CSCI4969-6969 Machine Learning in Bioinformatics

This course focuses on machine learning algorithms for analyzing biological data. The course will introduce the main topics in this area, such as analysis of protein/DNA sequences, protein structures, molecular graphs, and so on. The main focus is on the role of deep learning and data mining in computational biology and bioinformatics.

Class Hours: 10-11:50AM MR, Carnegie 201. Office Hours: 12-1PM MR
Online Class: https://rensselaer.webex.com/meet/zakim

Syllabus: CSCI4969-6969 Syllabus

Campuswire: https://campuswire.com/c/G8B78468D

Submitty: https://submitty.cs.rpi.edu/courses/s22/csci4969

Assignments

Assign0: CSCI4969-6969 Assign0, Due: 13th Jan

Class schedule

Tentative course schedule is given below.

Date Topic Lectures Readings
Jan 10 Introduction I intro.pdf, lecture1 video Intro to Molecular Biology (on LMS)
Jan 13 Introduction II intro.pdf, lecture2 video
Jan 17 NO CLASS (MLK, Jr. Day)
Jan 20 Neural Networks (MLPs)
Jan 27 Deep MLPs
Jan 31 RNNs
Feb 03 LSTMs
Feb 07 CNNs
Feb 10 Attention
Feb 14 Transformer
Feb 17 Language Models
Feb 22(T) Masked Language Models
Feb 24 Protein Sequence & Structure
Feb 28 Protein Sequence Embeddings
Mar 03 Embeddings with Structure
Mar 07 NO CLASS (Spring Break)
Mar 10 NO CLASS (Spring Break)
Mar 14 Secondary Structure Prediction
Mar 17 GNNs I
Mar 21 GNNs II
Mar 24 3D Structure Prediction I
Mar 28 3D Structure Prediction II
Mar 31 Structure Prediction Implementation
Apr 04 Distance Geometry
Apr 07 Molecular Graphs
Apr 11 Molecular Graphs II
Apr 14 Generative Models
Apr 18 Generative Models II
Apr 21 Project Presentations I
Apr 25 Project Presentations II