phenocluster 0.1.0__tar.gz

phenocluster-0.1.0/LICENSE

@@ -0,0 +1,21 @@
+MIT License
+
+Copyright (c) 2026 Ettore Rocchi
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

phenocluster-0.1.0/PKG-INFO

@@ -0,0 +1,241 @@
+Metadata-Version: 2.4
+Name: phenocluster
+Version: 0.1.0
+Summary: Clinical Phenotype Discovery using Latent Class / Profile Analysis with Automatic Model Selection
+Author-email: Ettore Rocchi <ettore.rocchi3@unibo.it>
+Maintainer-email: Ettore Rocchi <ettore.rocchi3@unibo.it>
+License: MIT
+Project-URL: Homepage, https://github.com/EttoreRocchi/PhenoCluster
+Project-URL: Documentation, https://ettorerocchi.github.io/PhenoCluster
+Project-URL: Repository, https://github.com/EttoreRocchi/PhenoCluster
+Project-URL: Bug Tracker, https://github.com/EttoreRocchi/PhenoCluster/issues
+Project-URL: Changelog, https://github.com/EttoreRocchi/PhenoCluster/blob/main/docs/changelog.rst
+Keywords: clinical,phenotype,clustering,latent-class-analysis,latent-profile-analysis,machine-learning,bioinformatics,healthcare,data-science
+Classifier: Development Status :: 4 - Beta
+Classifier: Intended Audience :: Science/Research
+Classifier: Intended Audience :: Healthcare Industry
+Classifier: License :: OSI Approved :: MIT License
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Programming Language :: Python :: 3.13
+Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
+Classifier: Topic :: Scientific/Engineering :: Medical Science Apps.
+Classifier: Operating System :: OS Independent
+Requires-Python: >=3.11
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: numpy<2.0.0,>=1.21.0
+Requires-Dist: pandas>=2.1.0
+Requires-Dist: scikit-learn>=1.0.0
+Requires-Dist: scipy>=1.11.0
+Requires-Dist: pyyaml>=5.4.0
+Requires-Dist: joblib>=1.3.0
+Requires-Dist: stepmix>=2.1.0
+Requires-Dist: statsmodels>=0.14.0
+Requires-Dist: plotly>=5.3.0
+Requires-Dist: typer>=0.9.0
+Requires-Dist: rich>=13.0.0
+Requires-Dist: tqdm>=4.62.0
+Requires-Dist: lifelines>=0.30.0
+Provides-Extra: dev
+Requires-Dist: pytest>=7.0; extra == "dev"
+Requires-Dist: ruff>=0.4.0; extra == "dev"
+Provides-Extra: docs
+Requires-Dist: sphinx>=7.0; extra == "docs"
+Requires-Dist: sphinx-click>=5.0; extra == "docs"
+Requires-Dist: furo; extra == "docs"
+Dynamic: license-file
+
+<p align="center">
+  <img src="docs/phenocluster_logo.png" alt="PhenoCluster" width="280"/>
+</p>
+
+<p align="center">
+  <strong>A flexible data-driven framework for identifying clinical phenotypes using latent class and profile analysis</strong>
+</p>
+
+[![PyPI version](https://img.shields.io/pypi/v/phenocluster)](https://pypi.org/project/phenocluster/)
+[![Python versions](https://img.shields.io/pypi/pyversions/phenocluster)](https://www.python.org/downloads/)
+[![MIT License](https://img.shields.io/badge/license-MIT-green)](https://opensource.org/licenses/MIT)
+[![CI](https://github.com/EttoreRocchi/PhenoCluster/actions/workflows/ci.yml/badge.svg)](https://github.com/EttoreRocchi/PhenoCluster/actions/workflows/ci.yml)
+[![Docs](https://img.shields.io/badge/docs-GitHub%20Pages-blue)](https://ettorerocchi.github.io/PhenoCluster)
+
+---
+
+## Overview
+
+PhenoCluster is a Python framework for unsupervised discovery of clinical phenotypes from heterogeneous patient data. It implements an end-to-end pipeline: from data preprocessing and latent class identification to outcome association analysis, survival modelling, and multistate transition modelling.
+
+The framework is **domain-agnostic** and can be applied to any clinical cohort study where the goal is to identify latent patient subgroups and characterise their relationship with clinical outcomes. Users supply a dataset and a YAML configuration file; PhenoCluster handles model selection, phenotype assignment, and downstream inference automatically.
