Set of models for classifcation of 3D volumes

Overview

Classification models 3D Zoo - Keras and TF.Keras

This repository contains 3D variants of popular CNN models for classification like ResNets, DenseNets, VGG, etc. It also contains weights obtained by converting ImageNet weights from the same 2D models.

This repository is based on great classification_models repo by @qubvel

Architectures:

Installation

pip install classification-models-3D

Examples

Loading model with imagenet weights:
# for keras
from classification_models_3D.keras import Classifiers

# for tensorflow.keras
# from classification_models_3D.tfkeras import Classifiers

ResNet18, preprocess_input = Classifiers.get('resnet18')
model = ResNet18(input_shape=(128, 128, 128, 3), weights='imagenet')

All possible nets for Classifiers.get() method: 'resnet18, 'resnet34', 'resnet50', 'resnet101', 'resnet152', 'seresnet18', 'seresnet34', 'seresnet50', 'seresnet101', 'seresnet152', 'seresnext50', 'seresnext101', 'senet154', 'resnext50', 'resnext101', 'vgg16', 'vgg19', 'densenet121', 'densenet169', 'densenet201', 'inceptionresnetv2', 'inceptionv3', 'mobilenet', 'mobilenetv2'

Convert imagenet weights (2D -> 3D)

Code to convert 2D imagenet weights to 3D variant is available here: convert_imagenet_weights_to_3D_models.py. Weights were obtained with TF2, but works OK with Keras + TF1 as well.

How to choose input shape

If initial 2D model had shape (512, 512, 3) then you can use shape (D, H, W, 3) where D * H * W ~= 512*512, so something like (64, 64, 64, 3) will be ok.

Training with single NVIDIA 1080Ti (11 GB) worked with:

  • DenseNet121, DenseNet169 and ResNet50 with shape (96, 128, 128, 3) and batch size 6
  • DenseNet201 with shape (96, 128, 128, 3) and batch size 5
  • ResNet18 with shape (128, 160, 160, 3) and batch size 6

Related repositories

Unresolved problems

  • There is no DepthwiseConv3D layer in keras, so repo used custom layer from this repo by @alexandrosstergiou which can be slower than native implementation.
  • There is no imagenet weights for 'inceptionresnetv2' and 'inceptionv3'.

Description

This code was used to get 1st place in DrivenData: Advance Alzheimer’s Research with Stall Catchers competition.

More details on ArXiv: https://arxiv.org/abs/2104.01687

Citation

If you find this code useful, please cite it as:

@InProceedings{RSolovyev_2021_stalled,
  author = {Solovyev, Roman and Kalinin, Alexandr A. and Gabruseva, Tatiana},
  title = {3D Convolutional Neural Networks for Stalled Brain Capillary Detection},
  booktitle = {Arxiv: 2104.01687},
  month = {April},
  year = {2021}
}
Comments
  • Update __init__.py

    Update __init__.py

    Using keras 2.9.0, import keras_applications as ka gives the following error:- ModuleNotFoundError: No module named 'keras_applications'

    Instead using from keras import applications as ka works!

    opened by msmuskan 0
  • Pushing current version to PyPI

    Pushing current version to PyPI

    Hello @ZFTurbo,

    if you have time, please push the current updated status (with ConvNeXt) of this repo to PyPI. :)

    Thanks again for the great work and your time!

    Cheers, Dominik

    opened by muellerdo 0
  • Grad cam issue

    Grad cam issue

    Hello ,

    base_model, preprocess_input = Classifiers.get('seresnext50') model = base_model(input_shape=(512, 512, 20, 1 ), weights=None , include_top = False ) x = Flatten()(model.output) x = Dense(1024, activation= 'sigmoid')(x) x = Dense(2, activation= 'sigmoid')(x)

    Trying to train a model , the accuracy is everything resides upto expectation, but the gradcam are quite off from the region of the focus - how the accuracy is good but the grad cam is off the focus of targeted area .

    Using the layer - 'activation-161' as output ref - https://github.com/fitushar/3D-Grad-CAM/blob/master/3DGrad-CAM.ipynb for the gradcam generation code , the results are always at the border of the image.

    opened by ntirupathirao18 0
  • ImportError: cannot import name 'VersionAwareLayers' from 'keras.layers'

    ImportError: cannot import name 'VersionAwareLayers' from 'keras.layers'

    Thank you for the great work.

