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Dev lane #249

Merged
merged 121 commits into from
Apr 17, 2024
Merged

Dev lane #249

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e50fefc
Adding escape for saving X_extra data (to deal with case of having fo…
rjacobs914 Mar 1, 2023
02355e3
Change recalibration_params dict to always have keys "a" and "b" for …
rjacobs914 Mar 1, 2023
a3b7c4b
Add option to have no feature selection, just build learning curve fr…
rjacobs914 Mar 1, 2023
7081917
Added ability to call models from linear-tree package
rjacobs914 Mar 1, 2023
a7c0f5c
Updated docs for elemental feature generator
rjacobs914 Mar 1, 2023
91c7efc
Fixed issue with KerasRegressor model saving
rjacobs914 Mar 1, 2023
89a3766
Added featurization methods from CBFV package
rjacobs914 Mar 1, 2023
367ec82
Added ability to control number of bins in RvE plots, and specify if …
rjacobs914 Mar 2, 2023
8b6d11a
Added another call to RvE bins and bin size (missed before)
rjacobs914 Mar 3, 2023
1468ce4
Changes made to have consistent input throughout generators: "featuri…
rjacobs914 Mar 3, 2023
5126851
Some updates to model.fit and model.predict to work with a PyTorch NN…
rjacobs914 Mar 6, 2023
6503de6
Added DeepChem featurizer that enables many feature methods for molec…
rjacobs914 Mar 6, 2023
1763574
For make_prediction, adding support for multiple featurizers, changin…
rjacobs914 Mar 6, 2023
721aaa7
Some minor updates because of python package reordering.
leschultz Mar 6, 2023
9cc4933
Working on simple domain implementation
leschultz Mar 13, 2023
f727b74
Still working on simple domain classification
leschultz Mar 13, 2023
1fbaf1e
Still working on simple domain classification
leschultz Mar 13, 2023
465dfc5
Now printing simple domain to split file
leschultz Mar 13, 2023
c37d55f
Now saved domains in notable folders
leschultz Mar 13, 2023
f1c04c0
Cleaned up some things
leschultz Mar 13, 2023
2d9d448
Now adding GPR
leschultz Mar 14, 2023
6c61163
Now added GPR
leschultz Mar 14, 2023
80c7b2e
Now dill domain models
leschultz Mar 14, 2023
1b5d87e
Adding CV to GPR for domain stuff
leschultz Mar 14, 2023
9dbb639
Added one example
leschultz Mar 14, 2023
9db6084
Added SymbolicRegressor model (genetic programming) from GPLearn package
rjacobs914 Mar 23, 2023
cc35566
Shap selector- added support for bar chart in addition to beeswarm pl…
rjacobs914 Mar 23, 2023
c49c6cf
Some small updates to docs and warnings for Shap selector regarding K…
rjacobs914 Mar 23, 2023
393a409
print correction
rjacobs914 Mar 23, 2023
254244d
added one missing instance of "domain" call to evaluate_split_sets
rjacobs914 Mar 23, 2023
757653f
added support for different number of recalibration parameters via "r…
rjacobs914 Mar 23, 2023
35d38b3
made updated make_prediction_dlhub function to coincide with updated …
rjacobs914 Mar 23, 2023
c0657b6
Added support for CrabNet regression model from Sparks' npj Comp Mat …
rjacobs914 Mar 24, 2023
094d7dd
Updated docs for CrabNet
rjacobs914 Mar 24, 2023
a691c51
Adding saving for all test and train model errors
rjacobs914 May 19, 2023
525dc6c
Cleanup of old domain code that isn't used, to prep for only using La…
rjacobs914 May 19, 2023
17b8a53
Made it so multiple domain assessment types can be performed in a sin…
rjacobs914 May 19, 2023
5ab4b8a
Changes to predict function to have column name indicate domain asses…
rjacobs914 May 19, 2023
bcfaad4
Adding feature range domain assessment
rjacobs914 May 19, 2023
c68d215
Small change to bin width calculation
