Doctoral Thesis Proposal: An Automatic Knowledge Discovery Strategy In Biomedical Images

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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.

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An Automatic Knowledge Discovery Strategy InBiomedical Images

Angel Alfonso Cruz Roa, Eng, M.Sc.Advisor: Fabio A. Gonzalez, Eng, M.Sc., Ph.D

BioIngenium Research Group - Universidad Nacional de Colombiahttp://www.bioingenium.unal.edu.co/

Doctoral Thesis ProposalDoctoral Program on Computer and Systems Engineering

December 1, 2011

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

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Outline

1 IntroductionMotivationResearch ProblemResearch Questions

2 Proposed ResearchObjectivesProposed Methodology

3 Preliminary WorkBag of Features Representation in Biomedical ImagesSemantic Biomedical Image RepresentationVisual Pattern Mining in Biomedical Images

Angel Alfonso Cruz Roa, Eng, M.Sc. Advisor: Fabio A. Gonzalez, Eng, M.Sc., Ph.D (BioIngenium Research Group - Universidad Nacional de Colombia http://www.bioingenium.unal.edu.co/)An Automatic Knowledge Discovery Strategy In Biomedical ImagesDoctoral Thesis Proposal Doctoral Program on Computer and Systems Engineering December 1, 2011 2

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MotivationClassical approach to biomedical image analysis

Angel Alfonso Cruz Roa, Eng, M.Sc. Advisor: Fabio A. Gonzalez, Eng, M.Sc., Ph.D (BioIngenium Research Group - Universidad Nacional de Colombia http://www.bioingenium.unal.edu.co/)An Automatic Knowledge Discovery Strategy In Biomedical ImagesDoctoral Thesis Proposal Doctoral Program on Computer and Systems Engineering December 1, 2011 3

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MotivationClassical approach to biomedical image analysis

Angel Alfonso Cruz Roa, Eng, M.Sc. Advisor: Fabio A. Gonzalez, Eng, M.Sc., Ph.D (BioIngenium Research Group - Universidad Nacional de Colombia http://www.bioingenium.unal.edu.co/)An Automatic Knowledge Discovery Strategy In Biomedical ImagesDoctoral Thesis Proposal Doctoral Program on Computer and Systems Engineering December 1, 2011 4

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MotivationAn alternative approach

Angel Alfonso Cruz Roa, Eng, M.Sc. Advisor: Fabio A. Gonzalez, Eng, M.Sc., Ph.D (BioIngenium Research Group - Universidad Nacional de Colombia http://www.bioingenium.unal.edu.co/)An Automatic Knowledge Discovery Strategy In Biomedical ImagesDoctoral Thesis Proposal Doctoral Program on Computer and Systems Engineering December 1, 2011 5

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Why?

Large volumes of dataComputationalcapabilityBetter results andinterpretabilityAutomatic KnowledgeDiscovery(biomarkers)

Angel Alfonso Cruz Roa, Eng, M.Sc. Advisor: Fabio A. Gonzalez, Eng, M.Sc., Ph.D (BioIngenium Research Group - Universidad Nacional de Colombia http://www.bioingenium.unal.edu.co/)An Automatic Knowledge Discovery Strategy In Biomedical ImagesDoctoral Thesis Proposal Doctoral Program on Computer and Systems Engineering December 1, 2011 6

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Trends

Angel Alfonso Cruz Roa, Eng, M.Sc. Advisor: Fabio A. Gonzalez, Eng, M.Sc., Ph.D (BioIngenium Research Group - Universidad Nacional de Colombia http://www.bioingenium.unal.edu.co/)An Automatic Knowledge Discovery Strategy In Biomedical ImagesDoctoral Thesis Proposal Doctoral Program on Computer and Systems Engineering December 1, 2011 7