+
+### Key capabilities
+
+- **Latent Class / Profile Analysis** via the [StepMix](https://github.com/Labo-Lacourse/stepmix) framework with native support for mixed continuous/categorical data and missing values
+- **Automatic model selection** using information criteria (BIC, AIC, ICL, CAIC, SABIC) with configurable cluster-size constraints
+- **Classification quality assessment** with per-phenotype Average Posterior Probability (AvePP) and assignment confidence metrics
+- **Outcome association analysis** with logistic regression yielding odds ratios, confidence intervals, and FDR-corrected p-values
+- **Survival analysis** with Cox proportional hazards models producing hazard ratios and log-rank tests
+- **Multistate modelling** with transition-specific Cox PH analysis, Monte Carlo simulation for state occupation probabilities with confidence interval bands, and clinical pathway enumeration
+- **Comprehensive output** including an interactive HTML report, forest plots with confidence intervals, Kaplan-Meier and Nelson-Aalen curves, heatmaps, and JSON/CSV data exports
+
+## Installation
+
+> **Requires Python ≥ 3.11**
+
+### From PyPI
+
+```bash
+pip install phenocluster
+```
+
+### From source
+
+```bash
+git clone https://github.com/EttoreRocchi/PhenoCluster.git
+cd PhenoCluster
+pip install -e ".[dev]"
+```
+
+## Quick start
+
+### 1. Generate a configuration file
+
+```bash
+phenocluster create-config -p complete -o config.yaml
+```
+
+### 2. Edit the configuration
+
+Open `config.yaml` and fill in your dataset-specific parameters:
+
+```yaml
+global:
+  project_name: "My Study"
+  output_dir: "results"
+  random_state: 42
+
+data:
+  continuous_columns:
+    - age
+    - bmi
+    - lab_value_1
+  categorical_columns:
+    - sex
+    - smoking_status
+    - disease_stage
+  split:
+    test_size: 0.2
+
+outcome:
+  enabled: true
+  outcome_columns:
+    - mortality_30d
+    - readmission_30d
+
+survival:
+  enabled: true
+  targets:
+    - name: "overall_survival"
+      time_column: "time_to_death"
+      event_column: "death_indicator"
+```
+
+### 3. Run the pipeline
+
+```bash
+phenocluster run -d data.csv -c config.yaml
+```
+
+### 4. Inspect results
+
+Results are written to the output directory (default: `results/`):
+
+| File | Description |
+|------|-------------|
+| `analysis_report.html` | Comprehensive HTML report with all results and visualisations |
+| `cluster_statistics.json` | Phenotype sizes, feature distributions, and classification quality |
+| `outcome_results.json` | Odds ratios with confidence intervals and p-values |
+| `survival_results.json` | Kaplan-Meier estimates and Cox PH hazard ratios |
+| `multistate_results.json` | Transition-specific hazard ratios, pathways, and state occupation |
+| `data/model_fit_metrics.csv` | Information criteria, entropy, and average posterior probabilities |
+| `data/phenotypes_data.csv` | Original data augmented with phenotype assignments |
+| `data/posterior_probabilities.csv` | Posterior class membership probabilities |
+| `results/model_selection_summary.json` | Model selection comparison table and best model info |
+| `results/feature_importance.json` | Feature characterisation per phenotype |
+| `results/validation_report.json` | Internal validation metrics (train/test comparison) |
+| `results/stability_results.json` | Consensus clustering stability metrics |
+| `results/split_info.json` | Train/test split details |
+| `results/external_validation_results.json` | External validation results (when enabled) |
+| `phenocluster.log` | Pipeline execution log |
+| `artifacts/` | Cached intermediate results for incremental re-runs |
+
+## Pipeline overview
+
+PhenoCluster executes the following stages in order:
+
+1. **Data quality assessment.** Missingness patterns, correlations, variance, and MCAR testing.
+2. **Train/test split.** Stratified splitting with configurable test size, performed before preprocessing to prevent data leakage.
+3. **Preprocessing.** Imputation, outlier handling, categorical encoding, standardization, and feature selection -- fit on training data only, then applied to the test set.
+4. **Model selection.** Cross-validated information criterion search over cluster counts (training set only).
+5. **Full-cohort refit.** Once K is selected, preprocessing and LCA/LPA model are refitted on the entire cohort; phenotypes reordered by size (largest = Phenotype 0).
