v3.0.0

Change Log

From v2.1.1 to v3.0.0

Fixes

• Fixed random seeds to give reproducible results. Each dataset is initialized with a
  single random state (either from the constructor or a random number generator) which
  is used in all subsequent random operations. Each model is initialized with a single
  random state as well: it uses the random state from the dataset, unless it's overriden
  in the constructor. When a dataset is saved to a file so is its random state, which is
  used by the dataset when the dataset is reloaded.
• fixed error with serialization of the DNNModel.params attribute, when no parameters
  are set.
• Fix bug with saving predictions from classification model
  when ModelAssessor.useProba set to False.
• Add missing implementation of QSPRDataset.removeProperty
• Improved behavior of the Papyrus data source (does not attempt to connect to the
  internet if the data set already exists).
• It is now possible to define new descriptor sets outside the package without errors.
• Basic consistency of models is also checked in the unit test suite, including in
  the qsprpred.extra package.
• Fixed a problem with feature standardizer being retrained on prediction data when a
  prediction from SMILES was invoked. This affected all versions of the package higher
  or equal to v2.1.0.
• Fixes to the fromMolTable method in various data set implementations, in particular
  in copying of the feature standardizer and other settings.
• Fixed not working cluster split and --imputation from data_CLI.py.
• Fixed a problem with ProteinDescriptorSet.getDescriptors returning descriptors in
  wrong order with Pandas <v2.2.0.

Changes

• The model is now independent of data sets. This means that the model no longer
  contains a reference to the data set it was trained on.
  • The fitAttached method was replaced with fitDataset, which takes the data set
    as
    an argument.
  • Assessors now also accept a data set as a second argument. Therefore, the same
    assessor
    can be used to assess different data sets with the same model settings.
  • The monitoring API was also slightly modified to reflect this change.
  • If a model requires initialization of some settings from data, this can be done in
    its initFromDataset method, which takes the data set as an argument. This method
    is called automatically before fitting, model assessment, and hyperparameter
    optimization.
• The whole package was refactored to simplify certain commonly used imports. The
  tutorial code was adjusted to reflect that.
• The jupyter notebooks in the tutorial now pass a random state to ensure consistent
  results.
• The default parameter values for STFullyConnected have changed from n_epochs =
  1000 to n_epochs = 100, from neurons_h1 = 4000 to neurons_h1 = 256
  and neurons_hx = 1000 to neurons_hx = 128.
• Rename HyperParameterOptimization to HyperparameterOptimization.
• TargetProperty.fromList and TargetProperty.fromDict now accept a both a string and
  a TargetTask as the task argument,
  without having to set the task_from_str argument, which is now deprecated.
• Make EarlyStopping.mode flexible for QSPRModel.fitDataset.
• save_params argument added to OptunaOptimization to save the best hyperparameters
  to the model (default: True).
• We now use jsonpickle for object serialization, which is more flexible than the
  non-standard approach before, but it also means previous models will not be compatible
  with this version.
• SklearnMetric was renamed to SklearnMetrics, it now also accepts an scikit-learn
  scorer name as input.
• QSPRModel.fitDataset now accepts a save_model (default: True)
  and save_dataset (default: False) argument to save the model and dataset to a file
  after fitting.
• Tutorials were completely rewritten and expanded. They can now be found in
  the tutorials folder instead of the tutorial folder.
• MetricsPlot now supports multi-class and multi-task classification models.
• CorrelationPlot now supports multi-task regression models.
• The behaviour of QSPRDataset was changed with regards to target properties. It now
  remembers the original state of any target property and all changes are performed in
  place on the original property column (i.e. conversion to multi-class classification).
  This is to always maintain the same property name and always have the option to reset
  it to the raw original state (i.e. if we switch to regression or want to repeat a
  transformation).
• The default log level for the package was changed from INFO to WARNING. A new
  tutorial
  was added to explain how to change the log level.
• RepeatsFilter argument year_name renamed to time_col and
  arugment additional_cols added.
• The perc argument of BorutaPy can now be set from the CLI.
• Descriptor calculators (previously used to aggregate and manage descriptor sets) were
  completely removed from the API and descriptor sets can now be added directly to the
  molecule tables.
• The rdkit-like descriptor and fingerprint retrieval functions were removed from the
  API because they complicated implementation of customized descriptors.
• The apply method was simplified and a new API was clearly defined for parallel
  processing of properties over data sets. To improve molecule processing,
  a processMols method was added to MoleculeTable.

New Features

• The qsprpred.benchmarks module was added, which contains functions to easily
  benchmark
  models on datasets.
• Most unit tests now have a variant that checks whether using a fixed random seed gives
  reproducible results.
• The build pipeline now contains a check that the jupyter notebooks give the same
  results as ones that were observed before.
• Added FitMonitor, AssessorMonitor, and HyperparameterOptimizationMonitor base
  classes to monitor the progress of fitting, assessing, and hyperparameter
  optimization, respectively.
• Added BaseMonitor class to internally keep track of the progress of a fitting,
  assessing, or hyperparameter optimization process.
• Added FileMonitor class to save the progress of a fitting, assessing, or
  hyperparameter optimization process to files.
• Added WandBMonitor class to save the progress of a fitting, assessing, or
  hyperparameter optimization process to Weights & Biases.
• Added NullMonitor class to ignore the progress of a fitting, assessing, or
  hyperparameter optimization process.
• Added ListMonitor class to combine multiple monitors.
• Cross-validation, testing, hyperparameter optimization and early-stopping were made
  more flexible by allowing custom splitting and fold generation strategies. A tutorial
  showcasing these features was created.
• Added a reset method to QSPRDataset, which resets splits and loads all descriptors
  into the training set matrix again.
• Added ConfusionMatrixPlot to plot confusion matrices.
• Added the searchWithIndex, searchOnProperty, searchWithSMARTS and sample
  to MoleculeTable to facilitate more advanced sampling from data.
• Assessors now have the split_multitask_scores flag that can be used to evaluate each
  task seperately with single-task metrics.
• MoleculeDataSets now has the smiles property to easily get smiles.
• A Docker-based runner in testing/runner can now be used to test GPU-enabled features
  and run the full CI pipeline.
• It is now possible to save PandasDataTables to a CSV file instead of the default
  pickle format (slower, but more human-readable).
• New RegressionPlot class WilliamsPlot added to plot Williams plots.
• Data sets can now be optionally stored in the csv format and not just as a pickle
  file. This makes it easier to debug and share data sets, but it is slower to load and
  save.
• Added ApplicabilityDomain class to calculate applicability domain and filter
  outliers from test sets.

Removed Features

• The Metric interface has been simplified in order to make it easier to implement
  custom metrics. The Metric interface now only requires the implementation of
  the __call__ method, which takes predictions and returns a float. The Metric
  interface no longer requires the implementation
  of needsDiscreteToScore, needsProbaToScore and supportsTask. However, this means
  the base functionality of checkMetricCompatibility, isClassificationMetric
  and isRegressionMetric are no longer available.
• Default hyperparameter search space file, no longer available.