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Outline

1 IntroductionMotivationResearch ProblemResearch Questions

2 Proposed ResearchObjectivesProposed Methodology

3 Preliminary WorkBag of Features Representation in Biomedical ImagesSemantic Biomedical Image RepresentationVisual Pattern Mining in Biomedical Images

Angel Alfonso Cruz Roa, Eng, M.Sc. Advisor: Fabio A. Gonzalez, Eng, M.Sc., Ph.D (BioIngenium Research Group - Universidad Nacional de Colombia http://www.bioingenium.unal.edu.co/)An Automatic Knowledge Discovery Strategy In Biomedical ImagesDoctoral Thesis Proposal Doctoral Program on Computer and Systems Engineering December 1, 2011 8

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Research Problem

How to perform automatic extraction of knowledge from biomedical imagecollections?

Specifically, how to find, automatically, visual patterns that compactlyexplain the visual richness of biomedical images, relationships betweenvisual patterns, and relationships between visual patterns and theirmeaning in a particular biomedical context?

Angel Alfonso Cruz Roa, Eng, M.Sc. Advisor: Fabio A. Gonzalez, Eng, M.Sc., Ph.D (BioIngenium Research Group - Universidad Nacional de Colombia http://www.bioingenium.unal.edu.co/)An Automatic Knowledge Discovery Strategy In Biomedical ImagesDoctoral Thesis Proposal Doctoral Program on Computer and Systems Engineering December 1, 2011 9

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Research Problem

How to perform automatic extraction of knowledge from biomedical imagecollections?

Specifically, how to find, automatically, visual patterns that compactlyexplain the visual richness of biomedical images, relationships betweenvisual patterns, and relationships between visual patterns and theirmeaning in a particular biomedical context?

Angel Alfonso Cruz Roa, Eng, M.Sc. Advisor: Fabio A. Gonzalez, Eng, M.Sc., Ph.D (BioIngenium Research Group - Universidad Nacional de Colombia http://www.bioingenium.unal.edu.co/)An Automatic Knowledge Discovery Strategy In Biomedical ImagesDoctoral Thesis Proposal Doctoral Program on Computer and Systems Engineering December 1, 2011 9

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Research ChallengesVisual content complexity

StainSkin of images (40X) stained with Hematoxilyn-eosin and Trichrome of Masson

MagnificationMuscular tissue in tongue stained with Trichrome of Masson (10X, 20X and 40X)

Type of CutCardiac striated muscular tissue, heart (HE), 1000X. Longitudinal and transverse cuts.

Angel Alfonso Cruz Roa, Eng, M.Sc. Advisor: Fabio A. Gonzalez, Eng, M.Sc., Ph.D (BioIngenium Research Group - Universidad Nacional de Colombia http://www.bioingenium.unal.edu.co/)An Automatic Knowledge Discovery Strategy In Biomedical ImagesDoctoral Thesis Proposal Doctoral Program on Computer and Systems Engineering December 1, 2011 10

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Research Challenges

Semantic gap and interpretability

?

Angel Alfonso Cruz Roa, Eng, M.Sc. Advisor: Fabio A. Gonzalez, Eng, M.Sc., Ph.D (BioIngenium Research Group - Universidad Nacional de Colombia http://www.bioingenium.unal.edu.co/)An Automatic Knowledge Discovery Strategy In Biomedical ImagesDoctoral Thesis Proposal Doctoral Program on Computer and Systems Engineering December 1, 2011 11

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Research Challenges

Semantic gap and interpretability

?

