autoencodix 0.2.0__py3-none-any.whl

autoencodix/xmodalix.py

@@ -0,0 +1,318 @@
+from typing import Dict, Optional, Type, Union, Literal
+import numpy as np
+
+import anndata as ad  # type: ignore
+
+from autoencodix.base._base_dataset import BaseDataset, DataSetTypes
+from autoencodix.base._base_loss import BaseLoss
+from autoencodix.base._base_pipeline import BasePipeline
+from autoencodix.base._base_trainer import BaseTrainer
+from autoencodix.base._base_visualizer import BaseVisualizer
+from autoencodix.base._base_preprocessor import BasePreprocessor
+from autoencodix.base._base_autoencoder import BaseAutoencoder
+from autoencodix.data._datasetcontainer import DatasetContainer
+from autoencodix.data._multimodal_dataset import MultiModalDataset
+
+from autoencodix.modeling._imagevae_architecture import ImageVAEArchitecture
+from autoencodix.data._datasplitter import DataSplitter
+from autoencodix.data.datapackage import DataPackage
+from autoencodix.modeling._varix_architecture import VarixArchitecture
+from autoencodix.data._xmodal_preprocessor import XModalPreprocessor
+from autoencodix.evaluate._xmodalix_evaluator import XModalixEvaluator
+from autoencodix.trainers._xmodal_trainer import XModalTrainer
+from autoencodix.utils._result import Result
+from autoencodix.configs.default_config import DefaultConfig
+from autoencodix.configs.xmodalix_config import XModalixConfig
+from autoencodix.utils._losses import XModalLoss
+from autoencodix.utils._utils import find_translation_keys
+from autoencodix.visualize._xmodal_visualizer import XModalVisualizer
+
+from mudata import MuData
+import torch  # type: ignore
+
+
+class XModalix(BasePipeline):
+    """XModalix specific version of the BasePipeline class.
+
+    Inherits preprocess, fit, evaluate, and visualize methods from BasePipeline.
+    Overrides predict
+
+    This class extends BasePipeline. See the parent class for a full list
+    of attributes and methods.
+
+    Additional Attributes:
+        _default_config: Is set to XModalixConfig here.
+
+    """
+
+    def __init__(
+        self,
+        data: Optional[Union[DataPackage, DatasetContainer]] = None,
+        trainer_type: Type[BaseTrainer] = XModalTrainer,
+        dataset_type: Type[BaseDataset] = MultiModalDataset,
+        model_type: Type[BaseAutoencoder] = VarixArchitecture,
+        loss_type: Type[BaseLoss] = XModalLoss,
+        preprocessor_type: Type[BasePreprocessor] = XModalPreprocessor,
+        visualizer: Optional[Type[BaseVisualizer]] = XModalVisualizer,
+        evaluator: Optional[Type[XModalixEvaluator]] = XModalixEvaluator,
+        result: Optional[Result] = None,
+        datasplitter_type: Type[DataSplitter] = DataSplitter,
+        custom_splits: Optional[Dict[str, np.ndarray]] = None,
+        config: Optional[DefaultConfig] = None,
+        model_map: Dict[DataSetTypes, Type[BaseAutoencoder]] = {
+            DataSetTypes.NUM: VarixArchitecture,
+            DataSetTypes.IMG: ImageVAEArchitecture,
+        },
+    ) -> None:
+        """See base class for full list of Args."""
+        self._default_config = XModalixConfig()
+        super().__init__(
+            data=data,
+            dataset_type=dataset_type,
+            trainer_type=trainer_type,
+            model_type=model_type,
+            loss_type=loss_type,
+            preprocessor_type=preprocessor_type,
+            visualizer=visualizer,
+            evaluator=evaluator,
+            result=result,
+            datasplitter_type=datasplitter_type,
+            config=config,
+            custom_split=custom_splits,
+            model_map=model_map,
+        )
+        if not isinstance(self.config, XModalixConfig):
+            raise TypeError(
+                f"For XModalix Pipeline, we only allow XModalixConfig as type for config, got {type(self.config)}"
+            )
+
+    def show_result(self):
+        """Displays key visualizations of model results.
