Multiple changes to interior order of operations #9
Conversation
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Likelihoods of individual columns (including the empty one) are now stored as p(c) * ||\nu|| rather than p(c) themselves.
Log-factorial is approximated using Stirling's formula. The constant term is removed, so all likelihoods are increased by log(sqrt(2*\pi)).
Value ||\nu|| * p(c0) is calculated without using matrix multiplication.
The order of additions for ||\nu||*p(c0) is changed in a way which enables cancellation with the exterior -||\nu||.
The only remaining intermediate value stored in Felsenstein's recursion for p(c0) is now equal to old \tilde{f}-1.
Numerical values in the test are adjusted to be more precise.
For detailed explanations see the pdf doc (to be written soon).
Codecov ReportAttention:
Additional details and impacted files@@ Coverage Diff @@
## main #9 +/- ##
==========================================
+ Coverage 93.56% 96.60% +3.04%
==========================================
Files 9 12 +3
Lines 823 1531 +708
Branches 139 230 +91
==========================================
+ Hits 770 1479 +709
+ Misses 49 47 -2
- Partials 4 5 +1 ☔ View full report in Codecov by Sentry. |
|
The "pdf doc" in question. https://github.com/acg-team/rust-phylo/files/13629444/Streamline.Notes.pdf EDIT: I proofred the doc and found a couple typos, this version is better: Streamline Notes.pdf |
junniest
pushed a commit
that referenced
this pull request
Apr 17, 2024
Likelihoods of individual columns (including the empty one) are now stored as p(c) * ||\nu|| rather than p(c) themselves.
Log-factorial is approximated using Stirling's formula. The constant term is removed, so all likelihoods are increased by log(sqrt(2*\pi)).
Value ||\nu|| * p(c0) is calculated without using matrix multiplication.
The order of additions for ||\nu||*p(c0) is changed in a way which enables cancellation with the exterior -||\nu||.
The only remaining intermediate value stored in Felsenstein's recursion for p(c0) is now equal to old \tilde{f}-1.
Numerical values in the test are adjusted to be more precise.
For detailed explanations see the pdf doc (to be written soon).
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
Add this suggestion to a batch that can be applied as a single commit.
This suggestion is invalid because no changes were made to the code.
Suggestions cannot be applied while the pull request is closed.
Suggestions cannot be applied while viewing a subset of changes.
Only one suggestion per line can be applied in a batch.
Add this suggestion to a batch that can be applied as a single commit.
Applying suggestions on deleted lines is not supported.
You must change the existing code in this line in order to create a valid suggestion.
Outdated suggestions cannot be applied.
This suggestion has been applied or marked resolved.
Suggestions cannot be applied from pending reviews.
Suggestions cannot be applied on multi-line comments.
Suggestions cannot be applied while the pull request is queued to merge.
Suggestion cannot be applied right now. Please check back later.
Likelihoods of individual columns (including the empty one) are now stored as p(c) * ||\nu|| rather than p(c) themselves.
Log-factorial is approximated using Stirling's formula. The constant term is removed, so all likelihoods are increased by log(sqrt(2*\pi)).
Value ||\nu|| * p(c0) is calculated without using matrix multiplication.
The order of additions for ||\nu|| * p(c0) is changed in a way which enables cancellation with the exterior -||\nu||.
The only remaining intermediate value stored in Felsenstein's recursion for p(c0) is now equal to old \tilde{f}-1.
Numerical values in the test are adjusted to be more precise.
For detailed explanations see the pdf doc (to be written soon).