+6. **Stability analysis.** Consensus clustering over subsampled runs.
+7. **Internal validation.** Train/test log-likelihood comparison, cluster proportion stability, and outcome OR consistency.
+8. **Outcome association.** Logistic regression for binary outcomes with FDR-corrected p-values (optional).
+9. **Survival analysis.** Kaplan-Meier curves, Nelson-Aalen estimators, log-rank tests, and Cox PH hazard ratios (optional).
+10. **Multistate modelling.** Transition-specific Cox PH models, transition hazard ratios, and Monte Carlo simulation (optional).
+11. **Report generation.** Interactive HTML report with all figures and tables.
+
+## CLI reference
+
+| Command | Description |
+|---------|-------------|
+| `phenocluster run -d DATA -c CONFIG [--force-rerun]` | Run the full pipeline |
+| `phenocluster create-config [-p PROFILE] [-o OUTPUT]` | Generate a config YAML from a profile template |
+| `phenocluster validate-config -c CONFIG [-d DATA]` | Validate config structure; cross-check columns against data |
+| `phenocluster version` | Show version, repository link, and documentation link |
+
+## Configuration profiles
+
+Profiles set sensible defaults for common use-cases. Generate one with `phenocluster create-config -p <profile>`:
+
+| Profile | Description | Inference | Stability | Multistate |
+|---------|-------------|:---------:|:---------:|:----------:|
+| `descriptive` | Phenotype discovery only, no statistical inference | off | on | off |
+| `complete` | All analyses enabled (outcomes, survival, multistate) | on | on | on |
+| `quick` | Fast iteration for development | on | off | off |
+
+## Configuration reference
+
+See the full [Configuration Reference](https://ettorerocchi.github.io/PhenoCluster/configuration.html) in the documentation.
+
+## Documentation
+
+Full documentation (statistical methods, configuration reference, output descriptions) is available at **[ettorerocchi.github.io/PhenoCluster](https://ettorerocchi.github.io/PhenoCluster)**.
+
+## Testing
+
+```bash
+pip install -e ".[dev]"
+pytest tests/ -v
+```
+
+## License
+
+This project is licensed under the [MIT](LICENSE) License.
+
+## Citation
+
+If you use **PhenoCluster** in your research, please cite:
+
+```bibtex
+
+```
+
+## Acknowledgment
+
+This project relies on **StepMix**, a Python package for pseudo-likelihood estimation of generalized mixture models with external variables. We thank the authors for making their work openly available.
+
+If you use this framework, please cite also:
+
+> Morin, S., Legault, R., Laliberté, F., Bakk, Z., Giguère, C.-É., de la Sablonnière, R., & Lacourse, É. (2025). StepMix: A Python Package for Pseudo-Likelihood Estimation of Generalized Mixture Models with External Variables. Journal of Statistical Software, 113(8), 1-39. doi: [10.18637/jss.v113.i08](https://doi.org/10.18637/jss.v113.i08)

phenocluster-0.1.0/README.md

@@ -0,0 +1,192 @@
+<p align="center">
+  <img src="docs/phenocluster_logo.png" alt="PhenoCluster" width="280"/>
+</p>
+
+<p align="center">
+  <strong>A flexible data-driven framework for identifying clinical phenotypes using latent class and profile analysis</strong>
+</p>
+
+[![PyPI version](https://img.shields.io/pypi/v/phenocluster)](https://pypi.org/project/phenocluster/)
+[![Python versions](https://img.shields.io/pypi/pyversions/phenocluster)](https://www.python.org/downloads/)
+[![MIT License](https://img.shields.io/badge/license-MIT-green)](https://opensource.org/licenses/MIT)
+[![CI](https://github.com/EttoreRocchi/PhenoCluster/actions/workflows/ci.yml/badge.svg)](https://github.com/EttoreRocchi/PhenoCluster/actions/workflows/ci.yml)
+[![Docs](https://img.shields.io/badge/docs-GitHub%20Pages-blue)](https://ettorerocchi.github.io/PhenoCluster)
+
+---
+
+## Overview
+
+PhenoCluster is a Python framework for unsupervised discovery of clinical phenotypes from heterogeneous patient data. It implements an end-to-end pipeline: from data preprocessing and latent class identification to outcome association analysis, survival modelling, and multistate transition modelling.
