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matsengrp
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gapml
GNU General Public License v3.0
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Missing tauGeodesic.jar
#180
mathiasbio
closed
3 years ago
2
Tutorial for new Gestalt data
#179
qinqian
opened
3 years ago
15
Unit test failure
#178
azwaans
closed
3 years ago
1
Sensitivity to indel errors
#177
jjfeng
closed
4 years ago
0
newick output
#176
jjfeng
closed
4 years ago
0
Remove boost parameters. Reparameterized trimming and insertion process
#175
jjfeng
closed
4 years ago
0
Failing unit tests
#174
seidels
closed
4 years ago
12
Constant paths specification
#173
seidels
closed
4 years ago
2
Neighbor joining
#172
wsdewitt
closed
6 years ago
0
update chad finder to be much faster and less dumb
#171
jjfeng
closed
6 years ago
0
Allow overall cut rate to vary
#170
jjfeng
closed
6 years ago
0
weight leaf sampling by abundance values
#169
jjfeng
closed
6 years ago
0
Update branch length penalty, update penalty parameter tuning, major code cleanup, also a target lambda penalty
#168
jjfeng
closed
6 years ago
0
Some random fixes
#167
jjfeng
closed
6 years ago
0
Fit final tree for simulations
#166
jjfeng
closed
6 years ago
0
Warm start during hanging chad tuning
#165
jjfeng
closed
6 years ago
0
Penalize transition probability away from target status, per target
#164
jjfeng
closed
6 years ago
0
Add chronos
#163
jjfeng
closed
6 years ago
0
Penalize list of targ stats
#162
jjfeng
closed
6 years ago
0
Fully solve partially penalized log lik problem
#161
jjfeng
closed
6 years ago
0
generate random chad faster
#160
jjfeng
closed
6 years ago
0
Properly warm start the branch lengths
#159
jjfeng
closed
6 years ago
0
Double redefine rate
#158
jjfeng
closed
6 years ago
0
have async and sync periods of cell lineage tree
#157
jjfeng
closed
6 years ago
0
Make additive hazard for double
#156
jjfeng
closed
6 years ago
0
Move all python notebooks to an appropriate folder
#155
jjfeng
opened
6 years ago
0
why does number of hanging chads change?
#154
jjfeng
closed
6 years ago
1
Brute force parsimony trees
#153
jjfeng
closed
6 years ago
0
Iterate through each hanging chad
#152
jjfeng
closed
6 years ago
0
add initial random rearrange
#151
jjfeng
closed
6 years ago
0
Warm start branch length estimates
#150
jjfeng
closed
6 years ago
0
Add tree stability scores
#149
jjfeng
closed
6 years ago
0
add model assessment class
#148
jjfeng
closed
6 years ago
0
Refactor the code like a crazy person
#147
jjfeng
closed
6 years ago
0
Hanging chads
#146
jjfeng
closed
6 years ago
0
Add subprocess and penalize only possible states
#145
jjfeng
closed
6 years ago
0
consider exponential growth rates. larval and dome simulation settings
#144
jjfeng
closed
6 years ago
0
New tree distance metric: correlation between times of internal nodes
#143
jjfeng
closed
6 years ago
1
Consider different lambda orderings
#142
jjfeng
closed
6 years ago
0
Add new rand tree generation
#141
jjfeng
closed
6 years ago
0
Tune by stability even for >1 barcode
#140
jjfeng
closed
6 years ago
0
Tune penalty param for one barcode based on model param stability
#139
jjfeng
closed
6 years ago
0
penalize spine length as a group in the bifurc situation
#138
jjfeng
closed
6 years ago
0
more train/val splits + resimulate alleles
#137
jjfeng
closed
6 years ago
0
split by immediate children of root
#136
jjfeng
closed
6 years ago
0
add placeholders to update known params
#135
jjfeng
closed
6 years ago
0
penalize spine appropriately
#134
jjfeng
closed
6 years ago
0
faster penalty parameter search by sharing the tensorflow models
#133
jjfeng
closed
6 years ago
0
"cross validation" for hyper parameter tuning for single barcode
#132
jjfeng
closed
6 years ago
0
Penalize diagonal of transition matrix to be closer to 1/2
#131
jjfeng
closed
6 years ago
0
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