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©2017 Xanadu Big Data, LLC All Rights Reserved www.xanadubigdata.com
Xanadu Based
Big Data Deep Learning
for Medical Data ...
©2017 Xanadu Big Data, LLC All Rights Reserved
Index for Part I
-Deep Learning for Medical Data Analysis Introduction
-Aut...
©2017 Xanadu Big Data, LLC All Rights Reserved
Index for Part II
-Deep Learning Introduction
-Convolution Process Details
...
©2017 Xanadu Big Data, LLC All Rights Reserved
Index for Part III
-Xanadu Functionality
-Xanadu Commodity Storage System U...
©2017 Xanadu Big Data, LLC All Rights Reserved
Medical Image Classification and Segmentation:
Analysis of X-ray, CT, MRI, ...
©2017 Xanadu Big Data, LLC All Rights Reserved
Dermatologist-level classification of skin cancer with deep
neural networks...
©2017 Xanadu Big Data, LLC All Rights Reserved
Google's Research In Artificial Intelligence Helps In
Preventing Blindness ...
©2017 Xanadu Big Data, LLC All Rights Reserved
Deep Learning for Predicting Glioblastoma Subtypes from MRI
Deep learning c...
©2017 Xanadu Big Data, LLC All Rights Reserved
A Survey on Medical Image Deep Learning Research
source: https://arxiv.org/...
©2017 Xanadu Big Data, LLC All Rights Reserved
Cardiologist-Level Arrhythmia Detection with Convolutional Neural
Networks
...
©2017 Xanadu Big Data, LLC All Rights Reserved
Deep Learning Helps Patient Care Decisions in Intensive Care Unit
Deep lear...
©2017 Xanadu Big Data, LLC All Rights Reserved
Deep Learning Introduction
Convolutional Neural Networks (CNNs): image/vide...
©2017 Xanadu Big Data, LLC All Rights Reserved
Convolution Process Details
input
1 filter
3x3 Kernel 15x15 Kernel
Activati...
©2017 Xanadu Big Data, LLC All Rights Reserved
Deep Learning Use Cases
CNN + RNN
for Real-time Object
Identification
Sourc...
©2017 Xanadu Big Data, LLC All Rights Reserved
Issues with Big Data Deep Learning
Big Data Deep Learning
Volume:
Size of D...
©2017 Xanadu Big Data, LLC All Rights Reserved
Distributed Deep Learning for Medical Big Data Analysis
Issues with medical...
©2017 Xanadu Big Data, LLC All Rights Reserved
Deep learning requires massive amount of training dataset as
accuracy of de...
©2017 Xanadu Big Data, LLC All Rights Reserved
CBIR is a way of searching image database using visual features of an
image...
©2017 Xanadu Big Data, LLC All Rights Reserved
Xanadu enables competitive big data management in the Clouds or
Enterprises...
©2017 Xanadu Big Data, LLC All Rights Reserved
Xanadu Performance BMT
©2017 Xanadu Big Data, LLC All Rights Reserved
Xanadu provides a composable architecture that can be integrated with
other...
©2017 Xanadu Big Data, LLC All Rights Reserved
Xanadu Commodity Storage System Use Case
©2017 Xanadu Big Data, LLC All Rights Reserved
Xanadu Cloud Computing Use Case
©2017 Xanadu Big Data, LLC All Rights Reserved
CNN/RNN architecture in
DeepLearning4J (DL4J)
Distributed deep leaning on
C...
©2017 Xanadu Big Data, LLC All Rights Reserved
Xanadu Medical Data Big Data Archive
Xanadu’s deduplication reduces the act...
©2017 Xanadu Big Data, LLC All Rights Reserved
Xanadu CBIR Demo
©2017 Xanadu Big Data, LLC All Rights Reserved
Thank you
Xanadu Big Data, LLC
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Xanadu Based Big Data Deep Learning for Medical Data Analysis

