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PHZ4710 - Introduction to Biological Physics
PHZ4710 - Introduction to Biological Physics
0. What is Biological Physics?
Spatial and temporal scales in Biology
1. Diffusion vs. Navigation
Random walk
Run-and-tumble
2. Probability and Statistics
Counting photons
Fluctuation test
3. Stochastic Processes
Birth-death process
Stochastic gene expression
4. Reaction Kinetics
Protein folding
Protein folding part2
Kinetic proofreading
5. Dynamical Systems
The
lac
Operon
Lotka-Volterra equations
The Lorenz system
6. Neural Networks
Hopfield network
Simple perceptron
Multi-layer networks
7. Data Analyses
Handwritten digits
Eigenworms
Cancer RNA-Seq data
8. Information and Strategy
Bet-hedging
Value of information
Evolutionary games
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Contents
1. Classification: Convolutional Neural Networks
Exercise:
Classification of handwritten digits
2. Dimensionality reduction: Principal Component Analysis
Exercise:
Quantifying worm behavior (“eigenworms”)
3. Data clustering: k-means
Exercise:
Cancer RNA-seq data analysis
Data Analyses
Contents
1. Classification: Convolutional Neural Networks
Exercise:
Classification of handwritten digits
2. Dimensionality reduction: Principal Component Analysis
Exercise:
Quantifying worm behavior (“eigenworms”)
3. Data clustering: k-means
Exercise:
Cancer RNA-seq data analysis
Data Analyses
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1. Classification: Convolutional Neural Networks
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alt text
Exercise:
Classification of handwritten digits
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2. Dimensionality reduction: Principal Component Analysis
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alt text
Exercise:
Quantifying worm behavior (“eigenworms”)
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3. Data clustering: k-means
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alt text
Exercise:
Cancer RNA-seq data analysis
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