An Automatic Knowledge Discovery Strategy In                           Biomedical Images                               Ang...
Outline   1    Introduction           Motivation           Research Problem           Research Questions   2    Proposed R...
Motivation                      Classical approach to biomedical image analysis                                           ...
Motivation                      Classical approach to biomedical image analysis                                           ...
Motivation                                          An alternative approach                                               ...
Why?                 Large volumes of data                 Computational                 capability                 Better...
Trends                                                                                       Doctoral Thesis Proposal Doct...
Outline   1    Introduction           Motivation           Research Problem           Research Questions   2    Proposed R...
Research Problem   How to perform automatic extraction of knowledge from biomedical image   collections?   Specifically, ho...
Research Problem   How to perform automatic extraction of knowledge from biomedical image   collections?   Specifically, ho...
Research Challenges                                         Visual content complexity         Stain                       ...
Research Challenges                                  Semantic gap and interpretability                                    ...
Research Challenges                                  Semantic gap and interpretability                                    ...
Research Challenges                                      Scalability for large databases                                  ...
Research Challenges               Scalability for large images (High resolution, 3D & 4D)                                 ...
Outline   1    Introduction           Motivation           Research Problem           Research Questions   2    Proposed R...
Research Questions           How to automatically learn a semantic enriched image representation           from a biomedic...
Research Questions           How to automatically learn a semantic enriched image representation           from a biomedic...
Research Questions           How to automatically learn a semantic enriched image representation           from a biomedic...
Research Questions           How to automatically learn a semantic enriched image representation           from a biomedic...
Research Questions           How to automatically learn a semantic enriched image representation           from a biomedic...
Outline   1    Introduction           Motivation           Research Problem           Research Questions   2    Proposed R...
Main Goal   To propose a strategy for automatic knowledge discovery in   biomedical image databases.                      ...
Specific Objectives           To propose/adapt a strategy for learning part-based image           representation from a col...
Specific Objectives           To propose/adapt a strategy for learning part-based image           representation from a col...
Specific Objectives           To propose/adapt a strategy for learning part-based image           representation from a col...
Outline   1    Introduction           Motivation           Research Problem           Research Questions   2    Proposed R...
Proposed Methodology                                                                                       Doctoral Thesis...
Part-based bioimage representation                                                                                       D...
Part-based bioimage representation                 Cells                 Tissues                 Organs                 Ar...
Part-based bioimage representation                 Bag of features                 Sparse                 Representation  ...
Semantic bioimage representation                                                                                       Doc...
Semantic bioimage representation                 Structural                 knowledge                 Labels and          ...
Semantic bioimage representation                 Latent Semantic                 Analysis                 Graphical models...
Biomedical knowledge discovery                                                                                       Docto...
Biomedical knowledge discovery                 Biomarkers                 Biological patterns                 Pathology fa...
Biomedical knowledge discovery                 Statistical learning                 Clustering                 Analysis   ...
Outline   1    Introduction           Motivation           Research Problem           Research Questions   2    Proposed R...
Bag of Features Representation in Biomedical Images                                                                       ...
Bag of Features Representation in Biomedical Images   Juan C. Caicedo, Angel Cruz-Roa, and Fabio A. Gonz´lez.. Histopathol...
Bag of Features Representation in Biomedical Images                                                                       ...
Bag of Features Representation in Biomedical Images   Angel Cruz-Roa, Juan C. Caicedo, Fabio A. Gonz´lez. Visual Pattern M...
Outline   1    Introduction           Motivation           Research Problem           Research Questions   2    Proposed R...
Semantic Biomedical Image Representation   Angel Cruz-Roa, Juan C. Caicedo and Fabio A. Gonz´lez. Visual Pattern Analysis ...
Semantic Biomedical Image Representation   Angel Cruz-Roa, Gloria D´ Eduardo Romero, Fabio A. Gonz´lez. Automatic Annotati...
Outline   1    Introduction           Motivation           Research Problem           Research Questions   2    Proposed R...
Visual Pattern Mining in Biomedical Images           Angel Cruz-Roa, Juan C. Caicedo, Fabio A. Gonz´lez. Visual Pattern Mi...