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Contents

Part I
Deep Learning for Medical Data Analysis Introduction
Automated Skin Cancer Classification
Automated Diabetic Retinopathy Classification
Brain Tumor Research
Alzheime Prediction
A Survey on Medical Image Deep Learning Research
Cardiac Arrhthymia Detection
ICU Patient Care

Part II
Deep Learning Introduction
Convolution Process Details
Issues with Big Data Deep Learning
Distributed Deep Learning for Medical Big Data Analysis
Challenges of Deep Learning for Medical Data Analysis
Content Based Image Retrieval (CBIR)

Part III
Xanadu Functionality
Xanadu Commodity Storage System Use Case
Xanadu Cloud Computing Use Case
Xanadu + Deep Learning + Hadoop + Spark Integration
Xanadu based Big Data Deep Learning System for Medical Data Analysis
Xanadu CBIR Demo

Published in: Healthcare
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Xanadu Based Big Data Deep Learning for Medical Data Analysis

  1. 1. ©2017 Xanadu Big Data, LLC All Rights Reserved www.xanadubigdata.com Xanadu Based Big Data Deep Learning for Medical Data Analysis November 9, 2017 Alex G. Lee (alexglee@xanadubigdata.com)
  2. 2. ©2017 Xanadu Big Data, LLC All Rights Reserved Index for Part I -Deep Learning for Medical Data Analysis Introduction -Automated Skin Cancer Classification -Automated Diabetic Retinopathy Classification -Brain Tumor Research -Alzheime Prediction -A Survey on Medical Image Deep Learning Research -Cardiac Arrhthymia Detection -ICU Patient Care
  3. 3. ©2017 Xanadu Big Data, LLC All Rights Reserved Index for Part II -Deep Learning Introduction -Convolution Process Details -Issues with Big Data Deep Learning -Distributed Deep Learning for Medical Big Data Analysis -Challenges of Deep Learning for Medical Data Analysis -Content Based Image Retrieval (CBIR)
  4. 4. ©2017 Xanadu Big Data, LLC All Rights Reserved Index for Part III -Xanadu Functionality -Xanadu Commodity Storage System Use Case -Xanadu Cloud Computing Use Case -Xanadu + Deep Learning + Hadoop + Spark Integration -Xanadu based Big Data Deep Learning System for Medical Data Analysis -Xanadu CBIR Demo
  5. 5. ©2017 Xanadu Big Data, LLC All Rights Reserved Medical Image Classification and Segmentation: Analysis of X-ray, CT, MRI, Ultrasound, PET, for Computer-Aided Diagnosis in Radiology, Cardiology, and Pathology Analysis of Microscopy Images for Disease Quantification Content Based Medical Image Retrieval for Diagnostic Decision Making Support Medical Monitoring Signal Classification and Prediction: Monitoring Signal Analysis for Automatic Health Risk Detection Predictive Analysis for Clinical Decision Making Support Deep Learning for Medical Data Analysis Introduction
  6. 6. ©2017 Xanadu Big Data, LLC All Rights Reserved Dermatologist-level classification of skin cancer with deep neural networks by Stanford University researchers Train Inception v3 CNN using a dataset of 129,450 clinical consisting of 2,032 different diseases: Test its performance against 21 board-certified dermatologists on biopsy-proven clinical images with two critical binary classification use cases: malignant carcinomas versus benign seborrheic keratoses; and malignant melanomas versus benign nevi. The deep learning CNN outperforms the average of the dermatologists at skin cancer classification . Automated Skin Cancer Classification source: https://cs.stanford.edu/people/esteva/nature/
  7. 7. ©2017 Xanadu Big Data, LLC All Rights Reserved Google's Research In Artificial Intelligence Helps In Preventing Blindness Caused by Diabetes Google Brain has collaborated with doctors in India and US to help them diagnose DR. The team has collected over 128,000 images that were each evaluated by 3-7 ophthalmologists from a panel of 54 ophthalmologists. These images were fed to a deep learning algorithm for creating a model to detect Diabetic Retinopathy. The predictions from Google Brain’s neural network algorithm were so close that it is considered to be on par with the diagnosis of experienced ophthalmologists. Automated Diabetic Retinopathy Classification source: https://www.youtube.com/watch?v=oOeZ7IgEN4o
