Course learing objectives

Biomedical Informatics 3 provides students the opportunity to develop their skills and understanding of algorithms in biomedical informatics. The course will provide a solid theoretical foundation on various algorithms, with an emphasis how to design algorithms for biomedical problems, and how these algorithms can be applied to biomedical problems. To facilitate the students’ skills for the application of algorithms for biomedical data analysis and to improve their problem-solving skills, the course also introduces sessions for advancing communication with biomedical scientists and software engineers.

Syllabus at a Glance

Topics: Algorithms

  • Algorithms and Complexity
  • Exhaustive Search
  • Greedy Algorithms
  • Dynamic Programming Algorithms
  • Divide-and-Conquer Algorithms
  • Graph Algorithms
  • Combinatorial Pattern Matching
  • Randomized Algorithms

Topics: Machine Learning

  • Dimensionality reduction - PCA, t-SNE, UMAP
  • Clustering and Trees
  • Hidden Markov Models
  • Logistic regression, decision tree, support vector machine
  • Neural Network theory and application in bioinformatics
This course is assessed by in-course assessment (ICA) only.

In order to pass the BMI3 course, you must:

  1. Submit all assessments that contribute to the ICA component of the course, AND
  2. obtain an overall ICA mark of at least 60% in the ICAs, AND
  3. obtain an ICA mark of at least 60% in the computer-based timed coding
  4. challenges.

In-Course Assessments (ICAs, 50%), Mini-project

  1. The deadline for this ICA presentation is during practical time on 12/16 13:00- 16:50
  2. The deadline for ICA report and code is 12/17 22:00
  3. Code (10%)
  4. Documentation (20%)
  5. Oral presentation (20%)
  6. You will receive your provisional marks and feedback for this ICA within 15 working days

Finals (50%) open book coding challenges

  1. This assessment is open-book, which means that you are allowed to bring and consult any notes you may have. However, you will not be allowed to access the internet and you will not be allowed to work with other students. Detailed instructions will be distributed prior to the assessment.
  2. You will receive your provisional marks and feedback for this ICA within 15 working days
  3. This ICA will be assessed anonymously by two independent markers and an average mark of their marks used.

For more information, please contact the TAs:

  1. Ziwei, 📧
  2. Ruonan, 📧
  3. Yixin, 📧