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  • 1. Introduction to class 1/4/2010 TCSS588A Isabelle Bichindaritz
  • 2. Outline
    • Introduction to class
    • Introduction to machine learning / data mining
    • Introduction to the Life Sciences
    • Example and importance of microarray data
    1/4/2010 TCSS588A Isabelle Bichindaritz
  • 3. Introduction to Class
    • This class focuses on learning how to apply data mining to biological and medical fields to solve some of their problems.
    • Does not require prior knowledge in the application areas.
    • Does not require prior knowledge in machine learning and/or data mining.
    1/4/2010 TCSS588A Isabelle Bichindaritz
  • 4. Introduction to Class
    • Data mining specialized in
      • Statistical data analysis and inference – SPSS, R-language
      • Clustering – SPSS, Gene Pattern
      • Machine learning - Rapid Miner
      • Classification – Rapid Miner ,R-language.
    • Requirement: use biological datasets and/or medical datasets.
    • Seattle area has many renowned research institutes.
    1/4/2010 TCSS588A Isabelle Bichindaritz
  • 5. 1/4/2010 TCSS588A Isabelle Bichindaritz Human Genome Program, U.S. Department of Energy, Genomics and Its Impact on Medicine and Society: A 2001 Primer, 2001
  • 6. The Human Genome Project
    • The Human Genome Project
    1/4/2010 TCSS588A Isabelle Bichindaritz
  • 7. Data Mining Motivation: “Necessity is the Mother of Invention”
    • Data explosion problem
      • Automated data collection tools and mature database technology lead to tremendous amounts of data stored in databases, data warehouses and other information repositories
    • We are drowning in data, but starving for knowledge!
    • Solution: Data warehousing and data mining
      • Data warehousing and on-line analytical processing
      • Extraction of interesting knowledge (rules, regularities, patterns, constraints) from data in large databases
    1/4/2010 TCSS588A Isabelle Bichindaritz
  • 8. What Is Data Mining?
    • Data mining (knowledge discovery in databases):
      • Extraction of interesting ( non-trivial, implicit , previously unknown and potentially useful) information or patterns from data in large databases
    • Alternative names and their “inside stories”:
      • Data mining: a misnomer?
      • Knowledge discovery(mining) in databases (KDD), knowledge extraction, data/pattern analysis, data archeology, data dredging, information harvesting, business intelligence, etc.
    • What is not data mining?
      • (Deductive) query processing.
      • Expert systems or small ML/statistical programs are often a part of data mining
    1/4/2010 TCSS588A Isabelle Bichindaritz
  • 9. What Is Data Mining?
    • Data mining (knowledge discovery in databases) is the process of discovering interesting knowledge from large amounts of data stored either in databases, data warehouses, or other information repositories.
    • Machine learning and knowledge discovery are interested in the process of discovering knowledge that may be structurally or semantically more complex: models, graphs, new theorems or theories … in particular to assist scientific discovery.
    1/4/2010 TCSS588A Isabelle Bichindaritz
  • 10. Data Mining: A KDD Process
      • Data mining: the core of knowledge discovery process.
    1/4/2010 TCSS588A Isabelle Bichindaritz Data Cleaning Data Integration Databases Data Warehouse Knowledge Task-relevant Data Selection Data Mining Pattern Evaluation
  • 11. Machine Learning Functionalities (1)
    • Concept description: Characterization and discrimination
      • Generalize, summarize, and contrast data characteristics, e.g., dry vs. wet regions
    • Association ( correlation and causality)
      • Multi-dimensional vs. single-dimensional association
      • age(X, “20..29”) ^ income(X, “20..29K”)  buys(X, “PC”) [support = 2%, confidence = 60%]
      • contains(T, “computer”)  contains(x, “software”) [1%, 75%]
      • Diaper  Beer [0.5%, 75%]
    1/4/2010 TCSS588A Isabelle Bichindaritz
  • 12. Machine Learning Functionalities (2)
    • Classification and Prediction
      • Finding models (functions) that describe and distinguish classes or concepts for future prediction
      • E.g., classify countries based on climate, or classify cars based on gas mileage
      • Presentation: decision-tree, classification rule, neural network
      • Prediction: Predict some unknown or missing numerical values
    • Cluster analysis
      • Class label is unknown: Group data to form new classes, e.g., cluster houses to find distribution patterns
      • Clustering based on the principle: maximizing the intra-class similarity and minimizing the interclass similarity
    1/4/2010 TCSS588A Isabelle Bichindaritz
  • 13. Machine Learning Functionalities (3)
    • Outlier analysis
      • Outlier: a data object that does not comply with the general behavior of the data
      • It can be considered as noise or exception but is quite useful in fraud detection, rare events analysis
    • Trend and evolution analysis
      • Trend and deviation: regression analysis
      • Sequential pattern mining, periodicity analysis
      • Similarity-based analysis
    • Other pattern-directed or statistical analyses
    1/4/2010 TCSS588A Isabelle Bichindaritz
  • 14. Are All the “Discovered” Patterns Interesting?
