Course 4541.773:

Molecular Machine Learning (Advanced AI)

School of Computer Science and Engineering,

Graduate Programs in Bioinformatics,

Brain Science, and Cognitive Science
Seoul National University


Prof. Byoung-Tak Zhang


Kyu-Baek Hwang (Room: 301-419, Tel.: 880-1847)




Tue, 10:30 ~ 11:45,   Thr,  10:30 ~ 11:45



  • Supplementary Materials
  1. A Bayesian Algorithm for In Vitro Molecular Evolution of Pattern Classifiers
  2. Molecular Machine Learning: A Personal Introduction
  3. Introduction to Probabilistic Graphical Models
  4. Bayesian Networks and Gene Expression Analysis
  5. Kernel Methods
  6. Sequence Design for DNA Computing 
  • Homework 1

Write an essay of one of the following books.

Due: October 14, 2004.

  • The Computer and the Brain, John von Neumann, Yale University Press, 2000.
  • Eniac: The Triumph and Tragedies of the World's First Computer, Scott McCartney, The Berkley Publishing Group, 1999.
  • The Difference Engine: Charles Babbage and the Quest to Build the First Computer, Doron Swade, The Penguin Group, 2001.
  • The Pattern on the Stone, W. Daniel Hillis, Basic Books, 1998.
  • Homework 2

Analyze one of the two datasets for term project using data mining tools.

Due: October 28, 2004. 

  • DNA Computing Workshop

Keywords for paper selection: DNA computing, in vitro selection, directed evolution, combinatorial chemistry

Time & date: Sat, November 20, 2004 (11:00 ~ 18:00).

Location: 301-421

Schedule & slides 

  • Term Project
  • Phase I

Data mining with machine learning tools

Due: October 28, 2004.

  • Phase II

DNA computing design for preliminary results

Due: December 7, 2004.

  • Phase III

Final report & presentation

Due: December 21, 2004.

  • Dataset 1 (text data)
  • Dataset 2 (gene expression data)
  • Final Exam

        Time & date: Thur, December 2, 10:30 - 11:45 AM


 -    Probabilistic Library Model (A Bayesian Algorithm for In Vitro Molecular Evolution of Pattern Classifiers, Zhang, B.-T. and Jang, H.-Y., Preliminary Proceedings of the Tenth International Meeting on DNA Computing, pp. 294-303, 2004)

      -    Kernel Machines (slide, An Introduction to Kernel-Based Learning Algorithms, Mueller, K.-R., Mika, S., Raetsch, G., Tsuda, K., and Schoelkopf, B., IEEE Transactions on Neural Networks, vol. 12, no. 2, 2001)

      -    Decision Trees (Machine Learning, Tom Mitchell, Chap. 3 (slide))

      -    Rule Learning (slide)

      -    Concept Learning (Machine Learning, Tom Mitchell, Chap. 2 (slide), Version Space Learning with DNA Molecules, Lim, H.-W., Yun, J.-E., Jang, H.-M., Chai, Y.-G., Yoo, S.-I., and Zhang, B.-T., Lecture Notes in Computer Science, vol. 2568, pp. 143-155, 2003) 

  • Data Mining Tools

This page is maintained by Kyu-Baek Hwang (kbhwang at, Last update: November 19, 2004