RSNA Intracranial Hemorrhage Detection with python

Related tags

Deep LearningIntracranial-Hemorrhage-Detection
Overview

RSNA Intracranial Hemorrhage Detection

This is the source code for the first place solution to the RSNA2019 Intracranial Hemorrhage Detection Challenge.

Solution write up: Link.

Solutuoin Overview

image

Dependencies

  • opencv-python==3.4.2
  • scikit-image==0.14.0
  • scikit-learn==0.19.1
  • scipy==1.1.0
  • torch==1.1.0
  • torchvision==0.2.1

CODE

  • 2DNet
  • 3DNet
  • SequenceModel

2D CNN Classifier

Pretrained models

Preprocessing

image

Prepare csv file:

download data.zip: https://drive.google.com/open?id=1buISR_b3HQDU4KeNc_DmvKTYJ1gvj5-3

  1. convert dcm to png
python3 prepare_data.py -dcm_path stage_1_train_images -png_path train_png
python3 prepare_data.py -dcm_path stage_1_test_images -png_path train_png
python3 prepare_data.py -dcm_path stage_2_test_images -png_path test_png
  1. train
python3 train_model.py -backbone DenseNet121_change_avg -img_size 256 -tbs 256 -vbs 128 -save_path DenseNet121_change_avg_256
python3 train_model.py -backbone DenseNet169_change_avg -img_size 256 -tbs 256 -vbs 128 -save_path DenseNet169_change_avg_256
python3 train_model.py -backbone se_resnext101_32x4d -img_size 256 -tbs 80 -vbs 40 -save_path se_resnext101_32x4d_256
  1. predict
python3 predict.py -backbone DenseNet121_change_avg -img_size 256 -tbs 4 -vbs 4 -spth DenseNet121_change_avg_256
python3 predict.py -backbone DenseNet169_change_avg -img_size 256 -tbs 4 -vbs 4 -spth DenseNet169_change_avg_256
python3 predict.py -backbone se_resnext101_32x4d -img_size 256 -tbs 4 -vbs 4 -spth se_resnext101_32x4d_256

After single models training, the oof files will be saved in ./SingleModelOutput(three folders for three pipelines).

After training the sequence model, the final submission will be ./FinalSubmission/final_version/submission_tta.csv

Sequence Models

Sequence Model 1

image

Sequence Model 2

image

Path Setup

Set data path in ./setting.py

download

download [csv.zip]

download [feature samples]

Sequence Model Training

CUDA_VISIBLE_DEVICES=0 python main.py

The final submissions are in the folder ../FinalSubmission/version2/submission_tta.csv

Final Submission

Private Leaderboard:

  • 0.04383

Reference

If you find our work useful in your research or if you use parts of this code please consider citing our paper:

  title={A deep learning algorithm for automatic detection and classification of acute intracranial hemorrhages in head CT scans},
  author={Wang, Xiyue and Shen, Tao and Yang, Sen and Lan, Jun and Xu, Yanming and Wang, Minghui and Zhang, Jing and Han, Xiao},
  journal={NeuroImage: Clinical},
  volume={32},
  pages={102785},
  year={2021},
  publisher={Elsevier}
}

TODO

  • Pre-trained models
  • 2DCNN + SeqModel end-to-end training
  • 3DCNN training
Owner
GitHub Repository
Lung Pattern Classification for Interstitial Lung Diseases Using a Deep Convolutional Neural Network

ild-cnn This is supplementary material for the manuscript: "Lung Pattern Classification for Interstitial Lung Diseases Using a Deep Convolutional Neur

22 Nov 05, 2022
A pytorch implementation of Detectron. Both training from scratch and inferring directly from pretrained Detectron weights are available.

Use this instead: https://github.com/facebookresearch/maskrcnn-benchmark A Pytorch Implementation of Detectron Example output of e2e_mask_rcnn-R-101-F

Roy 2.8k Dec 29, 2022
Scaling Vision with Sparse Mixture of Experts

Scaling Vision with Sparse Mixture of Experts This repository contains the code for training and fine-tuning Sparse MoE models for vision (V-MoE) on I

Google Research 290 Dec 25, 2022
Learning embeddings for classification, retrieval and ranking.