  8. 8. ©2017 Xanadu Big Data, LLC All Rights Reserved Deep Learning for Predicting Glioblastoma Subtypes from MRI Deep learning can identify people likely to develop Alzheimer’s in the next three years by studying positron emission tomography (PET) scans of the brain. Brain Tumor Research source: https://www.youtube.com/watch?v=LVJbvK_HAbY Alzheime Prediction source: https://www.technologyreview.com/s/604289/software-predicts-cognitive-decline-using- brain-images/
  9. 9. ©2017 Xanadu Big Data, LLC All Rights Reserved A Survey on Medical Image Deep Learning Research source: https://arxiv.org/abs/1702.05747
  10. 10. ©2017 Xanadu Big Data, LLC All Rights Reserved Cardiologist-Level Arrhythmia Detection with Convolutional Neural Networks The electrocardiogram (ECG) is a tool to detect the electrical signal, which could indicates malfunction of the heart. AF (Atrial Fibrillation) is the most common sustained cardiac arrhythmia, occurring in 1-2% of the general population and is associated with significant mortality and morbidity through association of risk of death, stroke, hospitalization, heart failure and coronary artery disease, etc. Cardiac Arrhthymia Detection source: https://physionet.org/challenge/2017/, https://www.youtube.com/watch?time_continue=130&v=XVDDEsmbjuE
  11. 11. ©2017 Xanadu Big Data, LLC All Rights Reserved Deep Learning Helps Patient Care Decisions in Intensive Care Unit Deep learning that takes large amounts of intensive-care-unit (ICU) data, from vitals and labs to notes and demographics, can determine what kinds of treatments are needed for different symptoms and who is at risk for mortality by real-time predictions. Analysis of electroencephalographic (EEG) recordings of brain activity for better treatment (e.g., epileptic seizure). ICU Patient Care source: https://www.eecs.mit.edu/news-events/announcements/using-machine-learning-improve- patient-care
  12. 12. ©2017 Xanadu Big Data, LLC All Rights Reserved Deep Learning Introduction Convolutional Neural Networks (CNNs): image/video analysis Source: Deep Learning A-Z™: Hands-On Artificial Neural Networks by SuperDataScience@udemy Recurrent Neural Networks (RNNs):time series analysis Reinforcement Learning (RL): automatically determine the ideal behaviour within a specific context, in order to maximize its performance for a specific goal Source: Reinforcement Learning in Python by Lazy Programmer Inc.@udemy
  13. 13. ©2017 Xanadu Big Data, LLC All Rights Reserved Convolution Process Details input 1 filter 3x3 Kernel 15x15 Kernel Activation 2x2 Pooling Activation + Pooling 3 filters Source: https://hackernoon.com/visualizing-parts-of-convolutional-neural-networks-using-keras-and-cats- 5cc01b214e59
  14. 14. ©2017 Xanadu Big Data, LLC All Rights Reserved Deep Learning Use Cases CNN + RNN for Real-time Object Identification Source: SoftPoint Consultores S.L. Deep RL for Self-driving Cars Source: Mobileye
  15. 15. ©2017 Xanadu Big Data, LLC All Rights Reserved Issues with Big Data Deep Learning Big Data Deep Learning Volume: Size of Data Increase in algorithm complexity and computing time Velocity: Data Processing Speed Difficulty in data learning process in a timely manner Variety: Different Types of Data Increase in data processing diversity for different data characteristics and behavior Veracity: Truthfulness of Data Significant increase in pre-processing of data
