Packages (downloads)	Tutorials		Models
	Ubuntu	macOS	Ubuntu	macOS

Flexynesis: deep learning toolkit for interpretable multi-omics integration and clinical outcome prediction

Flexynesis is a deep learning suite for multi-omics data integration, designed for (pre-)clinical endpoint prediction. It supports diverse neural architectures — from fully connected networks and supervised variational autoencoders to graph convolutional and multi-triplet models — with flexible options for omics layer fusion, automated feature selection, and hyperparameter optimization.

Built with interpretability in mind, Flexynesis incorporates integrated gradients (via Captum) for marker discovery, helping researchers move beyond black-box models.

The framework is continuously benchmarked on public datasets, particularly in oncology, and has been applied to tasks such as drug response prediction in patients and preclinical models (cell lines, PDXs), cancer subtype classification, and clinically relevant outcomes in regression, classification, survival, and cross-modality settings.

Installation

Flexynesis requires Python 3.11+.
You can install the latest release from PyPI:

pip install flexynesis

Citing our work

In order to refer to our work, please cite our manuscript published at Nature Communications.

Getting started with Flexynesis

Command-line tutorial

• Getting Started with Flexynesis

Jupyter notebooks for interactive usage

• Modeling Breast Cancer Subtypes
• Survival Markers of Lower Grade Gliomas
• Unsupervised Analysis of Bone Marrow Cells

Running Flexynesis on Galaxy

• See Galaxy Training Network Tutorials

Docker

• See how to run a Docker image of Flexynesis.

Benchmarks

For the latest benchmark results see: https://bimsbstatic.mdc-berlin.de/akalin/buyar/flexynesis-benchmark-datasets/dashboard.html

The code for the benchmarking pipeline is at: https://github.com/BIMSBbioinfo/flexynesis-benchmarks

Documentation

Flexynesis Documentation was generated using mkdocs

pip install mkdocstrings[python]
mkdocs build --clean

Contact

For questions, suggestions, or collaborations: Open an issue or create a discussion.

License

Flexynesis is released under a PolyForm Noncommercial License 1.0.0. Please contact us for permission to use it for commercial purposes. © 2025 Bioinformatics and Omic Data Science Platform, Max Delbrück Center for Molecular Medicine (MDC).