Angel Alfonso Cruz Roa, Eng, M.Sc. Advisor: Fabio A. Gonzalez, Eng, M.Sc., Ph.D (BioIngenium Research Group - Universidad Nacional de Colombia http://www.bioingenium.unal.edu.co/)An Automatic Knowledge Discovery Strategy In Biomedical ImagesDoctoral Thesis Proposal Doctoral Program on Computer and Systems Engineering December 1, 2011 11

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Research Challenges

Scalability for large databases

Angel Alfonso Cruz Roa, Eng, M.Sc. Advisor: Fabio A. Gonzalez, Eng, M.Sc., Ph.D (BioIngenium Research Group - Universidad Nacional de Colombia http://www.bioingenium.unal.edu.co/)An Automatic Knowledge Discovery Strategy In Biomedical ImagesDoctoral Thesis Proposal Doctoral Program on Computer and Systems Engineering December 1, 2011 12

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Research ChallengesScalability for large images (High resolution, 3D & 4D)

Angel Alfonso Cruz Roa, Eng, M.Sc. Advisor: Fabio A. Gonzalez, Eng, M.Sc., Ph.D (BioIngenium Research Group - Universidad Nacional de Colombia http://www.bioingenium.unal.edu.co/)An Automatic Knowledge Discovery Strategy In Biomedical ImagesDoctoral Thesis Proposal Doctoral Program on Computer and Systems Engineering December 1, 2011 13

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Outline

1 IntroductionMotivationResearch ProblemResearch Questions

2 Proposed ResearchObjectivesProposed Methodology

3 Preliminary WorkBag of Features Representation in Biomedical ImagesSemantic Biomedical Image RepresentationVisual Pattern Mining in Biomedical Images

Angel Alfonso Cruz Roa, Eng, M.Sc. Advisor: Fabio A. Gonzalez, Eng, M.Sc., Ph.D (BioIngenium Research Group - Universidad Nacional de Colombia http://www.bioingenium.unal.edu.co/)An Automatic Knowledge Discovery Strategy In Biomedical ImagesDoctoral Thesis Proposal Doctoral Program on Computer and Systems Engineering December 1, 2011 14

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Research Questions

How to automatically learn a semantic enriched image representationfrom a biomedical image collection?

How to use the learned representation to find interesting patterns thatconnect visual content and biomedical meaning?

Does this kind of representation improve the performance in taskssuch as automatic image annotation and segmentation?

How to use the learned representation to make image analysis modelsmore interpretable?

How to make algorithms scalable to large (hundreds of thousands ormillions) biomedical image collections?

Angel Alfonso Cruz Roa, Eng, M.Sc. Advisor: Fabio A. Gonzalez, Eng, M.Sc., Ph.D (BioIngenium Research Group - Universidad Nacional de Colombia http://www.bioingenium.unal.edu.co/)An Automatic Knowledge Discovery Strategy In Biomedical ImagesDoctoral Thesis Proposal Doctoral Program on Computer and Systems Engineering December 1, 2011 15

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Research Questions

How to automatically learn a semantic enriched image representationfrom a biomedical image collection?

How to use the learned representation to find interesting patterns thatconnect visual content and biomedical meaning?

Does this kind of representation improve the performance in taskssuch as automatic image annotation and segmentation?

How to use the learned representation to make image analysis modelsmore interpretable?

How to make algorithms scalable to large (hundreds of thousands ormillions) biomedical image collections?

Angel Alfonso Cruz Roa, Eng, M.Sc. Advisor: Fabio A. Gonzalez, Eng, M.Sc., Ph.D (BioIngenium Research Group - Universidad Nacional de Colombia http://www.bioingenium.unal.edu.co/)An Automatic Knowledge Discovery Strategy In Biomedical ImagesDoctoral Thesis Proposal Doctoral Program on Computer and Systems Engineering December 1, 2011 15

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Research Questions

How to automatically learn a semantic enriched image representationfrom a biomedical image collection?

How to use the learned representation to find interesting patterns thatconnect visual content and biomedical meaning?

Does this kind of representation improve the performance in taskssuch as automatic image annotation and segmentation?

How to use the learned representation to make image analysis modelsmore interpretable?

How to make algorithms scalable to large (hundreds of thousands ormillions) biomedical image collections?

