dadapy 0.3.2

Distance-based Analysis of DAta-manifolds in python

DADApy is a Python package for the characterization of manifolds in high-dimensional spaces.

Homepage

For more details and tutorials, visit the homepage at: https://dadapy.readthedocs.io/

Quick Example

import numpy as np
from dadapy.data import Data

# Generate a simple 3D gaussian dataset
X = np.random.normal(0, 1, (1000, 3))

# initialize the "Data" class with the set of coordinates
data = Data(X)

# compute distances up to the 100th nearest neighbor
data.compute_distances(maxk=100)

# compute the intrinsic dimension using 2nn estimator
id, id_error, id_distance = data.compute_id_2NN()

# compute the intrinsic dimension up to the 64th nearest neighbors using Gride
id_list, id_error_list, id_distance_list = data.return_id_scaling_gride(range_max=64)

# compute the density using PAk, a point adaptive kNN estimator
log_den, log_den_error = data.compute_density_PAk()

# find the peaks of the density profile through the ADP algorithm
cluster_assignment = data.compute_clustering_ADP()

# compute the neighborhood overlap with another dataset
X2 = np.random.normal(0, 1, (1000, 5))
overlap_x2 = data.return_data_overlap(X2)

# compute the neighborhood overlap with a set of labels
labels = np.repeat(np.arange(10), 100)
overlap_labels = data.return_label_overlap(labels)

Currently implemented algorithms

• Intrinsic dimension estimators

• Two-NN estimator

  Facco et al., Scientific Reports (2017)

• Gride estimator

  Denti et al., Scientific Reports (2022)

• I3D estimator (for both continuous and discrete spaces)

  Macocco et al., Physical Review Letters (2023)

• Density estimators

• kNN estimator

• k*NN estimator (kNN with an adaptive choice of k)

• PAk estimator

  Rodriguez et al., JCTC (2018)

• point-adaptive mean-shift gradient estimator

  Carli et al., ArXiv (2024)

• BMTI estimator

  Carli et al., ArXiv (2024)

• Density peaks clustering methods

• Density peaks clustering

  Rodriguez and Laio, Science (2014)

• Advanced density peaks clustering

  d’Errico et al., Information Sciences (2021)

• k-peak clustering

  Sormani, Rodriguez and Laio, JCTC (2020)

• Manifold comparison tools

• Neighbourhood overlap

  Doimo et al., NeurIPS (2020)

• Information imbalance

  Glielmo et al., PNAS Nexus (2022)

• Feature selection and weighting tool

• Differentiable Information Imbalance

Installation

The package is compatible with the Python versions 3.8, 3.9, 3.10, 3.11, and 3.12. The methods of the class DiffImbalance are only compatible with Python>=3.9. We currently only support Unix-based systems, including Linux and macOS. For Windows machines, we suggest using the Windows Subsystem for Linux (WSL).

The package requires numpy, scipy, scikit-learn, jax, jaxlib and matplotlib for the visualizations.

The package contains Cython-generated C extensions that are automatically compiled during installation.

The latest release is available through pip:

pip install dadapy

To install the latest development version, clone the source code from GitHub and install it with pip as follows:

pip install git+https://github.com/sissa-data-science/DADApy

Alternatively, if you'd like to modify the implementation of some function locally you can download the repository and install the package with:

git clone https://github.com/sissa-data-science/DADApy.git
cd DADApy
python setup.py build_ext --inplace
pip install .

The methods of the class DiffImbalance can be run on GPU, using a suitable installation of JAX on a GPU platform. The code has been tested using JAX v0.4.30 with CUDA 12, which can be installed with:

pip install --upgrade "jax[cuda12_pip]==0.4.30" -f https://storage.googleapis.com/jax-releases/jax_cuda_releases.html

For more information on the installation of the JAX library on GPUs see the official repository.

Citing DADApy

A description of the package is available here.

Please consider citing it if you found this package useful for your research:

@article{dadapy,
    title = {DADApy: Distance-based analysis of data-manifolds in Python},
    journal = {Patterns},
    pages = {100589},
    year = {2022},
    issn = {2666-3899},
    doi = {https://doi.org/10.1016/j.patter.2022.100589},
    url = {https://www.sciencedirect.com/science/article/pii/S2666389922002070},
    author = {Aldo Glielmo and Iuri Macocco and Diego Doimo and Matteo Carli and Claudio Zeni and Romina Wild and Maria d’Errico and Alex Rodriguez and Alessandro Laio},
    }