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[ENH] Neat and automated transfer learning with OPTIMADE API for auto-adjusted problem-specific ML model generation on the fly #16

Merged
merged 50 commits into from
Apr 4, 2024
Merged

[ENH] Neat and automated transfer learning with OPTIMADE API for auto-adjusted problem-specific ML model generation on the fly #16

merged 50 commits into from
Apr 4, 2024

Commits on Mar 27, 2024

  1. (modelAdjusters) set up scaffold for the submodule

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  2. (MA) documentation and initialization of LocalAdjuster

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  3. (MA) minor initialization additions and 2 plotting helper functions

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  4. (core) added plotly to the requirements

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  5. (MA) finalized the key adjust routine

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  6. (MA) aded returns to the adjust routine

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  7. (MA) add a message if ClearML is to be used in case someone does it o… 

    …n accident and gets an error
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Commits on Mar 28, 2024

  1. (MA) improved memory handling during adjustments

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  2. (MA) implemented a hyperparameter search matrix for 27 common options… 

    …; meant mostly for tuning to smaller datasets
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  3. (MA) implemented a hyperparameter search matrix for 27 common options… 

    …; meant mostly for tuning to smaller datasets
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  4. (MA) added optimade to the dev requirements

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  5. (MA) implemented initialization of OPTIMADEAdjuster and its docstrings

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  6. (MA) implemented querying OPTIMADE and passing structures to featuriz… 

    …ation in`OPTIMADEAdjuster`
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  7. (core) added [http_client] to the optimade requirement needed for… 

    … querying
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  8. (MA) added entry name collection to the OPTIMADEAdjuster

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  9. (MA) upped the default result number limit to 10000 and added it as… 

    … a parameter with documentation in `OPTIMADEAdjuster`
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  10. (core) removed info about importing from the top pysipfenn namespac… 

    …e in the top `__init__`
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  11. (MA) finalized the fetchAndFeturize routine of OPTIMADEAdjuster,… 

    … now collecting names, target data, and featurizing the obtained structures
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  12. (MA) add a message on possible degeneracy of datasets from overlappi… 

    …ng queries
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  13. (MA) added class parameter of validationLabels, assigned at every … 

    …adjustment, to display if a datapoint has been shown to the model at adjustment. Displayed when plotting unadjusted and adjusted models.
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  14. (MA) improved several printouts

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  15. (MA) added assertions that data to operate on is available before tu… 

    …ning
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Commits on Mar 29, 2024

  1. (MA) added automatic shuffling of the OPTIMADE-obtained data

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  2. (core) limit the convenience import scope of the top level `__init__… 

    ….py`
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  3. (MA) distributed optional dependency imports as needed

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  4. (deps) moved plotly from optional to required dependencies

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  5. (core) small addition to the top level imports

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  6. (core) reverted the __init__.py scope narrowing for the top level … 

    …import
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  7. (MA) aded tracking of the compositions coming in from OPTIMADE; not u… 

    …sed right now but important for future methods including crystALL
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  8. (MA) plotting style improvements

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  9. (MA) added a convenience function for highlighting points at given in… 

    …dices
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  10. (MA) added reduced formula homogenization just in case

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  11. (MA) added printout on the number of unique compositions at the end o… 

    …f OPTIMADE fetching
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  12. (MA) added population of validation labels with "Training" after data… 

    … is fetched from OPTIMADE but no training was done
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  13. (MA) improved target path documentation

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  14. (MA) added ETA printouts to the hyperparameter search

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Commits on Mar 30, 2024

  1. (MA) bugfix at CSV data ingestion which did not expect default pySIPF… 

    …ENN labeling
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  2. (MA) additional assertiona at the plotting step

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  3. (MA) general minor improvements including populating `self.validation… 

    …Labels` if no-validation adjustments were ran
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  4. (test) added an example NumPy file with stored descriptor data

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  5. (test) added an example CSV file with stored descriptor data

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  6. (test) added an example NumPy file with a stored target data array

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  7. (test) added an example CSV file with a stored target data table

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  8. (test) added a pretty complete testing suite for model adjusters; tes… 

    …ts all functions except for the optional, non-default ClearML connectivity
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  9. (test) improved ModelAdjusters test documentation

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Commits on Apr 3, 2024

  1. (MA) reduced hyperparameter search epoch *default* number to 20 and i… 

    …mproved description of the parameter to make it clear higher number is desired if GPU is present
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  2. (MA) added a set of assertions to the OPTIMADEAdjuster initialization

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  3. (MA) added an assertion more than no data was fetched, so that the er… 

    …ror message is more clear to the user
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  4. (MA) implemented endpointOverride parameter to allow user to specif… 

    …y the base URL to use and point to custom provider or a specific sub-database of a provider
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  5. (tests) added testing procedure for endpoint overriding

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