CleanML: A Study for Evaluating the Impact of Data Cleaning on ML Classification Tasks

Data quality affects machine learning (ML) model performances, and data scientists spend considerable amount of time on data cleaning before model training. However, to date, there does not exist a rigorous study on how exactly cleaning affects ML -- ML community usually focuses on developing ML algorithms that are robust to some particular noise types of certain distributions, while database (DB) community has been mostly studying the problem of data cleaning alone without considering how data is consumed by downstream ML analytics. We propose a CleanML study that systematically investigates the impact of data cleaning on ML classification tasks. The open-source and extensible CleanML study currently includes 14 real-world datasets with real errors, five common error types, seven different ML models, and multiple cleaning algorithms for each error type (including both commonly used algorithms in practice as well as state-of-the-art solutions in academic literature). We control the randomness in ML experiments using statistical hypothesis testing, and we also control false discovery rate in our experiments using the Benjamini-Yekutieli (BY) procedure. We analyze the results in a systematic way to derive many interesting and nontrivial observations. We also put forward multiple research directions for researchers.Comment: published in ICDE 202

Machine Learning and Integrative Analysis of Biomedical Big Data.

Recent developments in high-throughput technologies have accelerated the accumulation of massive amounts of omics data from multiple sources: genome, epigenome, transcriptome, proteome, metabolome, etc. Traditionally, data from each source (e.g., genome) is analyzed in isolation using statistical and machine learning (ML) methods. Integrative analysis of multi-omics and clinical data is key to new biomedical discoveries and advancements in precision medicine. However, data integration poses new computational challenges as well as exacerbates the ones associated with single-omics studies. Specialized computational approaches are required to effectively and efficiently perform integrative analysis of biomedical data acquired from diverse modalities. In this review, we discuss state-of-the-art ML-based approaches for tackling five specific computational challenges associated with integrative analysis: curse of dimensionality, data heterogeneity, missing data, class imbalance and scalability issues

On the role of pre and post-processing in environmental data mining

The quality of discovered knowledge is highly depending on data quality. Unfortunately real data use to contain noise, uncertainty, errors, redundancies or even irrelevant information. The more complex is the reality to be analyzed, the higher the risk of getting low quality data. Knowledge Discovery from Databases (KDD) offers a global framework to prepare data in the right form to perform correct analyses. On the other hand, the quality of decisions taken upon KDD results, depend not only on the quality of the results themselves, but on the capacity of the system to communicate those results in an understandable form. Environmental systems are particularly complex and environmental users particularly require clarity in their results. In this paper some details about how this can be achieved are provided. The role of the pre and post processing in the whole process of Knowledge Discovery in environmental systems is discussed

Multiple Imputation Ensembles (MIE) for dealing with missing data

Missing data is a significant issue in many real-world datasets, yet there are no robust methods for dealing with it appropriately. In this paper, we propose a robust approach to dealing with missing data in classification problems: Multiple Imputation Ensembles (MIE). Our method integrates two approaches: multiple imputation and ensemble methods and compares two types of ensembles: bagging and stacking. We also propose a robust experimental set-up using 20 benchmark datasets from the UCI machine learning repository. For each dataset, we introduce increasing amounts of data Missing Completely at Random. Firstly, we use a number of single/multiple imputation methods to recover the missing values and then ensemble a number of different classifiers built on the imputed data. We assess the quality of the imputation by using dissimilarity measures. We also evaluate the MIE performance by comparing classification accuracy on the complete and imputed data. Furthermore, we use the accuracy of simple imputation as a benchmark for comparison. We find that our proposed approach combining multiple imputation with ensemble techniques outperform others, particularly as missing data increases

The National Transport Data Framework

Report by Professor Peter Landshoff (Cambridge University) and Professor John Polak (Imperial College London) on a project for the Department for Transport. emails: [email protected] [email protected] NTDF is designed to be a resource for data owners to deposit descriptions into a central catalogue, so that people can search for data and find data and understand their characteristics. The value of this is to individuals, to commercial organizations, and to public bodies. For example, services that provide better information to travellers will help to make their journey less stressful and persuade them to make more use of public transport. Transport operators need very diverse information to help them plan developments to their services: demographic, geographical, economic etc. And policy makers need a similar range of information to help them decide how to divide their budget and afterwards to evaluate how valuable it has been.This work was supported by the Department for Transport (DfT)

How to Address the Data Quality Issues in Regression Models: A Guided Process for Data Cleaning

Today, data availability has gone from scarce to superabundant. Technologies like IoT, trends in social media and the capabilities of smart-phones are producing and digitizing lots of data that was previously unavailable. This massive increase of data creates opportunities to gain new business models, but also demands new techniques and methods of data quality in knowledge discovery, especially when the data comes from different sources (e.g., sensors, social networks, cameras, etc.). The data quality process of the data set proposes conclusions about the information they contain. This is increasingly done with the aid of data cleaning approaches. Therefore, guaranteeing a high data quality is considered as the primary goal of the data scientist. In this paper, we propose a process for data cleaning in regression models (DC-RM). The proposed data cleaning process is evaluated through a real datasets coming from the UCI Repository of Machine Learning Databases. With the aim of assessing the data cleaning process, the dataset that is cleaned by DC-RM was used to train the same regression models proposed by the authors of UCI datasets. The results achieved by the trained models with the dataset produced by DC-RM are better than or equal to that presented by the datasets' authors.This work has been also supported by the Spanish Ministry of Economy, Industry and Competitiveness (Projects TRA2015-63708-R and TRA2016-78886-C3-1-R)

Multiple Imputation Using Gaussian Copulas

Missing observations are pervasive throughout empirical research, especially in the social sciences. Despite multiple approaches to dealing adequately with missing data, many scholars still fail to address this vital issue. In this paper, we present a simple-to-use method for generating multiple imputations using a Gaussian copula. The Gaussian copula for multiple imputation (Hoff, 2007) allows scholars to attain estimation results that have good coverage and small bias. The use of copulas to model the dependence among variables will enable researchers to construct valid joint distributions of the data, even without knowledge of the actual underlying marginal distributions. Multiple imputations are then generated by drawing observations from the resulting posterior joint distribution and replacing the missing values. Using simulated and observational data from published social science research, we compare imputation via Gaussian copulas with two other widely used imputation methods: MICE and Amelia II. Our results suggest that the Gaussian copula approach has a slightly smaller bias, higher coverage rates, and narrower confidence intervals compared to the other methods. This is especially true when the variables with missing data are not normally distributed. These results, combined with theoretical guarantees and ease-of-use suggest that the approach examined provides an attractive alternative for applied researchers undertaking multiple imputations