divik 3.2.4
Divisive iK-means algorithm implementation
License: Apache-2.0
Requires Python: <4.0,>=3.7.1

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# divik

Python implementation of Divisive iK-means (DiviK) algorithm.

## Tools within this package

- Clustering at your command line with fit-clusters
- Set of algorithm implementations for unsupervised analyses
  - Clustering
    - DiviK - hands-free clustering method with built-in feature selection
    - K-Means with Dunn method for selecting the number of clusters
    - K-Means with GAP index for selecting the number of clusters
    - Modular K-Means implementation with custom distance metrics and initializations
  - Feature extraction
    - PCA with knee-based components selection
    - Locally Adjusted RBF Spectral Embedding
  - Feature selection
    - EXIMS
    - Gaussian Mixture Model based data-driven feature selection
      - High Abundance And Variance Selector - allows you to select highly variant features above noise level, based on GMM-decomposition
    - Outlier based Selector
      - Outlier Abundance And Variance Selector - allows you to select highly variant features above noise level, based on outlier detection
    - Percentage based Selector - allows you to select highly variant features above noise level with your predefined thresholds for each
  - Sampling
    - StratifiedSampler - generates samples of fixed number of rows from given dataset
    - UniformPCASampler - generates samples of random observations within boundaries of an original dataset, and preserving the rotation of the data
    - UniformSampler - generates samples of random observations within boundaries of an original dataset

## Installation

### Docker

The recommended way to use this software is through
[Docker](https://www.docker.com/). This is the most convenient way, if you want
to use `divik` application.

To install latest stable version use:

```bash
docker pull gmrukwa/divik
```

### Python package

Prerequisites for installation of base package:

- Python 3.7 / 3.8 / 3.9
- compiler capable of compiling the native C code and OpenMP support

#### Installation of OpenMP for Ubuntu / Debian

You should have it already installed with GCC compiler, but if somehow
not, try the following:

```bash
sudo apt-get install libgomp1
```

#### Installation of OpenMP for Mac

OpenMP is available as part of LLVM. You may need to install it with conda:

```bash
conda install -c conda-forge "compilers>=1.0.4,!=1.1.0" llvm-openmp
```

#### Installation of dependencied on Mac

You may see messages that some dependencies are invalid for the platform.
It is a [known bug](https://github.com/actions/setup-python/issues/469),
with [a workaround](https://github.com/actions/setup-python/issues/469#issuecomment-1192522949).

Use:

```bash
SYSTEM_VERSION_COMPAT=0 pip install divik
```

#### DiviK Installation

Having prerequisites installed, one can install latest base version of the
package:

```bash
pip install divik
```

If you want to have compatibility with
[`gin-config`](https://github.com/google/gin-config), you can install
necessary extras with:

```bash
pip install divik[gin]
```

**Note:** Remember about `\` before `[` and `]` in `zsh` shell.

You can install all extras with:

```bash
pip install divik[all]
```

## High-Volume Data Considerations

If you are using DiviK to run the analysis that could fail to fit RAM of your
computer, consider disabling the default parallelism and switch to
[dask](https://dask.org/). It's easy to achieve through configuration:

- set all parameters named `n_jobs` to `1`;
- set all parameters named `allow_dask` to `True`.

**Note:** Never set `n_jobs>1` and `allow_dask=True` at the same time, the
computations will freeze due to how `multiprocessing` and `dask` handle
parallelism.

## Known Issues

### Segmentation Fault

It can happen if the he `gamred_native` package (part of `divik` package) was
compiled with different numpy ABI than scikit-learn. This could happen if you
used different set of compilers than the developers of the scikit-learn
package.

In such a case, a handler is defined to display the stack trace. If the trace
comes from `_matlab_legacy.py`, the most probably this is the issue.

To resolve the issue, consider following the installation instructions once
again. The exact versions get updated to avoid the issue.

## Contributing

Contribution guide will be developed soon.

Format the code with:

```bash
isort -m 3 --fgw 3 --tc .
black -t py36 .
```

## References

This software is part of contribution made by [Data Mining Group of Silesian
University of Technology](http://www.zaed.polsl.pl/), rest of which is
published [here](https://github.com/ZAEDPolSl).

- [Mrukwa, G. and Polanska, J., 2020. DiviK: Divisive intelligent K-means for
hands-free unsupervised clustering in biological big data. *arXiv preprint
arXiv:2009.10706.*][1]

[1]: https://arxiv.org/abs/2009.10706