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raamana/confounds
Including causal discovery methods such as LiNGAM

Should we consider offering causal discovery based on LiNGAM ? For ex. Yang [2] applies LiNGAM for recognizing brain connectivity patterns with fMRI data. References 1. Python package for causal discovery ...
  • sinhaharsh
  • Opened 
    on Aug 23, 2023
  • #22

raamana/confounds
better validation of inputs to Deconfounders

the #19 reminds me of how some users can be confused given the code lets the second argument to .fit() and .transform() optional with y=None. The only reason we have y=None is to try follow sklearn conventions ...
  • raamana
  • 13
  • Opened 
    on Apr 29, 2022
  • #20

raamana/confounds
ValueError: Input contains NaN, infinity or a value too large for dtype('float64').

- confounds version:0.1.3 - Python version: 3.10 - Operating System: mac Having the error eventhough the data is clean, has no Na nor NaN values C_sample = graph_corr_1[confound_cols] X_sample ...
  • KingArnaiz
  • 4
  • Opened 
    on Apr 28, 2022
  • #19

raamana/confounds
drop-in replacements for cross_val_predict and cross_val_score etc

Pradeep, could something like this be of interest for the library? The idea would be to create a class that would do fit and predict including deconfounding and the use of the estimator in an encapsulated ...
  • jrasero
  • 14
  • Opened 
    on Feb 25, 2022
  • #18

raamana/confounds
Error fitting Residualize

- confounds version: 0.1.1 - Python version: 3.9.7 - Operating System: macOS 11.6 Description I tried to run the example code with some dummy data, but get an error when I try to fit Residualize ...
  • joebathelt
  • 5
  • Opened 
    on Oct 6, 2021
  • #17

raamana/confounds
Performance score stratified by confound

utils.score_stratified_by_confound() Helper to summarize the performance score (accuracy, MSE, MAE etc) for each level or variant of confound. This is helpful to assess any bias towards a particular value ...
  • raamana
  • 6
  • Opened 
    on Jun 17, 2020
  • #10

raamana/confounds
Adding more documentation

References to - literature on confounding in general and types of bias that are not due to confounding - Recent methods in the functional genomics literature such as RUV-4 and SCmerge - Papers evaluating ...
  • mnarayan
  • Opened 
    on Jun 16, 2020
  • #9

raamana/confounds
Add generator for simualted or real confounded datasets

  • dinga92
  • 2
  • Opened 
    on Jun 16, 2020
  • #8

raamana/confounds
Methods and metrics to quantify the level of confounding in a given a sample

May be more than a good first issue.. but depending on the skill level, this can be a good first issue.
good first issue
  • raamana
  • Opened 
    on Jun 16, 2020
  • #6

raamana/confounds
Add tests for DummyDeconfounding() method

good first issue
  • raamana
  • Opened 
    on Jun 16, 2020
  • #5
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