farabio 0.0.2

farabio - Deep learning for biomedical imaging

farabio

• What's New
• Introduction
• Features
• Biodatasets
• Models
• Getting Started (Installation)
• Credits
• Licenses
• Links

What's New

August 18, 2021

Release of farabio==0.0.2

April 21, 2021

This work is presented at PyTorch Ecosystem day. Poster is here.

April 2, 2021

Release of farabio==0.0.1

March 3, 2021

This work is selected for PyTorch Ecosystem Day.

Introduction

farabio is a minimal PyTorch toolkit for out-of-the-box deep learning support in biomedical imaging. For further information, see Wikis and Docs.

Features

• Biomedical datasets
• Common DL models
• Flexible trainers (*in progress)

Biodatasets

• Chest X-Ray Images (Pneumonia):
  https://www.kaggle.com/paultimothymooney/chest-xray-pneumonia
• 2018 Data Science Bowl:
  https://www.kaggle.com/c/data-science-bowl-2018/overview
• Histopathologic Cancer Detection:
  https://www.kaggle.com/c/histopathologic-cancer-detection/overview
• RANZCR CLiP - Catheter and Line Position Challenge:
  https://www.kaggle.com/c/ranzcr-clip-catheter-line-classification/overview
• APTOS 2019 Blindness Detection:
  https://www.kaggle.com/c/aptos2019-blindness-detection/overview

Models

• AlexNet - https://papers.nips.cc/paper/2012/file/c399862d3b9d6b76c8436e924a68c45b-Paper.pdf
• GoogLeNet - https://arxiv.org/pdf/1409.4842.pdf
• MobileNetV2 - https://arxiv.org/pdf/1801.04381.pdf
• MobileNetV3 - https://arxiv.org/pdf/1905.02244.pdf
• ResNet - https://arxiv.org/pdf/1512.03385.pdf
• ShuffleNetV2 - https://arxiv.org/pdf/1807.11164.pdf
• SqueezeNet - https://arxiv.org/pdf/1602.07360.pdf
• VGG - https://arxiv.org/pdf/1409.1556.pdf

Getting started (Installation)

1. Activate conda environment:

$ conda create -n myenv python=3.8
$ conda activate myenv

2. Install farabio:

A. With pip:

$ pip install farabio -f https://download.pytorch.org/whl/torch_stable.html

B. Setup from source:

$ git clone https://github.com/tuttelikz/farabio.git && cd farabio
$ pip install . -f https://download.pytorch.org/whl/torch_stable.html

Credits

If you like this repository, please click on Star.

Licenses

This work is licensed Apache 2.0.

Links

• API documentations: https://farabio.readthedocs.io
• Code: https://github.com/tuttelikz/farabio
• Issue tracker: https://github.com/tuttelikz/farabio/issues
• PyPI package: https://pypi.org/project/farabio/
• Wiki: https://github.com/tuttelikz/farabio/wiki