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Purpose: In China, individuals with substance use disorders (SUD) face severe stigma, but reliable stigma assessment tool is lacking. Therefore, this study aimed to validate the Chinese version of the Substance Use Stigma Mechanism Scale (SU-SMS-C) and set its cut-off point., Methods: We recruited 1005 individuals with SUDs from Chinese rehabilitation centers. These participants completed a battery of questionnaires that included the SU-SMS-C, The Multidimensional Scale of Perceived Social Support (MSPSS), Center for Epidemiologic Studies Depression Scale (CES-D), General Self-Efficacy Scale (GSES), and Perceived Devaluation and Discrimination (PDD). Confirmatory factor analysis was used to assess the construct validity of the scale. Additionally, the Naive Bayes classifier was used to establish the cut-off point for the SU-SMS-C. We additionally explored the correlation between patient demographic characteristics and stigma., Results: A confirmatory factor analysis was utilized, revealing a second-order five-factor model. Based on the Naive Bayes classifier, the area under the receiver operating characteristic (AUCROC) of 0.746, the cut-off point for the SU-SMS-C was established at 44.5. The prevalence of stigma observed in the study population was 49.05%. Significant disparities were observed in the distribution of stigma across genders, with males experiencing more pronounced stigma than females. Moreover, patients consuming different primary substances reported diverse levels of stigma. Notably, those primarily using heroin endured a higher degree of stigma than users of other substances., Conclusion: The study is the first to identify a cut-off point for the SU-SMS-C by Naive Bayes classifier, bridging a major gap in stigma measurement research. SU-SMS-C may help treat and manage SUDs by reducing stigma., (© 2024. The Author(s), under exclusive licence to Springer-Verlag GmbH Germany.)

Aim: To explore biomarkers that can predict the response of type 2 diabetes (T2D) patients to metformin at an early stage to provide better treatment for T2D., Methods: T2D patients with (responders) or without response (non-responders) to metformin were recruited, and their serum samples were used for metabolomic analysis to identify candidate biomarkers. Moreover, the efficacy of metformin was verified by insulin-resistant mice, and the candidate biomarkers were verified to determine the biomarkers. Five different machine learning methods were used to construct the integrated biomarker profiling (IBP) with the biomarkers to predict the response of T2D patients to metformin., Results: A total of 73 responders and 63 non-responders were recruited, and 88 differential metabolites were identified in the serum samples. After being verified in mice, 19 of the 88 were considered as candidate biomarkers. Next, after metformin regulation, nine candidate biomarkers were confirmed as the biomarkers. After comparing five machine learning models, the nine biomarkers were constructed into the IBP for predicting the response of T2D patients to metformin based on the Naïve Bayes classifier, which was verified with an accuracy of 89.70%., Conclusions: The IBP composed of nine biomarkers can be used to predict the response of T2D patients to metformin, enabling clinicians to start a combined medication strategy as soon as possible if T2D patients do not respond to metformin., (© 2024 John Wiley & Sons Ltd.)

Background: Self-grooming behavior in rodents serves as a valuable behavioral index for investigating stereotyped and perseverative responses. Most current grooming analyses rely on video observation, which lacks standardization, efficiency, and quantitative information about force. To address these limitations, we developed an automated paradigm to analyze grooming using a force-plate actometer., New Method: Grooming behavior is quantified by calculating ratios of relevant movement power spectral bands. These ratios are input into a naïve Bayes classifier, trained with manual video observations. The effectiveness of this method was tested using CIN-d mice, an animal model developed through early-life depletion of striatal cholinergic interneurons (CIN-d) and featuring prolonged grooming responses to acute stressors. Behavioral monitoring was simultaneously conducted on the force-place actometer and by video recording., Results: The naïve Bayes approach achieved 93.7% accurate classification and an area under the receiver operating characteristic curve of 0.894. We confirmed that male CIN-d mice displayed significantly longer grooming durations than controls. However, this elevation was not correlated with increases in grooming force. Notably, the dopaminergic antagonist haloperidol reduced grooming force and duration., Comparison With Existing Methods: In contrast to observation-based approaches, our method affords rapid, unbiased, and automated assessment of grooming duration, frequency, and force., Conclusions: Our novel approach enables fast and accurate automated detection of grooming behaviors. This method holds promise for high-throughput assessments of grooming stereotypies in animal models of neuropsychiatric disorders., Competing Interests: Declaration of Competing Interest The authors declare the following financial interests/personal relationships which may be considered as potential competing interests: Marco Bortolato reports financial support was provided by National Institutes of Health. Christopher Pittenger reports financial support was provided by National Institutes of Health. Stefan Pulst reports financial support was provided by National Institutes of Health., (Copyright © 2023 The Authors. Published by Elsevier B.V. All rights reserved.)

Introduction: A common task in the analysis of microbial communities involves assigning taxonomic labels to the sequences derived from organisms found in the communities. Frequently, such labels are assigned using machine learning algorithms that are trained to recognize individual taxonomic groups based on training data sets that comprise sequences with known taxonomic labels. Ideally, the training data should rely on labels that are experimentally verified-formal taxonomic labels require knowledge of physical and biochemical properties of organisms that cannot be directly inferred from sequence alone. However, the labels associated with sequences in biological databases are most commonly computational predictions which themselves may rely on computationally-generated data-a process commonly referred to as "transitive annotation.", Methods: In this manuscript we explore the implications of training a machine learning classifier (the Ribosomal Database Project's Bayesian classifier in our case) on data that itself has been computationally generated. We generate new training examples based on 16S rRNA data from a metagenomic experiment, and evaluate the extent to which the taxonomic labels predicted by the classifier change after re-training., Results: We demonstrate that even a few computationally-generated training data points can significantly skew the output of the classifier to the point where entire regions of the taxonomic space can be disturbed., Discussion and Conclusions: We conclude with a discussion of key factors that affect the resilience of classifiers to transitively-annotated training data, and propose best practices to avoid the artifacts described in our paper., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2024 Muralidharan, Fox and Pop.)

Cerebral microbleeds (CMBs) in the brain are the essential indicators of critical brain disorders such as dementia and ischemic stroke. Generally, CMBs are detected manually by experts, which is an exhaustive task with limited productivity. Since CMBs have complex morphological nature, manual detection is prone to errors. This paper presents a machine learning-based automated CMB detection technique in the brain susceptibility-weighted imaging (SWI) scans based on statistical feature extraction and classification. The proposed method consists of three steps: (1) removal of the skull and extraction of the brain; (2) thresholding for the extraction of initial candidates; and (3) extracting features and applying classification models such as random forest and naïve Bayes classifiers for the detection of true positive CMBs. The proposed technique is validated on a dataset consisting of 20 subjects. The dataset is divided into training data that consist of 14 subjects with 104 microbleeds and testing data that consist of 6 subjects with 63 microbleeds. We were able to achieve 85.7% sensitivity using the random forest classifier with 4.2 false positives per CMB, and the naïve Bayes classifier achieved 90.5% sensitivity with 5.5 false positives per CMB. The proposed technique outperformed many state-of-the-art methods proposed in previous studies., Competing Interests: The authors declare no conflict of interest in conducting the work.

