Pinebioml

description:
1. revise code in google style and using pdoc3 to generate api.
2. selection.Lasso: Default regression -> logistic regression + L1.
3. renaming

On going:
1. auto ml (auto sklearn, mljar, H2O)
2. document
a. API (Done)
b. tutorial (on going)
bug:
1. bagging:
- contradicts to log domain in selection method (the negative output of pca)
- the variance of feature will change during bagging (variance matters)
2. logistic regression + L1 grid search need to to modified. In temporary using binary search.
to do:
1. add parameter dict(json or yaml-like)
2. report
n. interactive interface or GUI (maybe nicegui/ plotly)

description:
1. gprofiler query
2. selection result with volcano plot
3. default parameter change:
i. normalizer will all do scaling and centering
ii. random_forest pruning (ccp_alpha = 1e-2)
iii. essemble will activate 8 method: dt, svm, lasso, multi-lasso, adaboost, xgboost, lightgbm, random_forest-gini
4. implement random_forest with oob + permutation importance.
i. single processing implement
ii. permutation method is super slow: O(n_trees* n_feature* n_repeat) ~ O(n_feature^2* n_repeat)
5. an optuna example of svm.
On going:
1. auto ml (auto sklearn, mljar, H2O)
2. document

bug:
1. bagging:
- contradicts to log domain in selection method (the negative output of pca)
- the variance of feature will change during bagging (variance matters)
to do:
1. add parameter dict(json or yaml-like)
2. report
n. interactive interface or GUI (maybe nicegui/ plotly)

description:
readme format changes

description:
Some changes about gradient boosting or IO functions was missed.

description:
1. add ablation notebook, GBM and ccRCC data.
2. fix variance of mean bug in global scale.
3. fix multi lasso scale problem.

bug:
1. bagging:
- contradicts to log domain in selection method (the negative output of pca)
- the variance of feature will change during bagging (variance matters)
to do:
1. add parameter dict(json or yaml-like)
2. auto ml (auto sklearn, mljar, H2O)
3. document (on going)
4. report
n. interactive interface or GUI

description:
1. check pipenv and readme