The growing on variety, volume and velocity of public biomedical databases in the last years have generate an explosion of big data in biology and medicine. Most of these databases comprise structural, molecular and genetic information from different kind of images acquisition modalities and associated metadata having a great potential, not yet exploited, as a source of information and knowledge which could impact biomedical research in different application fields. In fact, new research areas are emerging in this direction, known as bioimage informatics and computational pathology, which are areas basically attempting to apply different methods of image processing, pattern recognition, machine learning and data mining, in multimodal biomedical databases. However, the proposed tools and methods for image collection analysis have some research challenges coming with deluge of big data in biomedicine such as: visual appearance variability, semantic gap between image content and high-level meaning, structural and interpretable representation of image content, semantic inclusion of multimodal information sources, and scalability support with the increasing volume of databases. In this way, the research proposal is addressing the problem of automatic extraction of knowledge from biomedical image collections. Specifically, the goal is to devise methods to automatically find: visual patterns that compactly explain the visual richness of biomedical images, relationships between visual patterns, and relationships between visual patterns and their meaning in a particular biomedical context. In order to solve it, the proposed methodology has three main stages: part-based bioimage representation, semantic bioimage representation and biomedical knowledge discovery. Each stage of methodology state-of-the-art methods from computer vision, image processing, machine learning and data mining will be explored to provide interpretable learning methods supported by high-performance computing.

1. An Automatic Knowledge Discovery Strategy In
Biomedical Images
Angel Alfonso Cruz Roa, Eng, M.Sc.
Advisor: Fabio A. Gonz´lez, Eng, M.Sc., Ph.D
a
BioIngenium Research Group - Universidad Nacional de Colombia
http://www.bioingenium.unal.edu.co/
Doctoral Thesis Proposal
Doctoral Program on Computer and Systems Engineering
December 1, 2011
Doctoral Thesis Proposal Doctoral Program o
Angel Alfonso Cruz Roa, Eng, M.Sc. Advisor:An Automatic Knowledge M.Sc., Ph.D (BioIngenium Research Group - Universidad Naciona
Fabio A. Gonz´lez, Eng, Discovery Strategy In Biomedical Images
a / 41

2. Outline
1 Introduction
Motivation
Research Problem
Research Questions
2 Proposed Research
Objectives
Proposed Methodology
3 Preliminary Work
Bag of Features Representation in Biomedical Images
Semantic Biomedical Image Representation
Visual Pattern Mining in Biomedical Images
Doctoral Thesis Proposal Doctoral Program o
Angel Alfonso Cruz Roa, Eng, M.Sc. Advisor:An Automatic Knowledge M.Sc., Ph.D (BioIngenium Research Group - Universidad Naciona
Fabio A. Gonz´lez, Eng, Discovery Strategy In Biomedical Images
a / 41

3. Motivation
Classical approach to biomedical image analysis
Doctoral Thesis Proposal Doctoral Program o
Angel Alfonso Cruz Roa, Eng, M.Sc. Advisor:An Automatic Knowledge M.Sc., Ph.D (BioIngenium Research Group - Universidad Naciona
Fabio A. Gonz´lez, Eng, Discovery Strategy In Biomedical Images
a / 41

4. Motivation
Classical approach to biomedical image analysis
Doctoral Thesis Proposal Doctoral Program o
Angel Alfonso Cruz Roa, Eng, M.Sc. Advisor:An Automatic Knowledge M.Sc., Ph.D (BioIngenium Research Group - Universidad Naciona
Fabio A. Gonz´lez, Eng, Discovery Strategy In Biomedical Images
a / 41

5. Motivation
An alternative approach
Doctoral Thesis Proposal Doctoral Program o
Angel Alfonso Cruz Roa, Eng, M.Sc. Advisor:An Automatic Knowledge M.Sc., Ph.D (BioIngenium Research Group - Universidad Naciona
Fabio A. Gonz´lez, Eng, Discovery Strategy In Biomedical Images
a / 41