Fire debris analysis aims to detect and identify any ignitable liquid residues in burnt residues collected at a fire scene. Typically, the burnt residues are analysed using gas chromatography-mass spectrometry (GC-MS) and are manually interpreted. The interpretation process can be laborious due to the complexity and high dimensionality of the GC-MS data. Therefore, this study aims to compare the potential of classification and regression tree (CART) and naïve Bayes (NB) algorithms in analysing the pixel-level GC-MS data of fire debris. The data comprise 14 positive (i.e. fire debris with traces of gasoline) and 24 negative (i.e. fire debris without traces of gasoline) samples. The differences between the positive and negative samples were first inspected based on the mean chromatograms and scores plots of the principal component analysis technique. Then, CART and NB algorithms were independently applied to the GC-MS data. Stratified random resampling was applied to prepare three sets of 200 pairs of training and testing samples (i.e. split ratio of 7:3, 8:2, and 9:1) for estimating the prediction accuracies. Although both the positive and negative samples were hardly differentiated based on the mean chromatograms and scores plots of principal component analysis, the respective NB and CART predictive models produced satisfactory performances with the normalized GC-MS data, i.e. majority achieved prediction accuracy >70%. NB consistently outperformed CART based on the prediction accuracies of testing samples and the corresponding risk of overfitting except when evaluated using only 10% of samples. The accuracy of CART was found to be inversely proportional to the number of testing samples; meanwhile, NB demonstrated rather consistent performances across the three split ratios. In conclusion, NB seems to be much better than CART based on the robustness against the number of testing samples and the consistent lower risk of overfitting., (© The Author(s) 2023. Published by OUP on behalf of the Academy of Forensic Science.)

The current contribution aimed to evaluate the capacity of the naive Bayes classifier to predict the progression of dengue fever to severe infection in children based on a defined set of clinical conditions and laboratory parameters. This case-control study was conducted by reviewing patient files in two public hospitals in an endemic area in Mexico. All 99 qualifying files showed a confirmed diagnosis of dengue. The 32 cases consisted of patients who entered the intensive care unit, while the 67 control patients did not require intensive care. The naive Bayes classifier could identify factors predictive of severe dengue, evidenced by 78% sensitivity, 91% specificity, a positive predictive value of 8.7, a negative predictive value of 0.24, and a global yield of 0.69. The factors that exhibited the greatest predictive capacity in the model were seven clinical conditions (tachycardia, respiratory failure, cold hands and feet, capillary leak leading to the escape of blood plasma, dyspnea, and alterations in consciousness) and three laboratory parameters (hypoalbuminemia, hypoproteinemia, and leukocytosis). Thus, the present model showed a predictive and adaptive capacity in a small pediatric population. It also identified attributes (i.e., hypoalbuminemia and hypoproteinemia) that may strengthen the WHO criteria for predicting progression to severe dengue.

Essential oils are valuable in various industries, but their easy adulteration can cause adverse health effects. Electronic nasal sensors offer a solution for adulteration detection. This article proposes a new system for characterising essential oils based on low-cost sensor networks and machine learning techniques. The sensors used belong to the MQ family (MQ-2, MQ-3, MQ-4, MQ-5, MQ-6, MQ-7, and MQ-8). Six essential oils were used, including Cistus ladanifer , Pinus pinaster , and Cistus ladanifer oil adulterated with Pinus pinaster , Melaleuca alternifolia , tea tree, and red fruits. A total of up to 7100 measurements were included, with more than 118 h of measurements of 33 different parameters. These data were used to train and compare five machine learning algorithms: discriminant analysis, support vector machine, k-nearest neighbours, neural network, and naive Bayesian when the data were used individually or when hourly mean values were included. To evaluate the performance of the included machine learning algorithms, accuracy, precision, recall, and F1-score were considered. The study found that using k-nearest neighbours, accuracy, recall, F1-score, and precision values were 1, 0.99, 0.99, and 1, respectively. The accuracy reached 100% with k-nearest neighbours using only 2 parameters for averaged data or 15 parameters for individual data.

Despite the animal models' complexity, researchers tend to reduce the number of animals in experiments for expenses and ethical concerns. This tendency makes the risk of false-positive results, as statistical significance, the primary criterion to validate findings, often fails if testing small samples. This study aims to highlight such risks using an example from experimental regenerative therapy and propose a machine-learning solution to validate treatment effects. The example analysed was the pharmacological treatment of ear pinna punch wound healing in mice. Wound closure data analysed included eight groups treated with an epigenetic inhibitor, zebularine, and eight control groups receiving vehicle alone, of six mice each. We confirmed the zebularine healing effect for all 64 pairwise comparisons between treatment and control groups but also determined minor yet statistically significant differences between control groups in five of 28 possible comparisons. The occurrences of significant differences between the control groups, regardless of standardised experimental conditions, indicate a risk of statistically significant effects in the case a compound lacking the desired biological activity is tested. Since the criterion of statistical significance itself can be confusing, we demonstrate a machine-learning algorithm trained on datasets representing treatment and control experiments as a helpful tool for validating treatment outcomes. We tested two machine-learning approaches, Naïve Bayes and Support Vector Machine classifiers. In contrast to the Mann-Whitney U-test, indicating enhanced healing effects for some control groups receiving saline alone, both machine-learning algorithms faultlessly assigned all animal groups receiving saline to the controls., Competing Interests: Conflict of interest statement The authors declare that there are no conflicts of interest., (Copyright © 2023 The Authors. Published by Elsevier Masson SAS.. All rights reserved.)

Aim: Sepsis is a leading cause of morbidity and mortality in neonates. Early diagnosis is key but difficult due to non-specific signs. We investigate the predictive value of machine learning-assisted analysis of non-invasive, high frequency monitoring data and demographic factors to detect neonatal sepsis., Methods: Single centre study, including a representative cohort of 325 infants (2866 hospitalisation days). Personalised event timelines including interventions and clinical findings were generated. Time-domain features from heart rate, respiratory rate and oxygen saturation values were calculated and demographic factors included. Sepsis prediction was performed using Naïve Bayes algorithm in a maximum a posteriori framework up to 24 h before clinical sepsis suspicion., Results: Twenty sepsis cases were identified. Combining multiple vital signs improved algorithm performance compared to heart rate characteristics alone. This enabled a prediction of sepsis with an area under the receiver operating characteristics curve of 0.82, up to 24 h before clinical sepsis suspicion. Moreover, 10 h prior to clinical suspicion, the risk of sepsis increased 150-fold., Conclusion: The present algorithm using non-invasive patient data provides useful predictive value for neonatal sepsis detection. Machine learning-assisted algorithms are promising novel methods that could help individualise patient care and reduce morbidity and mortality., (© 2023 The Authors. Acta Paediatrica published by John Wiley & Sons Ltd on behalf of Foundation Acta Paediatrica.)

Sentiment analysis involves extricating and interpreting people's views, feelings, beliefs, etc., about diverse actualities such as services, goods, and topics. People intend to investigate the users' opinions on the online platform to achieve better performance. Regardless, the high-dimensional feature set in an online review study affects the interpretation of classification. Several studies have implemented different feature selection techniques; however, getting a high accuracy with a very minimal number of features is yet to be accomplished. This paper develops an effective hybrid approach based on an enhanced genetic algorithm (GA) and analysis of variance (ANOVA) to achieve this purpose. To beat the local minima convergence problem, this paper uses a unique two-phase crossover and impressive selection approach, gaining high exploration and fast convergence of the model. The use of ANOVA drastically reduces the feature size to minimize the computational burden of the model. Experiments are performed to estimate the algorithm performance using different conventional classifiers and algorithms like GA, Particle Swarm Optimization (PSO), Recursive Feature Elimination (RFE), Random Forest, ExtraTree, AdaBoost, GradientBoost, and XGBoost. The proposed novel approach gives impressive results using the Amazon Review dataset with an accuracy of 78.60 %, F1 score of 79.38 %, and an average precision of 0.87, and the Restaurant Customer Review dataset with an accuracy of 77.70 %, F1 score of 78.24 %, and average precision of 0.89 as compared to other existing algorithms. The result shows that the proposed model outperforms other algorithms with nearly 45 and 42% fewer features for the Amazon Review and Restaurant Customer Review datasets., Competing Interests: Conflict of interestThere is no conflict of interest for this study., (© The Author(s), under exclusive licence to Springer Science+Business Media, LLC, part of Springer Nature 2023, Springer Nature or its licensor (e.g. a society or other partner) holds exclusive rights to this article under a publishing agreement with the author(s) or other rightsholder(s); author self-archiving of the accepted manuscript version of this article is solely governed by the terms of such publishing agreement and applicable law.)

