diff --git a/docs/sphinx-builddir/doctrees/README.doctree b/docs/sphinx-builddir/doctrees/README.doctree index b98d40b..ac2cc78 100644 Binary files a/docs/sphinx-builddir/doctrees/README.doctree and b/docs/sphinx-builddir/doctrees/README.doctree differ diff --git a/docs/sphinx-builddir/doctrees/algorithms.doctree b/docs/sphinx-builddir/doctrees/algorithms.doctree index 3a05ee7..8f1344e 100644 Binary files a/docs/sphinx-builddir/doctrees/algorithms.doctree and b/docs/sphinx-builddir/doctrees/algorithms.doctree differ diff --git a/docs/sphinx-builddir/doctrees/descriptors.doctree b/docs/sphinx-builddir/doctrees/descriptors.doctree index fb48723..ca62090 100644 Binary files a/docs/sphinx-builddir/doctrees/descriptors.doctree and b/docs/sphinx-builddir/doctrees/descriptors.doctree differ diff --git a/docs/sphinx-builddir/doctrees/environment.pickle b/docs/sphinx-builddir/doctrees/environment.pickle index 79c358f..1cc3e03 100644 Binary files a/docs/sphinx-builddir/doctrees/environment.pickle and b/docs/sphinx-builddir/doctrees/environment.pickle differ diff --git a/docs/sphinx-builddir/doctrees/index.doctree b/docs/sphinx-builddir/doctrees/index.doctree index 60d62d9..236c9fd 100644 Binary files a/docs/sphinx-builddir/doctrees/index.doctree and b/docs/sphinx-builddir/doctrees/index.doctree differ diff --git a/docs/sphinx-builddir/doctrees/nbsphinx/notebooks/preprocess_data.ipynb b/docs/sphinx-builddir/doctrees/nbsphinx/notebooks/preprocess_data.ipynb index 0dd5da5..9853aed 100644 --- a/docs/sphinx-builddir/doctrees/nbsphinx/notebooks/preprocess_data.ipynb +++ b/docs/sphinx-builddir/doctrees/nbsphinx/notebooks/preprocess_data.ipynb @@ -1055,10 +1055,10 @@ " response_type=\"regression\",\n", " training_dataset_file=\"../tests/data/sdf/example.sdf\",\n", " deduplication_strategy=KeepAllNoDeduplication(),\n", - " log_transform=\"True\", # flags to use a transform\n", + " log_transform=True, # flags to use a transform\n", " log_transform_base=LogBase.LOG10, # Log10 base will be used\n", - " log_transform_negative=\"True\", # The negated log transform will be applied\n", - " log_transform_unit_conversion=6 # THe unit conversion for pXC50 values is 6\n", + " log_transform_negative=LogNegative.TRUE, # The negated log transform will be applied\n", + " log_transform_unit_conversion=6 # The unit conversion for pXC50 values is 6\n", ")\n", "\n", "pxc50_data = Dataset(\n", diff --git a/docs/sphinx-builddir/doctrees/notebooks/QSARtuna_Tutorial.doctree b/docs/sphinx-builddir/doctrees/notebooks/QSARtuna_Tutorial.doctree index 1e7523c..ebaf2d7 100644 Binary files a/docs/sphinx-builddir/doctrees/notebooks/QSARtuna_Tutorial.doctree and b/docs/sphinx-builddir/doctrees/notebooks/QSARtuna_Tutorial.doctree differ diff --git a/docs/sphinx-builddir/doctrees/notebooks/preprocess_data.doctree b/docs/sphinx-builddir/doctrees/notebooks/preprocess_data.doctree index 04b9457..145642a 100644 Binary files a/docs/sphinx-builddir/doctrees/notebooks/preprocess_data.doctree and b/docs/sphinx-builddir/doctrees/notebooks/preprocess_data.doctree differ diff --git a/docs/sphinx-builddir/doctrees/optunaz.config.doctree b/docs/sphinx-builddir/doctrees/optunaz.config.doctree index 816bded..70b28b9 100644 Binary files a/docs/sphinx-builddir/doctrees/optunaz.config.doctree and b/docs/sphinx-builddir/doctrees/optunaz.config.doctree differ diff --git a/docs/sphinx-builddir/doctrees/optunaz.doctree b/docs/sphinx-builddir/doctrees/optunaz.doctree index 9fed391..095c256 100644 Binary files a/docs/sphinx-builddir/doctrees/optunaz.doctree and b/docs/sphinx-builddir/doctrees/optunaz.doctree differ diff --git a/docs/sphinx-builddir/doctrees/optunaz.utils.doctree b/docs/sphinx-builddir/doctrees/optunaz.utils.doctree index ff5c180..e72ae3b 100644 Binary files a/docs/sphinx-builddir/doctrees/optunaz.utils.doctree and b/docs/sphinx-builddir/doctrees/optunaz.utils.doctree differ diff --git a/docs/sphinx-builddir/doctrees/transform.doctree b/docs/sphinx-builddir/doctrees/transform.doctree index 905f17d..c0512b3 100644 Binary files a/docs/sphinx-builddir/doctrees/transform.doctree and b/docs/sphinx-builddir/doctrees/transform.doctree differ diff --git a/docs/sphinx-builddir/html/.buildinfo b/docs/sphinx-builddir/html/.buildinfo index cca6452..7f97108 100644 --- a/docs/sphinx-builddir/html/.buildinfo +++ b/docs/sphinx-builddir/html/.buildinfo @@ -1,4 +1,4 @@ # Sphinx build info version 1 # This file hashes the configuration used when building these files. When it is not found, a full rebuild will be done. -config: b0c96d5f832cdd38d138271da4ddabf1 +config: cd8105a3e394e54ace4ef41b1def0634 tags: 645f666f9bcd5a90fca523b33c5a78b7 diff --git a/docs/sphinx-builddir/html/README.html b/docs/sphinx-builddir/html/README.html index f4998e9..1fb7f97 100644 --- a/docs/sphinx-builddir/html/README.html +++ b/docs/sphinx-builddir/html/README.html @@ -4,7 +4,7 @@ - QSARtuna 𓆛: QSAR using Optimization for Hyperparameter Tuning (formerly Optuna AZ and QPTUNA) — QSARtuna 3.1.2 documentation + QSARtuna 𓆛: QSAR using Optimization for Hyperparameter Tuning (formerly Optuna AZ and QPTUNA) — QSARtuna 3.1.3 documentation @@ -274,16 +274,14 @@

Run from Python/Jupyter Notebookfrom qsartuna.config.optconfig import ( OptimizationConfig, SVR, - RandomForest, + RandomForestRegressor, Ridge, Lasso, - PLS, - XGBregressor, + XGBRegressor, ) from qsartuna.datareader import Dataset -from qsartuna.descriptors import ECFP, MACCS_keys, ECFP_counts +from qsartuna.descriptors import ECFP, MACCS_keys, ECFP_counts, PathFP -## # Prepare hyperparameter optimization configuration. config = OptimizationConfig( data=Dataset( @@ -291,14 +289,13 @@

Run from Python/Jupyter Notebookresponse_column="molwt", training_dataset_file="tests/data/DRD2/subset-50/train.csv", ), - descriptors=[ECFP.new(), ECFP_counts.new(), MACCS_keys.new()], + descriptors=[ECFP.new(), ECFP_counts.new(), MACCS_keys.new(), PathFP.new()], algorithms=[ SVR.new(), - RandomForest.new(), + RandomForestRegressor.new(), Ridge.new(), Lasso.new(), - PLS.new(), - XGBregressor.new(), + XGBRegressor.new(), ], settings=OptimizationConfig.Settings( mode=ModelMode.REGRESSION, @@ -308,22 +305,17 @@

Run from Python/Jupyter Notebook), ) -## # Run Optuna Study. study = optimize(config, study_name="my_study") -## # Get the best Trial from the Study and make a Build (Training) configuration for it. buildconfig = buildconfig_best(study) -# Optional: write out JSON of the best configuration. -import json -print(json.dumps(buildconfig.json(), indent=2)) +with open("best_config.txt", "w") as f: + f.write(str(buildconfig.__dict__)) -## # Build (re-Train) and save the best model. build_best(buildconfig, "target/best.pkl") -## # Build (Train) and save the model on the merged train+test data. build_merged(buildconfig, "target/merged.pkl") diff --git a/docs/sphinx-builddir/html/_modules/index.html b/docs/sphinx-builddir/html/_modules/index.html index 0584c3d..cab673a 100644 --- a/docs/sphinx-builddir/html/_modules/index.html +++ b/docs/sphinx-builddir/html/_modules/index.html @@ -3,7 +3,7 @@ - Overview: module code — QSARtuna 3.1.2 documentation + Overview: module code — QSARtuna 3.1.3 documentation diff --git a/docs/sphinx-builddir/html/_modules/optunaz/automl.html b/docs/sphinx-builddir/html/_modules/optunaz/automl.html index 4c16cc2..b61bc27 100644 --- a/docs/sphinx-builddir/html/_modules/optunaz/automl.html +++ b/docs/sphinx-builddir/html/_modules/optunaz/automl.html @@ -3,7 +3,7 @@ - optunaz.automl — QSARtuna 3.1.2 documentation + optunaz.automl — QSARtuna 3.1.3 documentation diff --git a/docs/sphinx-builddir/html/_modules/optunaz/builder.html b/docs/sphinx-builddir/html/_modules/optunaz/builder.html index a5e5651..fd1b9ca 100644 --- a/docs/sphinx-builddir/html/_modules/optunaz/builder.html +++ b/docs/sphinx-builddir/html/_modules/optunaz/builder.html @@ -3,7 +3,7 @@ - optunaz.builder — QSARtuna 3.1.2 documentation + optunaz.builder — QSARtuna 3.1.3 documentation @@ -98,8 +98,27 @@

