Shuyib/Phylogenetic-tree-study

Issues

• Review DNA BERT

  #52 opened a year ago by Shuyib
  2

• Repeat the notebooks

  #55 opened a year ago by Shuyib
  0

• Use similarity metrics

  #54 opened a year ago by Shuyib
  7

• Review embeddings

  #53 opened a year ago by Shuyib
  0

• Add nine potential organisms to the 16S rRNA

  #21 opened 2 years ago by Shuyib
  5

• Consider using DictVectorizer and semi-supervised learning to see if any generalizations arise from using a neural network. Review contrastive loss and ideas here

  #44 opened 2 years ago by Shuyib
  1

• redo the making the phylogenetics tree with MEGA7, clustal and unsupervised learning

  #27 opened 2 years ago by Shuyib
  2

• Use KEGG or something else to find out the function of the motifs found by MEME. Refer to biopython.

  #28 opened 2 years ago by Shuyib
  3

• Use data from https://geneontology.org to build an embedding model suitable for search

  #42 opened 2 years ago by Shuyib
  1

• Add DVC for better dataset and experiment tracking

  #41 opened 2 years ago by Shuyib
  1

• Add CI/CD step with github actions.

  #40 opened 2 years ago by Shuyib
  1

• Use MEME to find motifs and improve clustering done before

  #26 opened 2 years ago by Shuyib
  3

• Add Dockerfile

  #30 opened 2 years ago by Shuyib
  2

• Add todo list with updated kanban

  #35 opened 2 years ago by Shuyib
  0

• Sample size for the 16S rRNA sequences 30 good, 90 better and 120 the best.

  #22 opened 2 years ago by Shuyib
  1

• Add Makefile

  #29 opened 2 years ago by Shuyib
  1

• Assign 2 microbes per person to speed up sequence discovery and replacement.

  #23 opened 2 years ago by Shuyib
  1

• Update project

  #1 opened 2 years ago by Shuyib
  0