    I am experiencing the following error over and over, even though I created a brand new tensorflow environment and installed all the necessary libraries in it. Could you please have a look on it and guide me how do I solve this problem? Thank you.

    ImportError: Unable to import 'VersionAwareLayers' from 'keras.layers' (/home/ubuntu/anaconda3/envs/cm_3d/lib/python3.7/site-packages/keras/layers/init.py)

    opened by nasir3843 2
  • 3D DenseNet

    3D DenseNet

    Hello and sorry to bother you beforehand,

    I am currently conducting my master thesis project and I am trying to implement a 3D DenseNet-121 with knee MRIs as input data. While I was searching on how to implement a 3D version of the DenseNet I came across your repository and tried to change it for my application.

    I have some issues regarding my try and I didn't know where else to ask about it and again I am sorry if I am completely of topic asking them here.

    Firstly, my input shapes are (250,320,18,1) and when I give them as input to the 3D DenseNet I developed with stride_size=1 for my Conv_block and pooling_size=(2,2,2) and strides=(2,2,1) for my AveragePooling3D layer in the transition block, the model is constructed properly with the specific input_size, while when I am trying to load a DenseNet121 from classification_models_3d.tfkeras classifiers I am unable to construct it with input_shape(250,320,18,1), stride_size=1 and kernel_size=2. It gives as an error "Negative dimension size... for node pool4_pool/AvgPool3D". Is there a way to specifically define the strides for AvgPool3D layer in the transition block?

    And secondly, I was thinking to load the 3D weights to my 3D DenseNet 121, is there a folder in your repository where I can find your pre-trained weights on imagenet??

    Again thank you for having this repository publicly available and sorry if I am completely of topic asking such things here.

    I look forward for you answer, Kind regards, Anastasis

    opened by alexopoulosanastasis 4
  • What are the limitations on Inceptionv3 input shape?

    What are the limitations on Inceptionv3 input shape?

    I seem to always get this error when I try to create InceptionV3 model no matter what input_shape. What are the limitations on input shape there?

    InvalidArgumentError: Negative dimension size caused by subtracting 3 from 2 for '{{node conv3d_314/Conv3D}} = 
    Conv3D[T=DT_FLOAT, data_format="NDHWC", dilations=[1, 1, 1, 1, 1], padding="VALID", strides=[1, 2, 2, 2, 1]](Placeholder, 
    conv3d_314/Conv3D/ReadVariableOp)' with input shapes: [?,2,17,17,192], [3,3,3,192,320].
    
    opened by mazatov 0
Releases(v1.0.4)
Deep GPs built on top of TensorFlow/Keras and GPflow

GPflux Documentation | Tutorials | API reference | Slack What does GPflux do? GPflux is a toolbox dedicated to Deep Gaussian processes (DGP), the hier

Secondmind Labs 107 Nov 02, 2022
PERIN is Permutation-Invariant Semantic Parser developed for MRP 2020

PERIN: Permutation-invariant Semantic Parsing David Samuel & Milan Straka Charles University Faculty of Mathematics and Physics Institute of Formal an

ÚFAL 40 Jan 04, 2023
Streaming Anomaly Detection Framework in Python (Outlier Detection for Streaming Data)

Python Streaming Anomaly Detection (PySAD) PySAD is an open-source python framework for anomaly detection on streaming multivariate data. Documentatio

Selim Firat Yilmaz 181 Dec 18, 2022
Revisiting Temporal Alignment for Video Restoration

Revisiting Temporal Alignment for Video Restoration [arXiv] Kun Zhou, Wenbo Li, Liying Lu, Xiaoguang Han, Jiangbo Lu We provide our results at Google

52 Dec 25, 2022
Example scripts for the detection of lanes using the ultra fast lane detection model in Tensorflow Lite.

TFlite Ultra Fast Lane Detection Inference Example scripts for the detection of lanes using the ultra fast lane detection model in Tensorflow Lite. So

Ibai Gorordo 12 Aug 27, 2022
Official repository for: Continuous Control With Ensemble DeepDeterministic Policy Gradients

Continuous Control With Ensemble Deep Deterministic Policy Gradients This repository is the official implementation of Continuous Control With Ensembl

4 Dec 06, 2021
This repository contains the code for the paper ``Identifiable VAEs via Sparse Decoding''.

Sparse VAE This repository contains the code for the paper ``Identifiable VAEs via Sparse Decoding''. Data Sources The datasets used in this paper wer

Gemma Moran 17 Dec 12, 2022
Deep Learning with PyTorch made easy 🚀 !