Source code for optunaz.builder

     estimator = buildconfig.algorithm.estimator()
     if merge_train_and_test_data:
         train_smiles, train_y, train_aux = buildconfig.data.get_merged_sets()
+        test_smiles, test_y, test_aux, test_X = None, None, None, None
     else:
-        train_smiles, train_y, train_aux, _, _, _ = buildconfig.data.get_sets()
+        (
+            train_smiles,
+            train_y,
+            train_aux,
+            test_smiles,
+            test_y,
+            test_aux,
+        ) = buildconfig.data.get_sets()
+        if test_smiles is not None and len(test_smiles) > 0:
+            test_X, failed_idx = descriptor_from_config(
+                test_smiles, buildconfig.descriptor, cache=cache
+            )
+            test_y, test_smiles, test_aux = remove_failed_idx(
+                failed_idx, test_y, test_smiles, test_aux
+            )
+            if test_aux is not None:
+                test_X = np.hstack((test_X, test_aux))
+        else:
+            test_X = None
 
     train_X, failed_idx = descriptor_from_config(
         train_smiles, buildconfig.descriptor, cache=cache
@@ -116,15 +135,22 @@ 
Source code for optunaz.builder
     estimator.X_ = train_X
     estimator.y_ = train_y
     estimator.aux_ = train_aux
-
-    if merge_train_and_test_data:
-        train_scores = get_merged_train_score(estimator, buildconfig, cache=cache)
-        test_scores = None
-    else:
+    estimator.test_smiles_ = test_smiles
+    estimator.test_X_ = test_X
+    estimator.test_y_ = test_y
+    estimator.test_aux_ = test_aux
+
+    if (
+        not merge_train_and_test_data
+        and test_smiles is not None
+        and len(test_smiles) > 0
+    ):
         train_scores, test_scores = get_train_test_scores(
-            estimator, buildconfig, cache=cache
+            estimator, buildconfig, train_X, train_y, test_X, test_y
         )
-
+    else:
+        train_scores = get_merged_train_score(estimator, buildconfig, train_X, train_y)
+        test_scores = None
     return estimator, train_scores, test_scores
diff --git a/docs/sphinx-builddir/html/_modules/optunaz/config.html b/docs/sphinx-builddir/html/_modules/optunaz/config.html index a5f8fc5..8c6d26f 100644 --- a/docs/sphinx-builddir/html/_modules/optunaz/config.html +++ b/docs/sphinx-builddir/html/_modules/optunaz/config.html @@ -3,7 +3,7 @@ - optunaz.config — QSARtuna 3.1.2 documentation + optunaz.config — QSARtuna 3.1.3 documentation diff --git a/docs/sphinx-builddir/html/_modules/optunaz/config/build_from_opt.html b/docs/sphinx-builddir/html/_modules/optunaz/config/build_from_opt.html index 2e95342..e057e04 100644 --- a/docs/sphinx-builddir/html/_modules/optunaz/config/build_from_opt.html +++ b/docs/sphinx-builddir/html/_modules/optunaz/config/build_from_opt.html @@ -3,7 +3,7 @@ - optunaz.config.build_from_opt — QSARtuna 3.1.2 documentation + optunaz.config.build_from_opt — QSARtuna 3.1.3 documentation diff --git a/docs/sphinx-builddir/html/_modules/optunaz/config/buildconfig.html b/docs/sphinx-builddir/html/_modules/optunaz/config/buildconfig.html index 5f9e7ae..977686f 100644 --- a/docs/sphinx-builddir/html/_modules/optunaz/config/buildconfig.html +++ b/docs/sphinx-builddir/html/_modules/optunaz/config/buildconfig.html @@ -3,7 +3,7 @@ - optunaz.config.buildconfig — QSARtuna 3.1.2 documentation + optunaz.config.buildconfig — QSARtuna 3.1.3 documentation @@ -124,8 +124,8 @@

Source code for optunaz.config.buildconfig

 class AdaBoostClassifier(Algorithm):
 
[docs]    @dataclass
     class AdaBoostClassifierParameters:
-        n_estimators: int = field(metadata=schema(min=1))
-        learning_rate: float = field(metadata=schema(min=0.0001))

+        n_estimators: int = field(default=1, metadata=schema(min=1))
+        learning_rate: float = field(default=0.1, metadata=schema(min=0.0001))
name: Literal["AdaBoostClassifier"] parameters: AdaBoostClassifierParameters @@ -198,7 +198,7 @@

Source code for optunaz.config.buildconfig

 
[docs]    @dataclass
     class LogisticRegressionParameters:
         solver: str
-        C: float = field(metadata=schema(min=0.001, max=1000))

+        C: float = field(default=1.0, metadata=schema(min=0.001, max=1000))
name: Literal["LogisticRegression"] parameters: LogisticRegressionParameters @@ -219,7 +219,7 @@

Source code for optunaz.config.buildconfig

 class PLSRegression(Algorithm):
 
[docs]    @dataclass
     class PLSParameters:
-        n_components: int = field(metadata=schema(min=1))

+        n_components: int = field(default=2, metadata=schema(min=1))
name: Literal["PLSRegression"] parameters: PLSParameters @@ -234,9 +234,9 @@

Source code for optunaz.config.buildconfig

 class RandomForestClassifier(Algorithm):
 
[docs]    @dataclass
     class RandomForestParameters:
-        max_depth: int = field(metadata=schema(min=1))
-        n_estimators: int = field(metadata=schema(min=1))
-        max_features: str

+        max_features: str
+        max_depth: int = field(default=None, metadata=schema(min=1))
+        n_estimators: int = field(default=100, metadata=schema(min=1))
name: Literal["RandomForestClassifier"] parameters: RandomForestParameters diff --git a/docs/sphinx-builddir/html/_modules/optunaz/config/optconfig.html b/docs/sphinx-builddir/html/_modules/optunaz/config/optconfig.html index 575ceb7..07401f3 100644 --- a/docs/sphinx-builddir/html/_modules/optunaz/config/optconfig.html +++ b/docs/sphinx-builddir/html/_modules/optunaz/config/optconfig.html @@ -3,7 +3,7 @@ - optunaz.config.optconfig — QSARtuna 3.1.2 documentation + optunaz.config.optconfig — QSARtuna 3.1.3 documentation diff --git a/docs/sphinx-builddir/html/_modules/optunaz/datareader.html b/docs/sphinx-builddir/html/_modules/optunaz/datareader.html index ef2ee88..0b87a1b 100644 --- a/docs/sphinx-builddir/html/_modules/optunaz/datareader.html +++ b/docs/sphinx-builddir/html/_modules/optunaz/datareader.html @@ -3,7 +3,7 @@ - optunaz.datareader — QSARtuna 3.1.2 documentation + optunaz.datareader — QSARtuna 3.1.3 documentation diff --git a/docs/sphinx-builddir/html/_modules/optunaz/descriptors.html b/docs/sphinx-builddir/html/_modules/optunaz/descriptors.html index cadfd5f..cdeb08d 100644 --- a/docs/sphinx-builddir/html/_modules/optunaz/descriptors.html +++ b/docs/sphinx-builddir/html/_modules/optunaz/descriptors.html @@ -3,7 +3,7 @@ - optunaz.descriptors — QSARtuna 3.1.2 documentation + optunaz.descriptors — QSARtuna 3.1.3 documentation @@ -114,7 +114,6 @@

Source code for optunaz.descriptors

 
 from rdkit.ML.Descriptors.MoleculeDescriptors import MolecularDescriptorCalculator
 from jazzy.api import molecular_vector_from_smiles
-from jazzy.exception import JazzyError
 from sklearn import preprocessing
 from joblib import Parallel, delayed, effective_n_jobs
 from optunaz.config import NameParameterDataclass
diff --git a/docs/sphinx-builddir/html/_modules/optunaz/evaluate.html b/docs/sphinx-builddir/html/_modules/optunaz/evaluate.html
index 1a24961..3d852b0 100644
--- a/docs/sphinx-builddir/html/_modules/optunaz/evaluate.html
+++ b/docs/sphinx-builddir/html/_modules/optunaz/evaluate.html
@@ -3,7 +3,7 @@
 
   
   
-  optunaz.evaluate — QSARtuna 3.1.2 documentation
+  optunaz.evaluate — QSARtuna 3.1.3 documentation
       
       
       
@@ -79,21 +79,13 @@
            

              
   
Source code for optunaz.evaluate
-import numpy as np
-from typing import Dict, List
-
-from sklearn.metrics import get_scorer
-
+from typing import List
+import numpy as np
+from sklearn.metrics import check_scoring
+from sklearn.calibration import calibration_curve
 from optunaz import objective
 from optunaz.config import ModelMode
 from optunaz.config.buildconfig import BuildConfig
-from optunaz.utils import remove_failed_idx
-from optunaz.descriptors import descriptor_from_config
-
-
-
[docs]def score_all(scores: List[str], estimator, X, y) -> Dict[str, float]:
-    result = {s: get_scorer(s)(estimator, X, y) for s in scores}
-    return result

 
 
 
[docs]def get_scores(mode: ModelMode) -> List[str]:
@@ -103,71 +95,39 @@ 
Source code for optunaz.evaluate
         scores = objective.classification_scores
     else:
         raise ValueError(f"Unrecognized mode: {mode}")
-
     return scores

 
 
-
[docs]def score_all_smiles(scores, estimator, smiles, descriptor, aux, y, cache=None):
-    X, failed_idx = descriptor_from_config(smiles, descriptor, cache=cache)
-    y, smiles, aux = remove_failed_idx(failed_idx, y, smiles, aux)
-    if aux is not None:
-        X = np.hstack((X, aux))
-    return score_all(scores, estimator, X, y)

-
-
-
[docs]def get_train_test_scores(estimator, buildconfig: BuildConfig, cache=None):
+
[docs]def get_train_test_scores(
+    estimator, buildconfig: BuildConfig, train_X, train_y, test_X, test_y
+):
     scores = get_scores(buildconfig.settings.mode)
-
-    (
-        train_smiles,
-        train_y,
-        train_aux,
-        test_smiles,
-        test_y,
-        test_aux,
-    ) = buildconfig.data.get_sets()
-
-    train_scores = score_all_smiles(
-        scores,
-        estimator,
-        train_smiles,
-        buildconfig.descriptor,
-        train_aux,
-        train_y,
-        cache=cache,
-    )
-    if test_smiles is not None and len(test_smiles) > 0:
-        test_scores = score_all_smiles(
-            scores,
-            estimator,
-            test_smiles,
-            buildconfig.descriptor,
-            test_aux,
-            test_y,
-            cache=cache,
-        )
-    else:
-        test_scores = None
-
+    train_scores = check_scoring(estimator, scoring=scores)(estimator, train_X, train_y)
+    test_scores = check_scoring(estimator, scoring=scores)(estimator, test_X, test_y)
     return train_scores, test_scores

 
 
-
[docs]def get_merged_train_score(estimator, buildconfig: BuildConfig, cache=None):
+
[docs]def get_merged_train_score(estimator, buildconfig: BuildConfig, train_X, train_y):
     scores = get_scores(buildconfig.settings.mode)
+    train_scores = check_scoring(estimator, scoring=scores)(estimator, train_X, train_y)
+    return train_scores

 
-    train_smiles, train_y, train_aux = buildconfig.data.get_merged_sets()
-
-    train_scores = score_all_smiles(
-        scores,
-        estimator,
-        train_smiles,
-        buildconfig.descriptor,
-        train_aux,
-        train_y,
-        cache=cache,
-    )
 
-    return train_scores

+
[docs]def calibration_analysis(y_test, y_pred):
+    try:
+        frac_true, frac_pred = calibration_curve(y_test, y_pred, n_bins=15)
+        bin_edges = frac_pred
+    except ValueError:
+        # weight each bin by the total number of values so that the sum of all bars equal unity
+        weights = np.ones_like(y_test) / len(y_test)
+        # calculate fraction of true points across uniform bins
+        frac_true, bin_edges = np.histogram(y_test, bins=15, weights=weights)
+        # calculate fraction of pred points across uniform true bins
+        frac_pred, _ = np.histogram(y_pred, bins=bin_edges, weights=weights)
+        # convert to cumulative sum for plotting
+        frac_true = np.cumsum(frac_true)
+        frac_pred = np.cumsum(frac_pred)
+    return list(zip(bin_edges, frac_true, frac_pred))

 

 
            

diff --git a/docs/sphinx-builddir/html/_modules/optunaz/explainability.html b/docs/sphinx-builddir/html/_modules/optunaz/explainability.html
index e42cbbf..7a5c478 100644
--- a/docs/sphinx-builddir/html/_modules/optunaz/explainability.html
+++ b/docs/sphinx-builddir/html/_modules/optunaz/explainability.html
@@ -3,7 +3,7 @@
 
   
   
-  optunaz.explainability — QSARtuna 3.1.2 documentation
+  optunaz.explainability — QSARtuna 3.1.3 documentation
       
