Commits · ca328b463546a94a080d92af88fad38d34a43198 · Jerry Dinan / bmDCA

May 12, 2020
- correct note on default value for 'output_binary' · ca328b46
  sudorook authored 4 years ago
  
  ca328b46
- create new config flag for saving best steps · 95ce9941
  sudorook authored 4 years ago
  
  95ce9941
- restarting bugfixes: · ec41fed8
  sudorook authored 4 years ago
```
1. fix reloading of runs after writing a step that is not a multiple of
   save_parameters
2. restore error_tot_min upon restart and consolidate state restore fxns
```
  ec41fed8
- no need to keep passing the model pointer · 0175f785
  sudorook authored 4 years ago
  
  0175f785
- tweak name of function for writing positional Di · 0f0e0521
  sudorook authored 4 years ago
  
  0f0e0521
- carry out convergence check in run loop; write steps with low error_tot · b42a24bc
  sudorook authored 4 years ago
  
  b42a24bc
- cleanup · 4a972c48
  sudorook authored 4 years ago
  
  4a972c48
- compute the root mean squared error of 1p and 2p frequencies · 543a3545
  sudorook authored 4 years ago
  
  543a3545
- add functions to compute rel entropy for N and N*Q · 2b747d3f
  sudorook authored 4 years ago
  
  2b747d3f
- use dynamic scheduler for correlation loops · 9ae7d8cf
  sudorook authored 4 years ago
  
  9ae7d8cf
- compute relative entropy at each position · 70e6afa1
  sudorook authored 4 years ago
  
  70e6afa1
- write full final step (helps with restarting) · e56f6080
  sudorook authored 4 years ago
  
  e56f6080
- write final step time to run log upon convergence · 3d8f5d39
  sudorook authored 4 years ago
  
  3d8f5d39
- binarize rel ent grad output and have ascii format match 1p stats · 96e4495f
  sudorook authored 4 years ago
  
  96e4495f
- clear old code from Graph (should rename this...) · 1da215a6
  sudorook authored 4 years ago
  
  1da215a6
- bump to v0.8.9 · c58d4497
  sudorook authored 4 years ago
  
  c58d4497
- clang-format (2) · 30222b49
  sudorook authored 4 years ago
  
  30222b49
- clang-format · a03c1560
  sudorook authored 4 years ago
  
  a03c1560
- fix grave inefficiency in mc sampler · c0ee0701
  sudorook authored 4 years ago
  
  c0ee0701
- use ARMA_NO_DEBUG rather than .at to disable bounds checks globally · f248f6ea
  sudorook authored 4 years ago
  
  f248f6ea
- use dynamic scheduler for two loops · d9f28c39
  sudorook authored 4 years ago
  
  d9f28c39
- clarify when to use OMP_NUM_THREADS · 7edc80c4
  sudorook authored 4 years ago
  
  7edc80c4
- remove superfluous 'weight_given' variable · 4e076017
  sudorook authored 4 years ago
  
  4e076017
- consolidate MSA constructors · 898ebc2c
  sudorook authored 4 years ago
  
  898ebc2c
- print msa info immediately · 447327c4
  sudorook authored 4 years ago
  
  447327c4
- add functions to compute hamming distance pairs for an MSA · 72879851
  sudorook authored 4 years ago
  
  72879851
- add notes on .bash_profile on macOS in README · 18ada0d3
  sudorook authored 4 years ago
  
  18ada0d3
- 'arma::raw_binary' not defined for fields · a8a30251
  sudorook authored 4 years ago
  
  a8a30251
- check for valid input in arma2ascii · 8648d5f7
  sudorook authored 4 years ago
  
  8648d5f7
- simplify bmdca.cpp · 17db5c72
  sudorook authored 4 years ago
  
  17db5c72
- write alignment stats as binaries · dfc79347
  sudorook authored 4 years ago
  
  dfc79347
- add threshold to usage message · a1cdd2be
  sudorook authored 4 years ago
  
  a1cdd2be
- 'Compat' -> 'Ascii' · dec8dc2a
  sudorook authored 4 years ago
  
  dec8dc2a
- fix default use_reparametrization=true · 2405f7dd
  sudorook authored 4 years ago
  
  2405f7dd
- add note on 'use_reparametrization' flag in README · 5807c023
  sudorook authored 4 years ago
  
  5807c023
- add param for not using reparametrized model · 28b9041e
  sudorook authored 4 years ago
  
  28b9041e
- remove option to change inference temperature · d69aebc9
  sudorook authored 4 years ago
  
  d69aebc9
- minor · 4f8597ff
  sudorook authored 4 years ago
  
  4f8597ff
- bugfix - h was being halved in the gradient update step · 794a5c90
  sudorook authored 4 years ago
  
  794a5c90
- parallelize sequence weighting · 133d83a4
  sudorook authored 4 years ago
  
  133d83a4