NMF

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• Summary
• Checks
• Past versions

Last updated: 2021-05-04

Checks: 2 0

Knit directory: website/

This reproducible R Markdown analysis was created with workflowr (version 1.6.2). The Checks tab describes the reproducibility checks that were applied when the results were created. The Past versions tab lists the development history.

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R Markdown file: up-to-date

Great! Since the R Markdown file has been committed to the Git repository, you know the exact version of the code that produced these results.

Repository version: e345579

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The results in this page were generated with repository version e345579. See the Past versions tab to see a history of the changes made to the R Markdown and HTML files.

Note that you need to be careful to ensure that all relevant files for the analysis have been committed to Git prior to generating the results (you can use wflow_publish or wflow_git_commit). workflowr only checks the R Markdown file, but you know if there are other scripts or data files that it depends on. Below is the status of the Git repository when the results were generated:

Ignored files:
    Ignored:    .RData
    Ignored:    .Rhistory

Unstaged changes:
    Deleted:    analysis/about.Rmd

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These are the previous versions of the repository in which changes were made to the R Markdown (analysis/NMF.Rmd) and HTML (docs/NMF.html) files. If you’ve configured a remote Git repository (see ?wflow_git_remote), click on the hyperlinks in the table below to view the files as they were in that past version.

File	Version	Author	Date	Message
Rmd	e345579	rbghks0126	2021-05-04	update To Do
html	8600d23	rbghks0126	2021-03-30	Build site.
Rmd	4813229	rbghks0126	2021-03-30	Update to do list
html	49c268d	rbghks0126	2021-03-22	Build site.
html	d657de6	rbghks0126	2021-03-22	Build site.
Rmd	eda95eb	rbghks0126	2021-03-22	Add NMF page

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To Do Lists

4/5/2021

• See if the implementation has functionality for returning the second factored matrix.
• Perform signature matching on BRCA100 data using their algorithm.
• Perform signature matching on BRCA100 data using my DS-SSVI and DS-Gibbs.

16/4/2021

• Find software/github implementation for Deciphering Signatures of Mutational Processes Operative in Human Cance.
  • See if they have some procedure for generating the data matrix for cancer mutation type and signatures (latent components).
• FOUND:

  • https://osf.io/zyknf/ (original authors’)

  • Github: https://github.com/ShixiangWang/sigminer (another person’s)

    • Tutorial: https://shixiangwang.gitee.io/sigminer-doc/sbssig.html#extract-signatures

30/3/2021

• Apply my DS-SSVI NMF (and gibbs sampling version too) on audio data for blind source separation. (testing the second factored matrix)
  • Compare the separation performance with:
    • BETA PROCESS SPARSE NONNEGATIVE MATRIX FACTORIZATION FOR MUSIC, Liang et al. (2013)
    • Beta Process Non-negative Matrix Factorization with Stochastic Structured Mean-Field Variational Inference, Liang et al. (2014)

22/3/2021

For me

• Check predictive log-likelihood for LAVI and CoGAPS.
• Look at the 2 real datasets from Doubly Nonparametric Sparse Nonnegative Matrix Factorization Based on Dependent Indian Buffet Processes, Xuan et al (2018) and Bayesian Nonnegative Matrix Factorization With Dirichlet Process Mixtures, Li et al (2020).
  • Try understand how they used these datasets and produced results.
  • Try see if I can apply my algorithm to these datasets.

For HJ

• Check (email) implementation for Doubly Nonparametric Sparse Nonnegative Matrix Factorization Based on Dependent Indian Buffet Processes, Xuan et al (2018) and Bayesian Nonnegative Matrix Factorization With Dirichlet Process Mixtures, Li et al (2020).