MissForest - nonparametric missing value imputation for mixed-type data

Modern data acquisition based on high-throughput technology is often facing the problem of missing data. Algorithms commonly used in the analysis of such large-scale data often depend on a complete set. Missing value imputation offers a solution to this problem. However, the majority of available imputation methods are restricted to one type of variable only: continuous or categorical. For mixed-type data the different types are usually handled separately. Therefore, these methods ignore possible relations between variable types. We propose a nonparametric method which can cope with different types of variables simultaneously. We compare several state of the art methods for the imputation of missing values. We propose and evaluate an iterative imputation method (missForest) based on a random forest. By averaging over many unpruned classification or regression trees random forest intrinsically constitutes a multiple imputation scheme. Using the built-in out-of-bag error estimates of random forest we are able to estimate the imputation error without the need of a test set. Evaluation is performed on multiple data sets coming from a diverse selection of biological fields with artificially introduced missing values ranging from 10% to 30%. We show that missForest can successfully handle missing values, particularly in data sets including different types of variables. In our comparative study missForest outperforms other methods of imputation especially in data settings where complex interactions and nonlinear relations are suspected. The out-of-bag imputation error estimates of missForest prove to be adequate in all settings. Additionally, missForest exhibits attractive computational efficiency and can cope with high-dimensional data.Comment: Submitted to Oxford Journal's Bioinformatics on 3rd of May 201

A systematic review of data quality issues in knowledge discovery tasks

Hay un gran crecimiento en el volumen de datos porque las organizaciones capturan permanentemente la cantidad colectiva de datos para lograr un mejor proceso de toma de decisiones. El desafío mas fundamental es la exploración de los grandes volúmenes de datos y la extracción de conocimiento útil para futuras acciones por medio de tareas para el descubrimiento del conocimiento; sin embargo, muchos datos presentan mala calidad. Presentamos una revisión sistemática de los asuntos de calidad de datos en las áreas del descubrimiento de conocimiento y un estudio de caso aplicado a la enfermedad agrícola conocida como la roya del café.Large volume of data is growing because the organizations are continuously capturing the collective amount of data for better decision-making process. The most fundamental challenge is to explore the large volumes of data and extract useful knowledge for future actions through knowledge discovery tasks, nevertheless many data has poor quality. We presented a systematic review of the data quality issues in knowledge discovery tasks and a case study applied to agricultural disease named coffee rust

Can k-NN imputation improve the performance of C4.5 with small software project data sets? A comparative evaluation

Missing data is a widespread problem that can affect the ability to use data to construct effective prediction systems. We investigate a common machine learning technique that can tolerate missing values, namely C4.5, to predict cost using six real world software project databases. We analyze the predictive performance after using the k-NN missing data imputation technique to see if it is better to tolerate missing data or to try to impute missing values and then apply the C4.5 algorithm. For the investigation, we simulated three missingness mechanisms, three missing data patterns, and five missing data percentages. We found that the k-NN imputation can improve the prediction accuracy of C4.5. At the same time, both C4.5 and k-NN are little affected by the missingness mechanism, but that the missing data pattern and the missing data percentage have a strong negative impact upon prediction (or imputation) accuracy particularly if the missing data percentage exceeds 40%

A Stochastic Method for Estimating Imputation Accuracy

This thesis describes a novel imputation evaluation method and shows how this method can be used to estimate the accuracy of the imputed values generated by any imputation technique. This is achieved by using an iterative stochastic procedure to repeatedly measure how accurately a set of randomly deleted values are “put back” by the imputation process. The proposed approach builds on the ideas underpinning uncertainty estimation methods, but differs from them in that it estimates the accuracy of the imputed values, rather than estimating the uncertainty inherent within those values. In addition, a procedure for comparing the accuracy of the imputed values in different data segments has been built into the proposed method, but uncertainty estimation methods do not include such procedures. This proposed method is implemented as a software application. This application is used to estimate the accuracy of the imputed values generated by the expectation-maximisation (EM) and nearest neighbour (NN) imputation algorithms. These algorithms are implemented alongside the method, with particular attention being paid to the use of implementation techniques which decrease algorithm execution times, so as to support the computationally intensive nature of the method. A novel NN imputation algorithm is developed and the experimental evaluation of this algorithm shows that it can be used to decrease the execution time of the NN imputation process for both simulated and real datasets. The execution time of the new NN algorithm was found to steadily decrease as the proportion of missing values in the dataset was increased. The method is experimentally evaluated and the results show that the proposed approach produces reliable and valid estimates of imputation accuracy when it is used to compare the accuracy of the imputed values generated by the EM and NN imputation algorithms. Finally, a case study is presented which shows how the method has been applied in practice, including a detailed description of the experiments that were performed in order to find the most accurate methods of imputing the missing values in the case study dataset. A comprehensive set of experimental results is given, the associated imputation accuracy statistics are analysed and the feasibility of imputing the missing case study data is assessed

Ensemble missing data techniques for software effort prediction

Constructing an accurate effort prediction model is a challenge in software engineering. The development and validation of models that are used for prediction tasks require good quality data. Unfortunately, software engineering datasets tend to suffer from the incompleteness which could result to inaccurate decision making and project management and implementation. Recently, the use of machine learning algorithms has proven to be of great practical value in solving a variety of software engineering problems including software prediction, including the use of ensemble (combining) classifiers. Research indicates that ensemble individual classifiers lead to a significant improvement in classification performance by having them vote for the most popular class. This paper proposes a method for improving software effort prediction accuracy produced by a decision tree learning algorithm and by generating the ensemble using two imputation methods as elements. Benchmarking results on ten industrial datasets show that the proposed ensemble strategy has the potential to improve prediction accuracy compared to an individual imputation method, especially if multiple imputation is a component of the ensemble

Multilevel Weighted Support Vector Machine for Classification on Healthcare Data with Missing Values

This work is motivated by the needs of predictive analytics on healthcare data as represented by Electronic Medical Records. Such data is invariably problematic: noisy, with missing entries, with imbalance in classes of interests, leading to serious bias in predictive modeling. Since standard data mining methods often produce poor performance measures, we argue for development of specialized techniques of data-preprocessing and classification. In this paper, we propose a new method to simultaneously classify large datasets and reduce the effects of missing values. It is based on a multilevel framework of the cost-sensitive SVM and the expected maximization imputation method for missing values, which relies on iterated regression analyses. We compare classification results of multilevel SVM-based algorithms on public benchmark datasets with imbalanced classes and missing values as well as real data in health applications, and show that our multilevel SVM-based method produces fast, and more accurate and robust classification results.Comment: arXiv admin note: substantial text overlap with arXiv:1503.0625