+
+        This method generates the following visualizations:
+        1. Loss Curves: Displays the absolute loss curves to provide insights into
+           the model's training and validation performance over epochs.
+        2. Latent Space Ridgeline Plot: Visualizes the distribution of the latent
+           space representations across different dimensions, offering a high-level
+           overview of the learned embeddings.
+        3. Latent Space 2D Scatter Plot: Projects the latent space into two dimensions
+           for a detailed view of the clustering or separation of data points.
+
+        These visualizations help in understanding the model's performance and
+        the structure of the latent space representations.
+        """
+        print("Creating plots ...")
+
+        self.visualizer.show_loss(plot_type="absolute")
+
+        self.visualizer.show_latent_space(result=self.result, plot_type="Ridgeline")
+
+        self.visualizer.show_latent_space(result=self.result, plot_type="2D-scatter")
+
+        dm_keys = find_translation_keys(
+            config=self.config,
+            trained_modalities=self._trainer._modality_dynamics.keys(),
+        )
+        if "IMG" in dm_keys["to"]:
+            self.visualizer.show_image_translation(
+                result=self.result,
+                from_key=dm_keys["from"],
+                to_key=dm_keys["to"],
+                split="test",
+            )
+
+    def _process_latent_results(
+        self, predictor_results: Result, predict_data: DatasetContainer
+    ):
+        """Processes latent space results into a single AnnData object for the source modality.
+
+        This method identifies the source ('from') modality used for translation,
+        extracts its latent space and sample IDs, and creates a single, informative
+        AnnData object. The original feature names from the source dataset are
+        also stored for reference.
+
+        The final AnnData object is stored in `self.result.adata_latent`.
+
+        Args:
+            predictor_results: The Result object returned by the `predict` method.
+            predict_data: The MultiModalDataset used for prediction, to access metadata.
+
+        Raises:
+            TypeError: if predicitonsresults arr no Dicts.
+            ValueError: if no translate direction can be found or no latentspace is stored for the specified modality.
+        """
+        print("Processing latent space results into a single AnnData object...")
+        all_latents = predictor_results.latentspaces.get(epoch=-1, split="test")
+        all_sample_ids = predictor_results.sample_ids.get(epoch=-1, split="test")
+        all_recons = predictor_results.reconstructions.get(epoch=-1, split="test")
+
+        if not all(
+            [isinstance(res, dict) for res in [all_latents, all_sample_ids, all_recons]]
+        ):
+            raise TypeError("Expected prediction results to be dictionaries.")
+
+        try:
+            predict_keys = find_translation_keys(
+                config=self.config,
+                trained_modalities=all_latents.keys(),  # type: ignore
+            )
+            from_key = predict_keys["from"]
+        except Exception as e:
+            # Provide a helpful error if the key can't be determined.
+            raise ValueError(
+                "Could not determine the 'from_key' for translation. "
+                "Ensure the translation direction is specified in the config."
+            ) from e
+
+        print(f"Identified source modality for latent space: '{from_key}'")
+
+        latent = all_latents.get(from_key)  # type: ignore
+        sample_ids = all_sample_ids.get(from_key)  # type: ignore
+
+        if latent is None:
+            raise ValueError(
+                f"Latent space for source modality '{from_key}' not found."
+            )
+
+        self.result.adata_latent = ad.AnnData(latent)
+        self.result.adata_latent.var_names = [
+            f"latent_{i}" for i in range(latent.shape[1])
+        ]
+
+        if sample_ids is not None:
+            self.result.adata_latent.obs_names = sample_ids
+
+        source_dataset = predict_data.test.datasets.get(from_key)  # type: ignore
+        if (
+            source_dataset
+            and hasattr(source_dataset, "feature_ids")
+            and source_dataset.feature_ids is not None
+        ):
+            self.result.adata_latent.uns["feature_ids"] = source_dataset.feature_ids
+            print(
+                f"  - Added {len(source_dataset.feature_ids)} source feature IDs to .uns"
+            )
+
+        self.result.update(predictor_results)
+        print("Finished processing latent results.")