       
       
diff --git a/docs/sphinx-builddir/html/_modules/optunaz/metircs.html b/docs/sphinx-builddir/html/_modules/optunaz/metircs.html
index 51ca9e2..0c924f4 100644
--- a/docs/sphinx-builddir/html/_modules/optunaz/metircs.html
+++ b/docs/sphinx-builddir/html/_modules/optunaz/metircs.html
@@ -3,7 +3,7 @@
 
   
   
-  optunaz.metircs — QSARtuna 3.1.2 documentation
+  optunaz.metircs — QSARtuna 3.1.3 documentation
       
       
       
diff --git a/docs/sphinx-builddir/html/_modules/optunaz/model_writer.html b/docs/sphinx-builddir/html/_modules/optunaz/model_writer.html
index d4423d2..59fff92 100644
--- a/docs/sphinx-builddir/html/_modules/optunaz/model_writer.html
+++ b/docs/sphinx-builddir/html/_modules/optunaz/model_writer.html
@@ -3,7 +3,7 @@
 
   
   
-  optunaz.model_writer — QSARtuna 3.1.2 documentation
+  optunaz.model_writer — QSARtuna 3.1.3 documentation
       
       
       
@@ -346,7 +346,9 @@ 
Source code for optunaz.model_writer
         pass
 
     with open(filename, "wb") as f:
-        pickle.dump(model, f)

+        pickle.dump(model, f)
+
+    return model
diff --git a/docs/sphinx-builddir/html/_modules/optunaz/objective.html b/docs/sphinx-builddir/html/_modules/optunaz/objective.html index 8fc64f4..b175bd1 100644 --- a/docs/sphinx-builddir/html/_modules/optunaz/objective.html +++ b/docs/sphinx-builddir/html/_modules/optunaz/objective.html @@ -3,7 +3,7 @@ - optunaz.objective — QSARtuna 3.1.2 documentation + optunaz.objective — QSARtuna 3.1.3 documentation diff --git a/docs/sphinx-builddir/html/_modules/optunaz/optbuild.html b/docs/sphinx-builddir/html/_modules/optunaz/optbuild.html index ad7d52b..f28e6f6 100644 --- a/docs/sphinx-builddir/html/_modules/optunaz/optbuild.html +++ b/docs/sphinx-builddir/html/_modules/optunaz/optbuild.html @@ -3,7 +3,7 @@ - optunaz.optbuild — QSARtuna 3.1.2 documentation + optunaz.optbuild — QSARtuna 3.1.3 documentation diff --git a/docs/sphinx-builddir/html/_modules/optunaz/predict.html b/docs/sphinx-builddir/html/_modules/optunaz/predict.html index cdd7407..6edfa2a 100644 --- a/docs/sphinx-builddir/html/_modules/optunaz/predict.html +++ b/docs/sphinx-builddir/html/_modules/optunaz/predict.html @@ -3,7 +3,7 @@ - optunaz.predict — QSARtuna 3.1.2 documentation + optunaz.predict — QSARtuna 3.1.3 documentation diff --git a/docs/sphinx-builddir/html/_modules/optunaz/schemagen.html b/docs/sphinx-builddir/html/_modules/optunaz/schemagen.html index ddf0f90..5708ced 100644 --- a/docs/sphinx-builddir/html/_modules/optunaz/schemagen.html +++ b/docs/sphinx-builddir/html/_modules/optunaz/schemagen.html @@ -3,7 +3,7 @@ - optunaz.schemagen — QSARtuna 3.1.2 documentation + optunaz.schemagen — QSARtuna 3.1.3 documentation @@ -82,7 +82,7 @@

Source code for optunaz.schemagen

 import inspect
 import json
 from textwrap import dedent
-from typing import Any, Tuple, Optional
+from typing import Any, Optional
 
 import apischema
 from apischema import schema
diff --git a/docs/sphinx-builddir/html/_modules/optunaz/three_step_opt_build_merge.html b/docs/sphinx-builddir/html/_modules/optunaz/three_step_opt_build_merge.html
index e527241..558a75e 100644
--- a/docs/sphinx-builddir/html/_modules/optunaz/three_step_opt_build_merge.html
+++ b/docs/sphinx-builddir/html/_modules/optunaz/three_step_opt_build_merge.html
@@ -3,7 +3,7 @@
 
   
   
-  optunaz.three_step_opt_build_merge — QSARtuna 3.1.2 documentation
+  optunaz.three_step_opt_build_merge — QSARtuna 3.1.3 documentation
       
       
       
@@ -352,7 +352,7 @@ 
Source code for optunaz.three_step_opt_build_merge
if main_score_val is not None:
         logger.info(f"{label.capitalize()} score {main_score}: {main_score_val}")
     logger.info(
-        f"All {label} cores: { {k: round(number=v, ndigits=3) for k, v in scores.items()} }"
+        f"All {label} scores: { {k: round(number=v, ndigits=3) for k, v in scores.items()} }"
     )

 
 
@@ -364,7 +364,7 @@ 
Source code for optunaz.three_step_opt_build_merge
    """Step 2. Build. Train a model with the best hyperparameters."""
 
     model, train_scores, test_scores = build(buildconfig, cache=cache)
-    save_model(
+    qsartuna_model = save_model(
         model,
         buildconfig,
         outfname,
@@ -379,7 +379,7 @@ 
Source code for optunaz.three_step_opt_build_merge
log_scores(test_scores, buildconfig.settings.scoring, "test")
 
     if buildconfig.settings.tracking_rest_endpoint is not None:
-        track_build(model, buildconfig)
+        track_build(qsartuna_model, buildconfig, test_scores)
 
     return buildconfig

 
diff --git a/docs/sphinx-builddir/html/_modules/optunaz/utils.html b/docs/sphinx-builddir/html/_modules/optunaz/utils.html
index aeafbf2..9849b9a 100644
--- a/docs/sphinx-builddir/html/_modules/optunaz/utils.html
+++ b/docs/sphinx-builddir/html/_modules/optunaz/utils.html
@@ -3,7 +3,7 @@
 
   
   
-  optunaz.utils — QSARtuna 3.1.2 documentation
+  optunaz.utils — QSARtuna 3.1.3 documentation
       
       
       
diff --git a/docs/sphinx-builddir/html/_modules/optunaz/utils/enums.html b/docs/sphinx-builddir/html/_modules/optunaz/utils/enums.html
index 12b65cc..8f8da55 100644
--- a/docs/sphinx-builddir/html/_modules/optunaz/utils/enums.html
+++ b/docs/sphinx-builddir/html/_modules/optunaz/utils/enums.html
@@ -3,7 +3,7 @@
 
   
   
-  optunaz.utils.enums — QSARtuna 3.1.2 documentation
+  optunaz.utils.enums — QSARtuna 3.1.3 documentation
       
       
       
diff --git a/docs/sphinx-builddir/html/_modules/optunaz/utils/enums/building_configuration_enum.html b/docs/sphinx-builddir/html/_modules/optunaz/utils/enums/building_configuration_enum.html
index 4217424..d503a2f 100644
--- a/docs/sphinx-builddir/html/_modules/optunaz/utils/enums/building_configuration_enum.html
+++ b/docs/sphinx-builddir/html/_modules/optunaz/utils/enums/building_configuration_enum.html
@@ -3,7 +3,7 @@
 
   
   
-  optunaz.utils.enums.building_configuration_enum — QSARtuna 3.1.2 documentation
+  optunaz.utils.enums.building_configuration_enum — QSARtuna 3.1.3 documentation
       
       
       
diff --git a/docs/sphinx-builddir/html/_modules/optunaz/utils/enums/configuration_enum.html b/docs/sphinx-builddir/html/_modules/optunaz/utils/enums/configuration_enum.html
index ace13f7..1d1aae3 100644
--- a/docs/sphinx-builddir/html/_modules/optunaz/utils/enums/configuration_enum.html
+++ b/docs/sphinx-builddir/html/_modules/optunaz/utils/enums/configuration_enum.html
@@ -3,7 +3,7 @@
 
   
   
-  optunaz.utils.enums.configuration_enum — QSARtuna 3.1.2 documentation
+  optunaz.utils.enums.configuration_enum — QSARtuna 3.1.3 documentation
       
       
       
diff --git a/docs/sphinx-builddir/html/_modules/optunaz/utils/enums/interface_enum.html b/docs/sphinx-builddir/html/_modules/optunaz/utils/enums/interface_enum.html
index 476982d..6637941 100644
--- a/docs/sphinx-builddir/html/_modules/optunaz/utils/enums/interface_enum.html
+++ b/docs/sphinx-builddir/html/_modules/optunaz/utils/enums/interface_enum.html
@@ -3,7 +3,7 @@
 
   
   
-  optunaz.utils.enums.interface_enum — QSARtuna 3.1.2 documentation
+  optunaz.utils.enums.interface_enum — QSARtuna 3.1.3 documentation
       
       
       
diff --git a/docs/sphinx-builddir/html/_modules/optunaz/utils/enums/model_runner_enum.html b/docs/sphinx-builddir/html/_modules/optunaz/utils/enums/model_runner_enum.html
index e4d1e03..0989b66 100644
--- a/docs/sphinx-builddir/html/_modules/optunaz/utils/enums/model_runner_enum.html
+++ b/docs/sphinx-builddir/html/_modules/optunaz/utils/enums/model_runner_enum.html
@@ -3,7 +3,7 @@
 
   
   
-  optunaz.utils.enums.model_runner_enum — QSARtuna 3.1.2 documentation
+  optunaz.utils.enums.model_runner_enum — QSARtuna 3.1.3 documentation
       
       
       
diff --git a/docs/sphinx-builddir/html/_modules/optunaz/utils/enums/objective_enum.html b/docs/sphinx-builddir/html/_modules/optunaz/utils/enums/objective_enum.html
index 20533ca..110a4df 100644
--- a/docs/sphinx-builddir/html/_modules/optunaz/utils/enums/objective_enum.html
+++ b/docs/sphinx-builddir/html/_modules/optunaz/utils/enums/objective_enum.html
@@ -3,7 +3,7 @@
 
   
   
-  optunaz.utils.enums.objective_enum — QSARtuna 3.1.2 documentation
+  optunaz.utils.enums.objective_enum — QSARtuna 3.1.3 documentation
       
       
       
diff --git a/docs/sphinx-builddir/html/_modules/optunaz/utils/enums/optimization_configuration_enum.html b/docs/sphinx-builddir/html/_modules/optunaz/utils/enums/optimization_configuration_enum.html
index 2fb091a..7fc1716 100644
--- a/docs/sphinx-builddir/html/_modules/optunaz/utils/enums/optimization_configuration_enum.html
+++ b/docs/sphinx-builddir/html/_modules/optunaz/utils/enums/optimization_configuration_enum.html
@@ -3,7 +3,7 @@
 
   
   
-  optunaz.utils.enums.optimization_configuration_enum — QSARtuna 3.1.2 documentation
+  optunaz.utils.enums.optimization_configuration_enum — QSARtuna 3.1.3 documentation
       
       
       
diff --git a/docs/sphinx-builddir/html/_modules/optunaz/utils/enums/prediction_configuration_enum.html b/docs/sphinx-builddir/html/_modules/optunaz/utils/enums/prediction_configuration_enum.html
index 6221ca5..3b36190 100644
--- a/docs/sphinx-builddir/html/_modules/optunaz/utils/enums/prediction_configuration_enum.html
+++ b/docs/sphinx-builddir/html/_modules/optunaz/utils/enums/prediction_configuration_enum.html
@@ -3,7 +3,7 @@
 
