Relative Entropy or Kullback Leibler divergence

Click For Summary
SUMMARY

The discussion focuses on calculating the Kullback-Leibler divergence, also known as relative entropy, between two frequency occurrence matrices representing sets of data. Set 1 and Set 2 consist of nucleotide counts (A, C, G, T), with Set 2 being a mutated version of Set 1. The user initially sought guidance on the calculation process but later confirmed they resolved the issue independently.

PREREQUISITES
  • Understanding of Kullback-Leibler divergence
  • Familiarity with frequency occurrence matrices
  • Basic knowledge of nucleotide sequences (A, C, G, T)
  • Proficiency in statistical analysis
NEXT STEPS
  • Study the mathematical formulation of Kullback-Leibler divergence
  • Explore Python libraries for statistical analysis, such as SciPy
  • Learn about mutation effects on frequency occurrence in biological data
  • Investigate applications of relative entropy in bioinformatics
USEFUL FOR

Researchers in bioinformatics, data analysts working with genetic data, and students studying statistics or computational biology will benefit from this discussion.

bowlbase
Messages
145
Reaction score
2

Homework Statement


I am suppose to calculate the relative entropy between two sets of data:
Base set
Set 1:
A C G T
0 0 0 10
0 0 0 10
0 0 10 0
0 10 0 0
10 0 0 0
* * * * //Randomized
0 0 0 10
0 10 0 0

Set 2:
A C G T
0 0 0 10
0 0 0 10
0 0 10 0
0 10 0 0
10 0 0 0
1 4 1 4
0 0 0 10
0 10 0 0These are frequency of occurrence matrices. Set 2 is a matrix created after a variable number of characters is mutated. In this case only 1 character in the 3rd from bottom row was mutated. Thats why this row has no 10s. Every other position didn't mutate so has the correct number of occurrences as compared to set 1. I have 70 other sets of this data with various number of mutations and lengths.

I am trying to read about this online but the information is convoluted and often seems to actively avoid defining variables. Can someone walk me through the process?

Homework Equations

The Attempt at a Solution

 
Physics news on Phys.org
Nevermind, I've got it!
 

Similar threads

  • · Replies 3 ·
Replies
3
Views
2K
  • · Replies 7 ·
Replies
7
Views
2K
Replies
33
Views
4K
  • · Replies 1 ·
Replies
1
Views
1K
Replies
5
Views
2K
Replies
6
Views
7K
  • · Replies 6 ·
Replies
6
Views
5K
  • · Replies 3 ·
Replies
3
Views
2K
  • · Replies 3 ·
Replies
3
Views
2K
  • · Replies 3 ·
Replies
3
Views
2K