+
+    def _validate_prediction_data(self, predict_data: BaseDataset):
+        """Validate that prediction data has required test split.
+
+        Args:
+            predict_data: Dataset for prediciton
+        Raises:
+            ValueError: if prediciton data is empty.
+
+        """
+        if predict_data is None:
+            raise ValueError(
+                f"The data for prediction need to be a DatasetContainer with a test attribute containing a `BaseDataset` child"
+                f"attribute, got: {predict_data}"
+            )
+
+    def _predict(
+        self,
+        predict_data: BaseDataset,
+        from_key: Optional[str] = None,
+        to_key: Optional[str] = None,
+        split: Literal["train", "valid", "test"] = "test",
+    ):
+        """Utility warpper of predict method of the trainer instance"""
+        self._validate_prediction_data(predict_data=predict_data)
+        return self._trainer.predict(
+            data=predict_data,
+            model=self.result.model,
+            from_key=from_key,
+            to_key=to_key,
+            split=split,
+        )  # type: ignore
+
+    def predict(
+        self,
+        data: Optional[
+            Union[
+                DataPackage,
+                DatasetContainer,
+                ad.AnnData,
+                MuData,  # ty: ignore[invalid-type-form]
+            ]
+        ] = None,
+        config: Optional[Union[None, DefaultConfig]] = None,
+        from_key: Optional[str] = None,
+        to_key: Optional[str] = None,
+        predict_all: bool = False,
+        **kwargs,
+    ):
+        """Generates predictions using the trained model.
+
+        Uses the trained model to make predictions on test data or new data
+        provided by the user. Processes the results and stores them in the
+        result container.
+
+        Args:
+            data: Optional new data for predictions.
+            config: Optional custom configuration for prediction.
+            from_key: string indicator of 'from' translation direction.
+            to_key: string indicator of 'to' translation direction.
+            **kwargs: Additional configuration parameters as keyword arguments.
+
+        Raises:
+            NotImplementedError: If required components aren't initialized.
+            ValueError: If no test data is available or data format is invalid.
+        """
+        self._validate_prediction_requirements()
+
+        original_input = data
+        predict_data = self._prepare_prediction_data(data=data)
+        if predict_data.test is None:
+            raise ValueError("No test data available for predictions.")
+        predictor_results = self._predict(
+            predict_data=predict_data.test,
+            from_key=from_key,
+            to_key=to_key,
+            split="test",
+        )
+
+        self._process_latent_results(
+            predictor_results=predictor_results, predict_data=predict_data
+        )
+        self._postprocess_reconstruction(
+            predictor_results=predictor_results,
+            original_input=original_input,
+            predict_data=predict_data,
+        )
+
+        if predict_all:
+            if self._datasets is None:
+                raise ValueError(
+                    "No training/validation data available for predictions."
+                )
+            train_pred_results = self._predict(
+                predict_data=self._datasets.train,
+                from_key=from_key,
+                to_key=to_key,
+                split="train",
+            )
+            self.result.update(other=train_pred_results)
+            if self._datasets.valid is None:
+                raise ValueError("No validation data available for predictions.")
+            valid_pred_results = self._predict(
+                predict_data=self._datasets.valid,
+                from_key=from_key,
+                to_key=to_key,
+                split="valid",
+            )
+            self.result.update(other=valid_pred_results)
+
+        return self.result
+
+    def sample_latent_space(
+        self,
+        n_samples: int,
+        split: str = "test",
+        epoch: int = -1,
+    ) -> torch.Tensor:
+        raise NotImplementedError(
+            "Sampling latent space is not implemented for XModalix."