   
   
-  optunaz.utils.enums.prediction_configuration_enum — QSARtuna 3.1.2 documentation
+  optunaz.utils.enums.prediction_configuration_enum — QSARtuna 3.1.3 documentation
       
       
       
diff --git a/docs/sphinx-builddir/html/_modules/optunaz/utils/enums/return_values_enum.html b/docs/sphinx-builddir/html/_modules/optunaz/utils/enums/return_values_enum.html
index d869b42..57c05cb 100644
--- a/docs/sphinx-builddir/html/_modules/optunaz/utils/enums/return_values_enum.html
+++ b/docs/sphinx-builddir/html/_modules/optunaz/utils/enums/return_values_enum.html
@@ -3,7 +3,7 @@
 
   
   
-  optunaz.utils.enums.return_values_enum — QSARtuna 3.1.2 documentation
+  optunaz.utils.enums.return_values_enum — QSARtuna 3.1.3 documentation
       
       
       
diff --git a/docs/sphinx-builddir/html/_modules/optunaz/utils/enums/visualization_enum.html b/docs/sphinx-builddir/html/_modules/optunaz/utils/enums/visualization_enum.html
index 3b4c92f..c328756 100644
--- a/docs/sphinx-builddir/html/_modules/optunaz/utils/enums/visualization_enum.html
+++ b/docs/sphinx-builddir/html/_modules/optunaz/utils/enums/visualization_enum.html
@@ -3,7 +3,7 @@
 
   
   
-  optunaz.utils.enums.visualization_enum — QSARtuna 3.1.2 documentation
+  optunaz.utils.enums.visualization_enum — QSARtuna 3.1.3 documentation
       
       
       
diff --git a/docs/sphinx-builddir/html/_modules/optunaz/utils/files_paths.html b/docs/sphinx-builddir/html/_modules/optunaz/utils/files_paths.html
index 427a3a1..9f58f03 100644
--- a/docs/sphinx-builddir/html/_modules/optunaz/utils/files_paths.html
+++ b/docs/sphinx-builddir/html/_modules/optunaz/utils/files_paths.html
@@ -3,7 +3,7 @@
 
   
   
-  optunaz.utils.files_paths — QSARtuna 3.1.2 documentation
+  optunaz.utils.files_paths — QSARtuna 3.1.3 documentation
       
       
       
diff --git a/docs/sphinx-builddir/html/_modules/optunaz/utils/load_json.html b/docs/sphinx-builddir/html/_modules/optunaz/utils/load_json.html
index 6cd9a8c..b14b058 100644
--- a/docs/sphinx-builddir/html/_modules/optunaz/utils/load_json.html
+++ b/docs/sphinx-builddir/html/_modules/optunaz/utils/load_json.html
@@ -3,7 +3,7 @@
 
   
   
-  optunaz.utils.load_json — QSARtuna 3.1.2 documentation
+  optunaz.utils.load_json — QSARtuna 3.1.3 documentation
       
       
       
diff --git a/docs/sphinx-builddir/html/_modules/optunaz/utils/mlflow.html b/docs/sphinx-builddir/html/_modules/optunaz/utils/mlflow.html
index 215903b..3ea3bbb 100644
--- a/docs/sphinx-builddir/html/_modules/optunaz/utils/mlflow.html
+++ b/docs/sphinx-builddir/html/_modules/optunaz/utils/mlflow.html
@@ -3,7 +3,7 @@
 
   
   
-  optunaz.utils.mlflow — QSARtuna 3.1.2 documentation
+  optunaz.utils.mlflow — QSARtuna 3.1.3 documentation
       
       
       
diff --git a/docs/sphinx-builddir/html/_modules/optunaz/utils/preprocessing/deduplicator.html b/docs/sphinx-builddir/html/_modules/optunaz/utils/preprocessing/deduplicator.html
index b66d9e8..9ac4243 100644
--- a/docs/sphinx-builddir/html/_modules/optunaz/utils/preprocessing/deduplicator.html
+++ b/docs/sphinx-builddir/html/_modules/optunaz/utils/preprocessing/deduplicator.html
@@ -3,7 +3,7 @@
 
   
   
-  optunaz.utils.preprocessing.deduplicator — QSARtuna 3.1.2 documentation
+  optunaz.utils.preprocessing.deduplicator — QSARtuna 3.1.3 documentation
       
       
       
diff --git a/docs/sphinx-builddir/html/_modules/optunaz/utils/preprocessing/splitter.html b/docs/sphinx-builddir/html/_modules/optunaz/utils/preprocessing/splitter.html
index 3992d5e..6e6a91f 100644
--- a/docs/sphinx-builddir/html/_modules/optunaz/utils/preprocessing/splitter.html
+++ b/docs/sphinx-builddir/html/_modules/optunaz/utils/preprocessing/splitter.html
@@ -3,7 +3,7 @@
 
   
   
-  optunaz.utils.preprocessing.splitter — QSARtuna 3.1.2 documentation
+  optunaz.utils.preprocessing.splitter — QSARtuna 3.1.3 documentation
       
       
       
diff --git a/docs/sphinx-builddir/html/_modules/optunaz/utils/preprocessing/transform.html b/docs/sphinx-builddir/html/_modules/optunaz/utils/preprocessing/transform.html
index 4c1b9e2..9558d06 100644
--- a/docs/sphinx-builddir/html/_modules/optunaz/utils/preprocessing/transform.html
+++ b/docs/sphinx-builddir/html/_modules/optunaz/utils/preprocessing/transform.html
@@ -3,7 +3,7 @@
 
   
   
-  optunaz.utils.preprocessing.transform — QSARtuna 3.1.2 documentation
+  optunaz.utils.preprocessing.transform — QSARtuna 3.1.3 documentation
       
       
       
@@ -375,13 +375,13 @@ 
Source code for optunaz.utils.preprocessing.transform
return np.array([list(Peptide(val).z_scales()) for val in auxiliary_data])

 
 
-
[docs]@dataclass
+
[docs]@dataclass
 class AmorProt(AuxTransformer):
     """AmorProt from column
 
     Calculates AmorProt for sequences or a predefined list of peptide/protein targets"""
 
-
[docs]    @apischema.type_name("AmorProtParams")
+
[docs]    @apischema.type_name("AmorProtParams")
     @dataclass
     class Parameters:
         pass

diff --git a/docs/sphinx-builddir/html/_modules/optunaz/utils/retraining.html b/docs/sphinx-builddir/html/_modules/optunaz/utils/retraining.html
index d633524..b6aa7d9 100644
--- a/docs/sphinx-builddir/html/_modules/optunaz/utils/retraining.html
+++ b/docs/sphinx-builddir/html/_modules/optunaz/utils/retraining.html
@@ -3,7 +3,7 @@
 
   
   
-  optunaz.utils.retraining — QSARtuna 3.1.2 documentation
+  optunaz.utils.retraining — QSARtuna 3.1.3 documentation
       
       
       
diff --git a/docs/sphinx-builddir/html/_modules/optunaz/utils/schema.html b/docs/sphinx-builddir/html/_modules/optunaz/utils/schema.html
index 3236f0c..e32f596 100644
--- a/docs/sphinx-builddir/html/_modules/optunaz/utils/schema.html
+++ b/docs/sphinx-builddir/html/_modules/optunaz/utils/schema.html
@@ -3,7 +3,7 @@
 
   
   
-  optunaz.utils.schema — QSARtuna 3.1.2 documentation
+  optunaz.utils.schema — QSARtuna 3.1.3 documentation
       
       
       
diff --git a/docs/sphinx-builddir/html/_modules/optunaz/utils/tracking.html b/docs/sphinx-builddir/html/_modules/optunaz/utils/tracking.html
index 4a03f5f..5e6041f 100644
--- a/docs/sphinx-builddir/html/_modules/optunaz/utils/tracking.html
+++ b/docs/sphinx-builddir/html/_modules/optunaz/utils/tracking.html
@@ -3,7 +3,7 @@
 
   
   
-  optunaz.utils.tracking — QSARtuna 3.1.2 documentation
+  optunaz.utils.tracking — QSARtuna 3.1.3 documentation
       
       
       
@@ -84,18 +84,15 @@ 
Source code for optunaz.utils.tracking
 import os
 from dataclasses import dataclass
 from typing import List, Dict
-
 import requests
 from apischema import serialize
 from optunaz.config.build_from_opt import remove_algo_hash
 from optuna import Study
 from optuna.trial import FrozenTrial
-
 from optunaz.config.build_from_opt import buildconfig_from_trial
 from optunaz.config.buildconfig import BuildConfig
 from optunaz.config.optconfig import OptimizationConfig
-from optunaz.evaluate import get_train_test_scores
-from optunaz.model_writer import wrap_model
+from optunaz.evaluate import calibration_analysis
 
 logger = logging.getLogger(__name__)
 
@@ -114,6 +111,7 @@ 
Source code for optunaz.utils.tracking
     trial_state: str
     all_cv_test_scores: Dict[str, List[float]]
     buildconfig: BuildConfig
+    algorith_hash: str
 
     def __post_init__(self):
         self.buildconfig.metadata = None  # Metadata is not essential - drop.
@@ -133,7 +131,7 @@ 
Source code for optunaz.utils.tracking
 
 
[docs]@dataclass
 class InternalTrackingCallback:
-    """Callback to track (log) progress using internal tracking format"""
+    """Callback to track (log) Optimization progress using internal tracking format"""
 
     optconfig: OptimizationConfig
     trial_number_offset: int
@@ -156,6 +154,7 @@ 
Source code for optunaz.utils.tracking
                 trial_state=trial.state.name,
                 all_cv_test_scores=round_scores(trial.user_attrs["test_scores"]),
                 buildconfig=buildconfig,
+                algorith_hash=trial.user_attrs["alg_hash"],
             )
 
             json_data = serialize(data)
@@ -181,35 +180,40 @@ 
Source code for optunaz.utils.tracking
     predicted: float

 
 
+
[docs]@dataclass
+class Calpoint:
+    bin_edges: float
+    frac_true: float
+    frac_pred: float

+
+
 
[docs]@dataclass
 class BuildTrackingData:
-    """Dataclass defining internal tracking format"""
+    """Dataclass defining internal Build tracking format"""
 
     response_column_name: str
-    test_scores: Dict[str, float]
-    test_points: List[Datapoint]

+    test_scores: Dict[str, float] | str
+    test_points: List[Datapoint]
+    cal_points: List[Calpoint] | None

 
 
-
[docs]def track_build(model, buildconfig: BuildConfig):
-    train_scores, test_scores = get_train_test_scores(model, buildconfig)
+
[docs]def track_build(qptuna_model, buildconfig: BuildConfig, test_scores):
+    test_smiles = qptuna_model.predictor.test_smiles_
+    test_aux = qptuna_model.predictor.test_aux_
+    expected = qptuna_model.predictor.test_y_
 
+    if test_smiles is None or len(test_smiles) < 1:
+        logger.warning("No test set.")
+        return
     rounded_test_scores = (
         {k: round(v, ndigits=3) for k, v in test_scores.items()}
         if test_scores is not None
-        else None
+        else ""
     )
 