rjacobs914 May 19, 2023
b169a80
Update saving of domain model files
rjacobs914 May 19, 2023
ff2f17a
Updates to mastml predictor functions to fix issue when featurizers a…
rjacobs914 May 19, 2023
8f2774a
Updates to setup.py
rjacobs914 May 22, 2023
bf1a895
Adding support for Docker-containerized models on DockerHub
rjacobs914 Jun 1, 2023
2b7b3fb
Using 1/-1 for in/out of domain instead of strings
rjacobs914 Jun 1, 2023
b806b17
Added tqdm to help better monitor fitting progress
rjacobs914 Jun 1, 2023
f3cd085
Added tqdm to help better monitor featurization progress for elementa…
rjacobs914 Jun 1, 2023
eb0432a
Some adjustments to verbosity behavior
rjacobs914 Jun 1, 2023
e43a590
Updates to refine metadata summaries in mastml. In lieu of old metada…
rjacobs914 Jun 2, 2023
ef34e05
First pass at integration of madml
leschultz Jul 5, 2023
1675a07
Now added a user defined function to the madml run
leschultz Jul 6, 2023
fcb3527
Some changes to the predictor to get things to run
leschultz Jul 7, 2023
2033b99
Now added the madml subroutine to mastml predictor.
leschultz Jul 10, 2023
84a3433
Added arugment for coefficient guess to be pased to madml
leschultz Jul 10, 2023
b572dd8
Update setup.py
rjacobs914 Jul 28, 2023
48896ef
Update requirements.txt
rjacobs914 Jul 28, 2023
a883283
Attempting to integrate google colab compatability
leschultz Sep 8, 2023
bbabc05
Attempting to integrate google colab compatability
leschultz Sep 8, 2023
0f8fbdf
Attempting to integrate google colab compatability
leschultz Sep 8, 2023
afddf66
Attempting to integrate google colab compatability
leschultz Sep 8, 2023
ae61fe0
Attempting to integrate google colab compatability
leschultz Sep 8, 2023
0776fca
Attempting to integrate google colab compatability
leschultz Sep 8, 2023
b933f0d
Trying to maek preidictor work
leschultz Sep 11, 2023
1b39b75
Updated predictor
leschultz Sep 11, 2023
1b1b958
Fixed Bug
leschultz Oct 9, 2023
d9f1448
Removed the feature dropping feature for the elemental feature genrator.
leschultz Oct 11, 2023
cb7c45f
Made dropping columns in feature genrator optional
leschultz Oct 11, 2023
2dae957
Revereted some stuff
leschultz Oct 17, 2023
b2ab751
Fixed a bug I introduced
leschultz Nov 1, 2023
8ad59f3
Fixed aditional bug
leschultz Nov 1, 2023
50ea866
Had to comment out something for the predictor to work.
leschultz Nov 1, 2023
1b8a641
Added some python only examples. Non of the jupterlab stuff.
leschultz Nov 1, 2023
ea75dc7
Fixed a bug on the mastml_predictor for the madml integration component.
leschultz Nov 1, 2023
73c93b7
Added the custom thresholds
leschultz Nov 2, 2023
e5b8b73
Added more user friendly prints
leschultz Nov 2, 2023
9aced1d
Added a madml jupyter example.
leschultz Nov 2, 2023
b32c33d
Working on a containerization example
leschultz Nov 6, 2023
5b06853
Updated requirements
leschultz Nov 7, 2023
287a2ce
Updating a local example for creating a container with domain and cal…
leschultz Nov 7, 2023
66a096e
Wrote jupyter lab tutorial for publishing models.
leschultz Nov 8, 2023
115e2ba
Renamed and cleaned
leschultz Nov 8, 2023
d52e6a8
Added more detail to the MADML domain tutorial and passed more parame…
leschultz Nov 16, 2023
8ea4a39
Cleaned tutorial ouptuts
leschultz Nov 16, 2023
55a19c8
Changed requirements
leschultz Nov 16, 2023
6a87b13
Made sure that the latest tutorial ran on google colabm
leschultz Nov 16, 2023
fb1076c
Added CDF plots for calibrated and uncalibrated z scores.
leschultz Nov 27, 2023
b6fb303
New features
leschultz Dec 1, 2023
7549b48