6. Why?
Large volumes of data
Computational
capability
Better results and
interpretability
Automatic Knowledge
Discovery
(biomarkers)
Doctoral Thesis Proposal Doctoral Program o
Angel Alfonso Cruz Roa, Eng, M.Sc. Advisor:An Automatic Knowledge M.Sc., Ph.D (BioIngenium Research Group - Universidad Naciona
Fabio A. Gonz´lez, Eng, Discovery Strategy In Biomedical Images
a / 41

7. Trends
Doctoral Thesis Proposal Doctoral Program o
Angel Alfonso Cruz Roa, Eng, M.Sc. Advisor:An Automatic Knowledge M.Sc., Ph.D (BioIngenium Research Group - Universidad Naciona
Fabio A. Gonz´lez, Eng, Discovery Strategy In Biomedical Images
a / 41

8. Outline
1 Introduction
Motivation
Research Problem
Research Questions
2 Proposed Research
Objectives
Proposed Methodology
3 Preliminary Work
Bag of Features Representation in Biomedical Images
Semantic Biomedical Image Representation
Visual Pattern Mining in Biomedical Images
Doctoral Thesis Proposal Doctoral Program o
Angel Alfonso Cruz Roa, Eng, M.Sc. Advisor:An Automatic Knowledge M.Sc., Ph.D (BioIngenium Research Group - Universidad Naciona
Fabio A. Gonz´lez, Eng, Discovery Strategy In Biomedical Images
a / 41

9. Research Problem
How to perform automatic extraction of knowledge from biomedical image
collections?
Specifically, how to find, automatically, visual patterns that compactly
explain the visual richness of biomedical images, relationships between
visual patterns, and relationships between visual patterns and their
meaning in a particular biomedical context?
Doctoral Thesis Proposal Doctoral Program o
Angel Alfonso Cruz Roa, Eng, M.Sc. Advisor:An Automatic Knowledge M.Sc., Ph.D (BioIngenium Research Group - Universidad Naciona
Fabio A. Gonz´lez, Eng, Discovery Strategy In Biomedical Images
a / 41

10. Research Problem
How to perform automatic extraction of knowledge from biomedical image
collections?
Specifically, how to find, automatically, visual patterns that compactly
explain the visual richness of biomedical images, relationships between
visual patterns, and relationships between visual patterns and their
meaning in a particular biomedical context?
Doctoral Thesis Proposal Doctoral Program o
Angel Alfonso Cruz Roa, Eng, M.Sc. Advisor:An Automatic Knowledge M.Sc., Ph.D (BioIngenium Research Group - Universidad Naciona
Fabio A. Gonz´lez, Eng, Discovery Strategy In Biomedical Images
a / 41

11. Research Challenges
Visual content complexity
Stain
Skin of images (40X) stained with Hematoxilyn-eosin and Trichrome of Masson
Magnification
Muscular tissue in tongue stained with Trichrome of Masson (10X, 20X and 40X)
Type of Cut
Cardiac striated muscular tissue, heart (HE), 1000X. Longitudinal and transverse cuts.
Doctoral Thesis Proposal Doctoral Program o
Angel Alfonso Cruz Roa, Eng, M.Sc. Advisor:An Automatic Knowledge M.Sc., Ph.D (BioIngenium Research Group - Universidad Naciona
Fabio A. Gonz´lez, Eng, Discovery Strategy In Biomedical Images
a / 41

12. Research Challenges
Semantic gap and interpretability
?
Doctoral Thesis Proposal Doctoral Program o
Angel Alfonso Cruz Roa, Eng, M.Sc. Advisor:An Automatic Knowledge M.Sc., Ph.D (BioIngenium Research Group - Universidad Naciona
Fabio A. Gonz´lez, Eng, Discovery Strategy In Biomedical Images
a / 41

13. Research Challenges
Semantic gap and interpretability
?
Doctoral Thesis Proposal Doctoral Program o
Angel Alfonso Cruz Roa, Eng, M.Sc. Advisor:An Automatic Knowledge M.Sc., Ph.D (BioIngenium Research Group - Universidad Naciona
Fabio A. Gonz´lez, Eng, Discovery Strategy In Biomedical Images
a / 41