-    _, _, _, smiles, expected, _ = buildconfig.data.get_sets()
-
-    if smiles is None or len(smiles) < 1:
-        logger.warning("No test set.")
-        return
-
-    mode = buildconfig.settings.mode
-    descriptor = buildconfig.descriptor
-    qsartuna_model = wrap_model(model, descriptor=descriptor, mode=mode)
-
-    predicted = qsartuna_model.predict_from_smiles(smiles)
+    predicted = qptuna_model.predict_from_smiles(test_smiles, aux=test_aux)
+    if qptuna_model.transform is not None:
+        expected = qptuna_model.transform.reverse_transform(expected)
 
     test_points = [
         Datapoint(
@@ -217,13 +221,28 @@ 
Source code for optunaz.utils.tracking
             expected=round(expval.item(), ndigits=3),  # item() converts numpy to float.
             predicted=round(predval.item(), ndigits=3),
         )
-        for smi, expval, predval in zip(smiles, expected, predicted)
+        for smi, expval, predval in zip(test_smiles, expected, predicted)
     ]
 
+    try:
+        cal_points = [
+            Calpoint(
+                bin_edges=round(bin_edges.item(), ndigits=3),
+                frac_true=round(frac_true.item(), ndigits=3),
+                frac_pred=round(frac_pred.item(), ndigits=3),
+            )
+            for bin_edges, frac_true, frac_pred in calibration_analysis(
+                expected, predicted
+            )
+        ]
+    except ValueError:
+        cal_points = ""
+
     data = BuildTrackingData(
         response_column_name=buildconfig.data.response_column,
         test_scores=rounded_test_scores,
         test_points=test_points,
+        cal_points=cal_points,
     )
 
     json_data = serialize(data)
@@ -238,7 +257,7 @@ 
Source code for optunaz.utils.tracking
     try:
         response = requests.post(url, json=json_data, headers=headers)
     except Exception as e:
-        logger.warning(f"Failed to report build results to {url}: {e}")

+        logger.warning(f"Failed to report build results {json_data} to {url}: {e}")

 

 
            

diff --git a/docs/sphinx-builddir/html/_modules/optunaz/visualizer.html b/docs/sphinx-builddir/html/_modules/optunaz/visualizer.html
index a30976e..574418d 100644
--- a/docs/sphinx-builddir/html/_modules/optunaz/visualizer.html
+++ b/docs/sphinx-builddir/html/_modules/optunaz/visualizer.html
@@ -3,7 +3,7 @@
 
   
   
-  optunaz.visualizer — QSARtuna 3.1.2 documentation
+  optunaz.visualizer — QSARtuna 3.1.3 documentation
       
       
       
diff --git a/docs/sphinx-builddir/html/_sources/README.md.txt b/docs/sphinx-builddir/html/_sources/README.md.txt
index 092bbee..2eadcce 100644
--- a/docs/sphinx-builddir/html/_sources/README.md.txt
+++ b/docs/sphinx-builddir/html/_sources/README.md.txt
@@ -161,16 +161,14 @@ from qsartuna.config import ModelMode, OptimizationDirection
 from qsartuna.config.optconfig import (
     OptimizationConfig,
     SVR,
-    RandomForest,
+    RandomForestRegressor,
     Ridge,
     Lasso,
-    PLS,
-    XGBregressor,
+    XGBRegressor,
 )
 from qsartuna.datareader import Dataset
-from qsartuna.descriptors import ECFP, MACCS_keys, ECFP_counts
+from qsartuna.descriptors import ECFP, MACCS_keys, ECFP_counts, PathFP
 
-##
 # Prepare hyperparameter optimization configuration.
 config = OptimizationConfig(
     data=Dataset(
@@ -178,14 +176,13 @@ config = OptimizationConfig(
         response_column="molwt",
         training_dataset_file="tests/data/DRD2/subset-50/train.csv",
     ),
-    descriptors=[ECFP.new(), ECFP_counts.new(), MACCS_keys.new()],
+    descriptors=[ECFP.new(), ECFP_counts.new(), MACCS_keys.new(), PathFP.new()],
     algorithms=[
         SVR.new(),
-        RandomForest.new(),
+        RandomForestRegressor.new(),
         Ridge.new(),
         Lasso.new(),
-        PLS.new(),
-        XGBregressor.new(),
+        XGBRegressor.new(),
     ],
     settings=OptimizationConfig.Settings(
         mode=ModelMode.REGRESSION,
@@ -195,22 +192,17 @@ config = OptimizationConfig(
     ),
 )
 
-##
 # Run Optuna Study.
 study = optimize(config, study_name="my_study")
 
-##
 # Get the best Trial from the Study and make a Build (Training) configuration for it.
 buildconfig = buildconfig_best(study)
-# Optional: write out JSON of the best configuration.
-import json
-print(json.dumps(buildconfig.json(), indent=2))
+with open("best_config.txt", "w") as f:
+    f.write(str(buildconfig.__dict__))
 
-##
 # Build (re-Train) and save the best model.
 build_best(buildconfig, "target/best.pkl")
 