Angel Alfonso Cruz Roa, Eng, M.Sc. Advisor: Fabio A. Gonzalez, Eng, M.Sc., Ph.D (BioIngenium Research Group - Universidad Nacional de Colombia http://www.bioingenium.unal.edu.co/)An Automatic Knowledge Discovery Strategy In Biomedical ImagesDoctoral Thesis Proposal Doctoral Program on Computer and Systems Engineering December 1, 2011 15

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Research Questions

How to automatically learn a semantic enriched image representationfrom a biomedical image collection?

How to use the learned representation to find interesting patterns thatconnect visual content and biomedical meaning?

Does this kind of representation improve the performance in taskssuch as automatic image annotation and segmentation?

How to use the learned representation to make image analysis modelsmore interpretable?

How to make algorithms scalable to large (hundreds of thousands ormillions) biomedical image collections?

Angel Alfonso Cruz Roa, Eng, M.Sc. Advisor: Fabio A. Gonzalez, Eng, M.Sc., Ph.D (BioIngenium Research Group - Universidad Nacional de Colombia http://www.bioingenium.unal.edu.co/)An Automatic Knowledge Discovery Strategy In Biomedical ImagesDoctoral Thesis Proposal Doctoral Program on Computer and Systems Engineering December 1, 2011 15

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Research Questions

How to automatically learn a semantic enriched image representationfrom a biomedical image collection?

How to use the learned representation to find interesting patterns thatconnect visual content and biomedical meaning?

Does this kind of representation improve the performance in taskssuch as automatic image annotation and segmentation?

How to use the learned representation to make image analysis modelsmore interpretable?

How to make algorithms scalable to large (hundreds of thousands ormillions) biomedical image collections?

Angel Alfonso Cruz Roa, Eng, M.Sc. Advisor: Fabio A. Gonzalez, Eng, M.Sc., Ph.D (BioIngenium Research Group - Universidad Nacional de Colombia http://www.bioingenium.unal.edu.co/)An Automatic Knowledge Discovery Strategy In Biomedical ImagesDoctoral Thesis Proposal Doctoral Program on Computer and Systems Engineering December 1, 2011 15

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Outline

1 IntroductionMotivationResearch ProblemResearch Questions

2 Proposed ResearchObjectivesProposed Methodology

3 Preliminary WorkBag of Features Representation in Biomedical ImagesSemantic Biomedical Image RepresentationVisual Pattern Mining in Biomedical Images

Angel Alfonso Cruz Roa, Eng, M.Sc. Advisor: Fabio A. Gonzalez, Eng, M.Sc., Ph.D (BioIngenium Research Group - Universidad Nacional de Colombia http://www.bioingenium.unal.edu.co/)An Automatic Knowledge Discovery Strategy In Biomedical ImagesDoctoral Thesis Proposal Doctoral Program on Computer and Systems Engineering December 1, 2011 16

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Main Goal

To propose a strategy for automatic knowledge discovery inbiomedical image databases.

Angel Alfonso Cruz Roa, Eng, M.Sc. Advisor: Fabio A. Gonzalez, Eng, M.Sc., Ph.D (BioIngenium Research Group - Universidad Nacional de Colombia http://www.bioingenium.unal.edu.co/)An Automatic Knowledge Discovery Strategy In Biomedical ImagesDoctoral Thesis Proposal Doctoral Program on Computer and Systems Engineering December 1, 2011 17

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Specific Objectives

To propose/adapt a strategy for learning part-based imagerepresentation from a collection of biomedical images.

To propose and validate a learning method that enriches the learnedimage representation with semantic content from a particularbiomedical domain.

To propose and validate a method for image collection analysis andvisual pattern mining in biomedical image collections.

Angel Alfonso Cruz Roa, Eng, M.Sc. Advisor: Fabio A. Gonzalez, Eng, M.Sc., Ph.D (BioIngenium Research Group - Universidad Nacional de Colombia http://www.bioingenium.unal.edu.co/)An Automatic Knowledge Discovery Strategy In Biomedical ImagesDoctoral Thesis Proposal Doctoral Program on Computer and Systems Engineering December 1, 2011 18

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Specific Objectives

To propose/adapt a strategy for learning part-based imagerepresentation from a collection of biomedical images.