Commenting out some old error plotting routines that aren't so useful…
rjacobs914 Jan 12, 2024
4765acb
Move plot_cdf to be its own function
rjacobs914 Jan 12, 2024
5db809a
Some small cleanup in rstat plotting functions
rjacobs914 Jan 12, 2024
a67cd28
Removing model as input for RvE plots to make for easier plotting, es…
rjacobs914 Jan 12, 2024
85a6a2d
Updates to documentation and some code cleanup
rjacobs914 Jan 12, 2024
cfd480c
Added name_str parameter for rstat and RvE plots to make running in p…
rjacobs914 Jan 12, 2024
46eb017
Adding plot of rstat (zscore) per bin
rjacobs914 Jan 25, 2024
cc81447
Added data output for other error plots
rjacobs914 Jan 25, 2024
34b53a2
Adding plot_cdf and plot_cdf_uncal_cal_overlay rather than calling ma…
rjacobs914 Jan 25, 2024
a25ea07
Adding cdf calls to make_plots
rjacobs914 Jan 25, 2024
9c7d522
Adding plot of CDF miscalibration per bin
rjacobs914 Jan 31, 2024
4fc7ed6
Added plot of CDF miscal area per bin with uncal and cal overlay
rjacobs914 Jan 31, 2024
897a9f9
added transfer learning
leschultz Apr 9, 2024
0814595
Added pre-trained elemnet
leschultz Apr 9, 2024
4926ff7
update to plots.py
rjacobs914 Apr 9, 2024
aa022e6
Update models.py
rjacobs914 Apr 9, 2024
5aa544b
Update domain.py
rjacobs914 Apr 9, 2024
3058b19
Update error_analysis.py
rjacobs914 Apr 9, 2024
a7b73df
Update data_splitters.py
rjacobs914 Apr 9, 2024
9d78ee0
Updates for latest sklearn version
rjacobs914 Apr 11, 2024
a862b84
Update MASTML_Tutorial_1_GettingStarted.ipynb
rjacobs914 Apr 11, 2024
b25cf16
Update MASTML_Tutorial_2_DataImport.ipynb
rjacobs914 Apr 11, 2024
cc4e20e
Update MASTML_Tutorial_3_FeatureEngineering.ipynb
rjacobs914 Apr 11, 2024
1f35076
Update MASTML_Tutorial_4_Models_and_Tests.ipynb
rjacobs914 Apr 11, 2024
65dcf46
Update tutorial names
rjacobs914 Apr 11, 2024
0788d79
Update data_splitters.py
rjacobs914 Apr 12, 2024
dacc4ef
Update MASTML_Tutorial_5_NestedCV_and_OptimizedModels.ipynb
rjacobs914 Apr 12, 2024
fd81227
Update MASTML_Tutorial_6_ErrorAnalysis_UncertaintyQuantification.ipynb
rjacobs914 Apr 12, 2024
c813eea
Update VERSION
rjacobs914 Apr 12, 2024
acfe183
Update setup.py
rjacobs914 Apr 12, 2024
f758554
Update data_splitters.py
rjacobs914 Apr 12, 2024
e89855d
Update MASTML_Tutorial_7_ModelPredictions_with_Guide_Rails.ipynb
rjacobs914 Apr 12, 2024
bbc6f80
Create requirements.txt
rjacobs914 Apr 17, 2024
c03dd5d
Merge branch 'master' into dev_lane
rjacobs914 Apr 17, 2024
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3 changes: 3 additions & 0 deletions README.md
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Expand Up @@ -35,6 +35,9 @@ MAST-ML is an open-source Python package designed to broaden and accelerate the
* Tutorial 7: Model predictions with calibrated error bars, model hosting on Foundry/DLHub:
[![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/uw-cmg/MAST-ML/blob/master/examples/MASTML_Tutorial_7_ModelPredictions_with_CalibratedErrorBars_HostModelonFoundry.ipynb)

* Tutorial 8: Model predictions with guide rails:
[![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/uw-cmg/MAST-ML/blob/master/examples/MASTML_Tutorial_8_ModelPredictions_with_Guide_Rails.ipynb)

## MAST-ML version 3.1.x Major Updates from July 2022
* Refinement of tutorials, addition of Tutorial 7, Colab links as badges added for easier use.

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3 changes: 2 additions & 1 deletion VERSION
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@@ -1 +1,2 @@
3.1.8
3.2.0

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