-##
 # Build (Train) and save the model on the merged train+test data.
 build_merged(buildconfig, "target/merged.pkl")
 ```
diff --git a/docs/sphinx-builddir/html/_sources/algorithms.rst.txt b/docs/sphinx-builddir/html/_sources/algorithms.rst.txt
index 4c7d25e..d6e584f 100644
--- a/docs/sphinx-builddir/html/_sources/algorithms.rst.txt
+++ b/docs/sphinx-builddir/html/_sources/algorithms.rst.txt
@@ -14,13 +14,13 @@ Lasso
 
 
 KNeighborsClassifier
-#####
+####################
 ..  autoclass:: optunaz.config.optconfig.KNeighborsClassifier
     :members:
 
 
 KNeighborsRegressor
-#####
+###################
 ..  autoclass:: optunaz.config.optconfig.KNeighborsRegressor
     :members:
 
@@ -103,8 +103,8 @@ ChemPropHyperoptRegressor
     :members:
 
 
-ChemPropRegressorPretrained
-#########################
+ChemPropHyperoptRegressorPretrained
+###################################
 ..  autoclass:: optunaz.config.optconfig.ChemPropRegressorPretrained
     :members:
 
diff --git a/docs/sphinx-builddir/html/_sources/descriptors.rst.txt b/docs/sphinx-builddir/html/_sources/descriptors.rst.txt
index d36f36b..5c2bc5d 100644
--- a/docs/sphinx-builddir/html/_sources/descriptors.rst.txt
+++ b/docs/sphinx-builddir/html/_sources/descriptors.rst.txt
@@ -19,7 +19,7 @@ ECFP_counts
 
 
 PathFP
-###########
+######
 ..  autoclass:: optunaz.descriptors.PathFP
     :members:
 
@@ -37,13 +37,13 @@ UnscaledPhyschemDescriptors
 
 
 UnscaledJazzyDescriptors
-###########################
+########################
 ..  autoclass:: optunaz.descriptors.UnscaledJazzyDescriptors
     :members:
 
 
 UnscaledZScalesDescriptors
-###########
+##########################
 ..  autoclass:: optunaz.descriptors.UnscaledZScalesDescriptors
     :members:
 
@@ -67,7 +67,7 @@ PrecomputedDescriptorFromFile
 
 
 ZScales
-###########
+#######
 ..  autoclass:: optunaz.descriptors.ZScalesDescriptors
     :members:
 
@@ -94,3 +94,39 @@ CompositeDescriptor
 ###################
 ..  autoclass:: optunaz.descriptors.CompositeDescriptor
     :members:
+
+
+AmorProtDescriptors
+###################
+..  autoclass:: optunaz.descriptors.AmorProtDescriptors
+    :members:
+
+
+PathFP
+######
+..  autoclass:: optunaz.descriptors.PathFP
+    :members:
+
+
+UnscaledMAPC
+############
+..  autoclass:: optunaz.descriptors.UnscaledMAPC
+    :members:
+
+
+UnscaledZScalesDescriptors
+##########################
+..  autoclass:: optunaz.descriptors.UnscaledZScalesDescriptors
+    :members:
+
+
+MAPC
+####
+..  autoclass:: optunaz.descriptors.MAPC
+    :members:
+
+
+ZScalesDescriptors
+##################
+..  autoclass:: optunaz.descriptors.ZScalesDescriptors
+    :members:
\ No newline at end of file
diff --git a/docs/sphinx-builddir/html/_sources/index.rst.txt b/docs/sphinx-builddir/html/_sources/index.rst.txt
index 43864b0..e48f662 100644
--- a/docs/sphinx-builddir/html/_sources/index.rst.txt
+++ b/docs/sphinx-builddir/html/_sources/index.rst.txt
@@ -28,4 +28,4 @@ Development
 -----------
 * `Test report <_static/pytest/pytest/index.html>`_
 * `Test coverage <_static/pytest/coverage/index.html>`_
-* `Public release (3.1.2)  `_
\ No newline at end of file
+* `Public release (3.1.3)  `_
\ No newline at end of file
diff --git a/docs/sphinx-builddir/html/_sources/notebooks/preprocess_data.ipynb.txt b/docs/sphinx-builddir/html/_sources/notebooks/preprocess_data.ipynb.txt
index 0dd5da5..9853aed 100644
--- a/docs/sphinx-builddir/html/_sources/notebooks/preprocess_data.ipynb.txt
+++ b/docs/sphinx-builddir/html/_sources/notebooks/preprocess_data.ipynb.txt
@@ -1055,10 +1055,10 @@
     "    response_type=\"regression\",\n",
     "    training_dataset_file=\"../tests/data/sdf/example.sdf\",\n",
     "    deduplication_strategy=KeepAllNoDeduplication(),\n",
-    "    log_transform=\"True\", # flags to use a transform\n",
+    "    log_transform=True, # flags to use a transform\n",
     "    log_transform_base=LogBase.LOG10, # Log10 base will be used\n",
-    "    log_transform_negative=\"True\", # The negated log transform will be applied\n",
-    "    log_transform_unit_conversion=6 # THe unit conversion for pXC50 values is 6\n",
+    "    log_transform_negative=LogNegative.TRUE, # The negated log transform will be applied\n",
+    "    log_transform_unit_conversion=6 # The unit conversion for pXC50 values is 6\n",
     ")\n",
     "\n",
     "pxc50_data = Dataset(\n",
diff --git a/docs/sphinx-builddir/html/_sources/transform.rst.txt b/docs/sphinx-builddir/html/_sources/transform.rst.txt
index aaee310..6e5139d 100644
--- a/docs/sphinx-builddir/html/_sources/transform.rst.txt
+++ b/docs/sphinx-builddir/html/_sources/transform.rst.txt
@@ -24,3 +24,10 @@ ZScales
 #######
 ..  autoclass:: optunaz.utils.preprocessing.transform.ZScales
     :members:
+
+
+AmorProt
+########
+..  autoclass:: optunaz.utils.preprocessing.transform.AmorProt
+    :members:
+
diff --git a/docs/sphinx-builddir/html/_static/documentation_options.js b/docs/sphinx-builddir/html/_static/documentation_options.js
index d853903..7c93622 100644
--- a/docs/sphinx-builddir/html/_static/documentation_options.js
+++ b/docs/sphinx-builddir/html/_static/documentation_options.js
@@ -1,6 +1,6 @@
 var DOCUMENTATION_OPTIONS = {
     URL_ROOT: document.getElementById("documentation_options").getAttribute('data-url_root'),
-    VERSION: '3.1.2',
+    VERSION: '3.1.3',
     LANGUAGE: 'en',
     COLLAPSE_INDEX: false,
     BUILDER: 'html',
diff --git a/docs/sphinx-builddir/html/algorithms.html b/docs/sphinx-builddir/html/algorithms.html
index 4055411..4a83b27 100644
--- a/docs/sphinx-builddir/html/algorithms.html
+++ b/docs/sphinx-builddir/html/algorithms.html
@@ -4,7 +4,7 @@
   
 
   
-  Available algorithms — QSARtuna 3.1.2 documentation
+  Available algorithms — QSARtuna 3.1.3 documentation
       
       
       
@@ -68,7 +68,7 @@
 
  • ChemPropClassifier
    • 
 
  • ChemPropHyperoptClassifier
    • 
 
  • ChemPropHyperoptRegressor
    • 
-
  • ChemPropRegressorPretrained
    • 
+
  • ChemPropHyperoptRegressorPretrained
    • 
 
  • CalibratedClassifierCVWithVA
    • 
 
  • Mapie
    • 
 
@@ -854,8 +854,8 @@ 
    ChemPropHyperoptRegressor
-
    ChemPropRegressorPretrained
    
+
    
+
    ChemPropHyperoptRegressorPretrained
    
 
    
 
    
 class optunaz.config.optconfig.ChemPropRegressorPretrained(name, parameters)[source]
    
diff --git a/docs/sphinx-builddir/html/deduplicator.html b/docs/sphinx-builddir/html/deduplicator.html
index b7f930d..989a1a7 100644
--- a/docs/sphinx-builddir/html/deduplicator.html
+++ b/docs/sphinx-builddir/html/deduplicator.html
@@ -4,7 +4,7 @@
   
 
   
-  Available deduplicators — QSARtuna 3.1.2 documentation
+  Available deduplicators — QSARtuna 3.1.3 documentation
       
       
       
diff --git a/docs/sphinx-builddir/html/descriptors.html b/docs/sphinx-builddir/html/descriptors.html
index e48cab5..137de2b 100644
--- a/docs/sphinx-builddir/html/descriptors.html
+++ b/docs/sphinx-builddir/html/descriptors.html
@@ -4,7 +4,7 @@
   
 
   
-  Available descriptors — QSARtuna 3.1.2 documentation
+  Available descriptors — QSARtuna 3.1.3 documentation
       
       
       
@@ -68,6 +68,12 @@
 
  • SmilesAndSideInfoFromFile
    • 
 
  • ScaledDescriptor
    • 
 
  • CompositeDescriptor
    • 
+
  • AmorProtDescriptors
    • 
+
  • PathFP
    • 
+
  • UnscaledMAPC
    • 
+
  • UnscaledZScalesDescriptors
    • 
+
  • MAPC
    • 
+
  • ZScalesDescriptors
    • 
 
 
 
  • List of available evaluation splits
    • 
@@ -577,6 +583,170 @@ 
    CompositeDescriptor
+
    AmorProtDescriptors
    
+
    
+
    
+class optunaz.descriptors.AmorProtDescriptors(name, parameters)[source]
    
+
    These descriptors are intended to be used with Peptide SMILES
    
+
    
+
    
+class Parameters[source]
    
+
    
+
+
    
+
    
+calculate_from_smi(smi)[source]
    
+
    Returns a descriptor (e.g. a fingerprint) for a given SMILES string.
    
+
    The descriptor is returned as a 1-d Numpy ndarray.
    
+
    
+
+
    
+
+
    
+
    
+
    PathFP
    
+
    
+
    
+class optunaz.descriptors.PathFP(name, parameters)[source]
    
+
    Path fingerprint based on RDKit FP Generator.
    
+
    This is a Path fingerprint.
    
+
    
+
    
+class Parameters(maxPath=3, fpSize=2048)[source]
    
+
    
+
    Parameters:
    
+
      
+
    • maxPath (int) – Maximum path for the fingerprint - minimum: 1, title: maxPath
      • 
+
    • fpSize (int) – Number size of the fingerprint, sometimes also called bit size. - minimum: 1, title: fpSize
      • 
+
    
+
    
+
    
+
    
+
+
    
+
    
+calculate_from_mol(mol)[source]
    
+
    Returns a descriptor (fingerprint) for a given RDKit Mol as a 1-d Numpy array.
    
+
    
+
+
    
+
+
    
+
    
+
    UnscaledMAPC
    
+
    
+
    
+class optunaz.descriptors.UnscaledMAPC(name, parameters)[source]
    
+
    Unscaled MAPC descriptors
    
+
    These MAPC descriptors are unscaled and should be used with caution. MinHashed Atom-Pair Fingerprint Chiral (see
+Orsi et al. One chiral fingerprint to find them all) is the original version of the MinHashed Atom-Pair
+fingerprint of radius 2 (MAP4) which combined circular substructure fingerprints and atom-pair fingerprints into
+a unified framework. This combination allowed for improved substructure perception and performance in small
+molecule benchmarks while retaining information about bond distances for molecular size and shape perception.
    
+
    These fingerprints expand the functionality of MAP4 to include encoding of stereochemistry into the fingerprint.
+CIP descriptors of chiral atoms are encoded into the fingerprint at the highest radius. This allows MAPC
+to modulate the impact of stereochemistry on fingerprints, making it scale with increasing molecular size
+without disproportionally affecting structural fingerprints/similarity.
    
+
    
+
    
+class Parameters(maxRadius=2, nPermutations=2048)[source]
    
+
    
+
    Parameters:
    
+
      
+
    • maxRadius (int) – Maximum radius of the fingerprint. - minimum: 1, title: maxRadius
      • 
+
    • nPermutations (int) – Number of permutations to perform. - minimum: 1, title: nPermutations
      • 
+
    
+
    
+
    
+
    
+
+
    
+
    
+calculate_from_mol(mol)[source]
    
+
    Returns a descriptor (fingerprint) for a given RDKit Mol as a 1-d Numpy array.
    
+
    
+
+
    
+
+
    
+
    
+
    UnscaledZScalesDescriptors
    
+
    
+
    
+class optunaz.descriptors.UnscaledZScalesDescriptors(name='UnscaledZScalesDescriptors', parameters=UnscaledZScalesDescriptors.Parameters())[source]
    
+
    Unscaled Z-Scales.
    
+
    Compute the Z-scales of a peptide SMILES. These Z-Scales descriptors are unscaled and should be used with caution.
    
+
    
+
    
+class Parameters[source]
    
+
    
+
+
    
+
    
+calculate_from_smi(smi)[source]
    
+
    Returns a descriptor (e.g. a fingerprint) for a given SMILES string.
    
+
    The descriptor is returned as a 1-d Numpy ndarray.
    
+
    
+
+
    
+
+
    
+
    
+
    MAPC
    
+
    
+
    
+class optunaz.descriptors.MAPC(parameters=MAPC.Parameters(maxRadius=2, nPermutations=2048, scaler=UnfittedSklearnScaler(mol_data=UnfittedSklearnScaler.MolData(file_path=None, smiles_column=None), name='UnfittedSklearnScaler'), descriptor=<class 'optunaz.descriptors.UnscaledMAPC'>), name='MAPC')[source]
    
