mllabiome 0.1.0__tar.gz

mllabiome-0.1.0/CHANGELOG.md

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+# Changelog
+
+## 0.1.0 - 2026-10-05
+
+Initial public release of `mllabiome`.

mllabiome-0.1.0/CITATION.cff

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+cff-version: 1.2.0
+message: "If you use mllabiome in research, please cite this software release using these metadata."
+title: "mllabiome"
+type: software
+version: "0.1.0"
+date-released: 2026-10-05
+authors:
+  - name: "Agata Polejowska"
+abstract: >-
+  mllabiome is a Python library for leakage-controlled machine learning on
+  microbiome data. It supports nested and subject-aware cross-validation,
+  leave-one-dataset-out evaluation, microbiota profile data representation
+  (MPDR) analysis, base and ensemble microbiota profile modelling algorithms
+  (MPMA-B and MPMA-E), multimodal modelling, explainable AI, robustness
+  analysis, statistical comparison, and research reporting. It is intended for research use only
+  and is not a medical device or clinical decision-support system.
+license: Apache-2.0
+repository-code: "https://github.com/CMG-GUTS/mllabiome"
+url: "https://github.com/CMG-GUTS/mllabiome"
+keywords:
+  - microbiome
+  - microbiota
+  - metagenomics
+  - machine learning
+  - microbiome machine learning
+  - nested cross-validation
+  - grouped cross-validation
+  - leave-one-dataset-out
+  - cross-cohort validation
+  - compositional data
+  - ensemble learning
+  - multimodal learning
+  - explainable AI
+  - SHAP
+  - LIME
+  - bioinformatics

mllabiome-0.1.0/LICENSE

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mllabiome-0.1.0/MANIFEST.in

@@ -0,0 +1,15 @@
+include README.md
+include LICENSE
+include CHANGELOG.md
+include CITATION.cff
+include pyproject.toml
+recursive-include tests *.py
+include mllabiome/py.typed
+recursive-include mllabiome/_r *.R
+global-exclude __pycache__
+global-exclude *.py[cod]
+global-exclude .DS_Store
+global-exclude ._*
+prune build
+prune dist
+prune *.egg-info

