6,983 research outputs found
Cross-validation based K nearest neighbor imputation for software quality datasets: An empirical study
Being able to predict software quality is essential, but also it pose significant challenges in software engineering. Historical software project datasets are often being utilized together with various machine learning algorithms for fault-proneness classification. Unfortunately, the missing values in datasets have negative impacts on the estimation accuracy and therefore, could lead to inconsistent results. As a method handling missing data, K nearest neighbor (KNN) imputation gradually gains acceptance in empirical studies by its exemplary performance and simplicity. To date, researchers still call for optimized parameter setting for KNN imputation to further improve its performance. In the work, we develop a novel incomplete-instance based KNN imputation technique, which utilizes a cross-validation scheme to optimize the parameters for each missing value. An experimental assessment is conducted on eight quality datasets under various missingness scenarios. The study also compared the proposed imputation approach with mean imputation and other three KNN imputation approaches. The results show that our proposed approach is superior to others in general. The relatively optimal fixed parameter settings for KNN imputation for software quality data is also determined. It is observed that the classification accuracy is improved or at least maintained by using our approach for missing data imputation
Adaptive imputation of missing values for incomplete pattern classification
In classification of incomplete pattern, the missing values can either play a
crucial role in the class determination, or have only little influence (or
eventually none) on the classification results according to the context. We
propose a credal classification method for incomplete pattern with adaptive
imputation of missing values based on belief function theory. At first, we try
to classify the object (incomplete pattern) based only on the available
attribute values. As underlying principle, we assume that the missing
information is not crucial for the classification if a specific class for the
object can be found using only the available information. In this case, the
object is committed to this particular class. However, if the object cannot be
classified without ambiguity, it means that the missing values play a main role
for achieving an accurate classification. In this case, the missing values will
be imputed based on the K-nearest neighbor (K-NN) and self-organizing map (SOM)
techniques, and the edited pattern with the imputation is then classified. The
(original or edited) pattern is respectively classified according to each
training class, and the classification results represented by basic belief
assignments are fused with proper combination rules for making the credal
classification. The object is allowed to belong with different masses of belief
to the specific classes and meta-classes (which are particular disjunctions of
several single classes). The credal classification captures well the
uncertainty and imprecision of classification, and reduces effectively the rate
of misclassifications thanks to the introduction of meta-classes. The
effectiveness of the proposed method with respect to other classical methods is
demonstrated based on several experiments using artificial and real data sets
Machine learning applied to enzyme turnover numbers reveals protein structural correlates and improves metabolic models.
Knowing the catalytic turnover numbers of enzymes is essential for understanding the growth rate, proteome composition, and physiology of organisms, but experimental data on enzyme turnover numbers is sparse and noisy. Here, we demonstrate that machine learning can successfully predict catalytic turnover numbers in Escherichia coli based on integrated data on enzyme biochemistry, protein structure, and network context. We identify a diverse set of features that are consistently predictive for both in vivo and in vitro enzyme turnover rates, revealing novel protein structural correlates of catalytic turnover. We use our predictions to parameterize two mechanistic genome-scale modelling frameworks for proteome-limited metabolism, leading to significantly higher accuracy in the prediction of quantitative proteome data than previous approaches. The presented machine learning models thus provide a valuable tool for understanding metabolism and the proteome at the genome scale, and elucidate structural, biochemical, and network properties that underlie enzyme kinetics
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