+
+The framework is **domain-agnostic** and can be applied to any clinical cohort study where the goal is to identify latent patient subgroups and characterise their relationship with clinical outcomes. Users supply a dataset and a YAML configuration file; PhenoCluster handles model selection, phenotype assignment, and downstream inference automatically.
+
+### Key capabilities
+
+- **Latent Class / Profile Analysis** via the [StepMix](https://github.com/Labo-Lacourse/stepmix) framework with native support for mixed continuous/categorical data and missing values
+- **Automatic model selection** using information criteria (BIC, AIC, ICL, CAIC, SABIC) with configurable cluster-size constraints
+- **Classification quality assessment** with per-phenotype Average Posterior Probability (AvePP) and assignment confidence metrics
+- **Outcome association analysis** with logistic regression yielding odds ratios, confidence intervals, and FDR-corrected p-values
+- **Survival analysis** with Cox proportional hazards models producing hazard ratios and log-rank tests
+- **Multistate modelling** with transition-specific Cox PH analysis, Monte Carlo simulation for state occupation probabilities with confidence interval bands, and clinical pathway enumeration
+- **Comprehensive output** including an interactive HTML report, forest plots with confidence intervals, Kaplan-Meier and Nelson-Aalen curves, heatmaps, and JSON/CSV data exports
+
+## Installation
+
+> **Requires Python ≥ 3.11**
+
+### From PyPI
+
+```bash
+pip install phenocluster
+```
+
+### From source
+
+```bash
+git clone https://github.com/EttoreRocchi/PhenoCluster.git
+cd PhenoCluster
+pip install -e ".[dev]"
+```
+
+## Quick start
+
+### 1. Generate a configuration file
+
+```bash
+phenocluster create-config -p complete -o config.yaml
+```
+
+### 2. Edit the configuration
+
+Open `config.yaml` and fill in your dataset-specific parameters:
+
+```yaml
+global:
+  project_name: "My Study"
+  output_dir: "results"
+  random_state: 42
+
+data:
+  continuous_columns:
+    - age
+    - bmi
+    - lab_value_1
+  categorical_columns:
+    - sex
+    - smoking_status
+    - disease_stage
+  split:
+    test_size: 0.2
+
+outcome:
+  enabled: true
+  outcome_columns:
+    - mortality_30d
+    - readmission_30d
+
+survival:
+  enabled: true
+  targets:
+    - name: "overall_survival"
+      time_column: "time_to_death"
+      event_column: "death_indicator"
+```
+
+### 3. Run the pipeline
+
+```bash
+phenocluster run -d data.csv -c config.yaml
+```
+
+### 4. Inspect results
+
+Results are written to the output directory (default: `results/`):
+
+| File | Description |
+|------|-------------|
+| `analysis_report.html` | Comprehensive HTML report with all results and visualisations |
+| `cluster_statistics.json` | Phenotype sizes, feature distributions, and classification quality |
+| `outcome_results.json` | Odds ratios with confidence intervals and p-values |
+| `survival_results.json` | Kaplan-Meier estimates and Cox PH hazard ratios |
+| `multistate_results.json` | Transition-specific hazard ratios, pathways, and state occupation |
+| `data/model_fit_metrics.csv` | Information criteria, entropy, and average posterior probabilities |
+| `data/phenotypes_data.csv` | Original data augmented with phenotype assignments |
+| `data/posterior_probabilities.csv` | Posterior class membership probabilities |
+| `results/model_selection_summary.json` | Model selection comparison table and best model info |
+| `results/feature_importance.json` | Feature characterisation per phenotype |
+| `results/validation_report.json` | Internal validation metrics (train/test comparison) |
+| `results/stability_results.json` | Consensus clustering stability metrics |
+| `results/split_info.json` | Train/test split details |
+| `results/external_validation_results.json` | External validation results (when enabled) |
+| `phenocluster.log` | Pipeline execution log |
+| `artifacts/` | Cached intermediate results for incremental re-runs |
+
+## Pipeline overview
+
+PhenoCluster executes the following stages in order:
+
+1. **Data quality assessment.** Missingness patterns, correlations, variance, and MCAR testing.
+2. **Train/test split.** Stratified splitting with configurable test size, performed before preprocessing to prevent data leakage.
+3. **Preprocessing.** Imputation, outlier handling, categorical encoding, standardization, and feature selection -- fit on training data only, then applied to the test set.
