Kaggle Ultrasound Nerve Segmentation competition [Keras]

Overview

Ultrasound nerve segmentation using Keras (1.0.7)

Kaggle Ultrasound Nerve Segmentation competition [Keras]

#Install (Ubuntu {14,16}, GPU)

cuDNN required.

###Theano

In ~/.theanorc

[global]
device = gpu0
[dnn]
enabled = True

###Keras

  • sudo apt-get install libhdf5-dev
  • sudo pip install h5py
  • sudo pip install pydot
  • sudo pip install nose_parameterized
  • sudo pip install keras

In ~/.keras/keras.json (it's very important, the project was running on theano backend, and some issues are possible in case of TensorFlow)

{
    "image_dim_ordering": "th",
    "epsilon": 1e-07,
    "floatx": "float32",
    "backend": "theano"
}

###Python deps

  • sudo apt-get install python-opencv
  • sudo apt-get install python-sklearn

#Prepare

Place train and test data into '../train' and '../test' folders accordingly.

mkdir np_data
python data.py

#Training

Single model training.

python train.py

Results will be generatated in "res/" folder. res/unet.hdf5 - best model

Generate submission:

python submission.py

Generate predection with a model in res/unet.hdf5

python current.py

#Model

Motivation's explained in my internal pres (slides: http://www.slideshare.net/Eduardyantov/ultrasound-segmentation-kaggle-review)

I used U-net like architecture (http://arxiv.org/abs/1505.04597). Main differences:

  • inception blocks instead of VGG like
  • Conv with stride instead of MaxPooling
  • Dropout, p=0.5
  • skip connections from encoder to decoder layers with residual blocks
  • BatchNorm everywhere
  • 2 heads training: auxiliary branch for scoring nerve presence (in the middle of the network), one branch for segmentation
  • ELU activation
  • sigmoid activation in output
  • Adam optimizer, without weight regularization in layers
  • Dice coeff loss, average per batch, without smoothing
  • output layers - sigmoid activation
  • batch_size=64,128 (for GeForce 1080 and Titan X respectively)

Augmentation:

  • flip x,y
  • random zoom
  • random channel shift
  • elastic transormation didn't help in this configuration

Augmentation generator (generate augmented data on the fly for each epoch) didn't improve the score. For prediction augmented images were used.

Validation:

For some reason validation split by patient (which is proper in this competition) didn't work for me, probably due to bug in the code. So I used random split.

Final prediction uses probability of a nerve presence: p_nerve = (p_score + p_segment)/2, where p_segment based on number of output pixels in the mask.

#Results and technical aspects

  • On GPU Titan X an epoch took about 6 minutes. Training early stops at 15-30 epochs.
  • For batch_size=64 6Gb GPU memory is required.
  • Best single model achieved 0.694 LB score.
  • An ensemble of 6 different k-fold ensembles (k=5,6,8) scored 0.70399

#Credits This code was originally based on https://github.com/jocicmarko/ultrasound-nerve-segmentation/

Automated image registration. Registrationimation was too much of a mouthful.

alignimation Automated image registration. Registrationimation was too much of a mouthful. This repo contains the code used for my blog post Alignimat

Ethan Rosenthal 9 Oct 13, 2022
Management Dashboard for Torchserve

Torchserve Dashboard Torchserve Dashboard using Streamlit Related blog post Usage Additional Requirement: torchserve (recommended:v0.5.2) Simply run:

Ceyda Cinarel 103 Dec 10, 2022
A curated list of neural network pruning resources.

A curated list of neural network pruning and related resources. Inspired by awesome-deep-vision, awesome-adversarial-machine-learning, awesome-deep-learning-papers and Awesome-NAS.

Yang He 1.7k Jan 09, 2023
ViSER: Video-Specific Surface Embeddings for Articulated 3D Shape Reconstruction

ViSER: Video-Specific Surface Embeddings for Articulated 3D Shape Reconstruction. NeurIPS 2021.

