ALOE - An overview of a service-oriented architecture for research in breast cancer diagnosis

Slides of our presentation in the IBERGRID workshop on biomedical image analysis celebrated on September 8th in Aveiro (Portugal)

Transcript

1. AN OVERVIEW OF A SERVICE-ORIENTED ARCHITECTURE FOR RESEARCH IN BREAST CANCER DIAGNOSIS JOSÉ MIGUEL FRANCO VALIENTE AVEIRO (PORTUGAL), SEPTEMBER 8TH, 2014
2. @josemi_fv josemiguel.franco@ciemat.es josemifv
3. CONTENTS Motivation and previous work What is ALOE? ALOE architecture Current status Future work Acknowledgements AN OVERVIEW OF A SERVICE-ORIENTED ARCHITECTURE FOR RESEARCH IN BREAST CANCER DIAGNOSIS
4. MOTIVATION Collaboration started in 2008 Research in breast cancer diagnosis – High mortality – Early detection is critical – Current techniques are expensive – Computer Assisted Diagnosis (CADx) AN OVERVIEW OF A SERVICE-ORIENTED ARCHITECTURE FOR RESEARCH IN BREAST CANCER DIAGNOSIS
5. PARTNERS AN OVERVIEW OF A SERVICE-ORIENTED ARCHITECTURE FOR RESEARCH IN BREAST CANCER DIAGNOSIS
6. FIRST RESULTS First Iberian Breast Cancer Digital Repository Workstation for Image Analysis and Diagnosis Machine Learning Classifiers AN OVERVIEW OF A SERVICE-ORIENTED ARCHITECTURE FOR RESEARCH IN BREAST CANCER DIAGNOSIS
7. AN OVERVIEW OF A SERVICE-ORIENTED ARCHITECTURE FOR RESEARCH IN BREAST CANCER DIAGNOSIS
8. MOTIVATION Reducing the rate of missed cancers by: 1. Support radiologist diagnosis through CADx AN OVERVIEW OF A SERVICE-ORIENTED ARCHITECTURE FOR RESEARCH IN BREAST CANCER DIAGNOSIS
9. MOTIVATION Reducing the rate of missed cancers by: 1. Support radiologist diagnosis through CADx 2. Improving the training process of new specialists AN OVERVIEW OF A SERVICE-ORIENTED ARCHITECTURE FOR RESEARCH IN BREAST CANCER DIAGNOSIS
10. MOTIVATION Reducing the rate of missed cancers by: 1. Support radiologist diagnosis through CADx 2. Improving the training process of new specialists AN OVERVIEW OF A SERVICE-ORIENTED ARCHITECTURE FOR RESEARCH IN BREAST CANCER DIAGNOSIS
11. WHAT IS ALOE? ALOE is a platform for radiologist training in breast cancer diagnosis AN OVERVIEW OF A SERVICE-ORIENTED ARCHITECTURE FOR RESEARCH IN BREAST CANCER DIAGNOSIS Lots of cases Auto-evaluation E-Learning Modulable E-Infrastructures
12. ALOE ARCHITECTURE AN OVERVIEW OF A SERVICE-ORIENTED ARCHITECTURE FOR RESEARCH IN BREAST CANCER DIAGNOSIS
13. BCDR MODULE AN OVERVIEW OF A SERVICE-ORIENTED ARCHITECTURE FOR RESEARCH IN BREAST CANCER DIAGNOSIS
14. BCDR MODULE Includes all components related to data Four components: • BCDR repository • MIWAD suite • BCDR-WS web service • BCDR.eu website AN OVERVIEW OF A SERVICE-ORIENTED ARCHITECTURE FOR RESEARCH IN BREAST CANCER DIAGNOSIS
15. BCDR REPOSITORY • A compilation of anonymous breast cancer cases annotated by expert radiologists • Contains clinical data, lesion outlines and image-based computed features Two subsets • BCDR-FM: 1010 cases. 720 x 1168 TIFF 8bits • BCDR-DM: 724 cases. 3328 x 4084 TIFF 14bits AN OVERVIEW OF A SERVICE-ORIENTED ARCHITECTURE FOR RESEARCH IN BREAST CANCER DIAGNOSIS
16. AN OVERVIEW OF A SERVICE-ORIENTED ARCHITECTURE FOR RESEARCH IN BREAST CANCER DIAGNOSIS
17. MIWAD Used by radiologists to segment and classify breast cancer cases Two applications: • MIWAD-DB: Manages BCDR content • MIWAD-CAD: Identify lesions. Feature extraction AN OVERVIEW OF A SERVICE-ORIENTED ARCHITECTURE FOR RESEARCH IN BREAST CANCER DIAGNOSIS
18. AN OVERVIEW OF A SERVICE-ORIENTED ARCHITECTURE FOR RESEARCH IN BREAST CANCER DIAGNOSIS
19. AN OVERVIEW OF A SERVICE-ORIENTED ARCHITECTURE FOR RESEARCH IN BREAST CANCER DIAGNOSIS
20. BCDR-WS WEB SERVICE Exposes BCDR content Restful approach Based on Eve (Flask, MongoDB and Redis) OpenID Connect (OAuth2 + JWT) • Federated Authentication AN OVERVIEW OF A SERVICE-ORIENTED ARCHITECTURE FOR RESEARCH IN BREAST CANCER DIAGNOSIS
