flexynesis 0.1.0__tar.gz

flexynesis-0.1.0/LICENCE.md

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flexynesis-0.1.0/PKG-INFO

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+Metadata-Version: 2.1
+Name: flexynesis
+Version: 0.1.0
+Summary: A deep-learning based multi-omics bulk sequencing
+Author-email: Bora Uyar <bora.uyar@mdc-berlin.de>, Taras Savchyn <Taras.Savchyn@mdc-berlin.de>
+Project-URL: homepage, https://github.com/BIMSBbioinfo/flexynesis
+Classifier: Development Status :: 3 - Alpha
+Classifier: Intended Audience :: Developers
+Classifier: Programming Language :: Python :: 3.11
+Requires-Python: <3.12,>=3.11
+Description-Content-Type: text/markdown
+License-File: LICENCE.md
+Requires-Dist: matplotlib
+Requires-Dist: numpy
+Requires-Dist: pandas
+Requires-Dist: lightning
+Requires-Dist: pyyaml
+Requires-Dist: scikit-optimize
+Requires-Dist: scipy
+Requires-Dist: seaborn
+Requires-Dist: torch
+Requires-Dist: torchvision
+Requires-Dist: tqdm
+Requires-Dist: umap-learn
+Requires-Dist: rich
+Requires-Dist: captum
+Requires-Dist: ipywidgets
+Requires-Dist: torch_geometric
+Requires-Dist: ipykernel
+Requires-Dist: lifelines
+Requires-Dist: papermill
+Requires-Dist: scikit-survival
+Requires-Dist: python-louvain
+Provides-Extra: test
+Requires-Dist: pytest; extra == "test"
+
+
+<p align="center">
+  <img alt="logo" src="https://github.com/BIMSBbioinfo/flexynesis/blob/main/img/logo.png" width="50%" height="50%">
+</p>
+
+![tests](https://github.com/BIMSBbioinfo/flexynesis/actions/workflows/tests.yml/badge.svg)
+![benchmarks](https://github.com/BIMSBbioinfo/flexynesis/actions/workflows/benchmarks.yml/badge.svg)
+![tutorials](https://github.com/BIMSBbioinfo/flexynesis/actions/workflows/tutorials.yml/badge.svg)
+![License: CC BY-NC-ND 4.0](https://img.shields.io/badge/License-CC_BY--NC--ND_4.0-lightgrey.svg)
+
+# flexynesis
+A deep-learning based multi-omics bulk sequencing data integration suite with a focus on (pre-)clinical 
+endpoint prediction. The package includes multiple types of deep learning architectures such as simple 
+fully connected networks, supervised variational autoencoders; different options of data layer fusion, 
+and automates feature selection and hyperparameter optimisation. The tools are continuosly benchmarked 
+on publicly available datasets mostly related to the study of cancer. Some of the applications of the methods 
+we develop are drug response modeling in cancer patients or preclinical models (such as cell lines and 
+patient-derived xenografts), cancer subtype prediction, or any other clinically relevant outcome prediction
+that can be formulated as a regression or classification problem. 
+
+<p align="center">
+  <img alt="workflow" src="https://github.com/BIMSBbioinfo/flexynesis/blob/main/img/graphical_abstract.jpg">
+</p>
+
+# Documentation
+
+A detailed documentation of classes and functions in this repository can be found [here](https://bimsbstatic.mdc-berlin.de/akalin/buyar/flexynesis/docs/flexynesis/index.html).
+
+# 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
+
+# Quick Start
+
+## Install 
+
+```
+git clone https://github.com/BIMSBbioinfo/flexynesis.git
+cd flexynesis
+# create an environment with python 3.11 
+conda create --name flexynesisenv --file spec-file.txt
+      # => alternatively: conda create --name flexynesisenv python==3.11
+# activate environment and install dependencies
+conda activate flexynesisenv 
+pip install -e .
+```
+
+## Options
+
+For a full set of command-line options:
+```
+flexynesis -h 
+```
+
+## Test the installation
+
+Download a dataset and test the flexynesis installation on a test run. 
+```
+curl -L -o dataset1.tgz \
+https://bimsbstatic.mdc-berlin.de/akalin/buyar/flexynesis-benchmark-datasets/dataset1.tgz
+
+tar -xzvf dataset1.tgz
+
+conda activate flexynesisenv
+
+flexynesis --data_path dataset1 \
+  --model_class DirectPred \
+  --target_variables Erlotinib \
+  --fusion_type early \
+  --hpo_iter 1 \
+  --features_min 50 \
+  --features_top_percentile 5 \
+  --log_transform False \
+  --data_types gex,cnv \
+  --outdir . \
+  --prefix erlotinib_direct \
+  --early_stop_patience 3 \
+  --use_loss_weighting False \
+  --evaluate_baseline_performance False
+```
+
+## Accelerating with GPUs
+
+If you have access to GPUs on your system, they can be used to accelerate the training of models. 
+However, making GPUs accessible to `torch` is system-specific. Please contact your system administrator 
+to make sure you have accessible GPUs and methods to access them. 
