Data Imputation for Symbolic Regression with Missing Values: A Comparative Study

Author(s):  
Baligh Al-Helali ◽  
Qi Chen ◽  
Bing Xue ◽  
Mengjie Zhang
2021 ◽  
Author(s):  
◽  
Baligh Al-Helali

<p><b>Symbolic regression is the process of constructing mathematical expressions that best fit given data sets, where a target variable is expressed in terms of input variables. Unlike traditional regression methods, which optimise the parameters of pre-defined models, symbolic regression learns both the model structure and its parameters simultaneously.</b></p> <p>Genetic programming (GP) is a biologically-inspired evolutionary algorithm, that automatically generates computer programs to solve a given task. The flexible representation of GP along with its ``white box" nature makes it a dominant method for symbolic regression. Moreover, GP has been successfully employed for different learning tasks such as feature selection and transfer learning.</p> <p>Data incompleteness is a pervasive problem in symbolic regression, and machine learning in general, especially when dealing with real-world data sets. One common approach to handling data missingness is data imputation. Data imputation is the process of estimating missing values based on existing data. Another approach to deal with incomplete data is to build learning algorithms that directly work with missing values.</p> <p>Although a number of methods have been proposed to tackle the data missingness issue in machine learning, most studies focus on classification tasks. Little attention has been paid to symbolic regression on incomplete data. The existing symbolic regression methods are only applicable when the given data set is complete.</p> <p>The overall goal of the thesis is to improve the performance of symbolic regression on incomplete data by using GP for data imputation, instance selection, feature selection, and transfer learning.</p> <p>This thesis develops an imputation method to handle missing values for symbolic regression. The method integrates the instance-based similarity of the k-nearest neighbour method with the feature-based predictability of GP to estimate the missing values. The results show that the proposed method outperforms existing popular imputation methods.</p> <p>This thesis develops an instance selection method for improving imputation for symbolic regression on incomplete data. The proposed method has the ability to simultaneously build imputation and symbolic regression models such that the performance is improved. The results show that involving instance selection with imputation advances the performance of using the imputation alone.</p> <p>High-dimensionality is a serious data challenge, which is even more difficult on incomplete data. To address this problem in symbolic regression tasks, this thesis develops a feature selection method that can select a good set of features directly from incomplete data. The method not only improves the regression accuracy, but also enhances the efficiency of symbolic regression on high-dimensional incomplete data.</p> <p>Another challenging problem is data shortage. This issue is even more challenging when the data is incomplete. To handle this situation, this thesis develops transfer learning methods to improve symbolic regression in domains with incomplete and limited data. These methods utilise two powerful abilities of GP: feature construction and feature selection. The results show the ability of these methods to achieve positive transfer learning from domains with complete data to different (but related) domains with incomplete data.</p> <p>In summary, the thesis develops a range of approaches to improving the effectiveness and efficiency of symbolic regression on incomplete data by developing a number of GP-based methods. The methods are evaluated using different types of data sets considering various missingness and learning scenarios.</p>


2021 ◽  
Author(s):  
◽  
Baligh Al-Helali

<p><b>Symbolic regression is the process of constructing mathematical expressions that best fit given data sets, where a target variable is expressed in terms of input variables. Unlike traditional regression methods, which optimise the parameters of pre-defined models, symbolic regression learns both the model structure and its parameters simultaneously.</b></p> <p>Genetic programming (GP) is a biologically-inspired evolutionary algorithm, that automatically generates computer programs to solve a given task. The flexible representation of GP along with its ``white box" nature makes it a dominant method for symbolic regression. Moreover, GP has been successfully employed for different learning tasks such as feature selection and transfer learning.</p> <p>Data incompleteness is a pervasive problem in symbolic regression, and machine learning in general, especially when dealing with real-world data sets. One common approach to handling data missingness is data imputation. Data imputation is the process of estimating missing values based on existing data. Another approach to deal with incomplete data is to build learning algorithms that directly work with missing values.</p> <p>Although a number of methods have been proposed to tackle the data missingness issue in machine learning, most studies focus on classification tasks. Little attention has been paid to symbolic regression on incomplete data. The existing symbolic regression methods are only applicable when the given data set is complete.</p> <p>The overall goal of the thesis is to improve the performance of symbolic regression on incomplete data by using GP for data imputation, instance selection, feature selection, and transfer learning.</p> <p>This thesis develops an imputation method to handle missing values for symbolic regression. The method integrates the instance-based similarity of the k-nearest neighbour method with the feature-based predictability of GP to estimate the missing values. The results show that the proposed method outperforms existing popular imputation methods.</p> <p>This thesis develops an instance selection method for improving imputation for symbolic regression on incomplete data. The proposed method has the ability to simultaneously build imputation and symbolic regression models such that the performance is improved. The results show that involving instance selection with imputation advances the performance of using the imputation alone.</p> <p>High-dimensionality is a serious data challenge, which is even more difficult on incomplete data. To address this problem in symbolic regression tasks, this thesis develops a feature selection method that can select a good set of features directly from incomplete data. The method not only improves the regression accuracy, but also enhances the efficiency of symbolic regression on high-dimensional incomplete data.</p> <p>Another challenging problem is data shortage. This issue is even more challenging when the data is incomplete. To handle this situation, this thesis develops transfer learning methods to improve symbolic regression in domains with incomplete and limited data. These methods utilise two powerful abilities of GP: feature construction and feature selection. The results show the ability of these methods to achieve positive transfer learning from domains with complete data to different (but related) domains with incomplete data.</p> <p>In summary, the thesis develops a range of approaches to improving the effectiveness and efficiency of symbolic regression on incomplete data by developing a number of GP-based methods. The methods are evaluated using different types of data sets considering various missingness and learning scenarios.</p>


