Inheritance metrics feats in unsupervised learning to classify unlabeled datasets and clusters in fault prediction
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ABSTRACT:
SUBMITTER: Aziz S
PROVIDER: S-EPMC8576544 | biostudies-literature |
REPOSITORIES: biostudies-literature
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Project description:Software Fault Prediction (SFP) assists in the identification of faulty classes, and software metrics provide us with a mechanism for this purpose. Besides others, metrics addressing inheritance in Object-Oriented (OO) are important as these measure depth, hierarchy, width, and overriding complexity of the software. In this paper, we evaluated the exclusive use, and viability of inheritance metrics in SFP through experiments. We perform a survey of inheritance metrics whose data sets are publicly available, and collected about 40 data sets having inheritance metrics. We cleaned, and filtered them, and captured nine inheritance metrics. After preprocessing, we divided selected data sets into all possible combinations of inheritance metrics, and then we merged similar metrics. We then formed 67 data sets containing only inheritance metrics that have nominal binary class labels. We performed a model building, and validation for Support Vector Machine(SVM). Results of Cross-Entropy, Accuracy, F-Measure, and AUC advocate viability of inheritance metrics in software fault prediction. Furthermore, ic, noc, and dit metrics are helpful in reduction of error entropy rate over the rest of the 67 feature sets.
| S-EPMC8189025 | biostudies-literature
Project description:Software is a complex entity, and its development needs careful planning and a high amount of time and cost. To assess quality of program, software measures are very helpful. Amongst the existing measures, coupling is an important design measure, which computes the degree of interdependence among the entities of a software system. Higher coupling leads to cognitive complexity and thus a higher probability occurrence of faults. Well in time prediction of fault-prone modules assists in saving time and cost of testing. This paper aims to capture important aspects of coupling and then assess the effectiveness of these aspects in determining fault-prone entities in the software system. We propose two coupling metrics, i.e., Vovel-in and Vovel-out, that capture the level of coupling and the volume of information flow. We empirically evaluate the effectiveness of the Vovel metrics in determining the fault-prone classes using five projects, i.e., Eclipse JDT, Equinox framework, Apache Lucene, Mylyn, and Eclipse PDE UI. Model building is done using univariate logistic regression and later Spearman correlation coefficient is computed with the existing coupling metrics to assess the coverage of unique information. Finally, the least correlated metrics are used for building multivariate logistic regression with and without the use of Vovel metrics, to assess the effectiveness of Vovel metrics. The results show the proposed metrics significantly improve the predicting of fault prone classes. Moreover, the proposed metrics cover a significant amount of unique information which is not covered by the existing well-known coupling metrics, i.e., CBO, RFC, Fan-in, and Fan-out. This paper, empirically evaluates the impact of coupling metrics, and more specifically the importance of level and volume of coupling in software fault prediction. The results advocate the prudent addition of proposed metrics due to their unique information coverage and significant predictive ability.
| S-EPMC8205299 | biostudies-literature
Project description:Pupylation plays a key role in regulating various protein functions as a crucial posttranslational modification of prokaryotes. In order to understand the molecular mechanism of pupylation, it is important to identify pupylation substrates and sites accurately. Several computational methods have been developed to identify pupylation sites because the traditional experimental methods are time-consuming and labor-sensitive. With the existing computational methods, the experimentally annotated pupylation sites are used as the positive training set and the remaining nonannotated lysine residues as the negative training set to build classifiers to predict new pupylation sites from the unknown proteins. However, the remaining nonannotated lysine residues may contain pupylation sites which have not been experimentally validated yet. Unlike previous methods, in this study, the experimentally annotated pupylation sites were used as the positive training set whereas the remaining nonannotated lysine residues were used as the unlabeled training set. A novel method named PUL-PUP was proposed to predict pupylation sites by using positive-unlabeled learning technique. Our experimental results indicated that PUL-PUP outperforms the other methods significantly for the prediction of pupylation sites. As an application, PUL-PUP was also used to predict the most likely pupylation sites in nonannotated lysine sites.