+        )

autoencodix-0.2.0.dist-info/METADATA

@@ -0,0 +1,143 @@
+Metadata-Version: 2.4
+Name: autoencodix
+Version: 0.2.0
+Summary: Framework for multi-omics data integration by autoencoders.
+Project-URL: Homepage, https://github.com/jan-forest/autoencodix_package
+Project-URL: Issues, https://github.com/jan-forest/autoencodix_package/issues
+Author-email: Maximilian Joas & Jan Ewald <jan.ewald@uni-leipzig.de>
+License-Expression: Apache-2.0
+Classifier: Operating System :: OS Independent
+Classifier: Programming Language :: Python :: 3
+Requires-Python: <3.13,>=3.9
+Requires-Dist: anndata==0.10.8
+Requires-Dist: captum==0.7.0
+Requires-Dist: dill>=0.4.0
+Requires-Dist: ipykernel>=6.29.5
+Requires-Dist: ipywidgets>=8.1.7
+Requires-Dist: lightning-fabric>=2.5.0.post0
+Requires-Dist: llvmlite>=0.43.0
+Requires-Dist: matplotlib>=3.9.4
+Requires-Dist: mistralai>=1.9.11
+Requires-Dist: mkdocs-material>=9.6.19
+Requires-Dist: mkdocstrings[python]>=0.30.0
+Requires-Dist: mudata==0.2.4
+Requires-Dist: numba>=0.60.0
+Requires-Dist: numpy>=2.0.2
+Requires-Dist: ollama>=0.6.1
+Requires-Dist: openai==2.31.0
+Requires-Dist: opencv-python>=4.11.0.86
+Requires-Dist: pandas-stubs>=2.2.2.240807
+Requires-Dist: pandas>=2.2.3
+Requires-Dist: pyarrow>=19.0.1
+Requires-Dist: pydantic>=2.10.6
+Requires-Dist: pyyaml>=6.0.2
+Requires-Dist: scanpy>=1.10.3
+Requires-Dist: scikit-learn>=1.6.1
+Requires-Dist: scipy>=1.13.1
+Requires-Dist: seaborn>=0.13.2
+Requires-Dist: tensorboard-plugin-profile==2.20.1
+Requires-Dist: tensorboard>=2.20.0
+Requires-Dist: torch<2.4.0,>=2.1.0
+Requires-Dist: umap-learn>=0.5.7
+Description-Content-Type: text/markdown
+
+# AUTOENCODIX
+Autoencoders are deep-learning-based networks for dimension reduction and embedding by a combination of a compressing encoder and decoder structure for non-linear and multi-modal data integration, with promising applications to complex biological data from large-scale omics measurements. Current ongoing research and publications provide many exciting architectures and implementations of autoencoders. However, there is a lack of easy-to-use and unified implementations covering the whole pipeline of autoencoder applications.
+Consequently, we present `AUTOENCODIX` with the following features:
+- Multi-modal data integration for any numerical or categorical data
+- Different autoencoder architectures:
+  - vanilla `vanillix`
+  - variational `varix`
+  - disentangled variational `disentanglix`
+  - hierarchical/stacked `stackix`
+  - ontology-based `ontix`
+  - masking `maskix`
+  - Image VAE (2D) `imagix`
+  - cross-modal autoencoder (translation between different data modalities) `x-modalix` (works for multiple modalities paired and unpaired)
+- A Python package with a scikit-learn-like interface
+
+## Requirements
+- Python>=3.8 <3.13
+- uv or another package manager (we recommend uv)
+- git or gh
+## Installation
+- `gh repo clone jan-forest/autoencodix_package`
+- `cd autoencodix_package`
+- `uv venv --python 3.10`
+- `source .venv/bin/activate`
+- `uv sync`
+
+## Sample Usage
+```python
+import autoencodix as acx
+from autoencodix.data.datapackage import DataPackage
+from autoencodix.configs.vanillix_config import VanillixConfig
+from autoencodix.configs.default_config import DataCase
+
+# If your data is stored in pandas DataFrames, you can easily pass them to our custom DataPackage.