14. Research Challenges
Scalability for large databases
Doctoral Thesis Proposal Doctoral Program o
Angel Alfonso Cruz Roa, Eng, M.Sc. Advisor:An Automatic Knowledge M.Sc., Ph.D (BioIngenium Research Group - Universidad Naciona
Fabio A. Gonz´lez, Eng, Discovery Strategy In Biomedical Images
a / 41

15. Research Challenges
Scalability for large images (High resolution, 3D & 4D)
Doctoral Thesis Proposal Doctoral Program o
Angel Alfonso Cruz Roa, Eng, M.Sc. Advisor:An Automatic Knowledge M.Sc., Ph.D (BioIngenium Research Group - Universidad Naciona
Fabio A. Gonz´lez, Eng, Discovery Strategy In Biomedical Images
a / 41

16. Outline
1 Introduction
Motivation
Research Problem
Research Questions
2 Proposed Research
Objectives
Proposed Methodology
3 Preliminary Work
Bag of Features Representation in Biomedical Images
Semantic Biomedical Image Representation
Visual Pattern Mining in Biomedical Images
Doctoral Thesis Proposal Doctoral Program o
Angel Alfonso Cruz Roa, Eng, M.Sc. Advisor:An Automatic Knowledge M.Sc., Ph.D (BioIngenium Research Group - Universidad Naciona
Fabio A. Gonz´lez, Eng, Discovery Strategy In Biomedical Images
a / 41

17. Research Questions
How to automatically learn a semantic enriched image representation
from a biomedical image collection?
How to use the learned representation to find interesting patterns that
connect visual content and biomedical meaning?
Does this kind of representation improve the performance in tasks
such as automatic image annotation and segmentation?
How to use the learned representation to make image analysis models
more interpretable?
How to make algorithms scalable to large (hundreds of thousands or
millions) biomedical image collections?
Doctoral Thesis Proposal Doctoral Program o
Angel Alfonso Cruz Roa, Eng, M.Sc. Advisor:An Automatic Knowledge M.Sc., Ph.D (BioIngenium Research Group - Universidad Naciona
Fabio A. Gonz´lez, Eng, Discovery Strategy In Biomedical Images
a / 41

18. Research Questions
How to automatically learn a semantic enriched image representation
from a biomedical image collection?
How to use the learned representation to find interesting patterns that
connect visual content and biomedical meaning?
Does this kind of representation improve the performance in tasks
such as automatic image annotation and segmentation?
How to use the learned representation to make image analysis models
more interpretable?
How to make algorithms scalable to large (hundreds of thousands or
millions) biomedical image collections?
Doctoral Thesis Proposal Doctoral Program o
Angel Alfonso Cruz Roa, Eng, M.Sc. Advisor:An Automatic Knowledge M.Sc., Ph.D (BioIngenium Research Group - Universidad Naciona
Fabio A. Gonz´lez, Eng, Discovery Strategy In Biomedical Images
a / 41

19. Research Questions
How to automatically learn a semantic enriched image representation
from a biomedical image collection?
How to use the learned representation to find interesting patterns that
connect visual content and biomedical meaning?
Does this kind of representation improve the performance in tasks
such as automatic image annotation and segmentation?
How to use the learned representation to make image analysis models
more interpretable?
How to make algorithms scalable to large (hundreds of thousands or
millions) biomedical image collections?
Doctoral Thesis Proposal Doctoral Program o
Angel Alfonso Cruz Roa, Eng, M.Sc. Advisor:An Automatic Knowledge M.Sc., Ph.D (BioIngenium Research Group - Universidad Naciona
Fabio A. Gonz´lez, Eng, Discovery Strategy In Biomedical Images
a / 41

20. Research Questions
How to automatically learn a semantic enriched image representation
from a biomedical image collection?
How to use the learned representation to find interesting patterns that
connect visual content and biomedical meaning?
Does this kind of representation improve the performance in tasks
such as automatic image annotation and segmentation?
How to use the learned representation to make image analysis models
more interpretable?
How to make algorithms scalable to large (hundreds of thousands or
millions) biomedical image collections?
Doctoral Thesis Proposal Doctoral Program o
Angel Alfonso Cruz Roa, Eng, M.Sc. Advisor:An Automatic Knowledge M.Sc., Ph.D (BioIngenium Research Group - Universidad Naciona
Fabio A. Gonz´lez, Eng, Discovery Strategy In Biomedical Images
a / 41

