All histopathology models are trained by Caffe version 1.0. Caffe is developed by Berkeley AI Research (BAIR)/The Berkeley Vision and Learning Center (BVLC) and community contributors and released under the BSD 2-Clause license. The source codes of this software dependency are included under the caffe directory.

Due to the file size limit of GitHub, we uploaded our convolutional neural networks models at the links below:

AlexNet-based Model: https://www.dropbox.com/s/cvom9wced4ltuhs/alexnet.caffemodel?dl=0

GoogLeNet-based Model: https://www.dropbox.com/s/l8gjebhvgpyre13/googlenet.caffemodel?dl=0

VGGNet-based Model: https://www.dropbox.com/s/w7zmkjsmpxxvikd/vgg.caffemodel?dl=0

AlexNet-based Model: https://www.dropbox.com/s/nou416u1b0gw3bg/alexnet.caffemodel?dl=0

GoogLeNet-based Model: https://www.dropbox.com/s/5v56ikpy6js29oc/googlenet.caffemodel?dl=0

VGGNet-based Model: https://www.dropbox.com/s/e9b4gnjksrjnt5o/vgg.caffemodel?dl=0

VGGNet-based Model: https://www.dropbox.com/s/7i9siypn1asp572/VggModel.h5?dl=0

The models for the differential expression analyses and predictive analyses are under omics_analyses/.

sudo apt-get install libprotobuf-dev libleveldb-dev libsnappy-dev libopencv-dev libhdf5-serial-dev protobuf-compiler
sudo apt-get install --no-install-recommends libboost-all-dev

sudo apt build-dep caffe-cpu        # dependencies for CPU-only version
sudo apt build-dep caffe-cuda       # dependencies for CUDA version

make all
make test
make runtest

caffe test -model model.prototxt -weights model.caffemodel

Caffe Installation: http://caffe.berkeleyvision.org/installation.html

Caffe Tutorial: http://caffe.berkeleyvision.org/tutorial/

Caffe Command Line Interfaces: https://caffe.berkeleyvision.org/tutorial/interfaces.html