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The naive diploid Viterbi algorithm doesn't scale well with the number of reference haplotypes, slowing testing (#65). @astheeggeggs suggested an alternative implementation that "merges" partial ances…
szhan updated
4 months ago
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## Expected Behavior
MAC realignment algorithm is enabled by default in hhsearch/hhblits/hhalign and
it's expected to improve the quality of hits' alignments.
## Current Behavior
In some c…
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This will give a boost to the project, there are a few scalable and open solutions to this problem.
In my short discussions @harsha2010, a HMM-based approach was mentioned.
@harsha2010: what is th…
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---
Author Name: **P. Horton** (P. Horton)
Original Redmine Issue: 2976, https://redmine.open-bio.org/issues/2976
Original Date: 2009-12-26
Original Assignee: Bioperl Guts
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Working with Bioperl-…
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Once the HMM is trained, it's show time !
We implement Viterbi algorithm with some smoothing mechanism (back-off to begin with)
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Right now I don't know much of what's going on when I use `run_HMM`.
I think we should have text output and progress bars for each long section, e.g.:
```
# Loading input files
**************…
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Hi Shaun,
I would like to use a list of different sequences (e.g. obtained from direct observations) for parameter tuning (using the Baum-Welch algorithm) before using Viterbi algorithm in a routin…
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* Use HMM's or viterbi to check whether new line number is logical in our current sequence
* Take a look at the streaming algorithms literature, as this is actually not a canonical ML problem.
* tal…
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Hi
I found your library and it appears to be the only HMM library in Rust. It's a bit of a shame that only viterbi is implemented and I'll see whether I can find the time and imement the forward ba…
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## I am reporting a bug
I have found that when I set the GaussianHMM with the following parameters, the accuracy of my model is different than when I use the default parameters. There is quite a la…