mllabiome-0.1.0/PKG-INFO

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+Metadata-Version: 2.4
+Name: mllabiome
+Version: 0.1.0
+Summary: Machine learning, ensemble learning, multimodal modeling, and explainable AI for microbiome data with end to end evaluation.
+Author: Agata Polejowska
+License-Expression: Apache-2.0
+Project-URL: Homepage, https://github.com/CMG-GUTS/mllabiome
+Project-URL: Documentation, https://cmg-guts.github.io/mllabiome/
+Project-URL: Repository, https://github.com/CMG-GUTS/mllabiome
+Project-URL: Issues, https://github.com/CMG-GUTS/mllabiome/issues
+Project-URL: Changelog, https://github.com/CMG-GUTS/mllabiome/blob/main/CHANGELOG.md
+Keywords: microbiome,microbiota,metagenomics,machine-learning,bioinformatics,microbiome-machine-learning,ensemble-learning,multimodal-learning,explainable-ai,xai,shap,lime,nested-cross-validation,cross-validation,compositional-data,biomarker-discovery
+Classifier: Development Status :: 3 - Alpha
+Classifier: Intended Audience :: Science/Research
+Classifier: Operating System :: OS Independent
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3.10
+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 :: Artificial Intelligence
+Requires-Python: >=3.10
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: numpy>=1.23
+Requires-Dist: pandas>=1.5
+Requires-Dist: scipy>=1.9
+Requires-Dist: scikit-learn>=1.6
+Requires-Dist: matplotlib>=3.6
+Requires-Dist: polars>=0.20
+Requires-Dist: pyarrow>=12
+Requires-Dist: xgboost>=2
+Requires-Dist: lightgbm>=4
+Requires-Dist: catboost>=1.2
+Requires-Dist: flaml>=2
+Requires-Dist: shap>=0.44
+Requires-Dist: lime>=0.2.0.1
+Requires-Dist: PyALE>=1.2.0
+Requires-Dist: scikit-bio>=0.7.0
+Requires-Dist: networkx>=3
+Requires-Dist: rich>=13
+Requires-Dist: tqdm>=4.66
+Requires-Dist: psutil>=7.2.2
+Dynamic: license-file
+
+<p>
+  <img
+    src="https://raw.githubusercontent.com/CMG-GUTS/mllabiome/main/assets/favicon.svg"
+    width="82"
+    height="82"
+    alt="mllabiome icon"
+  >
+  &nbsp;&nbsp;&nbsp;
+  <a href="https://cmg-guts.github.io/mllabiome/">
+    <img
+      src="https://raw.githubusercontent.com/CMG-GUTS/mllabiome/main/assets/mllabiome-readme-flow-symbols.svg"
+      width="350"
+      align="right"
+      alt="From microbiome abundance data through machine learning to learned patterns and interactions"
+    >
+  </a>
+</p>
+
+<b>E</b>valuate, <b>e</b>nsemble, <b>e</b>xplain machine learning for microbiota data analysis in single-modality and multimodality scenarios.
+
+> An integrated leakage-controlled framework for microbiome machine learning that jointly handles compositional preprocessing and taxonomic representation selection, subject/cohort-aware nested evaluation, inner-OOF ensemble and multimodal model construction, cross-fitted explanation, and uncertainty/robustness analysis.
+
+> mllabiome addresses a methodological gap between general-purpose machine-learning libraries and microbiome-specific analytical workflows. Its distinguishing feature is an evaluation architecture in which microbiome representation, preprocessing, model optimization, ensemble construction, and multimodal integration can be evaluated within the same nested, group-aware resampling hierarchy. This design allows analytical choices that are commonly fixed before cross-validation to be treated as model-selection decisions while maintaining an untouched outer evaluation set. The framework additionally propagates this separation to model interpretation and robustness analyses, providing a common provenance structure from preprocessing through prediction and explanation.
+
+`mllabiome` is a Python library for **microbiome machine learning**, designed for rigorous phenotype prediction, model benchmarking, ensemble learning, multimodal integration, explainable AI, and cross-cohort validation.
+
+It provides an end-to-end workflow for evaluating combinations of **microbiome representations, abundance transformations, taxonomic resolutions, machine-learning models, and ensembles** using nested validation procedures that keep preprocessing and model selection inside the training data.
+
+Use `mllabiome` when you need to build or benchmark predictive models from microbiome abundance data without leaking information from held-out samples.
+
+## What it does
+
+- **Nested cross-validation** and repeated nested cross-validation
+- **Subject-aware grouped splitting** for repeated or longitudinal samples
+- **Leave-one-dataset-out (LODO)** and cross-cohort evaluation
+- **Leakage-controlled preprocessing** fitted within training partitions
+- Microbiome transformations including relative abundance, presence/absence, Hellinger, arcsine-square-root, CLR, ALR, ILR, and prevalence filtering
+- Evaluation across **taxonomic resolutions**
+- Classification and regression
+- scikit-learn-compatible models plus XGBoost, LightGBM, CatBoost, AutoML, and SIAMCAT integration
+- **Ensemble learning** using inner out-of-fold predictions
+- **Multimodal learning** with early, intermediate, and late integration
+- **Explainable AI** using permutation importance, SHAP, ALE, LIME, and ALE interactions
+- Cross-fitted explanations based on held-out predictions
+- Robustness and feature-stability analyses
+- Exploratory microbiome analysis, including community-level statistics and differential abundance
+- Publication-oriented tables, figures, prediction files, and HTML reports
+
+## Why mllabiome?
+
+Microbiome machine-learning workflows are unusually vulnerable to optimistic performance estimates when feature filtering, transformations, model selection, repeated samples, or dataset structure are handled outside the validation procedure.
+
+`mllabiome` is designed around a simple rule:
+
+> **Information from a held-out sample must not influence the pipeline used to predict that sample.**
+
+Accordingly, preprocessing and candidate selection are performed within the appropriate training partitions, repeated samples can be kept at the subject level, and ensemble members are selected from inner out-of-fold predictions before evaluation on the outer test data.