+4. **Model selection.** Cross-validated information criterion search over cluster counts (training set only).
+5. **Full-cohort refit.** Once K is selected, preprocessing and LCA/LPA model are refitted on the entire cohort; phenotypes reordered by size (largest = Phenotype 0).
+6. **Stability analysis.** Consensus clustering over subsampled runs.
+7. **Internal validation.** Train/test log-likelihood comparison, cluster proportion stability, and outcome OR consistency.
+8. **Outcome association.** Logistic regression for binary outcomes with FDR-corrected p-values (optional).
+9. **Survival analysis.** Kaplan-Meier curves, Nelson-Aalen estimators, log-rank tests, and Cox PH hazard ratios (optional).
+10. **Multistate modelling.** Transition-specific Cox PH models, transition hazard ratios, and Monte Carlo simulation (optional).
+11. **Report generation.** Interactive HTML report with all figures and tables.
+
+## CLI reference
+
+| Command | Description |
+|---------|-------------|
+| `phenocluster run -d DATA -c CONFIG [--force-rerun]` | Run the full pipeline |
+| `phenocluster create-config [-p PROFILE] [-o OUTPUT]` | Generate a config YAML from a profile template |
+| `phenocluster validate-config -c CONFIG [-d DATA]` | Validate config structure; cross-check columns against data |
+| `phenocluster version` | Show version, repository link, and documentation link |
+
+## Configuration profiles
+
+Profiles set sensible defaults for common use-cases. Generate one with `phenocluster create-config -p <profile>`:
+
+| Profile | Description | Inference | Stability | Multistate |
+|---------|-------------|:---------:|:---------:|:----------:|
+| `descriptive` | Phenotype discovery only, no statistical inference | off | on | off |
+| `complete` | All analyses enabled (outcomes, survival, multistate) | on | on | on |
+| `quick` | Fast iteration for development | on | off | off |
+
+## Configuration reference
+
+See the full [Configuration Reference](https://ettorerocchi.github.io/PhenoCluster/configuration.html) in the documentation.
+
+## Documentation
+
+Full documentation (statistical methods, configuration reference, output descriptions) is available at **[ettorerocchi.github.io/PhenoCluster](https://ettorerocchi.github.io/PhenoCluster)**.
+
+## Testing
+
+```bash
+pip install -e ".[dev]"
+pytest tests/ -v
+```
+
+## License
+
+This project is licensed under the [MIT](LICENSE) License.
+
+## Citation
+
+If you use **PhenoCluster** in your research, please cite:
+
+```bibtex
+
+```
+
+## Acknowledgment
+
+This project relies on **StepMix**, a Python package for pseudo-likelihood estimation of generalized mixture models with external variables. We thank the authors for making their work openly available.
+
+If you use this framework, please cite also:
+
+> Morin, S., Legault, R., Laliberté, F., Bakk, Z., Giguère, C.-É., de la Sablonnière, R., & Lacourse, É. (2025). StepMix: A Python Package for Pseudo-Likelihood Estimation of Generalized Mixture Models with External Variables. Journal of Statistical Software, 113(8), 1-39. doi: [10.18637/jss.v113.i08](https://doi.org/10.18637/jss.v113.i08)

phenocluster-0.1.0/phenocluster/__init__.py

@@ -0,0 +1,190 @@
+"""
+PhenoCluster: Clinical Phenotype Discovery using Latent Class / Profile Analysis.
+
+A pipeline for identifying latent clinical phenotypes with automatic
+model selection, comprehensive validation, and advanced visualizations.
