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high_noise_clustering's Introduction

How to cluster datasets with important levels of noise or dropouts?

Let's start by defining the difference between noise and dropout:

Dropout = dataset non 0 values appear as 0 (single cell RNA-seq data)
Noise = the actual measured values have a certain additional noise (due to sensor calibration, experimental setup, etc)

This repository attempts to:

  • explain the theoretical notions behing spectral clustering and self tuned spectral clustering
  • implement the affinity matrix computation for self tuned spectral clustering
  • implement the eigenvalue gap heuristic for finding the optimal number of clusters

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high_noise_clustering's Issues

wrong results

the function used for calculating eigenvalues, does not return them sorted so the final results are wrong. One have to sort them manually before calculating eigengaps

Suggest np.linalg.eig for full symmetric matrices

Hi,

Firstly, your article and repo are excellent to explain spectral clustering with the gap heuristic.
I'd like to make a suggestion w.r.t. you eigenvalue computation, the scipy sparse eigsh code will warn (once) when you call it with a symmetric matrix (non sparse) and k=N, in the warning it falls back to the eigh call.
The confusing part is that for 100 function calls, it'll emit the warning once, so is easily missed.
May I suggest substituting this to np.linalg.eigh for full matrices?
Note that setting K < N affects the heuristic, whereas the full eigenvalues does not.
I'm referring to this notebook:
https://github.com/ciortanmadalina/high_noise_clustering/raw/master/spectral_clustering.ipynb

Thanks!

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