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

momentfm

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

geoanalytics

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

isotree

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

impyute

Cross-sectional and time-series data imputation algorithms

imputegap

A Library of Imputation Techniques for Time Series Data

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.

datawig

Imputation of missing values in tables.

disc

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

datafiller

Data imputation

hesseflux

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

rego

Automatic Time Series Forecasting and Missing Values Imputation

ae-imputer

A python package used for missing data imputation via autoencoders.

pycorruptor

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

imputena

Package that allows both automated and customized treatment of missing values in datasets using Python.

ml-impute

A package for synthetic data generation for imputation using single and multiple imputation methods.

missingdata

missing data handing: visualize and impute

sknnr

scikit-learn compatible estimators for various kNN imputation methods

utrees

Tabular data imputation and generation, with flexible modeling of quantitative features via hierarchical binning (TMLR, 2025)

phenoqc

PhenoQC is a lightweight, efficient, and user-friendly toolkit designed to perform comprehensive quality control (QC) on phenotypic datasets. It ensures that data adheres to standardized formats, maintains consistency, and is harmonized with recognized ontologies.