2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Nishith Kumar ◽  
Md. Aminul Hoque ◽  
Masahiro Sugimoto

AbstractMass spectrometry is a modern and sophisticated high-throughput analytical technique that enables large-scale metabolomic analyses. It yields a high-dimensional large-scale matrix (samples × metabolites) of quantified data that often contain missing cells in the data matrix as well as outliers that originate for several reasons, including technical and biological sources. Although several missing data imputation techniques are described in the literature, all conventional existing techniques only solve the missing value problems. They do not relieve the problems of outliers. Therefore, outliers in the dataset decrease the accuracy of the imputation. We developed a new kernel weight function-based proposed missing data imputation technique that resolves the problems of missing values and outliers. We evaluated the performance of the proposed method and other conventional and recently developed missing imputation techniques using both artificially generated data and experimentally measured data analysis in both the absence and presence of different rates of outliers. Performances based on both artificial data and real metabolomics data indicate the superiority of our proposed kernel weight-based missing data imputation technique to the existing alternatives. For user convenience, an R package of the proposed kernel weight-based missing value imputation technique was developed, which is available at https://github.com/NishithPaul/tWLSA.


Hydrology ◽  
2018 ◽  
Vol 5 (4) ◽  
pp. 63 ◽  
Author(s):  
Benjamin Nelsen ◽  
D. Williams ◽  
Gustavious Williams ◽  
Candace Berrett

Complete and accurate data are necessary for analyzing and understanding trends in time-series datasets; however, many of the available time-series datasets have gaps that affect the analysis, especially in the earth sciences. As most available data have missing values, researchers use various interpolation methods or ad hoc approaches to data imputation. Since the analysis based on inaccurate data can lead to inaccurate conclusions, more accurate data imputation methods can provide accurate analysis. We present a spatial-temporal data imputation method using Empirical Mode Decomposition (EMD) based on spatial correlations. We call this method EMD-spatial data imputation or EMD-SDI. Though this method is applicable to other time-series data sets, here we demonstrate the method using temperature data. The EMD algorithm decomposes data into periodic components called intrinsic mode functions (IMF) and exactly reconstructs the original signal by summing these IMFs. EMD-SDI initially decomposes the data from the target station and other stations in the region into IMFs. EMD-SDI evaluates each IMF from the target station in turn and selects the IMF from other stations in the region with periodic behavior most correlated to target IMF. EMD-SDI then replaces a section of missing data in the target station IMF with the section from the most closely correlated IMF from the regional stations. We found that EMD-SDI selects the IMFs used for reconstruction from different stations throughout the region, not necessarily the station closest in the geographic sense. EMD-SDI accurately filled data gaps from 3 months to 5 years in length in our tests and favorably compares to a simple temporal method. EMD-SDI leverages regional correlation and the fact that different stations can be subject to different periodic behaviors. In addition to data imputation, the EMD-SDI method provides IMFs that can be used to better understand regional correlations and processes.


2021 ◽  
Author(s):  
Panagiotis Anagnostou ◽  
Sotiris Tasoulis ◽  
Aristidis G. Vrahatis ◽  
Spiros Georgakopoulos ◽  
Matthew Prina ◽  
...  

