matsengrp/multidms

Issues

• Docs inline code formatting

  #155 opened 6 months ago by wsdewitt
  1

• No parameter transformation call needed for single condition model

  #160 opened 3 months ago by jgallowa07
  0

• Allow random init of beta params with desired variance.

  #161 opened 3 months ago by jgallowa07
  0

• How do we count "times seen" with non-identical encodings and parameter transformation?

  #162 opened 3 months ago by jgallowa07
  0

• Various TODO's in the code

  #153 opened 7 months ago by jgallowa07
  0

• Optimization improvements

  #156 opened 4 months ago by wsdewitt
  5

• `jax` disagreement with `pandarallel`

  #147 opened 7 months ago by jgallowa07
  1

• Model.get_mutations_df() output

  #158 opened 4 months ago by jgallowa07
  1

• Add back in gamma corrected infrastructure

  #159 opened 4 months ago by jgallowa07
  0

• Single-precision optimization

  #150 opened 6 months ago by wsdewitt
  2

• implement our own run() optimization loop

  #149 opened 6 months ago by jgallowa07
  0

• Allow for validation split as attribute of every `Data` object.

  #152 opened 7 months ago by jgallowa07
  0

• Allow user defined `site_map` in `Data` object

  #154 opened 7 months ago by jgallowa07
  0

• $\beta_m$ Ridge Regularization, and $\beta_0$ initialization value.

  #133 opened 7 months ago by jgallowa07
  3

• Troubleshooting Documentation

  #148 opened 7 months ago by jgallowa07
  0

• Warnings

  #130 opened 7 months ago by jgallowa07
  2

• Constraining the scale of the non-linearity.

  #143 opened 7 months ago by jgallowa07
  1

• Set default reported correlation to R^2

  #145 opened 7 months ago by jgallowa07
  0

• Convergence criteria

  #137 opened 7 months ago by jgallowa07
  5

• Simulations outline

  #125 opened 7 months ago by jgallowa07
  1

• Add Simulations and Spike analysis to documentation

  #132 opened 7 months ago by jgallowa07
  1

• conditional model training / validation loss.

  #140 opened 7 months ago by jgallowa07
  0

• simulation manuscript figures notebook.

  #139 opened 7 months ago by jgallowa07
  4

• Python 3.12 docs failure

  #136 opened 8 months ago by jgallowa07
  0

• global epistasis models give different results with `pandas` 2.2

  #128 opened 9 months ago by jbloom
  2

• remove data from notebooks/ directory

  #131 opened 9 months ago by jgallowa07
  0

• revise CONTRIBUTING

  #98 opened 9 months ago by wsdewitt
  4

• An idea to make things a little more modular.

  #91 opened 9 months ago by jgallowa07
  0

• mut_param_heatmap func bug.

  #126 opened 10 months ago by jgallowa07
  0

• Add code to automatically generate shrinkage plots from multidms paper

  #123 opened a year ago by Haddox
  0

• progress bar creates dependency on `ipywidgets`

  #114 opened a year ago by jbloom
  1

• consistency in output between versions

  #115 opened a year ago by jbloom
  1

• Add `ModelCollection` class

  #120 opened a year ago by jgallowa07
  1

• Link pre-print, and spike page up front in docs intro

  #118 opened a year ago by jgallowa07
  0

• indexing error.

  #116 opened a year ago by jgallowa07
  0

• Polyclonal dependency

  #101 opened a year ago by jgallowa07
  4

• Update all tqdm progress bars to ascii

  #108 opened a year ago by jgallowa07
  0

• make `multidms.plot.lineplot_and_heatmap` private

  #109 opened a year ago by jgallowa07
  0

• Biophysical docs notes

  #102 opened a year ago by jgallowa07
  0

• `get_mutations_df` returns ambiguously defined `predicted_func_score`

  #110 opened a year ago by jbloom
  1

• `Model.wildtype_df` BUG

  #106 opened a year ago by jgallowa07
  3

• citation

  #99 opened a year ago by wsdewitt
  3

• `nbsphinx` -> `MyST{NB}`

  #107 opened a year ago by jgallowa07
  0

• Lots of untested doctest code

  #104 opened a year ago by wsdewitt
  1

• CHANGELOG

  #96 opened a year ago by jbloom
  2

• Cleanup utils and plotting

  #94 opened a year ago by jgallowa07
  0

• What to do with Model.fit_reference_beta()

  #93 opened a year ago by jgallowa07
  0

• "func_score" -> "phenotype" nomenclature

  #89 opened a year ago by jgallowa07
  1

• model determinism

  #86 opened a year ago by jgallowa07
  0

• Property usage

  #88 opened a year ago by wsdewitt
  3