We examine the significance of the predictive potential of EPI cystatin C (EPI CysC) in combination with NTproBNP, sodium, and potassium in the evaluation of renal function in patients with cardiorenal syndrome using standard mathematical classification models from the domain of artificial intelligence. The criterion for the inclusion of subjects with combined impairment of heart and kidney function in the study was the presence of newly discovered or previously diagnosed clinically manifest cardiovascular disease and acute or chronic kidney disease in different stages of evolution. In this paper, five standard classifiers from the field of machine learning were used for the analysis of the obtained data: ensemble of neural networks (MLP), ensemble of k -nearest neighbors ( k -NN) and naive Bayes classifier, decision tree, and a classifier based on logistic regression. The results showed that in MLP, k -NN, and naive Bayes, EPI CysC had the highest predictive potential. Thus, our approach with utility classifiers recognizes the essence of the disorder in patients with cardiorenal syndrome and facilitates the planning of further treatment.

Background: In mammals, normal fertilization depends on the structural and functional integrity of the zona pellucida (ZP), which is an extracellular matrix surrounding oocytes. Mutations in ZP may affect oogenesis, fertilization and early embryonic development, which may cause female infertility., Methods: A PubMed literature search using the keywords 'zona pellucida', 'mutation' and 'variant' limited to humans was performed, with the last research on June 30, 2022. The mutation types, clinical phenotypes and pregnancy outcomes were summarized and analyzed. The naive Bayes classifier was used to predict clinical pregnancy outcomes for patients with ZP mutations., Results: A total of 29 publications were included in the final analysis. Sixty-nine mutations of the ZP genes were reported in 87 patients with different clinical phenotypes, including empty follicle syndrome (EFS), ZP-free oocytes (ZFO), ZP-thin oocytes (ZTO), degenerated and immature oocytes. The phenotypes of patients were influenced by the types and location of the mutations. The most common effects of ZP mutations are protein truncation and dysfunction. Three patients with ZP1 mutations, two with ZP2 mutations, and three with ZP4 mutations had successful pregnancies through Intracytoplasmic sperm injection (ICSI) from ZFO or ZTO. A prediction model of pregnancy outcome in patients with ZP mutation was constructed to assess the chance of pregnancy with the area under the curve (AUC) of 0.898. The normalized confusion matrix showed the true positive rate was 1.00 and the true negative rate was 0.38., Conclusion: Phenotypes in patients with ZP mutations might be associated with mutation sites or the degree of protein dysfunction. Successful pregnancy outcomes could be achieved in some patients with identified ZP mutations. Clinical pregnancy prediction model based on ZP mutations and clinical characteristics will be helpful to precisely evaluate pregnancy chance and provide references and guidance for the clinical treatment of relevant patients., (© 2022. The Author(s).)

Motivation: Application of chemical named entity recognition (CNER) algorithms allows retrieval of information from texts about chemical compound identifiers and creates associations with physical-chemical properties and biological activities. Scientific texts represent low-formalized sources of information. Most methods aimed at CNER are based on machine learning approaches, including conditional random fields and deep neural networks. In general, most machine learning approaches require either vector or sparse word representation of texts. Chemical named entities (CNEs) constitute only a small fraction of the whole text, and the datasets used for training are highly imbalanced., Methods and Results: We propose a new method for extracting CNEs from texts based on the naïve Bayes classifier combined with specially developed filters. In contrast to the earlier developed CNER methods, our approach uses the representation of the data as a set of fragments of text (FoTs) with the subsequent preparati`on of a set of multi-n-grams (sequences from one to n symbols) for each FoT. Our approach may provide the recognition of novel CNEs. For CHEMDNER corpus, the values of the sensitivity (recall) was 0.95, precision was 0.74, specificity was 0.88, and balanced accuracy was 0.92 based on five-fold cross validation. We applied the developed algorithm to the extracted CNEs of potential Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) main protease (Mpro) inhibitors. A set of CNEs corresponding to the chemical substances evaluated in the biochemical assays used for the discovery of Mpro inhibitors was retrieved. Manual analysis of the appropriate texts showed that CNEs of potential SARS-CoV-2 Mpro inhibitors were successfully identified by our method., Conclusion: The obtained results show that the proposed method can be used for filtering out words that are not related to CNEs; therefore, it can be successfully applied to the extraction of CNEs for the purposes of cheminformatics and medicinal chemistry., (© 2022. The Author(s).)

Research on upper-limb prostheses is typically laboratory-based. Evidence indicates that research has not yet led to prostheses that meet user needs. Inefficient communication loops between users, clinicians and manufacturers limit the amount of quantitative and qualitative data that researchers can use in refining their innovations. This paper offers a first demonstration of an alternative paradigm by which remote, beyond-the-laboratory prosthesis research according to user needs is feasible. Specifically, the proposed Internet of Things setting allows remote data collection, real-time visualization and prosthesis reprogramming through Wi-Fi and a commercial cloud portal. Via a dashboard, the user can adjust the configuration of the device and append contextual information to the prosthetic data. We evaluated this demonstrator in real-time experiments with three able-bodied participants. Results promise the potential of contextual data collection and system update through the internet, which may provide real-life data for algorithm training and reduce the complexity of send-home trials. This article is part of the theme issue 'Advanced neurotechnologies: translating innovation for health and well-being'.

Drug-induced liver injury (DILI) has been identified as one of the major causes for drugs withdrawn from the market, and even termination during the late stages of development. Therefore, it is imperative to evaluate the DILI potential of lead compounds during the research and development process. Although various computational models have been developed to predict DILI, most of which applied the DILI data were extracted from preclinical sources. In this investigation, the in silico prediction models for DILI were constructed based on 1140 FDA-approved drugs by using naïve Bayes classifier approach. The genetic algorithm method was applied for the molecular descriptors selection. Among these established prediction models, the NB-11 model based on eight molecular descriptors combined with ECFP_18 showed the best prediction performance for DILI, which gave 91.7% overall prediction accuracy for the training set, and 68.9% concordance for the external test set. Therefore, the established NB-11 prediction model can be used as a reliable virtual screening tool to predict DILI adverse effect in the early stages of drug design. In addition, some new structural alters for DILI were identified, which could be used for structural optimization in the future drug design by medicinal chemists., (Copyright © 2022 Elsevier Inc. All rights reserved.)