Visual Pattern Mining in Biomedical Images   Angel Cruz-Roa, Gloria D´ Fabio A. Gonz´lez. A Framework for Semantic Analysi...
Thanks for your attention                                                 Questions?                                      ...
Thanks for your attention                                                 Questions?                                      ...
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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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Doctoral Thesis Proposal: An Automatic Knowledge Discovery Strategy In Biomedical Images

  1. 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 oAngel 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. 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 oAngel 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. 3. Motivation Classical approach to biomedical image analysis Doctoral Thesis Proposal Doctoral Program oAngel 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. 4. Motivation Classical approach to biomedical image analysis Doctoral Thesis Proposal Doctoral Program oAngel 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. 5. Motivation An alternative approach Doctoral Thesis Proposal Doctoral Program oAngel 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. 6. Why? Large volumes of data Computational capability Better results and interpretability Automatic Knowledge Discovery (biomarkers) Doctoral Thesis Proposal Doctoral Program oAngel 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. 7. Trends Doctoral Thesis Proposal Doctoral Program oAngel 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. 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 oAngel 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. 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 oAngel 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. 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 oAngel 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. 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 oAngel 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. 12. Research Challenges Semantic gap and interpretability ? Doctoral Thesis Proposal Doctoral Program oAngel 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. 13. Research Challenges Semantic gap and interpretability ? Doctoral Thesis Proposal Doctoral Program oAngel 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. 14. Research Challenges Scalability for large databases Doctoral Thesis Proposal Doctoral Program oAngel 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. 15. Research Challenges Scalability for large images (High resolution, 3D & 4D) Doctoral Thesis Proposal Doctoral Program oAngel 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. 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 oAngel 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. 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 oAngel 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. 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 oAngel 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. 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 oAngel 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. 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 oAngel 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. 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 oAngel 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. 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 oAngel 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. 23. Main Goal To propose a strategy for automatic knowledge discovery in biomedical image databases. Doctoral Thesis Proposal Doctoral Program oAngel 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. 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 oAngel 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. 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 oAngel 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. 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 oAngel 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. 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 oAngel 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. 28. Proposed Methodology Doctoral Thesis Proposal Doctoral Program oAngel 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. 29. Part-based bioimage representation Doctoral Thesis Proposal Doctoral Program oAngel 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. 30. Part-based bioimage representation Cells Tissues Organs Architectural features Doctoral Thesis Proposal Doctoral Program oAngel 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. 31. Part-based bioimage representation Bag of features Sparse Representation Sparse Deep Belief Networks Doctoral Thesis Proposal Doctoral Program oAngel 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. 32. Semantic bioimage representation Doctoral Thesis Proposal Doctoral Program oAngel 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. 33. Semantic bioimage representation Structural knowledge Labels and concepts Annotations Descriptions Other modalities Doctoral Thesis Proposal Doctoral Program oAngel 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. 34. Semantic bioimage representation Latent Semantic Analysis Graphical models Non-negative Matrix Factorization Kernel Methods Doctoral Thesis Proposal Doctoral Program oAngel 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. 35. Biomedical knowledge discovery Doctoral Thesis Proposal Doctoral Program oAngel 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. 36. Biomedical knowledge discovery Biomarkers Biological patterns Pathology factors Patterns relations Data correlation Biological interpretation Diagnosis, prognosis and theragnosis Doctoral Thesis Proposal Doctoral Program oAngel 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. 37. Biomedical knowledge discovery Statistical learning Clustering Analysis Association Rules Structure Output Learning Decision trees Doctoral Thesis Proposal Doctoral Program oAngel 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. 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 oAngel 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. 39. Bag of Features Representation in Biomedical Images Doctoral Thesis Proposal Doctoral Program oAngel 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. 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 oAngel 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. 41. Bag of Features Representation in Biomedical Images Doctoral Thesis Proposal Doctoral Program oAngel 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. 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 oAngel 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. 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 oAngel 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. 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 oAngel 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. 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 oAngel 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. 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 oAngel 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. 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 oAngel 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. 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 oAngel 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. 49. Thanks for your attention Questions? Doctoral Thesis Proposal Doctoral Program oAngel 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. 50. Thanks for your attention Questions? Doctoral Thesis Proposal Doctoral Program oAngel 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

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