| S-EPMC4992543 | biostudies-literature
Project description:OBJECTIVES:To find and validate generalizable sepsis subtypes using data-driven clustering. DESIGN:We used advanced informatics techniques to pool data from 14 bacterial sepsis transcriptomic datasets from eight different countries (n = 700). SETTING:Retrospective analysis. SUBJECTS:Persons admitted to the hospital with bacterial sepsis. INTERVENTIONS:None. MEASUREMENTS AND MAIN RESULTS:A unified clustering analysis across 14 discovery datasets revealed three subtypes, which, based on functional analysis, we termed "Inflammopathic, Adaptive, and Coagulopathic." We then validated these subtypes in nine independent datasets from five different countries (n = 600). In both discovery and validation data, the Adaptive subtype is associated with a lower clinical severity and lower mortality rate, and the Coagulopathic subtype is associated with higher mortality and clinical coagulopathy. Further, these clusters are statistically associated with clusters derived by others in independent single sepsis cohorts. CONCLUSIONS:The three sepsis subtypes may represent a unifying framework for understanding the molecular heterogeneity of the sepsis syndrome. Further study could potentially enable a precision medicine approach of matching novel immunomodulatory therapies with septic patients most likely to benefit.
| S-EPMC5953807 | biostudies-literature
Project description:BackgroundThe incomplete ground truth of training data of B-cell epitopes is a demanding issue in computational epitope prediction. The challenge is that only a small fraction of the surface residues of an antigen are confirmed as antigenic residues (positive training data); the remaining residues are unlabeled. As some of these uncertain residues can possibly be grouped to form novel but currently unknown epitopes, it is misguided to unanimously classify all the unlabeled residues as negative training data following the traditional supervised learning scheme.ResultsWe propose a positive-unlabeled learning algorithm to address this problem. The key idea is to distinguish between epitope-likely residues and reliable negative residues in unlabeled data. The method has two steps: (1) identify reliable negative residues using a weighted SVM with a high recall; and (2) construct a classification model on the positive residues and the reliable negative residues. Complex-based 10-fold cross-validation was conducted to show that this method outperforms those commonly used predictors DiscoTope 2.0, ElliPro and SEPPA 2.0 in every aspect. We conducted four case studies, in which the approach was tested on antigens of West Nile virus, dihydrofolate reductase, beta-lactamase, and two Ebola antigens whose epitopes are currently unknown. All the results were assessed on a newly-established data set of antigen structures not bound by antibodies, instead of on antibody-bound antigen structures. These bound structures may contain unfair binding information such as bound-state B-factors and protrusion index which could exaggerate the epitope prediction performance. Source codes are available on request.
| S-EPMC4682424 | biostudies-literature
Project description:Protein pupylation is a type of post-translation modification, which plays a crucial role in cellular function of bacterial organisms in prokaryotes. To have a better insight of the mechanisms underlying pupylation an initial, but important, step is to identify pupylation sites. To date, several computational methods have been established for the prediction of pupylation sites which usually artificially design the negative samples using the verified pupylation proteins to train the classifiers. However, if this process is not properly done it can affect the performance of the final predictor dramatically. In this work, different from previous computational methods, we proposed an enhanced positive-unlabeled learning algorithm (EPuL) to the pupylation site prediction problem, which uses only positive and unlabeled samples. Firstly, we separate the training dataset into the positive dataset and the unlabeled dataset which contains the remaining non-annotated lysine residues. Then, the EPuL algorithm is utilized to select the reliably negative initial dataset and then iteratively pick out the non-pupylation sites. The performance of the proposed method was measured with an accuracy of 90.24%, an Area Under Curve (AUC) of 0.93 and an MCC of 0.81 by 10-fold cross-validation. A user-friendly web server for predicting pupylation sites was developed and was freely available at http://59.73.198.144:8080/EPuL.