Gengshan Yang 59 Nov 25, 2022
Activity tragle - Google is tracking everything, we just look at it

activity_tragle Google is tracking everything, we just look at it here. You need

BERNARD Guillaume 1 Feb 15, 2022
A commany has recently introduced a new type of bidding, the average bidding, as an alternative to the bid given to the current maximum bidding

Business Problem A commany has recently introduced a new type of bidding, the average bidding, as an alternative to the bid given to the current maxim

Kübra Bilinmiş 1 Jan 15, 2022
Implementation of Ag-Grid component for Streamlit

streamlit-aggrid AgGrid is an awsome grid for web frontend. More information in https://www.ag-grid.com/. Consider purchasing a license from Ag-Grid i

Pablo Fonseca 556 Dec 31, 2022
Weakly Supervised Learning of Instance Segmentation with Inter-pixel Relations, CVPR 2019 (Oral)

Weakly Supervised Learning of Instance Segmentation with Inter-pixel Relations The code of: Weakly Supervised Learning of Instance Segmentation with I

Jiwoon Ahn 472 Dec 29, 2022
A PyTorch implementation of "TokenLearner: What Can 8 Learned Tokens Do for Images and Videos?"

TokenLearner: What Can 8 Learned Tokens Do for Images and Videos? Source: Improving Vision Transformer Efficiency and Accuracy by Learning to Tokenize

Caiyong Wang 14 Sep 20, 2022
3DV 2021: Synergy between 3DMM and 3D Landmarks for Accurate 3D Facial Geometry

SynergyNet 3DV 2021: Synergy between 3DMM and 3D Landmarks for Accurate 3D Facial Geometry Cho-Ying Wu, Qiangeng Xu, Ulrich Neumann, CGIT Lab at Unive

Cho-Ying Wu 239 Jan 06, 2023
A programming language written with python

Kaoft A programming language written with python How to use A simple Hello World: c="Hello World" c Output: "Hello World" Operators: a=12

1 Jan 24, 2022
PyTorch implementation of Train Short, Test Long: Attention with Linear Biases Enables Input Length Extrapolation.

ALiBi PyTorch implementation of Train Short, Test Long: Attention with Linear Biases Enables Input Length Extrapolation. Quickstart Clone this reposit

Jake Tae 4 Jul 27, 2022
This is RFA-Toolbox, a simple and easy-to-use library that allows you to optimize your neural network architectures using receptive field analysis (RFA) and create graph visualizations of your architecture.

ReceptiveFieldAnalysisToolbox This is RFA-Toolbox, a simple and easy-to-use library that allows you to optimize your neural network architectures usin

84 Nov 23, 2022
Fast, general, and tested differentiable structured prediction in PyTorch

Fast, general, and tested differentiable structured prediction in PyTorch

HNLP 1.1k Dec 16, 2022
PolyphonicFormer: Unified Query Learning for Depth-aware Video Panoptic Segmentation

PolyphonicFormer: Unified Query Learning for Depth-aware Video Panoptic Segmentation Winner method of the ICCV-2021 SemKITTI-DVPS Challenge. [arxiv] [

Yuan Haobo 38 Jan 03, 2023
SNE-RoadSeg in PyTorch, ECCV 2020

SNE-RoadSeg Introduction This is the official PyTorch implementation of SNE-RoadSeg: Incorporating Surface Normal Information into Semantic Segmentati

242 Dec 20, 2022
Statistical-Rethinking-with-Python-and-PyMC3 - Python/PyMC3 port of the examples in " Statistical Rethinking A Bayesian Course with Examples in R and Stan" by Richard McElreath

Statistical Rethinking with Python and PyMC3 This repository has been deprecated in favour of this one, please check that repository for updates, for

Osvaldo Martin 786 Dec 29, 2022
RINDNet: Edge Detection for Discontinuity in Reflectance, Illumination, Normal and Depth, in ICCV 2021 (oral)

RINDNet RINDNet: Edge Detection for Discontinuity in Reflectance, Illumination, Normal and Depth Mengyang Pu, Yaping Huang, Qingji Guan and Haibin Lin

Mengyang Pu 75 Dec 15, 2022
Rainbow DQN implementation that outperforms the paper's results on 40% of games using 20x less data 🌈

Rainbow 🌈 An implementation of Rainbow DQN which reaches a median HNS of 205.7 after only 10M frames (the original Rainbow from Hessel et al. 2017 re

Dominik Schmidt 31 Dec 21, 2022
A python script to dump all the challenges locally of a CTFd-based Capture the Flag.

A python script to dump all the challenges locally of a CTFd-based Capture the Flag. Features Connects and logins to a remote CTFd instance. Dumps all

Podalirius 77 Dec 07, 2022