+
    Scaled MAPC descriptors
    
+
    MAPC (MinHashed Atom-Pair Fingerprint Chiral) (see Orsi et al. One chiral fingerprint to find them all) is the
+original version of the MinHashed Atom-Pair fingerprint of radius 2 (MAP4) which combined circular substructure
+fingerprints and atom-pair fingerprints into a unified framework. This combination allowed for improved
+substructure perception and performance in small molecule benchmarks while retaining information about bond
+distances for molecular size and shape perception.
    
+
    These fingerprints expand the functionality of MAP4 to include encoding of stereochemistry into the fingerprint.
+CIP descriptors of chiral atoms are encoded into the fingerprint at the highest radius. This allows MAPC
+to modulate the impact of stereochemistry on fingerprints, making it scale with increasing molecular size
+without disproportionally affecting structural fingerprints/similarity.
    
+
    
+
    
+class Parameters(maxRadius: int = 2, nPermutations: int = 2048, scaler: Union[optunaz.descriptors.FittedSklearnScaler, optunaz.descriptors.UnfittedSklearnScaler] = UnfittedSklearnScaler(mol_data=UnfittedSklearnScaler.MolData(file_path=None, smiles_column=None), name='UnfittedSklearnScaler'), descriptor: Union[optunaz.descriptors.Avalon, optunaz.descriptors.ECFP, optunaz.descriptors.ECFP_counts, optunaz.descriptors.PathFP, optunaz.descriptors.AmorProtDescriptors, optunaz.descriptors.MACCS_keys, optunaz.descriptors.PrecomputedDescriptorFromFile, optunaz.descriptors.UnscaledMAPC, optunaz.descriptors.UnscaledPhyschemDescriptors, optunaz.descriptors.UnscaledJazzyDescriptors, optunaz.descriptors.UnscaledZScalesDescriptors] = <class 'optunaz.descriptors.UnscaledMAPC'>)[source]
    
+
    
+
    
+descriptor
    
+
    alias of UnscaledMAPC
    
+
    
+
+
    
+
+
    
+
+
    
+
    
+
    ZScalesDescriptors
    
+
    
+
    
+class optunaz.descriptors.ZScalesDescriptors(parameters=ZScalesDescriptors.Parameters(scaler=UnfittedSklearnScaler(mol_data=UnfittedSklearnScaler.MolData(file_path=None, smiles_column=None), name='UnfittedSklearnScaler'), descriptor=<class 'optunaz.descriptors.UnscaledZScalesDescriptors'>), name='ZScalesDescriptors')[source]
    
+
    Scaled Z-Scales descriptors.
    
+
    Z-scales were proposed in Sandberg et al (1998) based on physicochemical properties of proteogenic and
+non-proteogenic amino acids, including NMR data and thin-layer chromatography (TLC) data. Refer to
+doi:10.1021/jm9700575 for the original publication. These descriptors capture 1. lipophilicity, 2. steric
+properties (steric bulk and polarizability), 3. electronic properties (polarity and charge),
+4. electronegativity (heat of formation, electrophilicity and hardness) and 5. another electronegativity.
+This fingerprint is the computed average of Z-scales of all the amino acids in the peptide.
    
+
    
+
    
+class Parameters(scaler: Union[optunaz.descriptors.FittedSklearnScaler, optunaz.descriptors.UnfittedSklearnScaler] = UnfittedSklearnScaler(mol_data=UnfittedSklearnScaler.MolData(file_path=None, smiles_column=None), name='UnfittedSklearnScaler'), descriptor: Union[optunaz.descriptors.Avalon, optunaz.descriptors.ECFP, optunaz.descriptors.ECFP_counts, optunaz.descriptors.PathFP, optunaz.descriptors.AmorProtDescriptors, optunaz.descriptors.MACCS_keys, optunaz.descriptors.PrecomputedDescriptorFromFile, optunaz.descriptors.UnscaledMAPC, optunaz.descriptors.UnscaledPhyschemDescriptors, optunaz.descriptors.UnscaledJazzyDescriptors, optunaz.descriptors.UnscaledZScalesDescriptors] = <class 'optunaz.descriptors.UnscaledZScalesDescriptors'>)[source]
    
+
    
+
    
+descriptor
    
+
    alias of UnscaledZScalesDescriptors
    
+
    
+
+
    
+
+
    
+
 
    
 
 
diff --git a/docs/sphinx-builddir/html/genindex.html b/docs/sphinx-builddir/html/genindex.html
index 60e8a59..6cdabae 100644
--- a/docs/sphinx-builddir/html/genindex.html
+++ b/docs/sphinx-builddir/html/genindex.html
@@ -3,7 +3,7 @@
 
   
   
-  Index — QSARtuna 3.1.2 documentation
+  Index — QSARtuna 3.1.3 documentation
       
       
       
@@ -168,6 +168,8 @@ 
    A
    
         
  • (optunaz.config.optconfig.ChemPropRegressor.Parameters attribute)
 
    • 
       
+      
  • algorith_hash (optunaz.utils.tracking.TrackingData attribute)
+
    • 
       
  • Algorithm (class in optunaz.config)
 
       
    • 
-      
  • AmorProt (class in optunaz.utils.preprocessing.transform)
+      
  • AmorProt (class in optunaz.utils.preprocessing.transform), [1]
 
    • 
-      
  • AmorProt.Parameters (class in optunaz.utils.preprocessing.transform)
+      
  • AmorProt.Parameters (class in optunaz.utils.preprocessing.transform), [1]
 
    • 
-      
  • AmorProtDescriptors (class in optunaz.descriptors)
+      
  • AmorProtDescriptors (class in optunaz.descriptors), [1]
 
    • 
       
  • AmorProtDescriptors.AmorProt (class in optunaz.descriptors)
 
    • 
-      
  • AmorProtDescriptors.Parameters (class in optunaz.descriptors)
+      
  • AmorProtDescriptors.Parameters (class in optunaz.descriptors), [1]
 
    • 
       
  • ArgsError
 
    • 
@@ -447,6 +449,8 @@ 
    B
    
       
  • best_trial (optunaz.config.buildconfig.BuildConfig.Metadata attribute)
 
    • 
       
  • best_value (optunaz.config.buildconfig.BuildConfig.Metadata attribute)
+
    • 
+      
  • bin_edges (optunaz.utils.tracking.Calpoint attribute)
 
    • 
       
  • bins (optunaz.utils.preprocessing.splitter.HistogramStratifiedShuffleSplit attribute)
 
@@ -509,6 +513,8 @@ 
    C
    
 
    • 
       
       
  • cache (optunaz.objective.Objective attribute)
+
    • 
+      
  • cal_points (optunaz.utils.tracking.BuildTrackingData attribute)
 
    • 
       
  • calcSlurmMem() (optunaz.automl.ModelDispatcher static method)
 
    • 
@@ -521,16 +527,16 @@ 
    C
    
 
         
  • (optunaz.descriptors.MACCS_keys method), [1]
 
    • 
-        
  • (optunaz.descriptors.PathFP method), [1]
+        
  • (optunaz.descriptors.PathFP method), [1], [2]
 
    • 
         
  • (optunaz.descriptors.RdkitDescriptor method)
 
    • 
-        
  • (optunaz.descriptors.UnscaledMAPC method)
+        
  • (optunaz.descriptors.UnscaledMAPC method), [1]
 
    • 
         
  • (optunaz.descriptors.UnscaledPhyschemDescriptors method), [1]
 
    • 
       
-      
  • calculate_from_smi() (optunaz.descriptors.AmorProtDescriptors method)
+      
  • calculate_from_smi() (optunaz.descriptors.AmorProtDescriptors method), [1]
 
       
+  
-  
    • 
-  
-  
+  
@@ -197,6 +197,12 @@ 
    Welcome to QSARtuna Documentation!SmilesAndSideInfoFromFile
 
  • ScaledDescriptor
    • 
 
  • CompositeDescriptor
    • 
+
  • AmorProtDescriptors
    • 
+
  • PathFP
    • 
+
  • UnscaledMAPC
    • 
+
  • UnscaledZScalesDescriptors
    • 
+
  • MAPC
    • 
+
  • ZScalesDescriptors
    • 
 
 
 
  • List of available evaluation splits
 
    • 
 
  • List of available deduplicators
 
 
diff --git a/docs/sphinx-builddir/html/modules.html b/docs/sphinx-builddir/html/modules.html
index f97b29c..f912afb 100644
--- a/docs/sphinx-builddir/html/modules.html
+++ b/docs/sphinx-builddir/html/modules.html
@@ -4,7 +4,7 @@
   
 
   
-  optunaz — QSARtuna 3.1.2 documentation
+  optunaz — QSARtuna 3.1.3 documentation
       
       
       
diff --git a/docs/sphinx-builddir/html/notebooks/QSARtuna_Tutorial.html b/docs/sphinx-builddir/html/notebooks/QSARtuna_Tutorial.html
index cf29fd9..fce4aa7 100644
--- a/docs/sphinx-builddir/html/notebooks/QSARtuna_Tutorial.html
+++ b/docs/sphinx-builddir/html/notebooks/QSARtuna_Tutorial.html
@@ -4,7 +4,7 @@
   
 
   
-  QSARtuna CLI Tutorial — QSARtuna 3.1.2 documentation
+  QSARtuna CLI Tutorial — QSARtuna 3.1.3 documentation
       
       
       
diff --git a/docs/sphinx-builddir/html/notebooks/preprocess_data.html b/docs/sphinx-builddir/html/notebooks/preprocess_data.html
index cc13eba..63426f9 100644
--- a/docs/sphinx-builddir/html/notebooks/preprocess_data.html
+++ b/docs/sphinx-builddir/html/notebooks/preprocess_data.html
@@ -4,7 +4,7 @@
   
 
   
-  Preprocessing data for QSARtuna — QSARtuna 3.1.2 documentation
+  Preprocessing data for QSARtuna — QSARtuna 3.1.3 documentation
       
       
       
@@ -1144,10 +1144,10 @@ 
    Performing data transform within the Datareaderresponse_type="regression",
     training_dataset_file="../tests/data/sdf/example.sdf",
     deduplication_strategy=KeepAllNoDeduplication(),
-    log_transform="True", # flags to use a transform
+    log_transform=True, # flags to use a transform
     log_transform_base=LogBase.LOG10, # Log10 base will be used
-    log_transform_negative="True", # The negated log transform will be applied
-    log_transform_unit_conversion=6 # THe unit conversion for pXC50 values is 6
+    log_transform_negative=LogNegative.TRUE, # The negated log transform will be applied
+    log_transform_unit_conversion=6 # The unit conversion for pXC50 values is 6
 )
 
 pxc50_data = Dataset(
diff --git a/docs/sphinx-builddir/html/notebooks/preprocess_data.ipynb b/docs/sphinx-builddir/html/notebooks/preprocess_data.ipynb
index 0dd5da5..9853aed 100644
--- a/docs/sphinx-builddir/html/notebooks/preprocess_data.ipynb
+++ b/docs/sphinx-builddir/html/notebooks/preprocess_data.ipynb
@@ -1055,10 +1055,10 @@
     "    response_type=\"regression\",\n",
     "    training_dataset_file=\"../tests/data/sdf/example.sdf\",\n",
     "    deduplication_strategy=KeepAllNoDeduplication(),\n",
-    "    log_transform=\"True\", # flags to use a transform\n",
+    "    log_transform=True, # flags to use a transform\n",
     "    log_transform_base=LogBase.LOG10, # Log10 base will be used\n",
-    "    log_transform_negative=\"True\", # The negated log transform will be applied\n",
-    "    log_transform_unit_conversion=6 # THe unit conversion for pXC50 values is 6\n",
+    "    log_transform_negative=LogNegative.TRUE, # The negated log transform will be applied\n",
+    "    log_transform_unit_conversion=6 # The unit conversion for pXC50 values is 6\n",
     ")\n",
     "\n",
     "pxc50_data = Dataset(\n",
diff --git a/docs/sphinx-builddir/html/objects.inv b/docs/sphinx-builddir/html/objects.inv
index 95e98eb..04574d3 100644
Binary files a/docs/sphinx-builddir/html/objects.inv and b/docs/sphinx-builddir/html/objects.inv differ
diff --git a/docs/sphinx-builddir/html/optunaz.config.html b/docs/sphinx-builddir/html/optunaz.config.html
index 540be15..a1f1b28 100644
--- a/docs/sphinx-builddir/html/optunaz.config.html
+++ b/docs/sphinx-builddir/html/optunaz.config.html
@@ -4,7 +4,7 @@
   
 
   
-  optunaz.config package — QSARtuna 3.1.2 documentation
+  optunaz.config package — QSARtuna 3.1.3 documentation
       
       
       
@@ -167,16 +167,16 @@ 
    SubmodulesAlgorithm
    
 
    
 
    
-class AdaBoostClassifierParameters(n_estimators: int, learning_rate: float)[source]
    
+class AdaBoostClassifierParameters(n_estimators: int = 1, learning_rate: float = 0.1)[source]
 
    Bases: object
    
 
    
 
    
-n_estimators
    
+n_estimators = 1
 
    
 
 
    
 
    
-learning_rate
    
+learning_rate = 0.1
 
    
 
 
    
@@ -320,7 +320,7 @@ 
    SubmodulesAlgorithm
    
 
    
 
    
