tanghuil / deep-learning-for-neuroimage

Deep Learning for Neuroimage

Deep Learning in general

• Textbook

  • Deep Learning Book (Yoshua Bengio) [html]

• Review papers

  • 2013 Representation learning: A review and new perspectives (Yushua Bengio) [pdf]
  • 2014 Deep learning for neuroimaging: a validation study [pdf]
  • 2015 Nature Deep learning (Yann LeCun, Yoshua Bengio, Geoffrey Hinton) [pdf]
  • 2015 Deep learning in neural networks: An overview (J. Schmidhuber) [pdf]
  • 2016 Understanding deep convolutional networks [pdf]
  • 2016 Deep Learning in medical imaging: overview and future promise of an exciting new technique [pdf]
  • 2016.07 Towards an integration of Deep Learning and Neuroscience [pdf]

• Network Models

  • 2012 ImageNet classification with deep convolutional neural networks (A. Krizhevsky et al. Hinton) [pdf]
  • 2015 Fully convolutional networks for semantic segmentation (J. Long et al.) [pdf]
  • 2014 Very deep convolutional networks for large-scale image recognition (K. Simonyan and A. Zisserman) [pdf]
  • 2014 Visualizing and understanding convolutional networks (M. Zeiler and R. Fergus) [pdf]
  • 2015 Fast R-CNN (R. Girshick) [pdf]
  • 2015 Going deeper with convolutions (C. Szegedy et al. Google) [pdf]
  • 2016 Deep residual learning for image recognition (K. He et al. Microsoft) [pdf]

• CNN

  • 2013 Decaf: A deep convolutional activation feature for generic visual recognition (J. Donahue et al.) [pdf]
  • 2014 DeepFace: Closing the Gap to Human-Level Performance in Face Verification (Y. Taigman et al.) [pdf]
  • 2015 Faster R-CNN: Towards Real-Time Object Detection with Region Proposal Networks (S. Ren et al.) [pdf]
  • 2015 Imagenet large scale visual recognition challenge (O. Russakovsky et al.) [pdf]
  • 2015 A Neural Algorithm of Artistic Style

• CNN visuatlization

  • Visualizing and understanding convolutional networks [pdf]
  • mNeuron: a Matlab plugin to visualize neurons from deep models [html]
  • Deep visualization toolbox [code]
  • 3D visualization of a convolutional neural network [demo]
  • Understanding neural networks through deep visualization [html]
  • Convolutional neural networks for visual recognition [html]
  • 2015 Deep Dream: visualizing every layer of GoogLeNet [html]
  • 2016 Visualization of deep convolutional neural networks [pdf]

• Articles

  • 2016.03 Deep learning in medical imaging: the not-so-near future [html]
  • 2016.04 Deep learning used to assist overburdened diagnosticians [html]
  • 2016.08 AI startups in Healthcare [html]
  • 2016.09 Machine Intelligence in Medical Imaging Conference – Report [html]
  • 2016.09 The role of AI in Healthcare [html]
  • 2016.09 DeepMind wants its healthcare AI to charge by results - but first it needs your data [html]
  • 2016.09 Microsoft announces new AI-powered health care initiatives targeting cancer [html]
  • 2016.09 Why deep learning is suddenly changing your life

• Link

  • Awesome - Most Cited Deep Learning Papers
  • Links to Deep Learning Subtopics
  • Book: Fundamental of Deep Learning
  • 머신러닝 튜토리얼

• Topic

  • 2016.09 인공지능이 작곡한 세계 최초의 음악이 공개되다

TensorFlow

• Tutorials

  • TensorFlow 공식 홈페이지
  • TensorFlow Github
  • TensorFlow Playground
  • Deep LEarning Docker Image
  • 텐서플로우 시작하기 (김정주)
  • 텐서플로우 코리아
  • 텐서플로우 튜토리얼 (텐서플로우 코리아)
  • Book: 텐서플로우 첫걸음
  • Lecture: 모두를 위한 딥러닝/머신러닝 강의 TensorFlow (김성)
  • Lecture: TensorFlow 로 시작하는 기계 학습과 딥 러닝 (CodeOnWeb)
  • TensorFlow Tutorial (SNU BILAB)
  • Deep learning/TensorFlow (문동선)
  • TFlearn