Background: Those who are found in close contact with COVID-19 patients and are also negative by polymerase chain reaction (PCR) test may act without waiting for the incubation period to elapse, can become infectious and spread the infection., Methods: A machine learning model that can evaluate the risk of infection in close contact with COVID-19 patients within the incubation period from the contact status reported from the index case was created using posterior probabilities. To confirm actual predictability, a verification test was conducted on 169 new close contacts, and the machine learning model was compared with four experienced healthcare workers for the predictability., Results: In a verification test, 33 of the 169 contacts were infected with COVID-19 during the incubation period, and 13 of 33 were negative on initial PCR test, after that the disease developed and their PCR test became positive. The machine learning model predicted the eventual infection in 12 of 13 patients who had negative results on the initial PCR test. In the verification test, the sensitivity of the machine learning model was 0.879 and the specificity was 0.588. The mean-standard deviation of the sensitivity and the specificity of the four health care workers was 0.568 (0.230) for sensitivity and 0.689 (0.103) for specificity., Conclusion: If it is possible to convey that individual risk of infection, the close contact may take suppressive action during the incubation period regardless of the result of the initial PCR test, thereby preventing secondary spread of infection., (Copyright © 2022 Japanese Society of Chemotherapy and The Japanese Association for Infectious Diseases. Published by Elsevier Ltd. All rights reserved.)

Infections such as COVID-19 are affecting the entire world and measures such as social distancing can be done so that the contact among people is reduced. IoT devices usage keeps on increasing every day thereby connecting the environments physically. Among the current technologies, machine learning can be employed along with IoT devices. Predicting the risk related with COVID-19, a novel method employing machine learning is proposed. Random forest and Naive Bayes classifier are used for the prediction from the data collected with the help of sensors. Groups of people are recognized and the disease impact can be reduced for the particular group with more population. The accuracy of RF is 97% and for NB it is 99%., Competing Interests: The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2022 Elsevier Ltd. All rights reserved. Selection and peer-review under responsibility of the scientific committee of the International Conference on Innovative Technology for Sustainable Development.)

Knowledge of animal behavior can be indicative of the well-being, health, productivity, and reproduction of animals. The use of accelerometers to classify and predict animal behavior can be a tool for continuous animal monitoring. Therefore, the aim of this study was to provide strategies for predicting more and less frequent beef cattle grazing behaviors. The behavior activities observed were grazing, ruminating, idle, water consumption frequency (WCF), feeding (supplementation) and walking. Three Machine Learning algorithms: Random Forest (RF), Support Vector Machine (SVM) and Naïve Bayes Classifier (NBC) and two resample methods: under and over-sampling, were tested. Overall accuracy was higher for RF models trained with the over-sampled dataset. The greatest sensitivity (0.808) for the less frequent behavior (WCF) was observed in the RF algorithm trained with the under-sampled data. The SVM models only performed efficiently when classifying the most frequent behavior (idle). The greatest predictor in the NBC algorithm was for ruminating behavior, with the over-sampled training dataset. The results showed that the behaviors of the studied animals were classified with high accuracy and specificity when the RF algorithm trained with the resampling methods was used. Resampling training datasets is a strategy to be considered, especially when less frequent behaviors are of interest.

American foulbrood is a dangerous disease of bee broods found worldwide, caused by the Paenibacillus larvae larvae L. bacterium. In an experiment, the possibility of detecting colonies of this bacterium on MYPGP substrates (which contains yeast extract, Mueller-Hinton broth, glucose, K2HPO4, sodium pyruvate, and agar) was tested using a prototype of a multi-sensor recorder of the MCA-8 sensor signal with a matrix of six semiconductors: TGS 823, TGS 826, TGS 832, TGS 2600, TGS 2602, and TGS 2603 from Figaro. Two twin prototypes of the MCA-8 measurement device, M1 and M2, were used in the study. Each prototype was attached to two laboratory test chambers: a wooden one and a polystyrene one. For the experiment, the strain used was P. l. larvae ATCC 9545, ERIC I. On MYPGP medium, often used for laboratory diagnosis of American foulbrood, this bacterium produces small, transparent, smooth, and shiny colonies. Gas samples from over culture media of one- and two-day-old foulbrood P. l. larvae (with no colonies visible to the naked eye) and from over culture media older than 2 days (with visible bacterial colonies) were examined. In addition, the air from empty chambers was tested. The measurement time was 20 min, including a 10-min testing exposure phase and a 10-min sensor regeneration phase. The results were analyzed in two variants: without baseline correction and with baseline correction. We tested 14 classifiers and found that a prototype of a multi-sensor recorder of the MCA-8 sensor signal was capable of detecting colonies of P. l. larvae on MYPGP substrate with a 97% efficiency and could distinguish between MYPGP substrates with 1-2 days of culture, and substrates with older cultures. The efficacy of copies of the prototypes M1 and M2 was shown to differ slightly. The weighted method with Canberra metrics (Canberra.811) and kNN with Canberra and Manhattan metrics (Canberra. 1nn and manhattan.1nn) proved to be the most effective classifiers.

Objective: To establish a risk prediction model of chemotherapy-induced nausea and vomiting based on naive Bayes classifier., Objective: We collected the basic information, treatment protocols and follow-up data from 300 patients receiving chemotherapy in the Oncology Department of Second Xiangya Hospital from July to September, 2020. Correlation analysis was carried out between the potential factors related to nausea and vomiting in the treatment plan and the individual characteristics of the patients. For the two characteristics with a correlation coefficient greater than 0.8, their contribution to the area under curve (AUC) was calculated, and the characteristic with a smaller contribution was removed. The naive Bayes classifier in the machine learning library scikit-learn was used as the prediction model of chemotherapy-induced nausea and vomiting, and 10-fold stratified-shuffled-split cross-validation was used to obtain the final result of the model. The machine learning model was trained using 70% of the samples, and 30% of the samples were used as the test set to assess the performance of the model., Objective: The sensitivity of the model for predicting the risk of nausea and vomiting due to acute chemotherapy was 0.83±0.04 (95% CI : 0.80-0.86) with a specificity of 0.45±0.03 (95% CI : 0.42-0.47) and an AUC of 0.72±0.04 (95% CI : 0.69-0.75). The sensitivity of the model for predicting the risk of delayed chemotherapy-induced nausea and vomiting was 0.84±0.01 (95% CI : 0.83-0.86) with a specificity of 0.48±0.03 (95% CI : 0.45-0.52) and an AUC of 0.74±0.02 (95% CI : 0.72-0.77)., Objective: The naive Bayes classifier model has a good performance in predicting the risk of chemotherapy-induced nausea and vomiting in Chinese cancer patients.

Development of reliable and efficient alternative in vivo methods for evaluation of the chemicals with potential neurotoxicity is an urgent need in the early stages of drug design. In this investigation, the computational prediction models for drug-induced neurotoxicity were developed by using the classical naïve Bayes classifier. Eight molecular properties closely relevant to neurotoxicity were selected. Then, 110 classification models were developed with using the eight important molecular descriptors and 10 types of fingerprints with 11 different maximum diameters. Among these 110 prediction models, the prediction model (NB-03) based on eight molecular descriptors combined with ECFP_10 fingerprints showed the best prediction performance, which gave 90.5% overall prediction accuracy for the training set and 82.1% concordance for the external test set. In addition, compared to naïve Bayes classifier, the recursive partitioning classifier displayed worse predictive performance for neurotoxicity. Therefore, the established NB-03 prediction model can be used as a reliable virtual screening tool to predict neurotoxicity in the early stages of drug design. Moreover, some structure alerts for characterizing neurotoxicity were identified in this research, which could give an important guidance for the chemists in structural modification and optimization to reduce the chemicals with potential neurotoxicity., (Copyright © 2020 Elsevier Ltd. All rights reserved.)