+# For any tabular data that is not single-cell, provide it as a dictionary to the "multi_bulk" attribute of DataPackage.
+# Note: "multi" might be misleading — it's valid to provide just one modality (1–n data modalities).
+# Here, we assume paired metadata. If you have separate metadata for each modality, use the same dict keys as in multi_bulk, e.g.:
+# annotation = {"rna": rna_annotation, "protein": protein_annotation}
+my_datapackage: DataPackage = DataPackage(
+    multi_bulk={"rna": raw_rna, "protein": raw_protein},
+    annotation={"paired": annotation},
+)
+
+myconfig: VanillixConfig = VanillixConfig(data_case=DataCase.MULTI_BULK, epochs=30, device="cpu")
+vanillix = acx.Vanillix(data=my_datapackage, config=myconfig)
+result = vanillix.run()
+```
+
+## Getting Started
+We provide extensive tutorials for all of our use cases. The best place to start is the `Vanillix Tutorial`. Here, we explain the design and features of our pipeline, which applies to other pipelines. From there, you can explore the tutorials for the more specialized architectures (`Varix`, `Ontix`, etc). We also provide tutorials for each pipeline, but the `Vanillix Tutorial` explains the general concepts, while the other tutorials go into the specifics of the corresponding pipeline. For even more details on extra functionality, such as visualizing or customizing we provide deep dive tutorials for these topics. You can find the tutorials here:
+
+- Best to get started: [Vanillix Tutorial](https://github.com/jan-forest/autoencodix_package/blob/main/Tutorials/PipelineTutorials/Vanillix.ipynb)
+- Tutorials for each specific pipeline (more advanced, do Vanillix first): [Pipeline Tutorials](https://github.com/jan-forest/autoencodix_package/tree/main/Tutorials/PipelineTutorials)
+- Tutorials for specific extra functionality, see [Deep Dives](https://github.com/jan-forest/autoencodix_package/tree/main/Tutorials/DeepDives)
+## Contributing
+Whether you have a feature request, found a bug, or have any other idea, we're always happy. For more details, refer to our [Guide](https://github.com/jan-forest/autoencodix_package/blob/main/DEVELOPER.md)
+
+## Read The Docs
+You can find our documentation [here](https://jan-forest.github.io/autoencodix_package/).
+
+## FAQ
+
+### Reproducibility and CUBLAS_WORKSPACE_CONFIG
+If you run for reproducibility with `FIX_RANDOMNESS: "all"` and you receive the following error:
+```
+RuntimeError: Deterministic behavior was enabled with either `torch.use_deterministic_algorithms(True)` or `at::Context::setDeterministicAlgorithms(true)`, but this operation is not deterministic because it uses CuBLAS and you have CUDA >= 10.2. 
+```
+You need to run the following in your terminal before running our pipeline: 
+```
+export CUBLAS_WORKSPACE_CONFIG=:16:8
+```
+
+
+## Cite
+
+While we are working on a new publication of the Python package version, we are referring to our previous publication in [Nature Computational Science](https://doi.org/10.1038/s43588-025-00916-4) 
+
+Please, use this to cite our work when using our framework: 
+
+```
+@article{joas2025autoencodix,
+  title={AUTOENCODIX: a generalized and versatile framework to train and evaluate autoencoders for biological representation learning and beyond},
+  author={Joas, Maximilian Josef and Jurenaite, Neringa and Pra{\v{s}}{\v{c}}evi{\'c}, Du{\v{s}}an and Scherf, Nico and Ewald, Jan},
+  journal={Nature Computational Science},
+  pages={1--13},
+  year={2025},
+  doi={}
+  publisher={Nature Publishing Group US New York}
+}
+```
+
+## License
+
+Copyright [2026] [Maximilian Josef Joas & Jan Ewald, ScaDS.AI, Leipzig University]
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+    http://www.apache.org/licenses/LICENSE-2.0

autoencodix-0.2.0.dist-info/RECORD

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