• Open-source TensorFlow Implementation

  • Syntax Net, Magenta, Image2Txt
  • https://github.com/TensorFlowKR/awesome_tensorflow_implementations

Deep learning for Neuroinformatics

• 2015 Deep Neural Networks: a new fraomework for modeling biological vision and brain information processing [pdf]

Deep learning for neurological disorder

• 2014 Deep learning for neuroimaging: a validation study [pdf]

Deep learning for Segmentation

• Electron Microscopy
  • 2013 Large-scale automatic reconstruction of neuroanl processes from electron microscopy images [pdf]
  • 2016 Deep learning trends for focal brain pathology segmentation in MRI [pdf]
• MRI
  • 2013 Machine learning in medical imaging [pdf]
  • `D

Deep learning for Brain Tumor Segmentation

• CODE
  • ISBI 2012 brain EM image segmentation [github]
  • Efficient multi-scale 3D convolution neural network for brain lesion segmentation [github]
• MRI
  • 2012 A comparative study of MRI data using various Machine Learning and pattern recognition algorithms to Detect Brain Abnormalities [pdf] = A novel machine learning approach for detecting the Brain Abnormalities from MRI structural images [html]
  • 2014 Survey of intelligent methods for Brain Tumor Detection [pdf]
  • 2015 Brain tumor detection and segmentation in multisequence MRI [pdf]
  • 2015 Automated glioma segmentation in MRI using deep convolutional networks [pdf]
  • 2015 Learning with Difference of Gaussian Features in the 3D Segmentation of Glioblastoma Brain Tumors [pdf]
  • 2015 Multi-scale 3D convolutional neural networks for lesion segmentation in brain MRI [pdf]
  • 2015 MICCAI-BRATS 2015 proceedings [pdf]
    • Structured prediction with convolutional neural networks for multimodal brain tumor segmentation
    • A convolutional neural network approach to brain tumor segmentation
    • Multimodal brain tumor segmentation (BRATS) using Sparse Coding and 2-layer Neural Network
    • Deep convolutional neural networks for the segmentation of gliomas in multi-sequence MRI
    • Brain tumor segmentation with Deep Learning
    • Multi-modal brain tumor segmentation using Stacked Denoising Autoencoders
  • 2015 Brain tumor detection and classification using deep learning classifier on MRI images [html]
  • 2015 Detection and segmentation of brain metastases with deep convolutional networks [pdf]
  • 2015 Deep Feature Learning with discrimination mechanism for brain tumor segmentation and diagnosis [pdf]
  • 2015 Plos One Automated glioblastoma segmentation based on a multiparametric structured unsupervised classification [pdf]
  • 2015 CVPR Deep neural networks for anatomical brain segmentation [pdf]
  • 2016 Brain Tumor Segmentation Using Convolutional Neural Networks in MRI Images [pdf]
  • 2016 Stanford Report A new algorithm for fully automatic brain tumor segmentation with 3D convolutional Neural Networks [pdf]
  • 2016 On image segmentation methods applied to glioblastoma: state of art and new trends [pdf]
  • 2016 Efficient multi-scale 3D CNN with fully connected CRF for accurate brain lesion segmentation [pdf]
• Pathology
  • 2012 Deep Neural Networks segment neuronal membranes in electron Microscopy images [pdf]

Deep learning for Brain Tumor Grading

• MRI
  • 2015 IEEE EMBS Brain tumor grading based on neural networks and convolutional neural netsworks [pdf]
  • 2016 Comput Math Methods Med Multiscale CNNs for brain tumor segmentation and diagnosis [pdf]
• PET
  • 2016 Convolutional neural network can help differentiate FDG PET images of brain tumor between glioblastoma and primary central nervous system lymphoma [html
• Brain pathology images
  • 2015 Automated grading of gliomas using deep learning in digital pathology images: a modular approach with ensemble of convolutional neural networks [pdf]
• Prostate/chest pathology images
  • 2016 Nature Sci.Rep. Deep learning as a tool for increased accuracy and efficiency of histopathological diagnosis [pdf]
  • 2015 Deep learning with non-medical training used for chest pathology identification [pdf]

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