DenseClus is a Python module for clustering mixed type data using UMAP and HDBSCAN

Related tags

Data Analysispythonclusteringembeddingmachinelearning-python
Overview

Amazon DenseClus

build PyPI version PyPI - Python Version PyPI - Wheel PyPI - License Code style: black Github Super-Linter

DenseClus is a Python module for clustering mixed type data using UMAP and HDBSCAN. Allowing for both categorical and numerical data, DenseClus makes it possible to incorporate all features in clustering.

Installation

python3 -m pip install Amazon-DenseClus

Usage

DenseClus requires a Panda's dataframe as input with both numerical and categorical columns. All preprocessing and extraction are done under the hood, just call fit and then retrieve the clusters!

from denseclus import DenseClus

clf = DenseClus(
    umap_combine_method="intersection_union_mapper",
)
clf.fit(df)

print(clf.score())

Examples

A hands-on example with an overview of how to use is currently available in the form of a Jupyter Notebook.

References

@article{mcinnes2018umap-software,
  title={UMAP: Uniform Manifold Approximation and Projection},
  author={McInnes, Leland and Healy, John and Saul, Nathaniel and Grossberger, Lukas},
  journal={The Journal of Open Source Software},
  volume={3},
  number={29},
  pages={861},
  year={2018}
}
@article{mcinnes2017hdbscan,
  title={hdbscan: Hierarchical density based clustering},
  author={McInnes, Leland and Healy, John and Astels, Steve},
  journal={The Journal of Open Source Software},
  volume={2},
  number={11},
  pages={205},
  year={2017}
}
Owner
Amazon Web Services - Labs
AWS Labs
Amazon Web Services - Labs
GitHub Repository https://aws.amazon.com/blogs/opensource/introducing-denseclus-an-open-source-clustering-package-for-mixed-type-data/
Falcon: Interactive Visual Analysis for Big Data

Falcon: Interactive Visual Analysis for Big Data Crossfilter millions of records without latencies. This project is work in progress and not documente

Vega 803 Dec 27, 2022
The official pytorch implementation of ViTAE: Vision Transformer Advanced by Exploring Intrinsic Inductive Bias

ViTAE: Vision Transformer Advanced by Exploring Intrinsic Inductive Bias Introduction | Updates | Usage | Results&Pretrained Models | Statement | Intr

104 Nov 27, 2022
A Python 3 library making time series data mining tasks, utilizing matrix profile algorithms

MatrixProfile MatrixProfile is a Python 3 library, brought to you by the Matrix Profile Foundation, for mining time series data. The Matrix Profile is

Matrix Profile Foundation 302 Dec 29, 2022
This project is the implementation template for HW 0 and HW 1 for both the programming and non-programming tracks

This project is the implementation template for HW 0 and HW 1 for both the programming and non-programming tracks

Donald F. Ferguson 4 Mar 06, 2022
Python Package for DataHerb: create, search, and load datasets.

The Python Package for DataHerb A DataHerb Core Service to Create and Load Datasets.

DataHerb 4 Feb 11, 2022
Toolchest provides APIs for scientific and bioinformatic data analysis.

Toolchest Python Client Toolchest provides APIs for scientific and bioinformatic data analysis. It allows you to abstract away the costliness of runni

Toolchest 11 Jun 30, 2022
ETL flow framework based on Yaml configs in Python

ETL framework based on Yaml configs in Python A light framework for creating data streams. Setting up streams through configuration in the Yaml file.

Павел Максимов 18 Jul 06, 2022
Validated, scalable, community developed variant calling, RNA-seq and small RNA analysis

Validated, scalable, community developed variant calling, RNA-seq and small RNA analysis. You write a high level configuration file specifying your in

Blue Collar Bioinformatics 917 Jan 03, 2023
PyChemia, Python Framework for Materials Discovery and Design

PyChemia, Python Framework for Materials Discovery and Design PyChemia is an open-source Python Library for materials structural search. The purpose o

Materials Discovery Group 61 Oct 02, 2022
A meta plugin for processing timelapse data timepoint by timepoint in napari

napari-time-slicer A meta plugin for processing timelapse data timepoint by timepoint. It enables a list of napari plugins to process 2D+t or 3D+t dat

Robert Haase 2 Oct 13, 2022
Efficient matrix representations for working with tabular data

Efficient matrix representations for working with tabular data

QuantCo 70 Dec 14, 2022
Hue Editor: Open source SQL Query Assistant for Databases/Warehouses

Hue Editor: Open source SQL Query Assistant for Databases/Warehouses

Cloudera 759 Jan 07, 2023
apricot implements submodular optimization for the purpose of selecting subsets of massive data sets to train machine learning models quickly.

Please consider citing the manuscript if you use apricot in your academic work! You can find more thorough documentation here. apricot implements subm

Jacob Schreiber 457 Dec 20, 2022
An Aspiring Drop-In Replacement for NumPy at Scale

Legate NumPy is a Legate library that aims to provide a distributed and accelerated drop-in replacement for the NumPy API on top of the Legion runtime. Using Legate NumPy you do things like run the f

Legate 502 Jan 03, 2023
PostQF is a user-friendly Postfix queue data filter which operates on data produced by postqueue -j.

PostQF Copyright © 2022 Ralph Seichter PostQF is a user-friendly Postfix queue data filter which operates on data produced by postqueue -j. See the ma

Ralph Seichter 11 Nov 24, 2022
AWS Glue ETL Code Samples

AWS Glue ETL Code Samples This repository has samples that demonstrate various aspects of the new AWS Glue service, as well as various AWS Glue utilit

AWS Samples 1.2k Jan 03, 2023
small package with utility functions for analyzing (fly) calcium imaging data

fly2p Tools for analyzing two-photon (2p) imaging data collected with Vidrio Scanimage software and micromanger. Loading scanimage data relies on scan

Hannah Haberkern 3 Dec 14, 2022
Implementation in Python of the reliability measures such as Omega.

reliabiliPy Summary Simple implementation in Python of the [reliability](https://en.wikipedia.org/wiki/Reliability_(statistics) measures for surveys:

Rafael Valero Fernández 2 Apr 27, 2022
Full automated data pipeline using docker images

Create postgres tables from CSV files This first section is only relate to creating tables from CSV files using postgres container alone. Just one of

1 Nov 21, 2021
AptaMat is a simple script which aims to measure differences between DNA or RNA secondary structures.

AptaMAT Purpose AptaMat is a simple script which aims to measure differences between DNA or RNA secondary structures. The method is based on the compa

GEC UTC 3 Nov 03, 2022