RSNA Intracranial Hemorrhage Detection with python

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
Code for Reciprocal Adversarial Learning for Brain Tumor Segmentation: A Solution to BraTS Challenge 2021 Segmentation Task

BRATS 2021 Solution For Segmentation Task This repo contains the supported pytorch code and configuration files to reproduce 3D medical image segmenta

Himashi Amanda Peiris 6 Sep 15, 2022
PyTorch Implementations for DeeplabV3 and PSPNet

Pytorch-segmentation-toolbox DOC Pytorch code for semantic segmentation. This is a minimal code to run PSPnet and Deeplabv3 on Cityscape dataset. Shor

Zilong Huang 746 Dec 15, 2022
Code of the lileonardo team for the 2021 Emotion and Theme Recognition in Music task of MediaEval 2021

Emotion and Theme Recognition in Music The repository contains code for the submission of the lileonardo team to the 2021 Emotion and Theme Recognitio

Vincent Bour 8 Aug 02, 2022
Plugin for Gaffer providing direct acess to asset from PolyHaven.com. Only HDRIs at the moment, Cycles and Arnold supported

GafferHaven Plugin for Gaffer providing direct acess to asset from PolyHaven.com. Only HDRIs are supported at the moment, in Cycles and Arnold lights.

Jakub Vondra 6 Jan 26, 2022
African language Speech Recognition - Speech-to-Text

Swahili-Speech-To-Text Table of Contents Swahili-Speech-To-Text Overview Scenario Approach Project Structure data: models: notebooks: scripts tests: l

2 Jan 05, 2023
A Sign Language detection project using Mediapipe landmark detection and Tensorflow LSTM's

sign-language-detection A Sign Language detection project using Mediapipe landmark detection and Tensorflow LSTM. The project is built for a vocabular

Hashim 4 Feb 06, 2022
NAVER BoostCamp Final Project

CV 14조 final project Super Resolution and Deblur module Inference code & Pretrained weight Repo SwinIR Deblur 실행 방법 streamlit run WebServer/Server_SRD

JiSeong Kim 5 Sep 06, 2022
Contra is a lightweight, production ready Tensorflow alternative for solving time series prediction challenges with AI

Contra AI Engine A lightweight, production ready Tensorflow alternative developed by Styvio styvio.com » How to Use · Report Bug · Request Feature Tab

styvio 14 May 25, 2022
TensorFlow GNN is a library to build Graph Neural Networks on the TensorFlow platform.

TensorFlow GNN This is an early (alpha) release to get community feedback. It's under active development and we may break API compatibility in the fut

889 Dec 30, 2022
LEDNet: A Lightweight Encoder-Decoder Network for Real-time Semantic Segmentation

LEDNet: A Lightweight Encoder-Decoder Network for Real-time Semantic Segmentation Table of Contents: Introduction Project Structure Installation Datas

Yu Wang 492 Dec 02, 2022
Syllabic Quantity Patterns as Rhythmic Features for Latin Authorship Attribution

Syllabic Quantity Patterns as Rhythmic Features for Latin Authorship Attribution Abstract Within the Latin (and ancient Greek) production, it is well

4 Dec 03, 2022
Learning the Beauty in Songs: Neural Singing Voice Beautifier; ACL 2022 (Main conference); Official code

Learning the Beauty in Songs: Neural Singing Voice Beautifier Jinglin Liu, Chengxi Li, Yi Ren, Zhiying Zhu, Zhou Zhao Zhejiang University ACL 2022 Mai

Jinglin Liu 257 Dec 30, 2022
PyTorchVideo is a deeplearning library with a focus on video understanding work

PyTorchVideo is a deeplearning library with a focus on video understanding work. PytorchVideo provides resusable, modular and efficient components needed to accelerate the video understanding researc

Facebook Research 2.7k Jan 07, 2023
Proof-Of-Concept Piano-Drums Music AI Model/Implementation

Rock Piano "When all is one and one is all, that's what it is to be a rock and not to roll." ---Led Zeppelin, "Stairway To Heaven" Proof-Of-Concept Pi

Alex 4 Nov 28, 2021
Image classification for projects and researches

This is a tool to help you quickly solve classification problems including: data analysis, training, report results and model explanation.

Nguyễn Trường Lâu 2 Dec 27, 2021
The project is an official implementation of our paper "3D Human Pose Estimation with Spatial and Temporal Transformers".

3D Human Pose Estimation with Spatial and Temporal Transformers This repo is the official implementation for 3D Human Pose Estimation with Spatial and

Ce Zheng 363 Dec 28, 2022
DiAne is a smart fuzzer for IoT devices

Diane Diane is a fuzzer for IoT devices. Diane works by identifying fuzzing triggers in the IoT companion apps to produce valid yet under-constrained

seclab 28 Jan 04, 2023
Application of the L2HMC algorithm to simulations in lattice QCD.

l2hmc-qcd 📊 Slides Recent talk on Training Topological Samplers for Lattice Gauge Theory from the Machine Learning for High Energy Physics, on and of

Sam Foreman 37 Dec 14, 2022
Pytorch implementation of Each Part Matters: Local Patterns Facilitate Cross-view Geo-localization https://arxiv.org/abs/2008.11646

[TCSVT] Each Part Matters: Local Patterns Facilitate Cross-view Geo-localization LPN [Paper] NEWs Prerequisites Python 3.6 GPU Memory = 8G Numpy 1.

46 Dec 14, 2022
BookMyShowPC - Movie Ticket Reservation App made with Tkinter

Book My Show PC What is this? Movie Ticket Reservation App made with Tkinter. Tk

The Nithin Balaji 3 Dec 09, 2022