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BioMarker Discovery Kit

Contents

  1. Goal of the Investigation
  2. Method of Examination
  3. Fingerprint-based versus Biomarker-based Classifiers
    1. What is the difference between fingerprint-based and biomarker-based classifiers?
    2. Common fingerprint-based classifiers
      1. Decision Trees
      2. Medoid Classification Algorithm
    3. Why are fingerprint-based classifiers not generalizable?
    4. Proposed biomarker-based classifier
  4. Concerns for any dataset or classifier
    1. Bias, chance and generalizability
    2. Coverage, Uniqueness and significance
  5. Identifying Putative Biomarkers
    1. Methods used in BMDK
      1. catboot
      2. student
      3. dtgini
      4. dtinfg
      5. nnfeat
      6. chisq
      7. kruswal
      8. kolsmir
      9. extreme
      10. vartest
    2. Comparisons and conclusions
  6. Form of a Biomarker-based Classifier
    1. Distance-Dependent K-Nearest Neighbor
  7. Need a Consistent Meaning for Terms
    1. Replace “panel of markers” with “battery of tests”
    2. Replace “personalized medicine” with “State-based diagnosis and treatment”
  8. Analyzing Spectroscopic Datasets
    1. Published Prostate Dataset
    2. Datasets Containing No Biological Information
  9. Datasets
    1. Structure of the Datasets
    2. Random Intensity Datasets
      1. 30 cases and 30 Controls
      2. 42 cases and 42 Controls
      3. 60 cases and 60 Controls
      4. 90 cases and 90 Controls
      5. 150 cases and 150 Controls
      6. 300 cases and 300 Controls
  10. References