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matsengrp
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multidms
Joint modeling of multiple deep mutational scanning experiments
https://matsengrp.github.io/multidms
MIT License
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jaxmodels
#164
wsdewitt
opened
1 month ago
3
160 161 transform normal init beta
#163
jgallowa07
closed
1 month ago
0
How do we count "times seen" with non-identical encodings and parameter transformation?
#162
jgallowa07
opened
2 months ago
0
Allow random init of beta params with desired variance.
#161
jgallowa07
closed
1 month ago
0
No parameter transformation call needed for single condition model
#160
jgallowa07
closed
1 month ago
0
Add back in gamma corrected infrastructure
#159
jgallowa07
opened
2 months ago
0
Model.get_mutations_df() output
#158
jgallowa07
closed
2 months ago
1
156 generalized lasso model
#157
jgallowa07
closed
2 months ago
0
Optimization improvements
#156
wsdewitt
closed
2 months ago
5
Docs inline code formatting
#155
wsdewitt
opened
5 months ago
1
Allow user defined `site_map` in `Data` object
#154
jgallowa07
opened
5 months ago
0
Various TODO's in the code
#153
jgallowa07
opened
5 months ago
0
Allow for validation split as attribute of every `Data` object.
#152
jgallowa07
opened
5 months ago
0
149 custom optimization loop
#151
jgallowa07
closed
5 months ago
6
Single-precision optimization
#150
wsdewitt
closed
5 months ago
2
implement our own run() optimization loop
#149
jgallowa07
closed
5 months ago
0
Troubleshooting Documentation
#148
jgallowa07
opened
5 months ago
0
`jax` disagreement with `pandarallel`
#147
jgallowa07
opened
5 months ago
1
added inference functionality to constraint of GE fx scaling
#146
jgallowa07
closed
5 months ago
0
Set default reported correlation to R^2
#145
jgallowa07
closed
5 months ago
0
Added optional fista acceleration, and convergence property to models
#144
jgallowa07
closed
5 months ago
0
Constraining the scale of the non-linearity.
#143
jgallowa07
closed
5 months ago
1
updated validation notebook to be compatible with latest multidms
#142
jgallowa07
closed
5 months ago
0
latest before moving spike analysis
#141
jgallowa07
closed
6 months ago
0
conditional model training / validation loss.
#140
jgallowa07
closed
6 months ago
0
simulation manuscript figures notebook.
#139
jgallowa07
closed
6 months ago
4
patch bug, update simulations to include more plotting
#138
jgallowa07
closed
6 months ago
0
Convergence criteria
#137
jgallowa07
closed
5 months ago
5
Python 3.12 docs failure
#136
jgallowa07
opened
6 months ago
0
added logging suppressor for falling back to cpu
#135
jgallowa07
closed
6 months ago
0
New simulations
#134
jgallowa07
closed
6 months ago
0
$\beta_m$ Ridge Regularization, and $\beta_0$ initialization value.
#133
jgallowa07
closed
5 months ago
3
Add Simulations and Spike analysis to documentation
#132
jgallowa07
closed
5 months ago
1
remove data from notebooks/ directory
#131
jgallowa07
opened
7 months ago
0
Warnings
#130
jgallowa07
closed
5 months ago
2
patched sorting bug
#129
jgallowa07
closed
7 months ago
0
global epistasis models give different results with `pandas` 2.2
#128
jbloom
closed
7 months ago
2
removed int cast and added test
#127
jgallowa07
closed
9 months ago
0
mut_param_heatmap func bug.
#126
jgallowa07
opened
9 months ago
0
Simulations outline
#125
jgallowa07
closed
5 months ago
1
Added shrinkage charts to `ModelCollection`
#124
jgallowa07
closed
10 months ago
0
Add code to automatically generate shrinkage plots from multidms paper
#123
Haddox
closed
10 months ago
0
120 model collection
#122
jgallowa07
closed
11 months ago
0
patch links for biophysical and example
#121
jgallowa07
closed
1 year ago
0
Add `ModelCollection` class
#120
jgallowa07
closed
11 months ago
1
updated docs
#119
jgallowa07
closed
1 year ago
0
Link pre-print, and spike page up front in docs intro
#118
jgallowa07
closed
1 year ago
0
reset index, and add_pheno_to_df index check
#117
jgallowa07
closed
1 year ago
0
indexing error.
#116
jgallowa07
closed
1 year ago
0
consistency in output between versions
#115
jbloom
closed
11 months ago
1
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