+
+This makes `mllabiome` particularly suited to **microbiome phenotype prediction, microbiome ML benchmarking, cross-study validation, and reproducible evaluation of predictive microbiome signatures**.
+
+## Install
+
+Python 3.10 or newer is required.
+
+```bash
+uv pip install mllabiome
+```
+
+or:
+
+```bash
+pip install mllabiome
+```
+
+To use benchmark datasets:
+```bash
+pip install -e ".[benchmark]"
+```
+
+For development from a checked-out repository:
+
+```bash
+uv venv
+source .venv/bin/activate
+uv pip install -e ".[dev]"
+uv run pytest -q
+```
+
+## Quick start
+
+Analyses are defined in Python configuration files and can be run end-to-end:
+
+```bash
+mllabiome examples/ncv__ptsd_configs_sweep.py
+```
+
+or stage by stage:
+
+```bash
+mllabiome examples/ncv__ptsd_configs_sweep.py --stage explore
+mllabiome examples/ncv__ptsd_configs_sweep.py --stage evaluate
+mllabiome examples/ncv__ptsd_configs_sweep.py --stage ensemble
+mllabiome examples/ncv__ptsd_configs_sweep.py --stage explain
+mllabiome examples/ncv__ptsd_configs_sweep.py --stage robustness
+mllabiome examples/ncv__ptsd_configs_sweep.py --stage report
+```
+
+For cross-study validation:
+
+```bash
+mllabiome examples/ibs_lodo_configs_sweep.py --stage evaluate
+```
+
+The main workflow is:
+
+```text
+explore → evaluate → ensemble → inference → explain → robustness → report
+```
+
+## Typical use cases
+
+`mllabiome` is intended for questions such as:
+
+- Which preprocessing and machine-learning pipeline generalizes best for a microbiome phenotype?
+- How should microbiome models be compared using nested cross-validation?
+- How well does a microbiome classifier generalize to unseen cohorts?
+- Which taxonomic resolution or abundance transformation is most useful for prediction?
+- Can multiple omics or clinical modalities improve prediction?
+- Does an ensemble improve over individual microbiome models?
+- Which microbial features consistently influence held-out predictions?
+- How stable are model explanations across folds, cohorts, and analysis choices?
+
+## Data
+
+`mllabiome` operates on already quantified feature or abundance tables together with sample metadata.
+
+Supported workflows include wide tabular data and feature-by-sample microbiome profiles such as MetaPhlAn-style taxonomic abundance tables.
+
+`mllabiome` is **not** a raw sequencing pipeline: read QC, assembly, taxonomic profiling, and generation of abundance tables should be performed upstream.
+
+## Models and representations
+
+Any compatible scikit-learn estimator can be included in a model sweep. Common workflows can combine models such as logistic regression, random forests, ExtraTrees, XGBoost, LightGBM, CatBoost, neural networks, SIAMCAT, and AutoML methods.
+
+Microbiome representations can be evaluated across taxonomic levels and abundance transformations within the same validation framework.
+
+## Multimodal analysis
+
+`mllabiome` supports unimodal and multimodal prediction, including:
+
+- early feature concatenation
+- modality-specific intermediate representations
+- joint intermediate representations
+- late prediction integration
+- weighted prediction integration
+- stacked / Super Learner-style integration
+
+Integration choices are evaluated within the same held-out evaluation framework.
+
+## Explainability
+
+Model interpretation is available for selected individual models and ensembles using:
+
+- permutation importance
+- SHAP
+- accumulated local effects (ALE)
+- ALE interactions
+- LIME
+
+Where applicable, explanations are generated from models for which the explained observations were held out during model fitting.
+
+Feature attribution should be interpreted as **model-based evidence and hypothesis generation**, not as proof of causal biological effects.
+
+## Outputs
+
+A run can produce:
+
+- out-of-fold predictions
+- classification or regression metrics
+- candidate rankings
+- selected model and ensemble specifications
+- statistical comparisons
+- explainability results
+- robustness analyses
+- publication-ready figures
+- machine-readable result tables
+- an integrated HTML report
+
+Tabular results can also be exported as TSV and figures as PNG or PDF.
+
+## Reproducibility
+
+`mllabiome` records analysis configurations and separates model selection from held-out performance estimation.
+
+For reproducible research, analyses should be run from a fixed `mllabiome` release together with the exact configuration, dataset version, software environment, and random seed used for the study.
+
+Optional R-backed functionality uses version-controlled integrations for SIAMCAT and ANCOM-BC2.
+
+## Examples
+
+Runnable configurations are available in [`examples/`](examples/), including:
+
+- grouped repeated nested cross-validation
+- leave-one-dataset-out evaluation
+- microbiome transformation and taxonomic-resolution sweeps
+- ensemble selection
+- explainability and robustness analysis
+
+## Scope
+
+`mllabiome` focuses on **rigorous evaluation of predictive microbiome models**.
+
+It complements upstream microbiome-processing tools and general-purpose machine-learning frameworks by providing microbiome-aware evaluation, representation search, cohort-aware validation, ensemble construction, explainability, and reporting in one workflow.
+
+## Citation
+
+If you use `mllabiome` in published research, please cite the software release and the accompanying methods paper.
+
+Citation information will be provided in `CITATION.cff`.
+
+## License
+
+`mllabiome` is released under the Apache License 2.0.
+
+## Keywords
+
+Microbiome machine learning · microbiota machine learning · metagenomics · phenotype prediction · nested cross-validation · grouped cross-validation · leave-one-dataset-out · cross-cohort validation · compositional data · ensemble learning · multimodal learning · explainable AI · SHAP · ALE · LIME · microbiome biomarker discovery · bioinformatics · classifying gut microbiome profiles to predict a health condition · taxonomic profiling data · comparing model performance across validation approaches