AbstractPreventive healthcare is a crucial pillar of health as it contributes to staying healthy and having immediate treatment when needed. Mining knowledge from longitudinal studies has the potential to significantly contribute to the improvement of preventive healthcare. Unfortunately, data originated from such studies are characterized by high complexity, huge volume and a plethora of missing values. Machine Learning, Data Mining and Data Imputation models are utilized as part of solving the aforementioned challenges, respectively. Towards this direction, we focus on the development of a complete methodology for the ATHLOS (Ageing Trajectories of Health: Longitudinal Opportunities and Synergies) Project - funded by the European Union’s Horizon 2020 Research and Innovation Program, which aims to achieve a better interpretation of the impact of aging on health. The inherent complexity of the provided dataset lie in the fact that the project includes 15 independent European and international longitudinal studies of aging. In this work, we particularly focus on the HealthStatus (HS) score, an index that estimates the human status of health, aiming to examine the effect of various data imputation models to the prediction power of classification and regression models. Our results are promising, indicating the critical importance of data imputation in enhancing preventive medicine’s crucial role.


2020 ◽  
Vol 69 ◽  
pp. 1255-1285
Author(s):  
Ricardo Cardoso Pereira ◽  
Miriam Seoane Santos ◽  
Pedro Pereira Rodrigues ◽  
Pedro Henriques Abreu

Missing data is a problem often found in real-world datasets and it can degrade the performance of most machine learning models. Several deep learning techniques have been used to address this issue, and one of them is the Autoencoder and its Denoising and Variational variants. These models are able to learn a representation of the data with missing values and generate plausible new ones to replace them. This study surveys the use of Autoencoders for the imputation of tabular data and considers 26 works published between 2014 and 2020. The analysis is mainly focused on discussing patterns and recommendations for the architecture, hyperparameters and training settings of the network, while providing a detailed discussion of the results obtained by Autoencoders when compared to other state-of-the-art methods, and of the data contexts where they have been applied. The conclusions include a set of recommendations for the technical settings of the network, and show that Denoising Autoencoders outperform their competitors, particularly the often used statistical methods.


2022 ◽  
Vol 16 (4) ◽  
pp. 1-24
Author(s):  
Kui Yu ◽  
Yajing Yang ◽  
Wei Ding

Causal feature selection aims at learning the Markov blanket (MB) of a class variable for feature selection. The MB of a class variable implies the local causal structure among the class variable and its MB and all other features are probabilistically independent of the class variable conditioning on its MB, this enables causal feature selection to identify potential causal features for feature selection for building robust and physically meaningful prediction models. Missing data, ubiquitous in many real-world applications, remain an open research problem in causal feature selection due to its technical complexity. In this article, we discuss a novel multiple imputation MB (MimMB) framework for causal feature selection with missing data. MimMB integrates Data Imputation with MB Learning in a unified framework to enable the two key components to engage with each other. MB Learning enables Data Imputation in a potentially causal feature space for achieving accurate data imputation, while accurate Data Imputation helps MB Learning identify a reliable MB of the class variable in turn. Then, we further design an enhanced kNN estimator for imputing missing values and instantiate the MimMB. In our comprehensively experimental evaluation, our new approach can effectively learn the MB of a given variable in a Bayesian network and outperforms other rival algorithms using synthetic and real-world datasets.


2020 ◽  
Vol 7 (1) ◽  
Author(s):  
Shahidul Islam Khan ◽  
Abu Sayed Md Latiful Hoque

Abstract In data analytics, missing data is a factor that degrades performance. Incorrect imputation of missing values could lead to a wrong prediction. In this era of big data, when a massive volume of data is generated in every second, and utilization of these data is a major concern to the stakeholders, efficiently handling missing values becomes more important. In this paper, we have proposed a new technique for missing data imputation, which is a hybrid approach of single and multiple imputation techniques. We have proposed an extension of popular Multivariate Imputation by Chained Equation (MICE) algorithm in two variations to impute categorical and numeric data. We have also implemented twelve existing algorithms to impute binary, ordinal, and numeric missing values. We have collected sixty-five thousand real health records from different hospitals and diagnostic centers of Bangladesh, maintaining the privacy of data. We have also collected three public datasets from the UCI Machine Learning Repository, ETH Zurich, and Kaggle. We have compared the performance of our proposed algorithms with existing algorithms using these datasets. Experimental results show that our proposed algorithm achieves 20% higher F-measure for binary data imputation and 11% less error for numeric data imputations than its competitors with similar execution time.


2021 ◽  
Author(s):  
Nwamaka Okafor ◽  
Declan Delaney

IoT sensors are becoming increasingly important supplement to traditional monitoring systems, particularly for in-situ based monitoring. However, data collection based on IoT sensors are often plagued with missing values usually occurring as a result of sensor faults, network failures, drifts and other operational issues. <br>


Sign in / Sign up

Export Citation Format

Share Document