21. Research Questions
How to automatically learn a semantic enriched image representation
from a biomedical image collection?
How to use the learned representation to find interesting patterns that
connect visual content and biomedical meaning?
Does this kind of representation improve the performance in tasks
such as automatic image annotation and segmentation?
How to use the learned representation to make image analysis models
more interpretable?
How to make algorithms scalable to large (hundreds of thousands or
millions) biomedical image collections?
Doctoral Thesis Proposal Doctoral Program o
Angel Alfonso Cruz Roa, Eng, M.Sc. Advisor:An Automatic Knowledge M.Sc., Ph.D (BioIngenium Research Group - Universidad Naciona
Fabio A. Gonz´lez, Eng, Discovery Strategy In Biomedical Images
a / 41

22. Outline
1 Introduction
Motivation
Research Problem
Research Questions
2 Proposed Research
Objectives
Proposed Methodology
3 Preliminary Work
Bag of Features Representation in Biomedical Images
Semantic Biomedical Image Representation
Visual Pattern Mining in Biomedical Images
Doctoral Thesis Proposal Doctoral Program o
Angel Alfonso Cruz Roa, Eng, M.Sc. Advisor:An Automatic Knowledge M.Sc., Ph.D (BioIngenium Research Group - Universidad Naciona
Fabio A. Gonz´lez, Eng, Discovery Strategy In Biomedical Images
a / 41

23. Main Goal
To propose a strategy for automatic knowledge discovery in
biomedical image databases.
Doctoral Thesis Proposal Doctoral Program o
Angel Alfonso Cruz Roa, Eng, M.Sc. Advisor:An Automatic Knowledge M.Sc., Ph.D (BioIngenium Research Group - Universidad Naciona
Fabio A. Gonz´lez, Eng, Discovery Strategy In Biomedical Images
a / 41

24. Specific Objectives
To propose/adapt a strategy for learning part-based image
representation from a collection of biomedical images.
To propose and validate a learning method that enriches the learned
image representation with semantic content from a particular
biomedical domain.
To propose and validate a method for image collection analysis and
visual pattern mining in biomedical image collections.
Doctoral Thesis Proposal Doctoral Program o
Angel Alfonso Cruz Roa, Eng, M.Sc. Advisor:An Automatic Knowledge M.Sc., Ph.D (BioIngenium Research Group - Universidad Naciona
Fabio A. Gonz´lez, Eng, Discovery Strategy In Biomedical Images
a / 41

25. Specific Objectives
To propose/adapt a strategy for learning part-based image
representation from a collection of biomedical images.
To propose and validate a learning method that enriches the learned
image representation with semantic content from a particular
biomedical domain.
To propose and validate a method for image collection analysis and
visual pattern mining in biomedical image collections.
Doctoral Thesis Proposal Doctoral Program o
Angel Alfonso Cruz Roa, Eng, M.Sc. Advisor:An Automatic Knowledge M.Sc., Ph.D (BioIngenium Research Group - Universidad Naciona
Fabio A. Gonz´lez, Eng, Discovery Strategy In Biomedical Images
a / 41

26. Specific Objectives
To propose/adapt a strategy for learning part-based image
representation from a collection of biomedical images.
To propose and validate a learning method that enriches the learned
image representation with semantic content from a particular
biomedical domain.
To propose and validate a method for image collection analysis and
visual pattern mining in biomedical image collections.
Doctoral Thesis Proposal Doctoral Program o
Angel Alfonso Cruz Roa, Eng, M.Sc. Advisor:An Automatic Knowledge M.Sc., Ph.D (BioIngenium Research Group - Universidad Naciona
Fabio A. Gonz´lez, Eng, Discovery Strategy In Biomedical Images
a / 41