To propose and validate a learning method that enriches the learnedimage representation with semantic content from a particularbiomedical domain.

To propose and validate a method for image collection analysis andvisual pattern mining in biomedical image collections.

Angel Alfonso Cruz Roa, Eng, M.Sc. Advisor: Fabio A. Gonzalez, Eng, M.Sc., Ph.D (BioIngenium Research Group - Universidad Nacional de Colombia http://www.bioingenium.unal.edu.co/)An Automatic Knowledge Discovery Strategy In Biomedical ImagesDoctoral Thesis Proposal Doctoral Program on Computer and Systems Engineering December 1, 2011 18

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Specific Objectives

To propose/adapt a strategy for learning part-based imagerepresentation from a collection of biomedical images.

To propose and validate a learning method that enriches the learnedimage representation with semantic content from a particularbiomedical domain.

To propose and validate a method for image collection analysis andvisual pattern mining in biomedical image collections.

Angel Alfonso Cruz Roa, Eng, M.Sc. Advisor: Fabio A. Gonzalez, Eng, M.Sc., Ph.D (BioIngenium Research Group - Universidad Nacional de Colombia http://www.bioingenium.unal.edu.co/)An Automatic Knowledge Discovery Strategy In Biomedical ImagesDoctoral Thesis Proposal Doctoral Program on Computer and Systems Engineering December 1, 2011 18

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Outline

1 IntroductionMotivationResearch ProblemResearch Questions

2 Proposed ResearchObjectivesProposed Methodology

3 Preliminary WorkBag of Features Representation in Biomedical ImagesSemantic Biomedical Image RepresentationVisual Pattern Mining in Biomedical Images

Angel Alfonso Cruz Roa, Eng, M.Sc. Advisor: Fabio A. Gonzalez, Eng, M.Sc., Ph.D (BioIngenium Research Group - Universidad Nacional de Colombia http://www.bioingenium.unal.edu.co/)An Automatic Knowledge Discovery Strategy In Biomedical ImagesDoctoral Thesis Proposal Doctoral Program on Computer and Systems Engineering December 1, 2011 19

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Proposed Methodology

Angel Alfonso Cruz Roa, Eng, M.Sc. Advisor: Fabio A. Gonzalez, Eng, M.Sc., Ph.D (BioIngenium Research Group - Universidad Nacional de Colombia http://www.bioingenium.unal.edu.co/)An Automatic Knowledge Discovery Strategy In Biomedical ImagesDoctoral Thesis Proposal Doctoral Program on Computer and Systems Engineering December 1, 2011 20

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Part-based bioimage representation

Angel Alfonso Cruz Roa, Eng, M.Sc. Advisor: Fabio A. Gonzalez, Eng, M.Sc., Ph.D (BioIngenium Research Group - Universidad Nacional de Colombia http://www.bioingenium.unal.edu.co/)An Automatic Knowledge Discovery Strategy In Biomedical ImagesDoctoral Thesis Proposal Doctoral Program on Computer and Systems Engineering December 1, 2011 21

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Part-based bioimage representation

CellsTissuesOrgansArchitecturalfeatures

Angel Alfonso Cruz Roa, Eng, M.Sc. Advisor: Fabio A. Gonzalez, Eng, M.Sc., Ph.D (BioIngenium Research Group - Universidad Nacional de Colombia http://www.bioingenium.unal.edu.co/)An Automatic Knowledge Discovery Strategy In Biomedical ImagesDoctoral Thesis Proposal Doctoral Program on Computer and Systems Engineering December 1, 2011 22

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Part-based bioimage representation

