Feyn Changelog

All notable changes to this project will be documented in this file.

The format is based on Keep a Changelog, and this project adheres to Semantic Versioning.

[3.0.1] - 2022-04-27

Changed

• Use of feyn is now fully local, using an improved and lightweight version of the QLattice bundled within feyn.
• You should now use feyn.QLattice() to get a QLattice. Notice that the previous functions feyn.connect_qlattice() and ql.reset() are now deprecated. They have been updated to match the new workflow to ensure previous code still works as intended, but will be removed in future releases of feyn.

Fixed

• plot_response_1d on a single-feature model no longer requires the by argument.
• plot_activation_flow now warns the user when more than one sample is given.
• Updated outdated LICENSE file.

[2.1.5] - 2022-03-25

Changed

• sklearn and sympy is now a dependency of feyn.

Fixed

• plot_roc_curve now correctly computes for large datasets.
• Minor performance improvements to the training.

[2.1.4] - 2022-01-13

Fixed

• Release windows versions missing in release 2.1.3.

[2.1.3] - 2022-01-11

Changed

• Build for python 3.10 for all major platforms.
• Drop support for python 3.6.

Fixed

• Fixed an issue with np.float128 type not supported on windows machines. Defaults to numpy.longdouble.

[2.1.2] - 2021-12-10

Added

• feyn.reference models now perform automatic categorical preprocessing. This is done using the optional stypes parameter in the constructor.

Changed

• feyn.plots.plot_model_response_2d now has a fixed scale for classification to make it easier to read and compare.

Fixed

• Fixed an issue where feyn.tools.estimate_priors would incorrectly rank the priors in some instances.
• The type checker now allows all numerical numpy dtypes in place of "float" and all integer types for "int", so you no longer have to upcast your dataframes.
• Input name truncation in the model plots now don't truncate if the length would result in a same-length or longer string.

[2.1.1] - 2021-10-27

Added

• Sympify:
  • feyn.tools.sympify() (also model.sympify()) now has parameter symbolic_cat that allows you to expand categories to their linear components to make it easier to port or evaluate a sympy expression.
  • feyn.tools.get_sympy_substitutions for easily converting a model and a sample to a substitution dictionary for use with <sympy_expr>.evalf(subs=...) with the new category changes.
• Exposed convenience functions used by auto_run to make it more composable by the user:
  • feyn.tools.infer_available_threads tries to guess how many threads you can use. Returns maximum - 1.
  • feyn.tools.get_progress_label gives a label for use with model.show that displays epoch count and an estimated time to finish (if elapsed seconds are given).
• Experimental feature for IPython environments only: ql.expand_auto_run is a function that takes all the same parameters as auto_run and creates a runnable code cell with the same code that makes it easier for you to fold out an auto_run loop to its primitive components. Note that this contains all of the error handling, general checking and safety measures of auto_run that you might not need, but could serve as a starting point.
• Added model.plot_pr_curve() to plot precision-recall curves.
• Added feyn.tools.estimate_priors function for computing prior probabilities of inputs based on mutual information.
• Added ql.update_priors function primitive for updating the QLattice with prior probabilities of inputs.

Changed

• feyn.get_diverse_models is now more likely to return up to n models, and has improved runtime.
• feyn.tools.get_model_parameters returns a slightly different structure for categories now. The category is the index, and the weight columns are now named as {input_name}\[_ix\]}. This makes it easier to relate to the specific places in the model, for example for use in substituting values in the sympy expression.
• model.inputs now returns a unique list of input names.
• The target parameter of models from feyn.reference has been renamed output_name.

Fixed

• Sympify model bugs:
  • Numerical input names now work correctly again.
  • Categorical input names are now identifiable if multiple inputs exist in a model with the same name.
  • Input names with sympy reserved characters should be better supported now (the characters get replaced).
• You can now install optional dependencies using pip install feyn[extras]
• Fix display of inputs in models that would sometimes result in hard to copy input names.
• Models with categorical registers should now be reproducible with seed and same version of feyn/qlattice.

[2.1.0] - 2021-09-27

Added

• Add feyn.get_diverse_models. User facing function to get diverse models given their lineage in the QLattice.
• Add feyn.tools.get_model_parameters (also model.get_parameters). User can extract the parameters of a certain feature in the model as a pandas DataFrame.
• Add option to save various plots:
  • plot_model_summary (also model.plot) plot as an html file.
  • plots in the majority of plotting functions.
• Add option to change the figsize of plots in the majority of plotting functions.
• Add more useful display of inputs in model when they share a common beginning.