Assessment of reproductive toxicity is one of the important safety considerations in drug development. Thus, in the present research, the naïve Bayes (NB)-classifier method was applied to develop binary classification models. Six important molecular descriptors for reproductive toxicity were selected by the genetic algorithm. Then, 110 classification models were developed using six molecular descriptors and10 types of fingerprints with 11 different maximum diameters. Among these established models, the model based on six molecular descriptors and the SciTegic extended-connectivity fingerprints with 20 maximum diameters (LCFC_20) displayed the best prediction performance for reproductive toxicity (NB-1), which gave a 0.884 receiver operating characteristic (ROC) score and 91.8% overall prediction accuracy for the Training Set, and produced a 0.888 ROC score and 83.0% overall accuracy for the external Test Set I. In addition, for the external rat multi-generation reproductive toxicity dataset (Test Set II), the NB-1 model generated a 0.806 ROC score and 85.1% concordance. The generated prediction results indicated that the NB-1 model could give robust and reliable predictions for a reproductive toxicity potential of chemicals. Thus, the established model could be applied to filter early-stage molecules for potential reproductive adverse effects. In addition, six important molecular descriptors and new structural alerts for reproductive toxicity were identified, which could help medicinal chemists rationally guide the optimization of lead compounds and select chemicals with the best prospects of being safe and effective., (© 2020 John Wiley & Sons, Ltd.)

Some drugs have the potential to cause cellular degeneration of cochlear and/or vestibular system, leading to temporary or permanent hearing loss, innitus, ataxia, dizziness, ear infections, hyperacusis, vertigo, nystagmus and other ear problems. Thus, precise assessment of ototoxicity has become a strong urge task for the toxicologist. In this research, the in silico prediction model of ototoxicity was developed based on 2612 diverse chemicals by using naïve Bayes classifier approach. A set of 7 molecular descriptors considered as important for ototoxicity was selected by genetic algorithm method, and some structural alerts for ototoxicity were identified. The established naïve Bayes prediction model produced 90.2% overall prediction accuracy for the training set and 88.7% for the external test set. We hope the established naïve Bayes prediction model should be employed as precise and convenient computational tool for assessing and screening the chemical-induced ototoxicity in drug development, and these important information of ototoxic chemical structures could provide theoretical guidance for hit and lead optimization in drug design., Competing Interests: Declaration of Competing Interest The authors declare no conflict of interest., (Copyright © 2020 Elsevier Ltd. All rights reserved.)

Background and Purpose: The unanticipated detection by magnetic resonance imaging (MRI) in the brain of asymptomatic subjects of white matter lesions suggestive of multiple sclerosis (MS) has been named radiologically isolated syndrome (RIS). As the difference between early MS [i.e. clinically isolated syndrome (CIS)] and RIS is the occurrence of a clinical event, it is logical to improve detection of the subclinical form without interfering with MRI as there are radiological diagnostic criteria for that. Our objective was to use machine-learning classification methods to identify morphometric measures that help to discriminate patients with RIS from those with CIS., Methods: We used a multimodal 3-T MRI approach by combining MRI biomarkers (cortical thickness, cortical and subcortical grey matter volume, and white matter integrity) of a cohort of 17 patients with RIS and 17 patients with CIS for single-subject level classification., Results: The best proposed models to predict the diagnosis of CIS and RIS were based on the Naive Bayes, Bagging and Multilayer Perceptron classifiers using only three features: the left rostral middle frontal gyrus volume and the fractional anisotropy values in the right amygdala and right lingual gyrus. The Naive Bayes obtained the highest accuracy [overall classification, 0.765; area under the receiver operating characteristic (AUROC), 0.782]., Conclusions: A machine-learning approach applied to multimodal MRI data may differentiate between the earliest clinical expressions of MS (CIS and RIS) with an accuracy of 78%., (© 2019 EAN.)

Background: Ontology has attracted substantial attention from both academia and industry. Handling uncertainty reasoning is important in researching ontology. For example, when a patient is suffering from cirrhosis, the appearance of abdominal vein varices is four times more likely than the presence of bitter taste. Such medical knowledge is crucial for decision-making in various medical applications but is missing from existing medical ontologies. In this paper, we aim to discover medical knowledge probabilities from electronic medical record (EMR) texts to enrich ontologies. First, we build an ontology by identifying meaningful entity mentions from EMRs. Then, we propose a symptom-dependency-aware naïve Bayes classifier (SDNB) that is based on the assumption that there is a level of dependency among symptoms. To ensure the accuracy of the diagnostic classification, we incorporate the probability of a disease into the ontology via innovative approaches., Results: We conduct a series of experiments to evaluate whether the proposed method can discover meaningful and accurate probabilities for medical knowledge. Based on over 30,000 deidentified medical records, we explore 336 abdominal diseases and 81 related symptoms. Among these 336 gastrointestinal diseases, the probabilities of 31 diseases are obtained via our method. These 31 probabilities of diseases and 189 conditional probabilities between diseases and the symptoms are added into the generated ontology., Conclusion: In this paper, we propose a medical knowledge probability discovery method that is based on the analysis and extraction of EMR text data for enriching a medical ontology with probability information. The experimental results demonstrate that the proposed method can effectively identify accurate medical knowledge probability information from EMR data. In addition, the proposed method can efficiently and accurately calculate the probability of a patient suffering from a specified disease, thereby demonstrating the advantage of combining an ontology and a symptom-dependency-aware naïve Bayes classifier.

Background: The placenta is a maternal-fetal organ that develops during pregnancy and provides nutrients, oxygen, and removal of waste products to the growing fetus. Better understanding of the placenta promises to help improve health of mothers and children, given its influence on health lasting a lifetime. However, the placenta is poorly understood due to its variability across different species and no live functions available after the baby is delivered. The Placenta Atlas Tool (PAT) project aims to leverage advanced computational approaches to meld numerous and diverse datasets into an integrated resource to encourage a "systems biology" approach for study of both normal and abnormal placental development and function throughout gestation., Methods: In this study, we introduced a multi-layer framework to automatically identify PAT relevant research from PubMed and develop a Placenta Curated Research Dataset (PCRD) to ultimately support placenta research. This framework functions by multiple well-known Natural Language Processing (NLP) components; including Medical Subject Headings (MeSH) based Naïve Bayes classifier, abstract based text similarity comparison and MeSH based article prioritization to systematically filter out PAT relevant research publications for further data curation. In addition, we developed a user-friendly web application to incorporate human judgement at the final stage of publication identification., Results: We obtained 22,047 articles from PubMed, and programmatically identified 6086 articles that are highly relevant to PAT via our framework. To assess performance of the framework, we manually reviewed a random set of articles by using our web tool. Based on our review, accuracy of article classification is greater than 90% and accuracy of prioritization is greater than 80%., Conclusions: We developed a multi-layer publication identification framework to systematically identify PAT relevant publications from PubMed. This framework not only demonstrates good performance in identifying placenta related research, but also can be easily extended to support research in other scientific fields., (Copyright © 2019 Elsevier Inc. All rights reserved.)

Here, we report two-class classification models for organic molecules ("ligands") able to bind various metal cations in water. The modeling was performed on 30 data sets, each corresponding to a particular metal, using the Naïve Bayes method and the ISIDA fragment descriptors. The ligands were classified on weak and strong binders according to threshold of the logarithm of the stability constant of the 1 : 1 (metal : ligand) complexes. The "consensus models" consisted each of 50 best individual models demonstrated a good predictive performance in 5-fold cross validation: the balanced accuracy (BA) varies from 0.965 (Yb 3+ ) to 0.767 (Mg 2+ ). The best predictions (BA>0.90) were obtained for the binders of rare-earth metals (Yb 3+ , Tm 3+ , Er 3+ , Lu 3+ , Ho 3+ , Gd 3+ and Dy 3+ ) and Pb 2+ . For 17 small external test sets of new ligands, BA varies from 0.800 to 1. The impact of variables selection on the predictive performance of the models is discussed., (© 2019 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.)