Bag of featuresSparseRepresentationSparse DeepBelief Networks

Angel Alfonso Cruz Roa, Eng, M.Sc. Advisor: Fabio A. Gonzalez, Eng, M.Sc., Ph.D (BioIngenium Research Group - Universidad Nacional de Colombia http://www.bioingenium.unal.edu.co/)An Automatic Knowledge Discovery Strategy In Biomedical ImagesDoctoral Thesis Proposal Doctoral Program on Computer and Systems Engineering December 1, 2011 23

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Semantic bioimage representation

Angel Alfonso Cruz Roa, Eng, M.Sc. Advisor: Fabio A. Gonzalez, Eng, M.Sc., Ph.D (BioIngenium Research Group - Universidad Nacional de Colombia http://www.bioingenium.unal.edu.co/)An Automatic Knowledge Discovery Strategy In Biomedical ImagesDoctoral Thesis Proposal Doctoral Program on Computer and Systems Engineering December 1, 2011 24

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Semantic bioimage representation

StructuralknowledgeLabels andconceptsAnnotationsDescriptionsOther modalities

Angel Alfonso Cruz Roa, Eng, M.Sc. Advisor: Fabio A. Gonzalez, Eng, M.Sc., Ph.D (BioIngenium Research Group - Universidad Nacional de Colombia http://www.bioingenium.unal.edu.co/)An Automatic Knowledge Discovery Strategy In Biomedical ImagesDoctoral Thesis Proposal Doctoral Program on Computer and Systems Engineering December 1, 2011 25

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Semantic bioimage representation

Latent SemanticAnalysisGraphical modelsNon-negativeMatrixFactorizationKernel Methods

Angel Alfonso Cruz Roa, Eng, M.Sc. Advisor: Fabio A. Gonzalez, Eng, M.Sc., Ph.D (BioIngenium Research Group - Universidad Nacional de Colombia http://www.bioingenium.unal.edu.co/)An Automatic Knowledge Discovery Strategy In Biomedical ImagesDoctoral Thesis Proposal Doctoral Program on Computer and Systems Engineering December 1, 2011 26

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Biomedical knowledge discovery

Angel Alfonso Cruz Roa, Eng, M.Sc. Advisor: Fabio A. Gonzalez, Eng, M.Sc., Ph.D (BioIngenium Research Group - Universidad Nacional de Colombia http://www.bioingenium.unal.edu.co/)An Automatic Knowledge Discovery Strategy In Biomedical ImagesDoctoral Thesis Proposal Doctoral Program on Computer and Systems Engineering December 1, 2011 27

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Biomedical knowledge discovery

BiomarkersBiological patternsPathology factorsPatterns relationsData correlationBiologicalinterpretationDiagnosis,prognosis andtheragnosis

Angel Alfonso Cruz Roa, Eng, M.Sc. Advisor: Fabio A. Gonzalez, Eng, M.Sc., Ph.D (BioIngenium Research Group - Universidad Nacional de Colombia http://www.bioingenium.unal.edu.co/)An Automatic Knowledge Discovery Strategy In Biomedical ImagesDoctoral Thesis Proposal Doctoral Program on Computer and Systems Engineering December 1, 2011 28

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Biomedical knowledge discovery

Statistical learningClusteringAnalysisAssociation RulesStructure OutputLearningDecision trees

Angel Alfonso Cruz Roa, Eng, M.Sc. Advisor: Fabio A. Gonzalez, Eng, M.Sc., Ph.D (BioIngenium Research Group - Universidad Nacional de Colombia http://www.bioingenium.unal.edu.co/)An Automatic Knowledge Discovery Strategy In Biomedical ImagesDoctoral Thesis Proposal Doctoral Program on Computer and Systems Engineering December 1, 2011 29

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Outline

1 IntroductionMotivationResearch ProblemResearch Questions

2 Proposed ResearchObjectivesProposed Methodology

3 Preliminary WorkBag of Features Representation in Biomedical ImagesSemantic Biomedical Image RepresentationVisual Pattern Mining in Biomedical Images