21. BCDR.EU WEBSITE AN OVERVIEW OF A SERVICE-ORIENTED ARCHITECTURE FOR RESEARCH IN BREAST CANCER DIAGNOSIS
22. AI MODULE AN OVERVIEW OF A SERVICE-ORIENTED ARCHITECTURE FOR RESEARCH IN BREAST CANCER DIAGNOSIS
23. AI MODULE Includes all components and services based on Artificial Intelligence techniques Three components: • Classifier engine • MLC-WS web service • Recommender engine AN OVERVIEW OF A SERVICE-ORIENTED ARCHITECTURE FOR RESEARCH IN BREAST CANCER DIAGNOSIS
24. CLASSIFIER ENGINE • Allows building, training and evaluating new Machine Learning Classifiers (MLCs) • Best performing MLCs are exposed through MLC-WS • Libraries supported: Python-Scykit, PSVM, Weka,… AN OVERVIEW OF A SERVICE-ORIENTED ARCHITECTURE FOR RESEARCH IN BREAST CANCER DIAGNOSIS
25. AN OVERVIEW OF A SERVICE-ORIENTED ARCHITECTURE FOR RESEARCH IN BREAST CANCER DIAGNOSIS
26. MLC-WS WEB SERVICE Allows the interaction with the AI module Restful approach Based on Eve (Flask, MongoDB and Redis) OpenID Connect (OAuth2 + JWT) • Federated Authentication AN OVERVIEW OF A SERVICE-ORIENTED ARCHITECTURE FOR RESEARCH IN BREAST CANCER DIAGNOSIS
27. RECOMMENDER ENGINE • Will allow the identification of relevant cases for ALOE users • User data + lesion data • Apache Mahout based • Early stage of development AN OVERVIEW OF A SERVICE-ORIENTED ARCHITECTURE FOR RESEARCH IN BREAST CANCER DIAGNOSIS
28. E-LEARNING MODULE AN OVERVIEW OF A SERVICE-ORIENTED ARCHITECTURE FOR RESEARCH IN BREAST CANCER DIAGNOSIS
29. E-LEARNING MODULE Enables the training activities in the ALOE platform Three components: • ALOE database • ALOE-WS web service • Breast Cancer Ontology Knowledge Base AN OVERVIEW OF A SERVICE-ORIENTED ARCHITECTURE FOR RESEARCH IN BREAST CANCER DIAGNOSIS
30. AN OVERVIEW OF A SERVICE-ORIENTED ARCHITECTURE FOR RESEARCH IN BREAST CANCER DIAGNOSIS
31. AN OVERVIEW OF A SERVICE-ORIENTED ARCHITECTURE FOR RESEARCH IN BREAST CANCER DIAGNOSIS
32. AN OVERVIEW OF A SERVICE-ORIENTED ARCHITECTURE FOR RESEARCH IN BREAST CANCER DIAGNOSIS
33. ALOE-WS WEB SERVICE Allows the interaction with the ALOE database Restful approach Based on Eve (Flask, MongoDB and Redis) OpenID Connect (OAuth2 + JWT) • Federated Authentication AN OVERVIEW OF A SERVICE-ORIENTED ARCHITECTURE FOR RESEARCH IN BREAST CANCER DIAGNOSIS
34. BREAST CANCER ONTOLOGY • Will store all concepts related to breast cancer diagnosis • Will support ALOE users training • Based on terms used at FMUP-HSJ • Work in progress… AN OVERVIEW OF A SERVICE-ORIENTED ARCHITECTURE FOR RESEARCH IN BREAST CANCER DIAGNOSIS
35. CURRENT STATUS ALOE platform is a work in progress • BCDR module: • BCDR 2.0 will be publicly released next month • MIWAD-SAAS (VDI) released • AI Module: • Classifier Engine on testing • Recommender system in early stages • E-Learning module: • First alpha version released (without Breast Cancer Ontology) AN OVERVIEW OF A SERVICE-ORIENTED ARCHITECTURE FOR RESEARCH IN BREAST CANCER DIAGNOSIS
36. FUTURE WORK • First production release at 2015Q1 • Enhancing social capabilities • Auto-evaluation via MLCs • Service migration to EGI Federated Cloud • New data sources addition • Support new diseases (kidney, lung, …) AN OVERVIEW OF A SERVICE-ORIENTED ARCHITECTURE FOR RESEARCH IN BREAST CANCER DIAGNOSIS
37. SUMMARY • ALOE platform aims at reducing the impact of breast cancer through: • Allowing the development of well-performing CADx systems • Improving the training of new radiologists • Provides specialized modules • Opened to researchers/students/professionals • Still in development AN OVERVIEW OF A SERVICE-ORIENTED ARCHITECTURE FOR RESEARCH IN BREAST CANCER DIAGNOSIS
38. ACKNOWLEDGEMENTS The four institutions express their gratitude for the support of the European Regional Development Fund (FEDER-ERDF) AN OVERVIEW OF A SERVICE-ORIENTED ARCHITECTURE FOR RESEARCH IN BREAST CANCER DIAGNOSIS
39. THANK YOU! AN OVERVIEW OF A SERVICE-ORIENTED ARCHITECTURE FOR RESEARCH IN BREAST CANCER DIAGNOSIS