The urinary tract toxicity is one of the major reasons for investigational drugs not coming into the market and even marketed drugs being restricted or withdrawn. The objective of this investigation is to develop an easily interpretable and practically applicable in silico prediction model of chemical-induced urinary tract toxicity by using naïve Bayes classifier. The genetic algorithm was used to select important molecular descriptors related to urinary tract toxicity, and the ECFP-6 fingerprint descriptors were applied to the urinary tract toxic/non-toxic fragments production. The established naïve Bayes classifier (NB-2) produced 87.3% overall accuracy of fivefold cross-validation for the training set and 84.2% for the external test set, which can be employed for the chemical-induced urinary tract toxicity assessment. Furthermore, six important molecular descriptors (e.g., number of N atoms, AlogP, molecular weight, number of H acceptors, number of H donors and molecular fractional polar surface area) and toxic and non-toxic fragments were obtained, which would help medicinal chemists interpret the mechanisms of urinary tract toxicity, and even provide theoretical guidance for hit and lead optimization.

The Lung nodules are very important to indicate the lung cancer, and its early detection enables timely treatment and increases the survival rate of patient. Even though lots of works are done in this area, still improvement in accuracy is required for improving the survival rate of the patient. The proposed method can classify the stages of lung cancer in addition to the detection of lung nodules. There are two parts in the proposed method, the first part is used for classifying normal/abnormal and second part is used for classifying stages of lung cancer. Totally 10 features from the lung region segmented image are considered for detection and classification. The first part of the proposed method classifies the input images with the aid of Naive Bayes classifier as normal or abnormal. The second part of the system classifies the four stages of lung cancer using Neuro Fuzzy classifier with Cuckoo Search algorithm. The results of proposed system show that the rate of accuracy of classification is improved and the results are compared with SVM, Neural Network and Neuro Fuzzy Classifiers.

In recent years, the successful implementation of human genome project has made people realize that genetic, environmental and lifestyle factors should be combined together to study cancer due to the complexity and various forms of the disease. The increasing availability and growth rate of 'big data' derived from various omics, opens a new window for study and therapy of cancer. In this paper, we will introduce the application of machine learning methods in handling cancer big data including the use of artificial neural networks, support vector machines, ensemble learning and naïve Bayes classifiers., (Copyright© Bentham Science Publishers; For any queries, please email at epub@benthamscience.net.)

Classification of abnormalities from medical images using computer-based approaches is of growing interest in medical imaging. Timely detection of abnormalities due to diabetic retinopathy and age-related macular degeneration is required in order to prevent the prognosis of the disease. Computer-aided systems using machine learning are becoming interesting to ophthalmologists and researchers. We present here one such technique, the Random Forest classifier, to aid medical practitioners in accurate diagnosis of the diseases. A computer-aided diagnosis system is proposed for detecting retina abnormalities, which combines K means-based segmentation of the retina image, after due preprocessing, followed by machine learning techniques, using several low level and statistical features. Abnormalities in the retina that are classified are caused by age-related macular degeneration and diabetic retinopathy. Performance measures used in the analysis are accuracy, sensitivity, specificity, F-measure, and Mathew correlation coefficient. A comparison with another machine learning technique, the Naïve Bayes classifier shows that the classification achieved by Random Forest classifier is 93.58% and it outperforms Naïve Bayes classifier which yields an accuracy of 83.63%. Graphical abstract Random Forest classifier for abnormality detection in retina images.

Respiratory toxicity is considered as main cause of drug withdrawal, which could seriously injure human health or even lead to death. The objective of this investigation was to develop an in silico prediction model of drug-induced respiratory toxicity by using naïve Bayes classifier. The genetic algorithm was used to select important molecular descriptors related to respiratory toxicity, and the ECFP_6 fingerprint descriptors were applied to the respiratory toxic/non-toxic fragments production. The established prediction model was validated by the internal 5-fold cross validation and external test set. The naïve Bayes classifier generated overall prediction accuracy of 91.8% for the training set and 84.3% for the external test set. Furthermore, six molecular descriptors (e.g., number of O atoms, number of N atoms, molecular weight, Apol, number of H acceptors and molecular polar surface area) considered as important for the drug-induced respiratory toxicity were identified, and some critical fragments related to the respiratory toxicity were achieved. We hope the established naïve Bayes prediction model could be used as a toxicological screening of chemicals for respiratory sensitization potential in drug development, and these obtained important information of respiratory toxic chemical structures could offer theoretical guidance for hit and lead optimization., (Copyright © 2018 Elsevier Ltd. All rights reserved.)

Predictive models permitting personalized prognostication for patients with cannulated screw fixation for the femoral neck fracture before operation are lacking. The objective of this study was to train, test, and cross-validate a Naive Bayes Classifier to predict the occurrence of postoperative osteonecrosis of cannulated screw fixation before the patient underwent the operation. The data for the classifier model were obtained from a ambispective cohort of 120 patients who had undergone closed reduction and cannulated screw fixation from January 2011 to June 2013. Three spatial displaced parameters of femoral neck: displacement of centre of femoral head, displacement of deepest of femoral head foveae and rotational displacement were measured from preoperative CT scans using a 3-dimensional software. The Naive Bayes Classifier was modelled with age, gender, side of fractures, mechanism of injury, preoperative traction, Pauwels angle and the three spatial parameters. After modelling, the ten-fold cross-validation method was used in this study to validate its performance. The ten-fold cross-validation method uses the whole dataset to be trained and tested by the given algorithm. Two of the three spatial parameters of femoral neck (displacement of center of femoral head and rotational displacement) were included successfully in the final Naive Bayes Classifier. The Classifier achieved good performance of the accuracy (74.4%), sensitivity (74.2%), specificity (75%), positive predictive value (92%), negative predictive value (42.9%) and AUC (0.746). We showed that the Naive Bayes Classifier have the potential utility to be used to predict the osteonecrosis of femoral head within 5 years after surgery. Although this study population was restricted to patients treated with cannulated screws fixation, Bayesian-derived models may be developed for application to patients with other surgical procedures at risk of osteonecrosis., (Copyright © 2018. Published by Elsevier Ltd.)

Grooving is widely used to improve airport runway pavement skid resistance during wet weather. However, runway grooves deteriorate over time due to the combined effects of traffic loading, climate, and weather, which brings about a potential safety risk at the time of the aircraft takeoff and landing. Accordingly, periodic measurement and evaluation of groove performance are critical for runways to maintain adequate skid resistance. Nevertheless, such evaluation is difficult to implement due to the lack of sufficient technologies to identify shallow or worn grooves and slab joints. This paper proposes a new strategy to automatically identify airport runway grooves and slab joints using high resolution laser profiling data. First, K-means clustering based filter and moving window traversal algorithm are developed to locate the deepest point of the potential dips (including noises, true grooves, and slab joints). Subsequently the improved moving average filter and traversal algorithms are used to determine the left and right endpoint positions of each identified dip. Finally, the modified heuristic method is used to separate out slab joints from the identified dips, and then the polynomial support vector machine is introduced to distinguish out noises from the candidate grooves (including noises and true grooves), so that PCC slab-based runway safety evaluation can be performed. The performance of the proposed strategy is compared with that of the other two methods, and findings indicate that the new method is more powerful in runway groove and joint identification, with the F-measure score of 0.98. This study would be beneficial in airport runway groove safety evaluation and the subsequent maintenance and rehabilitation of airport runway.