Angel Alfonso Cruz Roa, Eng, M.Sc. Advisor: Fabio A. Gonzalez, Eng, M.Sc., Ph.D (BioIngenium Research Group - Universidad Nacional de Colombia http://www.bioingenium.unal.edu.co/)An Automatic Knowledge Discovery Strategy In Biomedical ImagesDoctoral Thesis Proposal Doctoral Program on Computer and Systems Engineering December 1, 2011 30

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Bag of Features Representation in Biomedical Images

Angel Alfonso Cruz Roa, Eng, M.Sc. Advisor: Fabio A. Gonzalez, Eng, M.Sc., Ph.D (BioIngenium Research Group - Universidad Nacional de Colombia http://www.bioingenium.unal.edu.co/)An Automatic Knowledge Discovery Strategy In Biomedical ImagesDoctoral Thesis Proposal Doctoral Program on Computer and Systems Engineering December 1, 2011 31

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Bag of Features Representation in Biomedical ImagesJuan C. Caicedo, Angel Cruz-Roa, and Fabio A. Gonzalez.. Histopathology image classificationusing bag of features and kernel functions. Lecture Notes in Computer Science. ArtificialIntelligence in Medicine, AIME’09, pp 126-135, July 2009.Volume 5651/2009. ISSN 0302-9743

Angel Alfonso Cruz Roa, Eng, M.Sc. Advisor: Fabio A. Gonzalez, Eng, M.Sc., Ph.D (BioIngenium Research Group - Universidad Nacional de Colombia http://www.bioingenium.unal.edu.co/)An Automatic Knowledge Discovery Strategy In Biomedical ImagesDoctoral Thesis Proposal Doctoral Program on Computer and Systems Engineering December 1, 2011 32

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Bag of Features Representation in Biomedical Images

Angel Alfonso Cruz Roa, Eng, M.Sc. Advisor: Fabio A. Gonzalez, Eng, M.Sc., Ph.D (BioIngenium Research Group - Universidad Nacional de Colombia http://www.bioingenium.unal.edu.co/)An Automatic Knowledge Discovery Strategy In Biomedical ImagesDoctoral Thesis Proposal Doctoral Program on Computer and Systems Engineering December 1, 2011 33

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Bag of Features Representation in Biomedical ImagesAngel Cruz-Roa, Juan C. Caicedo, Fabio A. Gonzalez. Visual Pattern Mining in Histology ImageCollections Using Bag of Features. Journal Artificial Intelligence in Medicine. Vol 52 (2011) pp.91-106. ISSN 0933-3657.

Angel Alfonso Cruz Roa, Eng, M.Sc. Advisor: Fabio A. Gonzalez, Eng, M.Sc., Ph.D (BioIngenium Research Group - Universidad Nacional de Colombia http://www.bioingenium.unal.edu.co/)An Automatic Knowledge Discovery Strategy In Biomedical ImagesDoctoral Thesis Proposal Doctoral Program on Computer and Systems Engineering December 1, 2011 34

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Outline

1 IntroductionMotivationResearch ProblemResearch Questions

2 Proposed ResearchObjectivesProposed Methodology

3 Preliminary WorkBag of Features Representation in Biomedical ImagesSemantic Biomedical Image RepresentationVisual Pattern Mining in Biomedical Images

Angel Alfonso Cruz Roa, Eng, M.Sc. Advisor: Fabio A. Gonzalez, Eng, M.Sc., Ph.D (BioIngenium Research Group - Universidad Nacional de Colombia http://www.bioingenium.unal.edu.co/)An Automatic Knowledge Discovery Strategy In Biomedical ImagesDoctoral Thesis Proposal Doctoral Program on Computer and Systems Engineering December 1, 2011 35