Changed

• New QLattice algorithm that vastly improves performance and has better traversal of the search space:
  • QLattice.update now expects you to give all the models you have - sorted by your metric of choice - and it will figure out how best to update on its own.
  • New format for saving and loading models. Breaks backwards compatibility with previously saved models.
  • feyn.prune_models no longer supports dropout and decay parameters.
• plot_model_summary (also model.plot):
  • Is intended to plot the most useful metrics and report for your final model, and has been changed to reflect this.
  • Now displays a table of the inputs used in the model.
• plot_model_signal (also model.plot_signal) no longer plots the summary metrics, and the arguments have changed to reflect this.
• plot_partial_2d now has a deprecation warning, use plot_model_response_2d (model.plot_response_2d) instead.
• auto_run:
  • Now sorts best models based on the Bayesian information criterion (BIC) by default rather than loss.
  • No longer returns multiple models with identical mathematical expressions. This means that any number between one and ten models will be returned.
  • Now estimates a time to completion.
  • Starting models are now copied before being added to the fitting loop, meaning that your original models are left unchanged.

Removed

• Remove feyn.best_diverse_models. Replaced by feyn.get_diverse_models which has similar functionality.
• Remove semantic type "bool" which previously only used functions add, multiply, gaussian2. We now recommend using the numerical semantic type instead.
• Remove deprecated plot_partial. This functionality is covered by plot_model_response_1d.

Fixed

• auto_run has been reprimanded and will now properly honor your selected amount of threads.
• The query language can now be used in all cases - there is no longer a limitation to which queries will be feasible.

[2.0.7] - 2021-08-20

Added

• More informative error messages and type checks for all top-level functions, such as:
  • Primitives:
    • ql.auto_run,
    • ql.sample_models,
    • feyn.sample_models,
    • feyn.fit_models,
    • feyn.prune_models,
    • feyn.best_diverse_models,
    • ql.update,
  • Plotting:
    • feyn.plots.plot_partial2d,
    • feyn.plots.plot_roc_curve,
    • feyn.plots.plot_probability_scores,
    • feyn.plots.plot_activation_flow,
    • feyn.plots.plot_model_summary,
    • feyn.plots.plot_model_response_1d,
    • feyn.plots.plot_residuals,
    • feyn.plots.plot_regression
• Model.predict can now accept pd.Series.
• New function added called Model.plot_signal. This displays signal flow through model. This is the previous behaviour of Model.plot.
• New function make_regression and make_classification functions available in feyn.datasets module. These are wrappers of the sklearn functions in sklearn.datasets.
• Feyn now has a native package for Mac with Apple silicon (M1 chip) for Python 3.8 and 3.9

Changed

• plot_probability_scores parameter h_kwargs has been replaced with **kwargs. Now you can pass histogram kwargs as keyword arguments and not a dictionary
• Model.plot now displays performance figures underneath the model signal. For regressors these are:
  • plot_regression,
  • plot_residuals. For classifiers these are:
  • plot_roc_curve,
  • plot_confusion_matrix.

Removed

• ql.snapshots have been removed and the QLattice no longer has backup and restore functionality.

[2.0.4] - 2021-07-07

Changed

• plot_partial is now called plot_response_1d (feyn.plots.plot_model_response_1d)
  • The named argument fixed is now called input_constraints
  • plot_partial can still be called but now raises a FutureWarning about being deprecated.

[2.0.1] - 2021-06-29

Changed

• model.plot (feyn.plots.plot_model_summary) has been updated:
  • The named argument test is now called compare_data
  • Now supports labels param for custom labels for the summary metrics
  • Now supports a list of compare data, if you want to compare multiple things
  • Any additional metric added will be a more condensed column to make it easier to compare with the primary metrics

Fixed

• Model graphs being cut off by jupyter's viewport in some instances should now be fixed by automatic rescaling to fit in view.

[2.0.0] - 2021-06-18

Changed

• Graph is now called Model

• The QGraph no longer exists. Instead you now work on lists of Models.

• No longer directly instantiate a QLattice. Instead you call feyn.connect_qlattice().

• The common feyn workflow is now contained in one function called auto_run which lives on a connected QLattice.