StarSpace StarSpace is a general-purpose neural model for efficient learning of entity embeddings for solving a wide variety of problems: Learning wor

Facebook Research 3.8k Dec 22, 2022
MediaPipe is a an open-source framework from Google for building multimodal

MediaPipe is a an open-source framework from Google for building multimodal (eg. video, audio, any time series data), cross platform (i.e Android, iOS, web, edge devices) applied ML pipelines. It is

Bhavishya Pandit 3 Sep 30, 2022
Implementation of "Glancing Transformer for Non-Autoregressive Neural Machine Translation"

GLAT Implementation for the ACL2021 paper "Glancing Transformer for Non-Autoregressive Neural Machine Translation" Requirements Python = 3.7 Pytorch

117 Jan 09, 2023
fcn by tensorflow

Update An example on how to integrate this code into your own semantic segmentation pipeline can be found in my KittiSeg project repository. tensorflo

9 May 22, 2022
A tensorflow model that predicts if the image is of a cat or of a dog.

Quick intro Hello and thank you for your interest in my project! This is the backend part of a two-repo application. The other part can be found here

Tudor Matei 0 Mar 08, 2022
[ICML 2021] Break-It-Fix-It: Learning to Repair Programs from Unlabeled Data

Break-It-Fix-It: Learning to Repair Programs from Unlabeled Data This repo provides the source code & data of our paper: Break-It-Fix-It: Unsupervised

Michihiro Yasunaga 86 Nov 30, 2022
Supervised forecasting of sequential data in Python.

Supervised forecasting of sequential data in Python. Intro Supervised forecasting is the machine learning task of making predictions for sequential da

The Alan Turing Institute 54 Nov 15, 2022
Pytorch implementations of popular off-policy multi-agent reinforcement learning algorithms, including QMix, VDN, MADDPG, and MATD3.

Off-Policy Multi-Agent Reinforcement Learning (MARL) Algorithms This repository contains implementations of various off-policy multi-agent reinforceme

183 Dec 28, 2022
Code for Paper: Self-supervised Learning of Motion Capture

Self-supervised Learning of Motion Capture This is code for the paper: Hsiao-Yu Fish Tung, Hsiao-Wei Tung, Ersin Yumer, Katerina Fragkiadaki, Self-sup

Hsiao-Yu Fish Tung 87 Jul 25, 2022
Ankou: Guiding Grey-box Fuzzing towards Combinatorial Difference

Ankou Ankou is a source-based grey-box fuzzer. It intends to use a more rich fitness function by going beyond simple branch coverage and considering t

SoftSec Lab 54 Dec 24, 2022
Not Suitable for Work (NSFW) classification using deep neural network Caffe models.

Open nsfw model This repo contains code for running Not Suitable for Work (NSFW) classification deep neural network Caffe models. Please refer our blo

Yahoo 5.6k Jan 05, 2023
Dynamic Neural Representational Decoders for High-Resolution Semantic Segmentation

Dynamic Neural Representational Decoders for High-Resolution Semantic Segmentation Requirements This repository needs mmsegmentation Training To train

20 May 28, 2022
A Simple Example for Imitation Learning with Dataset Aggregation (DAGGER) on Torcs Env

Imitation Learning with Dataset Aggregation (DAGGER) on Torcs Env This repository implements a simple algorithm for imitation learning: DAGGER. In thi

Hao 66 Nov 23, 2022
PuppetGAN - Cross-Domain Feature Disentanglement and Manipulation just got way better! 🚀

Better Cross-Domain Feature Disentanglement and Manipulation with Improved PuppetGAN Quite cool... Right? Introduction This repo contains a TensorFlow

Giorgos Karantonis 5 Aug 25, 2022
Fader Networks: Manipulating Images by Sliding Attributes - NIPS 2017

FaderNetworks PyTorch implementation of Fader Networks (NIPS 2017). Fader Networks can generate different realistic versions of images by modifying at

Facebook Research 753 Dec 23, 2022
A Python library for common tasks on 3D point clouds

Point Cloud Utils (pcu) - A Python library for common tasks on 3D point clouds Point Cloud Utils (pcu) is a utility library providing the following fu

Francis Williams 622 Dec 27, 2022
The tool under this branch fork can be used to crack devices above A12 and up to A15. After cracking, you can also use SSH channel strong opening tool to open SSH channel and activate it with Demo or Shell script. The file can be extracted from my Github homepage, and the SSH channel opening tool can be extracted from Dr238 account.

Welcome to C0xy-A12-A15-Attack-Tool The tool under this branch fork can be used to crack devices above A12 and up to A15. After cracking, you can also

13 Dec 23, 2022