classifier performance, given hyper-parameters
    │    └── plotting.py                    <- Functionality to visualize results
    └── setup.py                            <- Makes 'hyper' pip-installable (pip install -e .)  

Data description

We use the handwritten digits dataset provided by scikit-learn. For details on this dataset, see scikit-learn's documentation:

https://scikit-learn.org/stable/datasets/toy_dataset.html#digits-dataset

Installation

This project is written for Python 3.9.5 (we recommend pyenv for Python version management).

All software dependencies of this project are managed with Python Poetry. All details about the used package versions are provided in pyproject.toml.

To clone this repository to your local machine, run:

git clone https://github.com/athms/reproducible-modelling

To install all dependencies with poetry, run:

cd reproducible-modelling/
poetry install

To reproduce our analyses, you additionally need to install our custom Python module (src/hyper) in your poetry environment:

cd src/
poetry run pip install -e .

Reproducing our analysis

Our analysis can be reproduced either by running scripts/run_analysis.sh:

cd scripts
poetry run bash run_analysis.sh

..or by the use of make:

poetry run make <ANALYSIS TARGET>

We provide the following targets for make:

Analysis target Description
all Runs the entire analysis pipeline
load Downloads scikit-learn's handwritten digit dataset
evaluate Runs our cross-validated hyper-parameter evaluation
plot Creates our results figure

This README file is strongly inspired by the Cookiecutter Data Science Structure

Owner
Armin Thomas
Ram and Vijay Shriram Data Science Fellow at Stanford Data Science
Armin Thomas
Good Classification Measures and How to Find Them

Good Classification Measures and How to Find Them This repository contains supplementary materials for the paper "Good Classification Measures and How

Yandex Research 7 Nov 13, 2022
Implementation of the ivis algorithm as described in the paper Structure-preserving visualisation of high dimensional single-cell datasets.

Implementation of the ivis algorithm as described in the paper Structure-preserving visualisation of high dimensional single-cell datasets.

beringresearch 285 Jan 04, 2023
Graph Self-Attention Network for Learning Spatial-Temporal Interaction Representation in Autonomous Driving

GSAN Introduction Code for paper GSAN: Graph Self-Attention Network for Learning Spatial-Temporal Interaction Representation in Autonomous Driving, wh

YE Luyao 6 Oct 27, 2022
Code for reproducing experiments in "Improved Training of Wasserstein GANs"

Improved Training of Wasserstein GANs Code for reproducing experiments in "Improved Training of Wasserstein GANs". Prerequisites Python, NumPy, Tensor

Ishaan Gulrajani 2.2k Jan 01, 2023
So-ViT: Mind Visual Tokens for Vision Transformer

So-ViT: Mind Visual Tokens for Vision Transformer        Introduction This repository contains the source code under PyTorch framework and models trai

Jiangtao Xie 44 Nov 24, 2022
A High-Performance Distributed Library for Large-Scale Bundle Adjustment

MegBA: A High-Performance and Distributed Library for Large-Scale Bundle Adjustment This repo contains an official implementation of MegBA. MegBA is a

旷视研究院 3D 组 336 Dec 27, 2022
Stream images from a connected camera over MQTT, view using Streamlit, record to file and sqlite

mqtt-camera-streamer Summary: Publish frames from a connected camera or MJPEG/RTSP stream to an MQTT topic, and view the feed in a browser on another

Robin Cole 183 Dec 16, 2022
Large Scale Multi-Illuminant (LSMI) Dataset for Developing White Balance Algorithm under Mixed Illumination

Large Scale Multi-Illuminant (LSMI) Dataset for Developing White Balance Algorithm under Mixed Illumination (ICCV 2021) Dataset License This work is l

DongYoung Kim 33 Jan 04, 2023
DNA-RECON { Automatic Web Reconnaissance Tool }

ABOUT TOOL : DNA-RECON is an automatic web reconnaissance tool written in python. This tool made for reconnaissance and information gathering with an

NIKUNJ BHATT 25 Aug 11, 2021
App customer segmentation cohort rfm clustering

CUSTOMER SEGMENTATION COHORT RFM CLUSTERING TỔNG QUAN VỀ HỆ THỐNG DỮ LIỆU Nên chuyển qua theme màu dark thì sẽ nhìn đẹp hơn https://customer-segmentat

hieulmsc 3 Dec 18, 2021
McGill Physics Hackathon 2021: Reaction-Diffusion Models for the Generation of Biological Patterns

DiffuseAnimals: Reaction-Diffusion Models for the Generation of Biological Patterns Introduction Reaction-diffusion equations can be utilized in order

Austin Szuminsky 2 Mar 07, 2022
BMVC 2021: This is the github repository for "Few Shot Temporal Action Localization using Query Adaptive Transformers" accepted in British Machine Vision Conference (BMVC) 2021, Virtual

FS-QAT: Few Shot Temporal Action Localization using Query Adaptive Transformer Accepted as Poster in BMVC 2021 This is an official implementation in P

Sauradip Nag 14 Dec 09, 2022
ACAV100M: Automatic Curation of Large-Scale Datasets for Audio-Visual Video Representation Learning. In ICCV, 2021.

ACAV100M: Automatic Curation of Large-Scale Datasets for Audio-Visual Video Representation Learning This repository contains the code for our ICCV 202

sangho.lee 28 Nov 08, 2022
PaddleViT: State-of-the-art Visual Transformer and MLP Models for PaddlePaddle 2.0+

PaddlePaddle Vision Transformers State-of-the-art Visual Transformer and MLP Models for PaddlePaddle 🤖 PaddlePaddle Visual Transformers (PaddleViT or

1k Dec 28, 2022
An experiment on the performance of homemade Q-learning AIs in Agar.io depending on their state representation and available actions

Agar.io_Q-Learning_AI An experiment on the performance of homemade Q-learning AIs in Agar.io depending on their state representation and available act

1 Jun 09, 2022
Video-face-extractor - Video face extractor with Python

Python face extractor Setup Create the srcvideos and faces directories Put your

2 Feb 03, 2022
An Open-Source Toolkit for Prompt-Learning.

An Open-Source Framework for Prompt-learning. Overview • Installation • How To Use • Docs • Paper • Citation • What's New? Nov 2021: Now we have relea

THUNLP 2.3k Jan 07, 2023
Official implementation of deep-multi-trajectory-based single object tracking (IEEE T-CSVT 2021).

DeepMTA_PyTorch Officical PyTorch Implementation of "Dynamic Attention-guided Multi-TrajectoryAnalysis for Single Object Tracking", Xiao Wang, Zhe Che

Xiao Wang(王逍) 7 Dec 03, 2022
Reinforcement learning algorithms in RLlib

raylab Reinforcement learning algorithms in RLlib and PyTorch. Installation pip install raylab Quickstart Raylab provides agents and environments to b

Ângelo 50 Sep 08, 2022
Least Square Calibration for Peer Reviews

Least Square Calibration for Peer Reviews Requirements gurobipy - for solving convex programs GPy - for Bayesian baseline numpy pandas To generate p

Sigma <a href=[email protected]"> 1 Nov 01, 2021