  16. 16. ©2017 Xanadu Big Data, LLC All Rights Reserved Distributed Deep Learning for Medical Big Data Analysis Issues with medical big data deep learning: High resolution/scale microscopy images 81,025 pixels by 86,273 pixels (roughly 6.99 gigapixels) requires 78.12 GB memory to store Trained on 1.28 M images and evaluated on 50 K images took 2 – 3 weeks using 8 GPU machine in MS ResNet Distributed training: In model parallelism, different machines in the distributed system are responsible for the computations in different parts of a single network - for example, each layer in the neural network may be assigned to a different machine. In data parallelism, different machines have a complete copy of the model; each machine simply gets a different portion of the data, and results from each are somehow combined. For details: Skymind web: http://engineering.skymind.io
  17. 17. ©2017 Xanadu Big Data, LLC All Rights Reserved Deep learning requires massive amount of training dataset as accuracy of deep learning is largely dependent on the quality and size of the dataset. Development of large medical image and signal data is very difficult as annotation requires extensive time from medical experts. Challenges of Deep Learning for Medical Data Analysis
  18. 18. ©2017 Xanadu Big Data, LLC All Rights Reserved CBIR is a way of searching image database using visual features of an image as a search term to find images that share the similar visual features. Content Based Image Retrieval (CBIR) source: http://www.sciencedirect.com/science/article/pii/S0925231217308445
  19. 19. ©2017 Xanadu Big Data, LLC All Rights Reserved Xanadu enables competitive big data management in the Clouds or Enterprises Xanadu Functionality K AnyTypes&SizeofData NoSQL Database Data De-duplication Data Replication Massively Scalable Fault Tolerance Data Store NoSQL Database ACID Compliance High Throughput Low Latency Data Access
  20. 20. ©2017 Xanadu Big Data, LLC All Rights Reserved Xanadu Performance BMT
  21. 21. ©2017 Xanadu Big Data, LLC All Rights Reserved Xanadu provides a composable architecture that can be integrated with other big data systems Xanadu Use Case + Total Integration Big Data Applications Big Data IT Infrastructure Xanadu Data Management Platform GPS / GLONASS WCDMA / LTE +
  22. 22. ©2017 Xanadu Big Data, LLC All Rights Reserved Xanadu Commodity Storage System Use Case
  23. 23. ©2017 Xanadu Big Data, LLC All Rights Reserved Xanadu Cloud Computing Use Case
  24. 24. ©2017 Xanadu Big Data, LLC All Rights Reserved CNN/RNN architecture in DeepLearning4J (DL4J) Distributed deep leaning on CPUs/GPUs (+Hadoop/Spark) Xanadu file system used to store images and load directly into DL4J Local Machines & AWS Clusters Xanadu + Deep Learning + Spark + Hadoop Integration Source: researchgate.net. Data Source: https://www.kaggle.com/c/diabetic-retinopathy-detection
  25. 25. ©2017 Xanadu Big Data, LLC All Rights Reserved Xanadu Medical Data Big Data Archive Xanadu’s deduplication reduces the actual storage footprint by recognizing duplicate data and maintaining only as many copies as it needs to assure its availability. Time stamping functionality provides inherent (built-in) backup of the database. ACID compliance guarantees reliable and consistent data update even in the face of the storage failure. Xanadu enables a fast content-based search system (e.g. CBIR) with massive scalability Xanadu provides database for real time big data deep learning Xanadu provides intra/inter hospital collaborative data sharing platform. Big Data Deep Learning integrated with Xanadu Medical Image Big Data Archive Customized deep learning for specific applications/dataset. High speed deep learning over multiple CPU/GPU machines. Xanadu based Big Data Deep Learning System for Medical Data Analysis
  26. 26. ©2017 Xanadu Big Data, LLC All Rights Reserved Xanadu CBIR Demo
  27. 27. ©2017 Xanadu Big Data, LLC All Rights Reserved Thank you Xanadu Big Data, LLC

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