cerebis / bin3C

Extract metagenome-assembled genomes (MAGs) from metagenomic data using Hi-C.
GNU Affero General Public License v3.0
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Poor time complexity of some algorithm choices #9

Closed cerebis closed 5 years ago

cerebis commented 7 years ago

For larger problems, time complexity makes some more precise algorithms a slow step and potentially impractical once timing estimation is carried out.

These include:

  1. optimal leaving ordering in Hclust order module of map_ordering.
  2. Jonkers-Volgenant algorithm employed within seriation.

Once the process settles, these could be made optional features.

cerebis commented 7 years ago

For JV, we could simply use it at the end of a convergence run of the faster heuristic method. Currently, the heuristic method is orders of magnitude faster due largely to the implicitly parallel matrix calculations, while JV is known to be a sequential algorithm.

cerebis commented 5 years ago

This issue pertains to unincluded features but is saved for future reference.