Imputation Python Packages

tsdb

a Python toolbox loads 173 public time series datasets for machine/deep learning with a single line of code. Datasets from multiple domains including healthcare, financial, power, traffic, weather, and etc.

pypots

A Python toolkit/library for reality-centric machine/deep learning & data mining on partially-observed time series, with 50+ SOTA neural network models for scientific analysis tasks (imputation, classification, clustering, forecasting, anomaly detection, cleaning) on incomplete industrial irregularly-sampled multivariate TS with NaN missing values

pygrinder

PyGrinder: a Python toolkit for grinding data beans into the incomplete for real-world data simulation by introducing missing values with different missingness patterns, including MCAR (complete at random), MAR (at random), MNAR (not at random), sub sequence missing, and block missing

knnimpute

Python implementations of kNN imputation

handyspark

HandySpark - bringing pandas-like capabilities to Spark dataframes

geoanalytics

This software is being developed at the University of Aizu, Aizu-Wakamatsu, Fukushima, Japan

momentfm

MOMENT: A Family of Open Time-series Foundation Models, ICML'24

isotree

(Python, R, C/C++) Isolation Forest and variations such as SCiForest and EIF, with some additions (outlier detection + similarity + NA imputation)

datawig

Imputation for tables with missing values

univi

UniVI is a scalable multi-modal VAE toolkit for aligning heterogeneous single-cell datasets into a shared latent space—supporting unimodal, dual-modal, and tri-modal (and beyond) integration. It can additionally be used for cross-modal imputation, data generation of biologically-relevant synthetic samples, data denoising, and structured evaluation.

pi-metaboqc

A comprehensive LC-MS metabolomics quality-control and preprocessing package that provides an object-oriented pipeline for dataset construction, sample and feature filtering, signal drift and batch-effect correction, missing-value imputation, normalization, quality assessment, and report generation.

datafiller

Data imputation

imputegap

ImputeGAP is a comprehensive Python library for imputation of missing values in time series data. It implements user-friendly APIs to easily visualize, analyze, and repair incomplete time series datasets.

impyute

Data imputations library to preprocess datasets with missing data

simpute

Python package that imputes missing values column-by-column using machine-learning and adaptive profiling.

disc

A highly scalable and accurate inference of gene expression and structure for single-cell transcriptomes using semi-supervised deep learning.

rego

Automatic Time Series Forecasting and Missing Values Imputation

did-imputation

Borusyak-Jaravel-Spiess (2024) difference-in-differences imputation estimator with event-study plots for Python.

hesseflux

hesseflux: a Python library to process and post-process Eddy covariance data

pycorruptor

A Python Toolbox for Data Corruption

ae-imputer

a python package used for missing data imputation via autoencoders

missingdata

missing data visualization and imputation

puredatalib

Automatic data cleaning and silent incompatibility detection for Python

data-cleaning

Data Cleaning is a python package for data preprocessing. This cleans the CSV file and returns the cleaned data frame. It does the work of imputation, removing duplicates, replacing special characters, and many more.