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Semantic Biomedical Image RepresentationAngel Cruz-Roa, Juan C. Caicedo and Fabio A. Gonzalez. Visual Pattern Analysis inHistopathology Images Using Bag of Features. Lecture Notes in Computer Science. 14thIberoamerican Congress on Pattern Recognition. CIARP 2009. pp 521-528. Volume 5856/2009.November 2009. ISBN 978-3-642-10267-7. ISSN 0302-9743

Angel Alfonso Cruz Roa, Eng, M.Sc. Advisor: Fabio A. Gonzalez, Eng, M.Sc., Ph.D (BioIngenium Research Group - Universidad Nacional de Colombia http://www.bioingenium.unal.edu.co/)An Automatic Knowledge Discovery Strategy In Biomedical ImagesDoctoral Thesis Proposal Doctoral Program on Computer and Systems Engineering December 1, 2011 36

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Semantic Biomedical Image Representation

Angel Cruz-Roa, Gloria Dıaz, Eduardo Romero, Fabio A. Gonzalez. Automatic Annotation ofHistopathological Images Using a Latent Topic Model Based On Non-negative MatrixFactorization. Journal of Pathology Informatics. (To appear 2011)

Angel Alfonso Cruz Roa, Eng, M.Sc. Advisor: Fabio A. Gonzalez, Eng, M.Sc., Ph.D (BioIngenium Research Group - Universidad Nacional de Colombia http://www.bioingenium.unal.edu.co/)An Automatic Knowledge Discovery Strategy In Biomedical ImagesDoctoral Thesis Proposal Doctoral Program on Computer and Systems Engineering December 1, 2011 37

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Outline

1 IntroductionMotivationResearch ProblemResearch Questions

2 Proposed ResearchObjectivesProposed Methodology

3 Preliminary WorkBag of Features Representation in Biomedical ImagesSemantic Biomedical Image RepresentationVisual Pattern Mining in Biomedical Images

Angel Alfonso Cruz Roa, Eng, M.Sc. Advisor: Fabio A. Gonzalez, Eng, M.Sc., Ph.D (BioIngenium Research Group - Universidad Nacional de Colombia http://www.bioingenium.unal.edu.co/)An Automatic Knowledge Discovery Strategy In Biomedical ImagesDoctoral Thesis Proposal Doctoral Program on Computer and Systems Engineering December 1, 2011 38

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Visual Pattern Mining in Biomedical Images

Angel Cruz-Roa, Juan C. Caicedo, Fabio A. Gonzalez. Visual Pattern Mining in HistologyImage Collections Using Bag of Features. Journal Artificial Intelligence in Medicine. Vol52 (2011) pp. 91-106. ISSN 0933-3657.

Angel Alfonso Cruz Roa, Eng, M.Sc. Advisor: Fabio A. Gonzalez, Eng, M.Sc., Ph.D (BioIngenium Research Group - Universidad Nacional de Colombia http://www.bioingenium.unal.edu.co/)An Automatic Knowledge Discovery Strategy In Biomedical ImagesDoctoral Thesis Proposal Doctoral Program on Computer and Systems Engineering December 1, 2011 39

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Visual Pattern Mining in Biomedical ImagesAngel Cruz-Roa, Gloria Dıaz, Fabio A. Gonzalez. A Framework for Semantic Analysis ofHistopathological Images Using Nonnegative Matrix Factorization. 6th Colombian ComputingCongress (CCC), 2011. May 4-6 2011. Universidad Nacional de Colombia, Sede Manizales.Manizales (Colombia). ISBN: 978-1-4577-0285-3

Angel Alfonso Cruz Roa, Eng, M.Sc. Advisor: Fabio A. Gonzalez, Eng, M.Sc., Ph.D (BioIngenium Research Group - Universidad Nacional de Colombia http://www.bioingenium.unal.edu.co/)An Automatic Knowledge Discovery Strategy In Biomedical ImagesDoctoral Thesis Proposal Doctoral Program on Computer and Systems Engineering December 1, 2011 40

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Thanks for your attentionQuestions?

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

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Thanks for your attentionQuestions?

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

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