-class LogisticRegressionParameters(solver: str, C: float)[source]
    
+class LogisticRegressionParameters(solver: str, C: float = 1.0)[source]
 
    Bases: object
    
 
    
 
    
@@ -329,7 +329,7 @@ 
    Submodules
 
    
-C
    
+C = 1.0
    
 
    
 
 
    
@@ -357,11 +357,11 @@ 
    SubmodulesAlgorithm
    
 
    
 
    
-class PLSParameters(n_components: int)[source]
    
+class PLSParameters(n_components: int = 2)[source]
 
    Bases: object
    
 
    
 
    
-n_components
    
+n_components = 2
 
    
 
 
    
@@ -389,21 +389,21 @@ 
    SubmodulesAlgorithm
    
 
    
 
    
-class RandomForestParameters(max_depth: int, n_estimators: int, max_features: str)[source]
    
+class RandomForestParameters(max_features: str, max_depth: int = None, n_estimators: int = 100)[source]
 
    Bases: object
    
 
    
-
    
-max_depth
    
+
    
+max_features
    
 
    
 
 
    
-
    
-n_estimators
    
+
    
+max_depth = None
    
 
    
 
 
    
-
    
-max_features
    
+
    
+n_estimators = 100
    
 
    
 
 
    
diff --git a/docs/sphinx-builddir/html/optunaz.html b/docs/sphinx-builddir/html/optunaz.html
index 2663f27..5cafa26 100644
--- a/docs/sphinx-builddir/html/optunaz.html
+++ b/docs/sphinx-builddir/html/optunaz.html
@@ -4,7 +4,7 @@
   
 
   
-  optunaz package — QSARtuna 3.1.2 documentation
+  optunaz package — QSARtuna 3.1.3 documentation
       
       
       
@@ -163,7 +163,7 @@ 
    Submodules
    optunaz.automl module
    
 
    
 
    
-class optunaz.automl.ModelAutoML(output_path=None, input_data=None, n_cores=- 1, email=None, user_name=None, smiles_col=None, activity_col=None, task_col=None, dry_run=False, timestr='20240828-174523')[source]
    
+class optunaz.automl.ModelAutoML(output_path=None, input_data=None, n_cores=- 1, email=None, user_name=None, smiles_col=None, activity_col=None, task_col=None, dry_run=False, timestr='20240916-165004')[source]
 
    Bases: object
    
 
    Prepares the data ready for the model training with ModelDispatcher.
 The ModelAutoML will also store activity for new tasks pending enough data.
    
@@ -1772,29 +1772,24 @@ 
    Submodules
 
    optunaz.evaluate module
    
-
    
-
    
-optunaz.evaluate.score_all(scores, estimator, X, y)[source]
    
-
    
-
 
    
 
    
 optunaz.evaluate.get_scores(mode)[source]
    
 
    
 
 
    
-
    
-optunaz.evaluate.score_all_smiles(scores, estimator, smiles, descriptor, aux, y, cache=None)[source]
    
+
    
+optunaz.evaluate.get_train_test_scores(estimator, buildconfig, train_X, train_y, test_X, test_y)[source]
    
 
    
 
 
    
-
    
-optunaz.evaluate.get_train_test_scores(estimator, buildconfig, cache=None)[source]
    
+
    
+optunaz.evaluate.get_merged_train_score(estimator, buildconfig, train_X, train_y)[source]
    
 
    
 
 
    
-
    
-optunaz.evaluate.get_merged_train_score(estimator, buildconfig, cache=None)[source]
    
+
    
+optunaz.evaluate.calibration_analysis(y_test, y_pred)[source]
    
 
    
 
 
@@ -1922,7 +1917,7 @@ 
    Submodules
 
    
-class optunaz.model_writer.QSARtunaModel(predictor: Predictor, descriptor: Union[Avalon, ECFP, ECFP_counts, PathFP, AmorProtDescriptors, MACCS_keys, PrecomputedDescriptorFromFile, UnscaledMAPC, UnscaledPhyschemDescriptors, UnscaledJazzyDescriptors, UnscaledZScalesDescriptors, ScaledDescriptor, MAPC, PhyschemDescriptors, JazzyDescriptors, ZScalesDescriptors, CompositeDescriptor, SmilesFromFile, SmilesAndSideInfoFromFile], mode: ModelMode, transform: Optional[ModelDataTransform] = None, aux_transform: Union[VectorFromColumn, ZScales, AmorProt, NoneType] = None, metadata: Optional[Dict] = None)[source]
    
+class optunaz.model_writer.QSARtunaModel(predictor: Predictor, descriptor: Union[Avalon, ECFP, ECFP_counts, PathFP, AmorProtDescriptors, MACCS_keys, PrecomputedDescriptorFromFile, UnscaledMAPC, UnscaledPhyschemDescriptors, UnscaledJazzyDescriptors, UnscaledZScalesDescriptors, ScaledDescriptor, MAPC, PhyschemDescriptors, JazzyDescriptors, ZScalesDescriptors, CompositeDescriptor, SmilesFromFile, SmilesAndSideInfoFromFile], mode: ModelMode, transform: Optional[ModelDataTransform] = None, aux_transform: Union[VectorFromColumn, ZScales, AmorProt, NoneType] = None, metadata: Optional[Dict] = None)[source]
 
    Bases: ABC
    
 
    
 
    
diff --git a/docs/sphinx-builddir/html/optunaz.utils.enums.html b/docs/sphinx-builddir/html/optunaz.utils.enums.html
index 1d91df8..43cb1ff 100644
--- a/docs/sphinx-builddir/html/optunaz.utils.enums.html
+++ b/docs/sphinx-builddir/html/optunaz.utils.enums.html
@@ -4,7 +4,7 @@
   
 
   
-  optunaz.utils.enums package — QSARtuna 3.1.2 documentation
+  optunaz.utils.enums package — QSARtuna 3.1.3 documentation
       
       
       
diff --git a/docs/sphinx-builddir/html/optunaz.utils.html b/docs/sphinx-builddir/html/optunaz.utils.html
index fc7a184..7f5a61d 100644
--- a/docs/sphinx-builddir/html/optunaz.utils.html
+++ b/docs/sphinx-builddir/html/optunaz.utils.html
@@ -4,7 +4,7 @@
   
 
   
-  optunaz.utils package — QSARtuna 3.1.2 documentation
+  optunaz.utils package — QSARtuna 3.1.3 documentation
       
       
       
@@ -391,7 +391,7 @@ 
    Submodules
 
    
-class optunaz.utils.tracking.TrackingData(trial_number, trial_value, scoring, trial_state, all_cv_test_scores, buildconfig)[source]
    
+class optunaz.utils.tracking.TrackingData(trial_number, trial_value, scoring, trial_state, all_cv_test_scores, buildconfig, algorith_hash)[source]
    
 
    Bases: object
    
 
    Dataclass defining internal tracking format
    
 
    
@@ -424,6 +424,11 @@ 
    Submodulesbuildconfig
 
    
 
+
    
+
    
+algorith_hash
    
+
    
+
 
    
 
 
    
@@ -440,7 +445,7 @@ 
    Submodules
 class optunaz.utils.tracking.InternalTrackingCallback(optconfig, trial_number_offset)[source]
 
    Bases: object
    
-
    Callback to track (log) progress using internal tracking format
    
+
    Callback to track (log) Optimization progress using internal tracking format
    
 
    
 
    
 optconfig
    
@@ -474,11 +479,32 @@ 
    Submodules
+
    
+class optunaz.utils.tracking.Calpoint(bin_edges: float, frac_true: float, frac_pred: float)[source]
    
+
    Bases: object
    
+
    
+
    
+bin_edges
    
+
    
+
+
    
+
    
+frac_true
    
+
    
+
+
    
+
    
+frac_pred
    
+
    
+
+
    
+
 
    
 
    
-class optunaz.utils.tracking.BuildTrackingData(response_column_name, test_scores, test_points)[source]
    
+class optunaz.utils.tracking.BuildTrackingData(response_column_name, test_scores, test_points, cal_points)[source]
 
    Bases: object
    
-
    Dataclass defining internal tracking format
    
+
    Dataclass defining internal Build tracking format
    
 
    
 
    
 response_column_name
    
@@ -494,11 +520,16 @@ 
    Submodulestest_points
 
    
 
+
    
+
    
+cal_points
    
+
    
+
 
    
 
 
    
 
    
-optunaz.utils.tracking.track_build(model, buildconfig)[source]
    
+optunaz.utils.tracking.track_build(qptuna_model, buildconfig, test_scores)[source]
 
    
 
 
diff --git a/docs/sphinx-builddir/html/optunaz.utils.preprocessing.html b/docs/sphinx-builddir/html/optunaz.utils.preprocessing.html
index ff60db7..85e72c5 100644
--- a/docs/sphinx-builddir/html/optunaz.utils.preprocessing.html
+++ b/docs/sphinx-builddir/html/optunaz.utils.preprocessing.html
@@ -4,7 +4,7 @@
   
 
   
-  optunaz.utils.preprocessing package — QSARtuna 3.1.2 documentation
+  optunaz.utils.preprocessing package — QSARtuna 3.1.3 documentation
       
       
       
diff --git a/docs/sphinx-builddir/html/py-modindex.html b/docs/sphinx-builddir/html/py-modindex.html
index 1935f53..59e526c 100644
--- a/docs/sphinx-builddir/html/py-modindex.html
+++ b/docs/sphinx-builddir/html/py-modindex.html
@@ -3,7 +3,7 @@
 
   
   
-  Python Module Index — QSARtuna 3.1.2 documentation
+  Python Module Index — QSARtuna 3.1.3 documentation
       
       
       
diff --git a/docs/sphinx-builddir/html/search.html b/docs/sphinx-builddir/html/search.html
index 64cd560..ecfba5b 100644
--- a/docs/sphinx-builddir/html/search.html
+++ b/docs/sphinx-builddir/html/search.html
@@ -3,7 +3,7 @@
 
   
   
-  Search — QSARtuna 3.1.2 documentation
+  Search — QSARtuna 3.1.3 documentation
       
       
       
diff --git a/docs/sphinx-builddir/html/searchindex.js b/docs/sphinx-builddir/html/searchindex.js
index 7e87d59..2e70d65 100644
--- a/docs/sphinx-builddir/html/searchindex.js
+++ b/docs/sphinx-builddir/html/searchindex.js
@@ -1 +1 @@
-Search.setIndex({"docnames": ["README", "algorithms", "deduplicator", "descriptors", "index", "modules", "notebooks/QSARtuna_Tutorial", "notebooks/preprocess_data", "optunaz", "optunaz.config", "optunaz.utils", "optunaz.utils.enums", "optunaz.utils.preprocessing", "splitters", "transform"], "filenames": ["README.md", "algorithms.rst", "deduplicator.rst", "descriptors.rst", "index.rst", "modules.rst", "notebooks/QSARtuna_Tutorial.ipynb", "notebooks/preprocess_data.ipynb", "optunaz.rst", "optunaz.config.rst", "optunaz.utils.rst", "optunaz.utils.enums.rst", "optunaz.utils.preprocessing.rst", "splitters.rst", "transform.rst"], "titles": ["QSARtuna \ud80c\udd9b: QSAR using Optimization for Hyperparameter Tuning (formerly Optuna AZ and QPTUNA)", "Available algorithms", "Available deduplicators", "Available descriptors", "Welcome to QSARtuna Documentation!", "optunaz", "QSARtuna CLI Tutorial", "Preprocessing data for QSARtuna", "optunaz package", "optunaz.config package", "optunaz.utils 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\ No newline at end of file
diff --git a/docs/sphinx-builddir/html/splitters.html b/docs/sphinx-builddir/html/splitters.html
index e104585..ae4fd80 100644
--- a/docs/sphinx-builddir/html/splitters.html
+++ b/docs/sphinx-builddir/html/splitters.html
@@ -4,7 +4,7 @@
   
 
   
-  Available splitters — QSARtuna 3.1.2 documentation
+  Available splitters — QSARtuna 3.1.3 documentation
       
       
       
diff --git a/docs/sphinx-builddir/html/transform.html b/docs/sphinx-builddir/html/transform.html
index 7692d3d..d4a789d 100644
--- a/docs/sphinx-builddir/html/transform.html
+++ b/docs/sphinx-builddir/html/transform.html
@@ -4,7 +4,7 @@
   
 
   
-  Available transform — QSARtuna 3.1.2 documentation
+  Available transform — QSARtuna 3.1.3 documentation
       
       
       
@@ -58,6 +58,7 @@
 
  • ModelDataTransform
    • 
 
  • VectorFromColumn
    • 
 
  • ZScales
    • 
+
  • AmorProt
    • 
 
 
    • 
 
  • List of available deduplicators
    • 
@@ -192,6 +193,21 @@ 
    ZScales
+
    AmorProt
    
+
    
+
    
+class optunaz.utils.preprocessing.transform.AmorProt(name='AmorProt', parameters=AmorProt.Parameters())[source]
    
+
    AmorProt from column
    
+
    Calculates AmorProt for sequences or a predefined list of peptide/protein targets
    
+
    
+
    
+class Parameters[source]
    
+
    
+
+
    
+
 
 
 
diff --git a/docs/sphinx-source/index.rst b/docs/sphinx-source/index.rst
index 43864b0..e48f662 100644
--- a/docs/sphinx-source/index.rst
+++ b/docs/sphinx-source/index.rst
@@ -28,4 +28,4 @@ Development
 -----------
 * `Test report <_static/pytest/pytest/index.html>`_
 * `Test coverage <_static/pytest/coverage/index.html>`_
-* `Public release (3.1.2)  `_
\ No newline at end of file
+* `Public release (3.1.3)  `_
\ No newline at end of file