• In addition to the above automatic workflow, we now have a more expressive set of functions to replace the old:

  • A list of Models can now be sampled from a connected QLattice using sample_models. This replaces part of the behaviour of the previous get_regressor and get_classifier on the QGraph.
  • You now fit a list of Models using feyn.fit_models. This takes a list of Models as an input and returns a list of fitted Models. This replaces part of the previous fit step on the QGraph.
  • You now prune the worst Models from a list using prune_models. This replaces part of the previous fit step on the QGraph. Default behaviour removes duplicate Models, has a decay function on Models and dropout.
  • You get the best diverse Models using feyn.best_diverse_models. This replaces QGraph.best.
  • Now that you operate on a list of Models, you have the freedom of using the native python filter function.
    • You still have a list of useful feyn.filter functions but instead apply to the native python filter. These functions are. Refer to the documentation for more details:
      • Complexity
      • ContainsInputs
      • ExcludeFunctions
      • ContainsFunctions
  • You can display a Model as a graph using the show_model function.
    • show_model detects whether you are in a Jupyter environment and decides what to display.

• Other changes:

  • plot_summary is now known as plot that lives on a Model.
  • The output of sympify has changed:
    • Categorical input features are now referenced as <feature_name>_cat.
    • Numerical input names get suffixed with _in.
    • Underscores and spaces in input names are truncated.
  • sympify now supports include_weights=False which gives an equation without weights and bias.
  • sympify now gives consistent results on up to 15 significant digits.
  • plot_goodness_of_fit is now called plot_regression.
  • plot_regression_metrics has been removed - its uses should be covered by plot_regression.

Added

• plot_roc_curve has a threshold parameter that will plot on the false positive rate and true positive rate at the given threshold.
• plot_confusion_matrix has a threshold parameter.

Removed

• Our experimental feature module __future__ has for now outlived its purpose and has been removed.

[1.6.1] - 2021-05-04

[1.6.0] - 2021-05-04

Added

• (future) Graph Recorder object that incorporates barcode and feature frequency matrix and heatmaps (now called feature occurrence)

Fixed

• Fixed a warning from matplotlib about duplicate cmap registering for newer versions of mpl.

[1.5.6] - 2021-04-23

Fixed

• Fixed bug in ROC plot function.

[1.5.5] - 2021-04-21

Fixed

• Fixed bug in qlattice migration script.

[1.5.4] - 2021-04-21

Added

• New sematic type "bool" which will only use functions that makes sense for boolean data types (add, multiply, gaussian2)
• New statistical plots, plot_goodness_of_fit and plot_residuals to feyn.plots.
• New transient QLattice feature.
• plot summary improvements:
  • Pearson correlation is now default - and now properly displays negative instead of absolute correlation
  • MI correlation now follows a simple linear colormap that better represents it.
  • Spearman correlation is now available as an alternative correlation function
• Introduce plot_flow and a Jupyter-widget-enabled plot_flow_interactive for graphs, allowing you to play around with samples and see the activations through the graph.
• (future) Barcode plot and feature frequency matrix and heatmap plots.
• Query language available through feyn.filters updated
  • New matching starts from the output of the graph.
  • Can write queries using + and * operators.
  • Wildcards matching any subgraph _, complexity can be constrained with edge count in brackets.
• New show_threshold parameter in plot_roc_curve that colours the ROC curve by thresholds.

Changed

• Backwards compatability QLattice-urls has been removed from feyn.QLattice(). Now the only accepted usages are:
  • feyn.QLattice(qlattice="<qlattice-id>", api_token="<token>").
  • feyn.QLattice(config="<name of a section in your config file>").
  • feyn.QLattice() # First section in your config file.

[1.5.3] - 2021-03-26

Changed

• General algorithm improvements.

Added

• Support for up to 2000 registers (Input features). Previously 200.
• Made it easier to trigger the hover information on graphs in notebooks.

[1.5.2] - 2021-03-11

Fixed

• Fixed bug in random seed, which caused QLattice.reset() to always use the same seed.

[1.5.1] - 2021-03-10

Changed

• Improve deprecation warning, so that it is obvious how to migrate the old configuration file.

[1.5.0] - 2021-03-10

Changed

• The parameters for the QLattice initializer has changed. You now only have to specify the qlattice and the token instead of the full url.
• With this, also the configuration-file format has changed accordingly. url has been replaced by server and qlattice. The old format still works, but support for it will be removed in a future release. A compatibility warning will be displayed for now.

Fixed

• plot_partial2d: Fixed to use new contract when getting graph state.

[1.4.8] - 2021-02-26

Changed

• The QGraph.fit supports using Akaike Information Criterion (AIC) or Bayesian information criterion (BIC). This may become the default in the future, reducing the need for limiting depth and edges manually
• Default threads used for fitting ans sorting changed from 1 to 4

[1.4.7] - 2021-02-12

Changed

• General performance improvements in finding good graphs.