Presynaptic neurotoxins and postsynaptic neurotoxins are two important neurotoxins isolated from venoms of venomous animals and have been proven to be potential effective in neurosciences and pharmacology. With the number of toxin sequences appeared in the public databases, there was a need for developing a computational method for fast and accurate identification and classification of the novel presynaptic neurotoxins and postsynaptic neurotoxins in the large databases. In this study, the Multinomial Naive Bayes Classifier (MNBC) had been developed to discriminate the presynaptic neurotoxins and postsynaptic neurotoxins based on the different kinds of features. The Minimum Redundancy Maximum Relevance (MRMR) feature selection method was used for ranking 400 pseudo amino acid (PseAA) compositions and 50 top ranked PseAA compositions were selected for improving the prediction results. The motif features, 400 PseAA compositions and 50 PseAA compositions were combined together, and selected as the input parameters of MNBC. The best correlation coefficient (CC) value of 0.8213 was obtained when the prediction quality was evaluated by the jackknife test. It was anticipated that the algorithm presented in this study may become a useful tool for identification of presynaptic neurotoxin and postsynaptic neurotoxin sequences and may provide some useful help for in-depth investigation into the biological mechanism of presynaptic neurotoxins and postsynaptic neurotoxins., (Copyright © 2018 Elsevier Ltd. All rights reserved.)

Mitochondrial dysfunction has been considered as an important contributing factor in the etiology of drug-induced organ toxicity, and even plays an important role in the pathogenesis of some diseases. The objective of this investigation was to develop a novel prediction model of drug-induced mitochondrial toxicity by using a naïve Bayes classifier. For comparison, the recursive partitioning classifier prediction model was also constructed. Among these methods, the prediction performance of naïve Bayes classifier established here showed best, which yielded average overall prediction accuracies for the internal 5-fold cross validation of the training set and external test set were 95 ± 0.6% and 81 ± 1.1%, respectively. In addition, four important molecular descriptors and some representative substructures of toxicants produced by ECFP_6 fingerprints were identified. We hope the established naïve Bayes prediction model can be employed for the mitochondrial toxicity assessment, and these obtained important information of mitochondrial toxicants can provide guidance for medicinal chemists working in drug discovery and lead optimization., (Copyright © 2017 Elsevier Ltd. All rights reserved.)

Toxicological testing associated with developmental toxicity endpoints are very expensive, time consuming and labor intensive. Thus, developing alternative approaches for developmental toxicity testing is an important and urgent task in the drug development filed. In this investigation, the naïve Bayes classifier was applied to develop a novel prediction model for developmental toxicity. The established prediction model was evaluated by the internal 5-fold cross validation and external test set. The overall prediction results for the internal 5-fold cross validation of the training set and external test set were 96.6% and 82.8%, respectively. In addition, four simple descriptors and some representative substructures of developmental toxicants were identified. Thus, we hope the established in silico prediction model could be used as alternative method for toxicological assessment. And these obtained molecular information could afford a deeper understanding on the developmental toxicants, and provide guidance for medicinal chemists working in drug discovery and lead optimization., (Copyright © 2017 Elsevier Inc. All rights reserved.)

Prediction of drug candidates for mutagenicity is a regulatory requirement since mutagenic compounds could pose a toxic risk to humans. The aim of this investigation was to develop a novel prediction model of mutagenicity by using a naïve Bayes classifier. The established model was validated by the internal 5-fold cross validation and external test sets. For comparison, the recursive partitioning classifier prediction model was also established and other various reported prediction models of mutagenicity were collected. Among these methods, the prediction performance of naïve Bayes classifier established here displayed very well and stable, which yielded average overall prediction accuracies for the internal 5-fold cross validation of the training set and external test set I set were 89.1±0.4% and 77.3±1.5%, respectively. The concordance of the external test set II with 446 marketed drugs was 90.9±0.3%. In addition, four simple molecular descriptors (e.g., Apol, No. of H donors, Num-Rings and Wiener) related to mutagenicity and five representative substructures of mutagens (e.g., aromatic nitro, hydroxyl amine, nitroso, aromatic amine and N-methyl-N-methylenemethanaminum) produced by ECFP_14 fingerprints were identified. We hope the established naïve Bayes prediction model can be applied to risk assessment processes; and the obtained important information of mutagenic chemicals can guide the design of chemical libraries for hit and lead optimization., (Copyright © 2017 Elsevier B.V. All rights reserved.)

Objectives: Variable prevalence and treatment of breakthrough pain (BTP) in different clinical contexts are partially due to the lack of reliable/validated diagnostic tools with prognostic capability. We report the statistical basis and performance analysis of a novel BTP scoring system based on the naïve Bayes classifier (NBC) approach and an 11-item IQ-BTP validated questionnaire. This system aims at classifying potential BTP presence in three likelihood classes: "High," "Intermediate," and "Low.", Methods: Out of a training set of n=120 mixed chronic pain patients, predictors associated with the BTP likelihood variables (Pearson's χ 2 and/or Fisher's exact test) were employed for the NBC planning. Adjusting the binary classification to a three-likelihood classes case enabled the building of a scoring algorithm and to retrieve the score of each predictor's answer options and the Patient's Global Score (PGS). The latter medians were used to establish the NBC thresholds, needed to evaluate the scoring system performance (leave-one-out cross-validation)., Results: Medians of PGS in the "High," "Intermediate," and "Low" likelihood classes were 3.44, 1.53, and -2.84, respectively. Leading predictors for the model (based on score differences) were flair frequency (ΔS=1.31), duration (ΔS=5.25), and predictability (ΔS=1.17). Percentages of correct classification were 63.6% for the "High" and of 100.0% for either the "Intermediate" and "Low" likelihood classes; overall accuracy of the scoring system was 90.9%., Conclusion: The NBC-based BTP scoring system showed satisfactory performance in classifying potential BTP in three likelihood classes. The reliability, flexibility, and simplicity of this statistical approach may have significant relevance for BTP epidemiology and management. These results need further impact studies to generalize our findings., Competing Interests: Disclosure The authors report no conflicts of interest in this work.

The carcinogenicity prediction has become a significant issue for the pharmaceutical industry. The purpose of this investigation was to develop a novel prediction model of carcinogenicity of chemicals by using a naïve Bayes classifier. The established model was validated by the internal 5-fold cross validation and external test set. The naïve Bayes classifier gave an average overall prediction accuracy of 90 ± 0.8% for the training set and 68 ± 1.9% for the external test set. Moreover, five simple molecular descriptors (e.g., AlogP, Molecular weight (M W ), No. of H donors, Apol and Wiener) considered as important for the carcinogenicity of chemicals were identified, and some substructures related to the carcinogenicity were achieved. Thus, we hope the established naïve Bayes prediction model could be applied to filter early-stage molecules for this potential carcinogenicity adverse effect; and the identified five simple molecular descriptors and substructures of carcinogens would give a better understanding of the carcinogenicity of chemicals, and further provide guidance for medicinal chemists in the design of new candidate drugs and lead optimization, ultimately reducing the attrition rate in later stages of drug development., (Copyright © 2016 Elsevier Ltd. All rights reserved.)

