Syllabus for Knowledge-Based Systems in Bioinformatics

Kunskapsbaserade system inom bioinformatik

  • 5 credits
  • Course code: 1MB416
  • Education cycle: Second cycle
  • Main field(s) of study and in-depth level: Technology A1N, Bioinformatics A1N

    Explanation of codes

    The code indicates the education cycle and in-depth level of the course in relation to other courses within the same main field of study according to the requirements for general degrees:

    First cycle

    • G1N: has only upper-secondary level entry requirements
    • G1F: has less than 60 credits in first-cycle course/s as entry requirements
    • G1E: contains specially designed degree project for Higher Education Diploma
    • G2F: has at least 60 credits in first-cycle course/s as entry requirements
    • G2E: has at least 60 credits in first-cycle course/s as entry requirements, contains degree project for Bachelor of Arts/Bachelor of Science
    • GXX: in-depth level of the course cannot be classified

    Second cycle

    • A1N: has only first-cycle course/s as entry requirements
    • A1F: has second-cycle course/s as entry requirements
    • A1E: contains degree project for Master of Arts/Master of Science (60 credits)
    • A2E: contains degree project for Master of Arts/Master of Science (120 credits)
    • AXX: in-depth level of the course cannot be classified

  • Grading system: Fail (U), Pass (3), Pass with credit (4), Pass with distinction (5)
  • Established: 2010-03-16
  • Established by:
  • Revised: 2021-10-22
  • Revised by: The Faculty Board of Science and Technology
  • Applies from: Autumn 2022
  • Entry requirements: Alt 1. 120 credits including Genomics and Bioinformatics, Probability and Statistics, and Computer Programming II. Alt 2. Introduction to Bioinformatics, Introduction to Programming, Scientific Computing and Statistics, and Programming in Python. Alt 3. 30 credits mathematics and 30 credits computer science. Introduction to Bioinformatics, and Script Programming. Alt 4. Participation in Introduction to Bioinformatics, Computer Programming I, Computational Methods for Scientific Applications, and Introduction to Statistics for Life Sciences. Alt 5. 30 credits mathematics and 30 credits computer science. Participation in Introduction to Bioinformatics, and Introduction to Statistics for Life Sciences. Proficiency in English equivalent to the Swedish upper secondary course English 6.
  • Responsible department: Biology Education Centre

Learning outcomes

The course aims to provide a good understanding how logic-based methods can be applied in the construction of knowledge-based systems within Life Sciences. The flood of large and very large data sets such as gene expressions, molecular interactions and taxonomies requires efficient handling. Specifically, the course leads to an advanced understanding of how learning methods can be applied to solve several bioinformatics problems.

On completion of the course, the student should be able to

  • use and describe definitions and mathematical notation for information and decision systems, rough sets and rule systems
  • use other methods for machine learning such as clustering, decision trees, and relate them to rough sets
  • apply knowledge of rule-based systems and Monte Carlo-based selection methods to formulate and solve classification problems in Life Sciences

Content

Introduction to Boolean functions. Transformation and simplification of Boolean expressions. Information, decision systems and rough sets. Features and their synthesis and selection. Training and validation of models. Statistical properties of models. Examples of applications inLifeSciences include: classification of expressions , prediction of gene functions from time profiles and genomic databases, modelling of transcriptional mechanisms, ligand receptor bindings, drug resistance, prediction of protein function from structure and modelling with clinical and genomic data. Lectures are interspaced with computer labs using real and synthetic data. Ontologies. Machine learning: clustering, rough sets, decision trees, Monte Carlo-based selection, statistical model validity and significance.

Instruction

Lectures, computer exercises, project and problem solving exercises.

Assessment

Written closed-book exam at the end of the course (3 credits). Written and computer exercises (1 credit).Project (1 credit).
If there are special reasons for doing so, an examiner may make an exception from the method of assessment indicated and allow a student to be assessed by another method. An example of special reasons might be a certificate regarding special pedagogical support from the disability coordinator of the university.

Reading list

The reading list is missing. For further information, please contact the responsible department.