| S-EPMC6151806 | biostudies-other
Project description:MotivationProtein phosphorylation is a post-translational modification that underlines various aspects of cellular signaling. A key step to reconstructing signaling networks involves identification of the set of all kinases and their substrates. Experimental characterization of kinase substrates is both expensive and time-consuming. To expedite the discovery of novel substrates, computational approaches based on kinase recognition sequence (motifs) from known substrates, protein structure, interaction and co-localization have been proposed. However, rarely do these methods take into account the dynamic responses of signaling cascades measured from in vivo cellular systems. Given that recent advances in mass spectrometry-based technologies make it possible to quantify phosphorylation on a proteome-wide scale, computational approaches that can integrate static features with dynamic phosphoproteome data would greatly facilitate the prediction of biologically relevant kinase-specific substrates.ResultsHere, we propose a positive-unlabeled ensemble learning approach that integrates dynamic phosphoproteomics data with static kinase recognition motifs to predict novel substrates for kinases of interest. We extended a positive-unlabeled learning technique for an ensemble model, which significantly improves prediction sensitivity on novel substrates of kinases while retaining high specificity. We evaluated the performance of the proposed model using simulation studies and subsequently applied it to predict novel substrates of key kinases relevant to insulin signaling. Our analyses show that static sequence motifs and dynamic phosphoproteomics data are complementary and that the proposed integrated model performs better than methods relying only on static information for accurate prediction of kinase-specific substrates.Availability and implementationExecutable GUI tool, source code and documentation are freely available at https://github.com/PengyiYang/KSP-PUEL.Contactpengyi.yang@nih.gov or jothi@mail.nih.govSupplementary informationSupplementary data are available at Bioinformatics online.
| S-EPMC4739180 | biostudies-literature
Project description:The aim of our study was to classify scoliosis compared to to healthy patients using non-invasive surface acquisition via Video-raster-stereography, without prior knowledge of radiographic data. Data acquisitions were made using Rasterstereography; unsupervised learning was adopted for clustering and supervised learning was used for prediction model Support Vector Machine and Deep Network architectures were compared. A M-fold cross validation procedure was performed to evaluate the results. The accuracy and balanced accuracy of the best supervised model were close to 85%. Classification rates by class were measured using the confusion matrix, giving a low percentage of unclassified patients. Rasterstereography has turned out to be a good tool to distinguish subject with scoliosis from healthy patients limiting the exposure to unnecessary radiations.
| S-EPMC8699618 | biostudies-literature
Project description:BackgroundDrug-target interaction (DTI) plays a vital role in drug discovery. Identifying drug-target interactions related to wet-lab experiments are costly, laborious, and time-consuming. Therefore, computational methods to predict drug-target interactions are an essential task in the drug discovery process. Meanwhile, computational methods can reduce search space by proposing potential drugs already validated on wet-lab experiments. Recently, deep learning-based methods in drug-target interaction prediction have gotten more attention. Traditionally, DTI prediction methods' performance heavily depends on additional information, such as protein sequence and molecular structure of the drug, as well as deep supervised learning.ResultsThis paper proposes a method based on deep unsupervised learning for drug-target interaction prediction called AutoDTI++. The proposed method includes three steps. The first step is to pre-process the interaction matrix. Since the interaction matrix is sparse, we solved the sparsity of the interaction matrix with drug fingerprints. Then, in the second step, the AutoDTI approach is introduced. In the third step, we post-preprocess the output of the AutoDTI model.ConclusionsExperimental results have shown that we were able to improve the prediction performance. To this end, the proposed method has been compared to other algorithms using the same reference datasets. The proposed method indicates that the experimental results of running five repetitions of tenfold cross-validation on golden standard datasets (Nuclear Receptors, GPCRs, Ion channels, and Enzymes) achieve good performance with high accuracy.
| S-EPMC8056558 | biostudies-literature
Project description:MicroRNAs (miRNAs) are short non-coding RNAs which bind to mRNAs and regulate their expression. MiRNAs have been found to be associated with initiation and progression of many complex diseases. Investigating miRNAs and their targets can thus help develop new therapies by designing anti-miRNA oligonucleotides. While existing computational approaches can predict miRNA targets, these predictions have low accuracy. In this paper, we propose a two-step approach to refine the results of sequence-based prediction algorithms. The first step, which is based on our previous work, uses an ensemble learning approach that combines multiple existing methods. The second step utilizes support vector machine (SVM) classifiers in one- and two-class modes to infer miRNA-mRNA interactions based on both binding features, as well as network features extracted from gene regulatory network. Experimental results using two real data sets from TCGA indicate that the use of two-class SVM classification significantly improves the precision of miRNA-mRNA prediction.
| S-EPMC7001746 | biostudies-literature