27. Outline
1 Introduction
Motivation
Research Problem
Research Questions
2 Proposed Research
Objectives
Proposed Methodology
3 Preliminary Work
Bag of Features Representation in Biomedical Images
Semantic Biomedical Image Representation
Visual Pattern Mining in Biomedical Images
Doctoral Thesis Proposal Doctoral Program o
Angel Alfonso Cruz Roa, Eng, M.Sc. Advisor:An Automatic Knowledge M.Sc., Ph.D (BioIngenium Research Group - Universidad Naciona
Fabio A. Gonz´lez, Eng, Discovery Strategy In Biomedical Images
a / 41

28. Proposed Methodology
Doctoral Thesis Proposal Doctoral Program o
Angel Alfonso Cruz Roa, Eng, M.Sc. Advisor:An Automatic Knowledge M.Sc., Ph.D (BioIngenium Research Group - Universidad Naciona
Fabio A. Gonz´lez, Eng, Discovery Strategy In Biomedical Images
a / 41

29. Part-based bioimage representation
Doctoral Thesis Proposal Doctoral Program o
Angel Alfonso Cruz Roa, Eng, M.Sc. Advisor:An Automatic Knowledge M.Sc., Ph.D (BioIngenium Research Group - Universidad Naciona
Fabio A. Gonz´lez, Eng, Discovery Strategy In Biomedical Images
a / 41

30. Part-based bioimage representation
Cells
Tissues
Organs
Architectural
features
Doctoral Thesis Proposal Doctoral Program o
Angel Alfonso Cruz Roa, Eng, M.Sc. Advisor:An Automatic Knowledge M.Sc., Ph.D (BioIngenium Research Group - Universidad Naciona
Fabio A. Gonz´lez, Eng, Discovery Strategy In Biomedical Images
a / 41

31. Part-based bioimage representation
Bag of features
Sparse
Representation
Sparse Deep
Belief Networks
Doctoral Thesis Proposal Doctoral Program o
Angel Alfonso Cruz Roa, Eng, M.Sc. Advisor:An Automatic Knowledge M.Sc., Ph.D (BioIngenium Research Group - Universidad Naciona
Fabio A. Gonz´lez, Eng, Discovery Strategy In Biomedical Images
a / 41

32. Semantic bioimage representation
Doctoral Thesis Proposal Doctoral Program o
Angel Alfonso Cruz Roa, Eng, M.Sc. Advisor:An Automatic Knowledge M.Sc., Ph.D (BioIngenium Research Group - Universidad Naciona
Fabio A. Gonz´lez, Eng, Discovery Strategy In Biomedical Images
a / 41

33. Semantic bioimage representation
Structural
knowledge
Labels and
concepts
Annotations
Descriptions
Other modalities
Doctoral Thesis Proposal Doctoral Program o
Angel Alfonso Cruz Roa, Eng, M.Sc. Advisor:An Automatic Knowledge M.Sc., Ph.D (BioIngenium Research Group - Universidad Naciona
Fabio A. Gonz´lez, Eng, Discovery Strategy In Biomedical Images
a / 41

34. Semantic bioimage representation
Latent Semantic
Analysis
Graphical models
Non-negative
Matrix
Factorization
Kernel Methods
Doctoral Thesis Proposal Doctoral Program o
Angel Alfonso Cruz Roa, Eng, M.Sc. Advisor:An Automatic Knowledge M.Sc., Ph.D (BioIngenium Research Group - Universidad Naciona
Fabio A. Gonz´lez, Eng, Discovery Strategy In Biomedical Images
a / 41

35. Biomedical knowledge discovery
Doctoral Thesis Proposal Doctoral Program o
Angel Alfonso Cruz Roa, Eng, M.Sc. Advisor:An Automatic Knowledge M.Sc., Ph.D (BioIngenium Research Group - Universidad Naciona
Fabio A. Gonz´lez, Eng, Discovery Strategy In Biomedical Images
a / 41

36. Biomedical knowledge discovery
Biomarkers
Biological patterns
Pathology factors
Patterns relations
Data correlation
Biological
interpretation
Diagnosis,
prognosis and
theragnosis
Doctoral Thesis Proposal Doctoral Program o
Angel Alfonso Cruz Roa, Eng, M.Sc. Advisor:An Automatic Knowledge M.Sc., Ph.D (BioIngenium Research Group - Universidad Naciona
Fabio A. Gonz´lez, Eng, Discovery Strategy In Biomedical Images
a / 41

