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:

Syllabus: CSCI4969-6969 Syllabus




Capstone2: CSCI4969-6969 Capstone2 , Due: 25th Apr

Capstone1: CSCI4969-6969 Capstone1 , Due: 19th Apr

Assign6: CSCI4969-6969 Assign6 , Due: 7th Apr

Assign5: CSCI4949-6969 Assign5, Due: 25th Mar

Assign4: CSCI4949-6969 Assign4, Due: 6th Mar

Assign3: CSCI4949-6969 Assign3, Due: 22nd Feb

Assign2: CSCI4969-6969 Assign2, Due: 9th Feb

Assign1: CSCI4969-6969 Assign1, Due: 1st Feb

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) lecture3.pdf, lecture3 video
Jan 24 MLPs II lecture4.pdf, lecture4 video
Jan 27 RNNs lecture5.pdf, lecture5 video
Jan 31 RNNs, LSTMs lecture6.pdf, lecture6 video
Feb 03 CNNs lecture7.pdf, lecture7 video
Feb 07 Word Embeddings lecture8.pdf, lecture8 video
Feb 10 Attention lecture9.pdf, lecture9 video
Feb 14 Transformer lecture10.pdf, lecture10 video
Feb 17 Language Models (BERT) lecture11.pdf, lecture11 video
Feb 22(T) Graph Neural Networks (GNNs) lecture12.pdf, lecture12 video
Feb 24 GNN IIs lecture13.pdf, lecture13 video
Feb 28 BERT for Proteins lecture14.pdf, lecture14 video
Mar 03 GNNs III lecture15.pdf, lecture15 video
Mar 07 NO CLASS (Spring Break)
Mar 10 NO CLASS (Spring Break)
Mar 14 Pytorch Implementation Tips lecture16.pdf, lecture16 video
Mar 17 GNN Assignment & Protein Structure lecture17.pdf, lecture17 video
Mar 21 Protein Structure Prediction lecture18.pdf, lecture18 video
Mar 24 AlphaFold1 I lecture19.pdf, lecture19 video
Mar 31 Alphafold1 II lecture20.pdf, lecture20 video
Apr 04 Alphafold1 III lecture21.pdf, lecture21 video
Apr 07 Alphafold2 I lecture22.pdf, lecture22 video
Apr 11 Alpahafold2: Evoformer lecture23.pdf, lecture23 video
Apr 14 Alphafold2: Evoformer II lecture24.pdf, lecture24 video
Apr 18 Alphafold2: Structure Prediction I lecture25.pdf, lecture25 video
Apr 21 Alphafold2: Structure Prediction II lecture26.pdf, lecture26 video
Apr 25 Wrap Up lecture27.pdf, lecture27 video