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
Select, weight and analyze complex sample data

Sample Analytics In large-scale surveys, often complex random mechanisms are used to select samples. Estimates derived from such samples must reflect

samplics 37 Dec 15, 2022
Object detection evaluation metrics using Python.

Object detection evaluation metrics using Python.

Louis Facun 2 Sep 06, 2022
Official code for UnICORNN (ICML 2021)

UnICORNN (Undamped Independent Controlled Oscillatory RNN) [ICML 2021] This repository contains the implementation to reproduce the numerical experime

Konstantin Rusch 21 Dec 22, 2022
An original implementation of "MetaICL Learning to Learn In Context" by Sewon Min, Mike Lewis, Luke Zettlemoyer and Hannaneh Hajishirzi

MetaICL: Learning to Learn In Context This includes an original implementation of "MetaICL: Learning to Learn In Context" by Sewon Min, Mike Lewis, Lu

Meta Research 141 Jan 07, 2023
Official PyTorch implementation of "Edge Rewiring Goes Neural: Boosting Network Resilience via Policy Gradient".

Edge Rewiring Goes Neural: Boosting Network Resilience via Policy Gradient This repository is the official PyTorch implementation of "Edge Rewiring Go

Shanchao Yang 4 Dec 12, 2022
Training code and evaluation benchmarks for the "Self-Supervised Policy Adaptation during Deployment" paper.

Self-Supervised Policy Adaptation during Deployment PyTorch implementation of PAD and evaluation benchmarks from Self-Supervised Policy Adaptation dur

Nicklas Hansen 101 Nov 01, 2022
A transformer model to predict pathogenic mutations

MutFormer MutFormer is an application of the BERT (Bidirectional Encoder Representations from Transformers) NLP (Natural Language Processing) model wi

Wang Genomics Lab 2 Nov 29, 2022
Contrastive Learning Inverts the Data Generating Process

Official code to reproduce the results and data presented in the paper Contrastive Learning Inverts the Data Generating Process.

71 Nov 25, 2022
Credit fraud detection in Python using a Jupyter Notebook

Credit-Fraud-Detection - Credit fraud detection in Python using a Jupyter Notebook , using three classification models (Random Forest, Gaussian Naive Bayes, Logistic Regression) from the sklearn libr

Ali Akram 4 Dec 28, 2021
Refactoring dalle-pytorch and taming-transformers for TPU VM

Text-to-Image Translation (DALL-E) for TPU in Pytorch Refactoring Taming Transformers and DALLE-pytorch for TPU VM with Pytorch Lightning Requirements

Kim, Taehoon 61 Nov 07, 2022
🍅🍅🍅YOLOv5-Lite: lighter, faster and easier to deploy. Evolved from yolov5 and the size of model is only 1.7M (int8) and 3.3M (fp16). It can reach 10+ FPS on the Raspberry Pi 4B when the input size is 320×320~

YOLOv5-Lite:lighter, faster and easier to deploy Perform a series of ablation experiments on yolov5 to make it lighter (smaller Flops, lower memory, a

pogg 1.5k Jan 05, 2023
Weak-supervised Visual Geo-localization via Attention-based Knowledge Distillation

Weak-supervised Visual Geo-localization via Attention-based Knowledge Distillation Introduction WAKD is a PyTorch implementation for our ICPR-2022 pap

2 Oct 20, 2022
The repo of the preprinting paper "Labels Are Not Perfect: Inferring Spatial Uncertainty in Object Detection"

Inferring Spatial Uncertainty in Object Detection A teaser version of the code for the paper Labels Are Not Perfect: Inferring Spatial Uncertainty in

ZINING WANG 21 Mar 03, 2022
SASM - simple crossplatform IDE for NASM, MASM, GAS and FASM assembly languages

SASM (SimpleASM) - простая кроссплатформенная среда разработки для языков ассемблера NASM, MASM, GAS, FASM с подсветкой синтаксиса и отладчиком. В SA

Dmitriy Manushin 5.6k Jan 06, 2023
Pytorch Implementation of "Desigining Network Design Spaces", Radosavovic et al. CVPR 2020.

RegNet Pytorch Implementation of "Desigining Network Design Spaces", Radosavovic et al. CVPR 2020. Paper | Official Implementation RegNet offer a very

Vishal R 2 Feb 11, 2022
Learning Calibrated-Guidance for Object Detection in Aerial Images

Learning Calibrated-Guidance for Object Detection in Aerial Images arxiv We propose a simple yet effective Calibrated-Guidance (CG) scheme to enhance

51 Sep 22, 2022
Hl classification bc - A Network-Based High-Level Data Classification Algorithm Using Betweenness Centrality

A Network-Based High-Level Data Classification Algorithm Using Betweenness Centr

Esteban Vilca 3 Dec 01, 2022
A Graph Neural Network Tool for Recovering Dense Sub-graphs in Random Dense Graphs.

PYGON A Graph Neural Network Tool for Recovering Dense Sub-graphs in Random Dense Graphs. Installation This code requires to install and run the graph

Yoram Louzoun's Lab 0 Jun 25, 2021
audioLIME: Listenable Explanations Using Source Separation

audioLIME This repository contains the Python package audioLIME, a tool for creating listenable explanations for machine learning models in music info

Institute of Computational Perception 27 Dec 01, 2022
A code implementation of AC-GC: Activation Compression with Guaranteed Convergence, in NeurIPS 2021.

Code For AC-GC: Lossy Activation Compression with Guaranteed Convergence This code is intended to be used as a supplemental material for submission to

Dave Evans 2 Nov 01, 2022