37. Biomedical knowledge discovery
Statistical learning
Clustering
Analysis
Association Rules
Structure Output
Learning
Decision trees
Doctoral Thesis Proposal Doctoral Program o
Angel Alfonso Cruz Roa, Eng, M.Sc. Advisor:An Automatic Knowledge M.Sc., Ph.D (BioIngenium Research Group - Universidad Naciona
Fabio A. Gonz´lez, Eng, Discovery Strategy In Biomedical Images
a / 41

38. Outline
1 Introduction
Motivation
Research Problem
Research Questions
2 Proposed Research
Objectives
Proposed Methodology
3 Preliminary Work
Bag of Features Representation in Biomedical Images
Semantic Biomedical Image Representation
Visual Pattern Mining in Biomedical Images
Doctoral Thesis Proposal Doctoral Program o
Angel Alfonso Cruz Roa, Eng, M.Sc. Advisor:An Automatic Knowledge M.Sc., Ph.D (BioIngenium Research Group - Universidad Naciona
Fabio A. Gonz´lez, Eng, Discovery Strategy In Biomedical Images
a / 41

39. Bag of Features Representation in Biomedical Images
Doctoral Thesis Proposal Doctoral Program o
Angel Alfonso Cruz Roa, Eng, M.Sc. Advisor:An Automatic Knowledge M.Sc., Ph.D (BioIngenium Research Group - Universidad Naciona
Fabio A. Gonz´lez, Eng, Discovery Strategy In Biomedical Images
a / 41

40. Bag of Features Representation in Biomedical Images
Juan C. Caicedo, Angel Cruz-Roa, and Fabio A. Gonz´lez.. Histopathology image classification
a
using bag of features and kernel functions. Lecture Notes in Computer Science. Artificial
Intelligence in Medicine, AIME’09, pp 126-135, July 2009.Volume 5651/2009. ISSN 0302-9743
Doctoral Thesis Proposal Doctoral Program o
Angel Alfonso Cruz Roa, Eng, M.Sc. Advisor:An Automatic Knowledge M.Sc., Ph.D (BioIngenium Research Group - Universidad Naciona
Fabio A. Gonz´lez, Eng, Discovery Strategy In Biomedical Images
a / 41

41. Bag of Features Representation in Biomedical Images
Doctoral Thesis Proposal Doctoral Program o
Angel Alfonso Cruz Roa, Eng, M.Sc. Advisor:An Automatic Knowledge M.Sc., Ph.D (BioIngenium Research Group - Universidad Naciona
Fabio A. Gonz´lez, Eng, Discovery Strategy In Biomedical Images
a / 41

42. Bag of Features Representation in Biomedical Images
Angel Cruz-Roa, Juan C. Caicedo, Fabio A. Gonz´lez. Visual Pattern Mining in Histology Image
a
Collections Using Bag of Features. Journal Artificial Intelligence in Medicine. Vol 52 (2011) pp.
91-106. ISSN 0933-3657.
Doctoral Thesis Proposal Doctoral Program o
Angel Alfonso Cruz Roa, Eng, M.Sc. Advisor:An Automatic Knowledge M.Sc., Ph.D (BioIngenium Research Group - Universidad Naciona
Fabio A. Gonz´lez, Eng, Discovery Strategy In Biomedical Images
a / 41

43. Outline
1 Introduction
Motivation
Research Problem
Research Questions
2 Proposed Research
Objectives
Proposed Methodology
3 Preliminary Work
Bag of Features Representation in Biomedical Images
Semantic Biomedical Image Representation
Visual Pattern Mining in Biomedical Images
Doctoral Thesis Proposal Doctoral Program o
Angel Alfonso Cruz Roa, Eng, M.Sc. Advisor:An Automatic Knowledge M.Sc., Ph.D (BioIngenium Research Group - Universidad Naciona
Fabio A. Gonz´lez, Eng, Discovery Strategy In Biomedical Images
a / 41