    • A data mining or machine learning system/query may generate thousands of patterns, not all of them are interesting.
      • Suggested approach: Human-centered, query-based, focused mining
    • Interestingness measures : A pattern is interesting if it is easily understood by humans, valid on new or test data with some degree of certainty, potentially useful , novel, or validates some hypothesis that a user seeks to confirm
    • Objective vs. subjective interestingness measures:
      • Objective: based on statistics and structures of patterns, e.g., support, confidence, etc.
      • Subjective: based on user’s belief in the data, e.g., unexpectedness, novelty, actionability, etc.
    1/4/2010 TCSS588A Isabelle Bichindaritz
  • 15. Can We Find All and Only Interesting Patterns?
    • Find all the interesting patterns: Completeness
      • Can a data mining or machine learning system find all the interesting patterns?
      • Association vs. classification vs. clustering
    • Search for only interesting patterns: Optimization
      • Can a data mining or machine learning system find only the interesting patterns?
      • Approaches
        • First general all the patterns and then filter out the uninteresting ones.
        • Generate only the interesting patterns — mining query optimization
    1/4/2010 TCSS588A Isabelle Bichindaritz
  • 16. Data Mining: Confluence of Multiple Disciplines 1/4/2010 TCSS588A Isabelle Bichindaritz Data Mining Database Technology Statistics Other Disciplines Information Science Machine Learning Visualization
  • 17. Data Mining: Classification Schemes
    • General functionality
      • Descriptive data mining
      • Predictive data mining
    • Different views, different classifications
      • Kinds of databases to be mined
      • Kinds of knowledge to be discovered
      • Kinds of techniques utilized
      • Kinds of applications adapted
    1/4/2010 TCSS588A Isabelle Bichindaritz
  • 18. Architecture of a Typical Data Mining System 1/4/2010 TCSS588A Isabelle Bichindaritz Data Warehouse Data cleaning & data integration Filtering Databases Database or data warehouse server Data mining engine Pattern evaluation Graphical user interface Knowledge-base
  • 19. Introduction to the Life Sciences
    • What is human DNA ?
      • DNA stands for DeoxyriboNucleic Acid
      • DNA stores the genetic material chromosomes in each cell nucleus
      • DNA is transcribed into RNA out of the nucleus ( transcription )
      • RNA stands for RiboNucleic Acid
      • RNA is translated into proteins in a cytoplasm organism called a ribosome ( translation )
      • DNA  RNA  proteins
    1/4/2010 TCSS588A Isabelle Bichindaritz
  • 20. Introduction to the Life Sciences 1/4/2010 TCSS588A Isabelle Bichindaritz DNA mRNA rRNA tRNA transcription Ribosome Protein translation
  • 21. Introduction to the Life Sciences
    • Gene expressions are any molecular compound produced from genes (ex: RNA) Genes are expressed by being transcribed into RNA, and this transcript may then be translated into protein.
    1/4/2010 TCSS588A Isabelle Bichindaritz
  • 22. Introduction to the Life Sciences
    • DNA and RNA are composed of
      • Nucleotides (nucleic acid molecules)
        • Pyrimidines
          • Cytosine (C) (DNA & RNA)
          • Thymine (T) (DNA)
          • Uracil (U) (RNA)
        • purines
          • Adenine (A) (DNA & RNA)
          • Guanine (G) (DNA & RNA)
      • Oses (Ribose for RNA, Deoxyribose for DNA)
    1/4/2010 TCSS588A Isabelle Bichindaritz
  • 23. Introduction to the Life Sciences
    • Succession of nucleotides composes a single strand in DNA
    • Two strands of DNA pair themselves in the 3-D shape of a double helix, where bases are paired (bp = base pair)
    • Pairing of the bases (A=T, G C) provides chemical bonds responsible for the double helix shape.