+
+Author: Ettore Rocchi <ettore.rocchi3@unibo.it>
+License: MIT
+"""
+
+__version__ = "0.1.0"
+__author__ = "Ettore Rocchi"
+__email__ = "ettore.rocchi3@unibo.it"
+
+# Configuration classes
+from .config import (
+    CacheConfig,
+    CategoricalEncodingConfig,
+    CategoricalFlowConfig,
+    DataQualityConfig,
+    DataSplitConfig,
+    ExternalValidationConfig,
+    FeatureCharacterizationConfig,
+    FeatureSelectionConfig,
+    ImputationConfig,
+    InferenceConfig,
+    LoggingConfig,
+    ModelSelectionConfig,
+    MultistateConfig,
+    MultistateState,
+    MultistateTransition,
+    OutcomeConfig,
+    OutlierConfig,
+    PhenoClusterConfig,
+    ReferenceConfig,
+    RowFilterConfig,
+    StabilityConfig,
+    StepMixConfig,
+    SurvivalConfig,
+    SurvivalTarget,
+    VisualizationConfig,
+)
+
+# Core exceptions
+from .core.exceptions import (
+    DataSplitError,
+    FeatureSelectionError,
+    ModelNotFittedError,
+    PhenoClusterError,
+)
+
+# Core types
+from .core.types import (
+    DataSplitResult,
+    ModelSelectionResult,
+)
+
+# Data handling
+from .data import DataPreprocessor, DataSplitter
+
+# Evaluation
+from .evaluation import (
+    ClusterEvaluator,
+    ClusterStatistics,
+    DataQualityAssessor,
+    ExternalValidator,
+    FeatureCharacterizer,
+    MonteCarloResults,
+    MultistateAnalyzer,
+    MultistateResults,
+    OutcomeAnalyzer,
+    StabilityAnalyzer,
+    SurvivalAnalyzer,
+)
+
+# Feature selection
+from .feature_selection import (
+    BaseFeatureSelector,
+    CorrelationSelector,
+    LassoSelector,
+    MixedDataFeatureSelector,
+    MutualInfoSelector,
+    VarianceSelector,
+)
+
+# Model selection
+from .model_selection import (
+    AVAILABLE_CRITERIA,
+    StepMixModelSelector,
+    aic_score,
+    bic_score,
+    caic_score,
+    create_scorer,
+    get_all_criteria,
+    icl_score,
+    relative_entropy_score,
+    sabic_score,
+)
+
+# Pipeline
+from .pipeline import PhenoClusterPipeline, run_pipeline
+
+# Config profiles
+from .profiles import create_config_yaml, get_profile, list_profiles
+
+# Utils
+from .utils import PhenoClusterLogger
+
+# Visualization
+from .visualization import Visualizer
+
+__all__ = [
+    # Main pipeline
+    "PhenoClusterPipeline",
+    "run_pipeline",
+    # Configuration
+    "PhenoClusterConfig",
+    "CacheConfig",
+    "CategoricalEncodingConfig",
+    "CategoricalFlowConfig",
+    "DataQualityConfig",
+    "DataSplitConfig",
+    "FeatureCharacterizationConfig",
+    "FeatureSelectionConfig",
+    "ExternalValidationConfig",
+    "InferenceConfig",
+    "ImputationConfig",
+    "LoggingConfig",
+    "ModelSelectionConfig",
+    "MultistateConfig",
+    "MultistateState",
+    "MultistateTransition",
+    "OutcomeConfig",
+    "OutlierConfig",
+    "ReferenceConfig",
+    "RowFilterConfig",
+    "StabilityConfig",
+    "StepMixConfig",
+    "SurvivalConfig",
+    "SurvivalTarget",
+    "VisualizationConfig",
+    # Config profiles
+    "list_profiles",
+    "get_profile",
+    "create_config_yaml",
+    # Data handling
+    "DataPreprocessor",
+    "DataSplitter",
+    "DataSplitResult",
+    # Evaluation
+    "ClusterEvaluator",
+    "ClusterStatistics",
+    "OutcomeAnalyzer",
+    "FeatureCharacterizer",
+    "StabilityAnalyzer",
+    "SurvivalAnalyzer",
+    "DataQualityAssessor",
+    "ExternalValidator",
+    "MultistateAnalyzer",
+    "MultistateResults",
+    "MonteCarloResults",
+    # Visualization
+    "Visualizer",
+    # Utils
+    "PhenoClusterLogger",
+    # Feature selection
+    "BaseFeatureSelector",
+    "VarianceSelector",
+    "CorrelationSelector",
+    "MutualInfoSelector",
+    "LassoSelector",
+    "MixedDataFeatureSelector",
+    # Model selection
+    "StepMixModelSelector",
+    "bic_score",
+    "aic_score",
+    "caic_score",
+    "sabic_score",
+    "icl_score",
+    "relative_entropy_score",
+    "create_scorer",
+    "get_all_criteria",
+    "AVAILABLE_CRITERIA",
+    "ModelSelectionResult",
+    # Exceptions
+    "PhenoClusterError",
+    "ModelNotFittedError",
+    "FeatureSelectionError",
+    "DataSplitError",
+]