Added

• Add roc_auc_score to feyn.metrics which will calculate the AUC of a graph. (Also accessible on graph.roc_auc_score).
• Plotting style improvements:
  • 'light' is now usable as alias to 'default' when setting theme.
  • Matplotlib plot styling now matches the theme choice.
  • Added colormaps to use with matplotlib: 'feyn', 'feyn-diverging'. 'feyn-partial', 'feyn-primary', 'feyn-secondary', 'feyn-highlight', 'feyn-accent'.
• Added FeatureImportanceTable to feyn.insights. (The equivalent functionality was previous in pdheatmap from __future__).
• (future) Add various stats functions. graph_f_score and plot_graph_p_value.

[1.4.6] - 2021-01-08

Added

• Targeted Maximum Likelihood Estimation (TMLE) introduced in feyn.inference. See more in our docs

Changed

• Default graphs sort back to loss_value instead of bic.
• feyn.tools.simpify_graph default option is now to not formulate the logistic function, but instead output “logreg(…)“. Use argument symbolic_lr=True if you want to keep previous behavior.
• Categorical variables rendered in the sympify function from category(<X_featurename>) to category_.

[1.4.5] - 2020-12-18

Added

• Python 3.9 support

Fixed

• Fix memory bug when handling many registers (>165) in QLattice.

[1.4.4] - 2020-12-18

Removed

• metrics.get_mutual_information(), metrics.get_pearson_correlations(), metrics.get_summary_information(). The functionality is now covered by metrics.calculate_mi(), metrics.calculate_pc() in the public API.

Changed

• Even more general performance improvements.

[1.4.3] - 2020-12-04

Changed

• General performance improvements.

Added

• Graph.plot_partial() and Graph.plot_partial2d() to analyze the graph response.
• metrics.calculate_mi(), metrics.calculate_pc() to calculate mutual information and pearson correlations.

[1.4.2] - 2020-10-26

• Graph.sympify() which returns a sympy expression mathcing the graph
• Mutual information and pearson correlations are now calculated on entire data set, giving more accurate results
• Graph.fit() function which can be used to fit or refit a single graph on a dataset
• Adding support to both numerical and categorical partial dependence plots
• Bugfix: 1d plots with categoricals ordered wrt their weights
• Bugfix: Fix support np-dict for graph_summary

[1.4.1] - 2020-10-09

• Added linear and constant reference models (in feyn.reference) to compare with and calculate p-values (lives in feyn.metrics).
• Graph vizualizations rewritten and much improved.
• Dark theme support!

[1.4.0] - 2020-09-03

• ql.update now accepts either a single graph or a list of graphs.
• Added methods: QLattice.get_regressor and QLattice.get_classifier to replace QLattice.get_qgraph.
• New mathematical functions: add, exp and log.
• You can now control functions in graphs with new filters: feyn.filters.Functions(["add", "multiply"]) and feyn.filters.ExcludeFunctions("sine").
• New plot. ROC-curves.

[1.3.3] - 2020-08-14

• Shorthands for plotting and score utility functions on feyn.Graph
• New approach to damping learning rates lead to more accurate fits
• Max-depth filter is less strict on which type of integers it accepts.
• Add automatric retries on failed http-requests
• Configurations can now also be stored in <home_folder>/.config/.feynrc

[1.3.1] - 2020-07-07

• The new automatic scalar is now default on both input and output.
• Alternative input and output semantic types (f#) that does not scaling

[1.3.0] - 2020-07-06

• Added a new scaler: f$. It is more automatic.

[1.2.1] - 2020-06-16

• Changed the configuration environment variable QLATTICE_BASE_URI to FEYN_QLATTICE_URL.
• Changed the configuration environment variable FEYN_TOKEN to FEYN_QLATTICE_API_TOKEN.
• Support for configuration via config file. feyn.ini or .feynrc located in your home folder.
• Breaks compatibility with qlattice <= 1.1.2
  • Removed the neeed to add registers via qlattice.registers.get (and removed qlattice.registers.get)
  • New parameter to get_qgraph function to choose the semantic type of the data colums (this replaces the need cat/fixed register types)
• Fixes bug with numpy 1.15 and multiarray import in windows 64bit

[1.1.2] - 2020-05-11

• Added Windows Support!
• Removed dependency to GraphViz
• Removed dependency to scikit-learn