Drug-induced liver injury (DILI) is one of the major safety concerns in drug development. Although various toxicological studies assessing DILI risk have been developed, these methods were not sufficient in predicting DILI in humans. Thus, developing new tools and approaches to better predict DILI risk in humans has become an important and urgent task. In this study, we aimed to develop a computational model for assessment of the DILI risk with using a larger scale human dataset and Naïve Bayes classifier. The established Naïve Bayes prediction model was evaluated by 5-fold cross validation and an external test set. For the training set, the overall prediction accuracy of the 5-fold cross validation was 94.0 %. The sensitivity, specificity, positive predictive value and negative predictive value were 97.1, 89.2, 93.5 and 95.1 %, respectively. The test set with the concordance of 72.6 %, sensitivity of 72.5 %, specificity of 72.7 %, positive predictive value of 80.4 %, negative predictive value of 63.2 %. Furthermore, some important molecular descriptors related to DILI risk and some toxic/non-toxic fragments were identified. Thus, we hope the prediction model established here would be employed for the assessment of human DILI risk, and the obtained molecular descriptors and substructures should be taken into consideration in the design of new candidate compounds to help medicinal chemists rationally select the chemicals with the best prospects to be effective and safe.

Background: The taxonomic and phylogenetic classification based on sequence analysis of the ITS1 genomic region has become a crucial component of fungal ecology and diversity studies. Nowadays, there is no accurate alignment-free classification tool for fungal ITS1 sequences for large environmental surveys. This study describes the development of a machine learning-based classifier for the taxonomical assignment of fungal ITS1 sequences at the genus level., Results: A fungal ITS1 sequence database was built using curated data. Training and test sets were generated from it. A Naïve Bayesian classifier was built using features from the primary sequence with an accuracy of 87 % in the classification at the genus level., Conclusions: The final model was based on a Naïve Bayes algorithm using ITS1 sequences from 510 fungal genera. This classifier, denoted as Mycofier, provides similar classification accuracy compared to BLASTN, but the database used for the classification contains curated data and the tool, independent of alignment, is more efficient and contributes to the field, given the lack of an accurate classification tool for large data from fungal ITS1 sequences. The software and source code for Mycofier are freely available at https://github.com/ldelgado-serrano/mycofier.git .

MicroRNAs (miRNAs) are important regulatory molecules in eukaryotic organisms. Existing methods for the identification of mature miRNA sequences in plants rely extensively on the search for stem-loop structures, leading to high false negative rates. Here, we describe a probabilistic method for ranking putative plant miRNAs using a naïve Bayes classifier and its publicly available implementation. We use a number of properties to construct the classifier, including sequence length, number of observations, existence of detectable predicted miRNA* sequences, the distribution of nearby reads and mapping multiplicity. We apply the method to small RNA sequence data from soybean, peach, Arabidopsis and rice and provide experimental validation of several predictions in soybean. The approach performs well overall and strongly enriches for known miRNAs over other types of sequences. By utilizing a Bayesian approach to rank putative miRNAs, our method is able to score miRNAs that would be eliminated by other methods, such as those that have low counts or lack detectable miRNA* sequences. As a result, we are able to detect several soybean miRNA candidates, including some that are 24 nucleotides long, a class that is almost universally eliminated by other methods., (© 2016 The Authors The Plant Journal © 2016 John Wiley & Sons Ltd.)

Oscillations of electroencephalographic signals represent the cognitive processes arose from the behavioral task and sensory representations across the mental state activity. Previous studies have shown the relation between event-related EEG and sensory-cognitive representation and revealed that categorization of presented object can be successfully recognized using recorded EEG signals when subjects view objects. Here, EEG signals in conjunction with a multivariate pattern recognition technique were used for investigating the possibility to identify conceptual representation based on the presentation of 12 semantic categories of objects (5 exemplars per category). Using multivariate stimulus decoding methods, surprisingly, we demonstrate that how objects are discriminated from phase pattern of EEG signals across the time in low-frequency band (1-4 Hz), but not from power of oscillatory brain signals in the same frequency band. In contrast, discrimination accuracy from the power of EEG signals has significantly higher than the performance from phase of EEG signal in the high-frequency band (20-30 Hz). Moreover, our results indicate that how the accuracy of prediction changes between various areas of brain continuously across the time. In particular, we find that, during the object categorization task, the inter-trial phase coherence in low-frequency band is significantly higher than other frequency in various regions of interests. This measure is associated with decoding pattern across the time. These results suggest that the mechanism underlying conceptual representation can be mediated by the phase of oscillatory neural activity.

Drug-induced myelotoxicity usually leads to decrease the production of platelets, red cells, and white cells. Thus, early identification and characterization of myelotoxicity hazard in drug development is very necessary. The purpose of this investigation was to develop a prediction model of drug-induced myelotoxicity by using a Naïve Bayes classifier. For comparison, other prediction models based on support vector machine and single-hidden-layer feed-forward neural network  methods were also established. Among all the prediction models, the Naïve Bayes classification model showed the best prediction performance, which offered an average overall prediction accuracy of [Formula: see text] for the training set and [Formula: see text] for the external test set. The significant contributions of this study are that we first developed a Naïve Bayes classification model of drug-induced myelotoxicity adverse effect using a larger scale dataset, which could be employed for the prediction of drug-induced myelotoxicity. In addition, several important molecular descriptors and substructures of myelotoxic compounds have been identified, which should be taken into consideration in the design of new candidate compounds to produce safer and more effective drugs, ultimately reducing the attrition rate in later stages of drug development.

Despite the relatively high accuracy of the naïve Bayes (NB) classifier, there may be several instances where it is not optimal, i.e. does not have the same classification performance as the Bayes classifier utilizing the joint distribution of the examined attributes. However, the Bayes classifier can be computationally intractable due to its required knowledge of the joint distribution. Therefore, we introduce a "pairwise naïve" Bayes (PNB) classifier that incorporates all pairwise relationships among the examined attributes, but does not require specification of the joint distribution. In this paper, we first describe the necessary and sufficient conditions under which the PNB classifier is optimal. We then discuss sufficient conditions for which the PNB classifier, and not NB, is optimal for normal attributes. Through simulation and actual studies, we evaluate the performance of our proposed classifier relative to the Bayes and NB classifiers, along with the HNB, AODE, LBR and TAN classifiers, using normal density and empirical estimation methods. Our applications show that the PNB classifier using normal density estimation yields the highest accuracy for data sets containing continuous attributes. We conclude that it offers a useful compromise between the Bayes and NB classifiers.

Experimental evidence for the entire human proteome has been defined in the Human Proteome Project, and it is publicly available in the neXtProt database. However, there are still human proteins for which reliable experimental evidence does not exist, and the identification of such information has become one of the overriding objectives in the chromosome-centric study of the human proteome. With this aim and considering the complexity of protein detection using shotgun and targeted proteomics, the research community has addressed the integration of transcriptomics and proteomics landscapes. Here, we describe an analytical pipeline that predicts the probability of a missing protein being expressed in a biological sample based on (1) gene sequence characteristics, (2) the probability of an expressed gene being a coding gene of a missing protein in a certain sample, and (3) the probability of a gene being expressed in a transcriptomic experiment. More than 3400 microarray experiments were analyzed corresponding to three biological sources: cell lines, normal tissues, and cancer samples. A gene classification based on gene expression profiles distinguished among ubiquitous, nonubiquitous, nonexpressed, and coding genes of missing proteins. In addition, a different tissue-specific expression pattern for the coding genes of missing proteins is reported. Our results underline the relevance of selecting an appropriate sample for the detection of missing proteins and provide a comprehensive method to score their expression probability. Testis, brain, and skeletal muscle are the most promising normal tissues.