44. Semantic Biomedical Image Representation
Angel Cruz-Roa, Juan C. Caicedo and Fabio A. Gonz´lez. Visual Pattern Analysis in
a
Histopathology Images Using Bag of Features. Lecture Notes in Computer Science. 14th
Iberoamerican Congress on Pattern Recognition. CIARP 2009. pp 521-528. Volume 5856/2009.
November 2009. ISBN 978-3-642-10267-7. ISSN 0302-9743
Doctoral Thesis Proposal Doctoral Program o
Angel Alfonso Cruz Roa, Eng, M.Sc. Advisor:An Automatic Knowledge M.Sc., Ph.D (BioIngenium Research Group - Universidad Naciona
Fabio A. Gonz´lez, Eng, Discovery Strategy In Biomedical Images
a / 41

45. Semantic Biomedical Image Representation
Angel Cruz-Roa, Gloria D´ Eduardo Romero, Fabio A. Gonz´lez. Automatic Annotation of
ıaz, a
Histopathological Images Using a Latent Topic Model Based On Non-negative Matrix
Factorization. Journal of Pathology Informatics. (To appear 2011)
Doctoral Thesis Proposal Doctoral Program o
Angel Alfonso Cruz Roa, Eng, M.Sc. Advisor:An Automatic Knowledge M.Sc., Ph.D (BioIngenium Research Group - Universidad Naciona
Fabio A. Gonz´lez, Eng, Discovery Strategy In Biomedical Images
a / 41

46. Outline
1 Introduction
Motivation
Research Problem
Research Questions
2 Proposed Research
Objectives
Proposed Methodology
3 Preliminary Work
Bag of Features Representation in Biomedical Images
Semantic Biomedical Image Representation
Visual Pattern Mining in Biomedical Images
Doctoral Thesis Proposal Doctoral Program o
Angel Alfonso Cruz Roa, Eng, M.Sc. Advisor:An Automatic Knowledge M.Sc., Ph.D (BioIngenium Research Group - Universidad Naciona
Fabio A. Gonz´lez, Eng, Discovery Strategy In Biomedical Images
a / 41

47. Visual Pattern Mining in Biomedical Images
Angel Cruz-Roa, Juan C. Caicedo, Fabio A. Gonz´lez. Visual Pattern Mining in Histology
a
Image Collections Using Bag of Features. Journal Artificial Intelligence in Medicine. Vol
52 (2011) pp. 91-106. ISSN 0933-3657.
Doctoral Thesis Proposal Doctoral Program o
Angel Alfonso Cruz Roa, Eng, M.Sc. Advisor:An Automatic Knowledge M.Sc., Ph.D (BioIngenium Research Group - Universidad Naciona
Fabio A. Gonz´lez, Eng, Discovery Strategy In Biomedical Images
a / 41

48. Visual Pattern Mining in Biomedical Images
Angel Cruz-Roa, Gloria D´ Fabio A. Gonz´lez. A Framework for Semantic Analysis of
ıaz, a
Histopathological Images Using Nonnegative Matrix Factorization. 6th Colombian Computing
Congress (CCC), 2011. May 4-6 2011. Universidad Nacional de Colombia, Sede Manizales.
Manizales (Colombia). ISBN: 978-1-4577-0285-3
Doctoral Thesis Proposal Doctoral Program o
Angel Alfonso Cruz Roa, Eng, M.Sc. Advisor:An Automatic Knowledge M.Sc., Ph.D (BioIngenium Research Group - Universidad Naciona
Fabio A. Gonz´lez, Eng, Discovery Strategy In Biomedical Images
a / 41

49. Thanks for your attention
Questions?
Doctoral Thesis Proposal Doctoral Program o
Angel Alfonso Cruz Roa, Eng, M.Sc. Advisor:An Automatic Knowledge M.Sc., Ph.D (BioIngenium Research Group - Universidad Naciona
Fabio A. Gonz´lez, Eng, Discovery Strategy In Biomedical Images
a / 41

50. Thanks for your attention
Questions?
Doctoral Thesis Proposal Doctoral Program o
Angel Alfonso Cruz Roa, Eng, M.Sc. Advisor:An Automatic Knowledge M.Sc., Ph.D (BioIngenium Research Group - Universidad Naciona
Fabio A. Gonz´lez, Eng, Discovery Strategy In Biomedical Images
a / 41