This repository was created to maintain the assignments of UW CSEP 527. We worked on some interesting problems using Hidden Markov Models, Viterbi algorithm, Gillespie algorithm, Smith–Waterman algorithm, and many others.
| Biological Problem | Attempted Algorithm |
|---|---|
| Population Evolution | Gillespie |
| Genome Alignment | Smith Waterman |
| RNA Transcript Abundance Estimation | Expectation Maximization |
| Cluster Cell Types Based On Gene Expression (Single-Cell Analysis) | Dimensionality Reduction (T-SNE) / K-Means Clustering |
| Differential Analysis | T-tests |
| Learning Sequences from Observed Data | Viterbi / Hidden Markov Models |
| Alternative Splicing Prediction | Gradient Descent for L2 Regularized KL-Loss Logistic Regression |