    1/4/2010 TCSS588A Isabelle Bichindaritz
  • 24. Introduction to the Life Sciences 1/4/2010 TCSS588A Isabelle Bichindaritz
  • 25. 1/4/2010 TCSS588A Isabelle Bichindaritz Human Genome Program, U.S. Department of Energy, Genomics and Its Impact on Medicine and Society: A 2001 Primer, 2001
  • 26. Introduction to the Life Sciences
    • Genes
      • A gene is a part of the genome that can be translated
      • A gene may encode a protein or RNA sequence
      • Genes are separated by non coding regions
      • Genes are concentrated in certain regions of the genome rich in G and C
      • Regions rich in A and T do not contain genes
      • Between the two, CpG islands (repetition of C and G) separate coding regions from non coding ones
      • Non coding regions can be parts of genes
    1/4/2010 TCSS588A Isabelle Bichindaritz
  • 27. Introduction to the Life Sciences
    • Genomes, diversity, size, structure
      • Profound diversity of living organisms genome.
      • DNA (cells), DNA or RNA (phage, virus)
      • Direction: from 5’ to 3’ of molecule (double stranded DNA), or both directions (single stranded)
      • Genome organized or not in chromosomes
      • Human genome: 22 chromosomes, 3 billion bases, 30,000 genes
      • Other species genome vary in size and number of genes
      • Human genome has only twice as many genes than a primitive worm
      • GenBank database
    1/4/2010 TCSS588A Isabelle Bichindaritz
  • 28. Introduction to the Life Sciences
    • Proteomes
      • The proteome is the set of proteins that can be expressed from a genome
      • Determination of:
        • Sequence of encoding genes
        • Location of the genes
        • Function of protein encoding genes
        • Different biochemical states (phosphorylation, glycosylation, co-enzymes…)
    1/4/2010 TCSS588A Isabelle Bichindaritz
  • 29. Introduction to the Life Sciences
    • Gene ontologies
      • Gene ontology consortium
        • Dynamic controlled vocabulary to describe
          • Molecular function (Ex: DNA polymerase, …)
          • Biological process (Ex: DNA synthesis, respiration, …)
          • Cellular component (Ex: nucleus, ribosome, …)
    1/4/2010 TCSS588A Isabelle Bichindaritz
  • 30. Principles of Bioinformatics
    • Biological information
      • Molecules at the basis of life can be represented as digital symbol strings (DNA, RNA, …)
      • Digital symbols (monomers) constitute an alphabet
      • Unique representation
      • Importance of probabilistic models
    1/4/2010 TCSS588A Isabelle Bichindaritz
  • 31. Principles of Bioinformatics
    • Database annotation quality
      • In addition to natural noise, data are distorted by people’s annotations (curation of the data)
      • Resulting error is very significant
      • Reasons:
        • Storage of positions in a sequence, not content
        • Difficulty of storing content
      • Need to check the data
    1/4/2010 TCSS588A Isabelle Bichindaritz
  • 32. Principles of Bioinformatics
    • Database redundancy
      • Different representations: RNA, cDNA (corresponding complementary)
      • Different methods: single-pass sequence, multi-fold repetition of a sequence
      • Different fragments: pre-mRNA can lead to several levels of splicing in cDNA, alternative splicing
      • Redundancy is source of error:
        • Bias of over represented fragments for closely related segments
        • Bias of over represented fragments for correlations
        • Overestimate prediction if input and output are related
    1/4/2010 TCSS588A Isabelle Bichindaritz
  • 33. Principles of Bioinformatics
    • Database redundancy
      • Better to clean the data first
      • Data mining cleaning methods apply
      • Difficulty to differentiate between true analogous sequences, and related ones
      • Sequence profile describes amino acid variation in a family of sequences
    1/4/2010 TCSS588A Isabelle Bichindaritz
  • 34. Principles of Bioinformatics
    • Main bioinformatics questions
      • Determine the exact transition between coding and non coding regions of genes
      • Find genes in prokaryotes and eukaryotes
      • Determine transcription initiation and termination
      • Sequence clustering and cluster topology
      • Protein structure prediction
      • Protein function prediction
      • Protein family classification
    1/4/2010 TCSS588A Isabelle Bichindaritz
  • 35. Principles of Bioinformatics
    • Question
      • Propose questions pertinent for bioinformatics
      • Propose questions pertinent for medical informatics
    1/4/2010 TCSS588A Isabelle Bichindaritz