Deep Learning with PyTorch made easy 🚀 ! Carefree? carefree-learn aims to provide CAREFREE usages for both users and developers. It also provides a c

381 Dec 22, 2022
This implements the learning and inference/proposal algorithm described in "Learning to Propose Objects, Krähenbühl and Koltun"

Learning to propose objects This implements the learning and inference/proposal algorithm described in "Learning to Propose Objects, Krähenbühl and Ko

Philipp Krähenbühl 90 Sep 10, 2021
Plaything for Autistic Children (demo for PaddlePaddle/Wechaty/Mixlab project)

星星的孩子 - 一款为孤独症孩子设计的聊天机器人游戏 孤独症儿童是目前常常被忽视的一类群体。他们有着类似性格内向的特征,实际却受着广泛性发育障碍的折磨。 项目背景 这类儿童在与人交往时存在着沟通障碍,其特点表现在: 社交交流差,互动障碍明显 认知能力有限,被动认知 兴趣狭窄,重复刻板,缺乏变化和想象

Tianyi Pan 35 Nov 24, 2022
The official implementation of the Interspeech 2021 paper WSRGlow: A Glow-based Waveform Generative Model for Audio Super-Resolution.

WSRGlow The official implementation of the Interspeech 2021 paper WSRGlow: A Glow-based Waveform Generative Model for Audio Super-Resolution. Audio sa

Kexun Zhang 96 Jan 03, 2023
Easy-to-use library to boost AI inference leveraging state-of-the-art optimization techniques.

NEW RELEASE How Nebullvm Works • Tutorials • Benchmarks • Installation • Get Started • Optimization Examples Discord | Website | LinkedIn | Twitter Ne

Nebuly 1.7k Dec 31, 2022
Towards Open-World Feature Extrapolation: An Inductive Graph Learning Approach

This repository holds the implementation for paper Towards Open-World Feature Extrapolation: An Inductive Graph Learning Approach Download our preproc

Qitian Wu 42 Dec 27, 2022
This is the code for the paper "Jinkai Zheng, Xinchen Liu, Wu Liu, Lingxiao He, Chenggang Yan, Tao Mei: Gait Recognition in the Wild with Dense 3D Representations and A Benchmark. (CVPR 2022)"

Gait3D-Benchmark This is the code for the paper "Jinkai Zheng, Xinchen Liu, Wu Liu, Lingxiao He, Chenggang Yan, Tao Mei: Gait Recognition in the Wild

82 Jan 04, 2023
[ICCV' 21] "Unsupervised Point Cloud Pre-training via Occlusion Completion"

OcCo: Unsupervised Point Cloud Pre-training via Occlusion Completion This repository is the official implementation of paper: "Unsupervised Point Clou

Hanchen 204 Dec 24, 2022
CV backbones including GhostNet, TinyNet and TNT, developed by Huawei Noah's Ark Lab.

CV Backbones including GhostNet, TinyNet, TNT (Transformer in Transformer) developed by Huawei Noah's Ark Lab. GhostNet Code TinyNet Code TNT Code Pyr

HUAWEI Noah's Ark Lab 3k Jan 08, 2023
PyTorch implementation of NIPS 2017 paper Dynamic Routing Between Capsules

Dynamic Routing Between Capsules - PyTorch implementation PyTorch implementation of NIPS 2017 paper Dynamic Routing Between Capsules from Sara Sabour,

Adam Bielski 475 Dec 24, 2022
PyTorch implementations of algorithms for density estimation

pytorch-flows A PyTorch implementations of Masked Autoregressive Flow and some other invertible transformations from Glow: Generative Flow with Invert

Ilya Kostrikov 546 Dec 05, 2022
Official implementation for paper: A Latent Transformer for Disentangled Face Editing in Images and Videos.

A Latent Transformer for Disentangled Face Editing in Images and Videos Official implementation for paper: A Latent Transformer for Disentangled Face

InterDigital 108 Dec 09, 2022
Repository For Programmers Seeking a platform to show their skills

Programming-Nerds Repository For Programmers Seeking Pull Requests In hacktoberfest ❓ What's Hacktoberfest 2021? Hacktoberfest is the easiest way to g

42 Oct 29, 2022