+
+### With Slurm 
+
+If you have [Slurm Workload Manager] in your system, you can call `flexynesis` as follows: 
+
+```
+conda activate flexynesisenv
+srun --gpus=1 --pty flexynesis --use_gpu ...otherarguments
+```
+
+### GridEngine
+
+If you have an HPC sytem running GridEngine with GPU nodes, you may be allowed to request a node with 
+GPUs. The important thing here is to request a GPU node with the proper **CUDA** version installed on it. 
+
+```
+# request 1 GPU device node with CUDA version 12
+qrsh -l gpu=1,cuda12
+# activate your environment
+conda activate flexynesisenv
+flexynesis --use_gpu ...otherarguments 
+```
+
+# Input Dataset Structure
+
+```txt
+InputFolder/
+| --  train 
+|    |-- omics1.csv 
+|    |-- omics2.csv
+|    |--  ... 
+|    |-- clin.csv
+
+| --  test 
+|    |-- omics1.csv 
+|    |-- omics2.csv
+|    |--  ... 
+|    |-- clin.csv
+```
+
+## File contents
+
+### clin.csv
+`clin.csv` contains the sample metadata. The first column contains unique sample identifiers. 
+The other columns contain sample-associated clinical variables. 
+`NA` values are allowed in the clinical variables. 
+
+```csv
+v1,v2
+s1,a,b
+s2,c,d
+s3,e,f
+```
+
+### omics.csv 
+The first column of the feature tables must be unique feature identifiers (e.g. gene names). 
+The column names must be sample identifiers that should overlap with those in the `clin.csv`. 
+They don't have to be completely identical or in the same order. Samples from the `clin.csv` that are not represented
+in the omics table will be dropped. 
+
+```txt
+s1,s2,s3
+g1,0,1,2
+g2,3,3,5
+g3,2,3,4
+```
+
+### Concordance between train/test splits
+The corresponding omics files in train/test splits must contain overlapping feature names (they don't 
+have to be identical or in the same order). 
+The `clin.csv` files in train/test must contain matching clinical variables. 
+
+# Guix
+
+You can also create a reproducible development environment or build a reproducible package of Flexynesis with [GNU Guix](https://guix.gnu.org).  You will need at least the Guix channels listed in `channels.scm`.  It also helps to have authorized the Inria substitute server to get binaries for CUDA-enabled packages.  See [this page](https://hpc.guix.info/channels/non-free/) for instructions on how to configure fetching binary substitutes from the build servers.
+
+You can build a Guix package from the current committed state of your git checkout and using the specified state of Guix like this:
+
+```sh
+guix time-machine -C channels.scm -- \
+    build --no-grafts -f guix.scm
+```
+
+To enter an environment containing just Flexynesis:
+
+```sh
+guix time-machine -C channels.scm -- \
+    shell --no-grafts -f guix.scm
+```
+
+To enter a development environment to hack on Flexynesis:
+
+```sh
+guix time-machine -C channels.scm -- \
+    shell --no-grafts -Df guix.scm
+```
+
+Do this to build a Docker image containing this package together with a matching Python installation:
+
+```sh
+guix time-machine -C channels.scm -- \
+  pack -C none \
+  -e '(load "guix.scm")' \
+  -f docker \
+  -S /bin=bin -S /lib=lib -S /share=share \
+  glibc-locales coreutils bash python
+```
+
+# Defining Kernel for Jupyter Notebook
+
+For interactively using flexynesis on Jupyter notebooks, one can define the kernel to make
+flexynesis and its dependencies available on the jupyter session. 
+
+Assuming you have already defined an environment and installed the package: 
+```
+conda activate flexynesisenv 
+python -m ipykernel install --user --name "flexynesisenv" --display-name "flexynesisenv"
+```
+
+# Compiling Notebooks
+
+`papermill` can be used to compile the tutorials under `examples/tutorials`. 
+
+If the purpose is to quickly check if the notebook can be run; set HPO_ITER to 1. 
+This sets hyperparameter optimisation steps to 1. 
+For longer training runs to see more meaningful results from the notebook, increase this number to e.g. 50. 
+
+Example: 
+
+```
+papermill examples/tutorials/brca_subtypes.ipynb brca_subtypes.ipynb -p HPO_ITER 1 
+```
+
+The output from papermill can be converted to an html file as follows:
+
+```
+jupyter nbconvert --to html brca_subtypes.ipynb 
+```
+
+
+# Testing
+
+Run unit tests
+```python
+pytest -vvv tests/unit
+```
+
+This will run all the unit tests in the tests directory.
+
+# Contributing
+If you would like to contribute to the project, please open an issue or a pull request on the GitHub repository.
+
+
+# Documentation
+
+```
+pdoc --html --output-dir docs --force flexynesis 
+```
+
+
+