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A review on the computational approaches for gene regulatory network construction

Chai LE, Loh SK, Low ST, Mohamad MS, Deris S, Zakaria Z

Comput Biol Med, 2014 May;48:55-65.
PMID: 24637147 DOI: 10.1016/j.compbiomed.2014.02.011

Many biological research areas such as drug design require gene regulatory networks to provide clear insight and understanding of the cellular process in living cells. This is because interactions among the genes and their products play an important role in many molecular processes. A gene regulatory network can act as a blueprint for the researchers to observe the relationships among genes. Due to its importance, several computational approaches have been proposed to infer gene regulatory networks from gene expression data. In this review, six inference approaches are discussed: Boolean network, probabilistic Boolean network, ordinary differential equation, neural network, Bayesian network, and dynamic Bayesian network. These approaches are discussed in terms of introduction, methodology and recent applications of these approaches in gene regulatory network construction. These approaches are also compared in the discussion section. Furthermore, the strengths and weaknesses of these computational approaches are described.

Matched MeSH terms: Bayes Theorem
New fragment weighting scheme for the Bayesian inference network in ligand-based virtual screening

Abdo A, Salim N

J Chem Inf Model, 2011 Jan 24;51(1):25-32.
PMID: 21155550 DOI: 10.1021/ci100232h

Many of the conventional similarity methods assume that molecular fragments that do not relate to biological activity carry the same weight as the important ones. One possible approach to this problem is to use the Bayesian inference network (BIN), which models molecules and reference structures as probabilistic inference networks. The relationships between molecules and reference structures in the Bayesian network are encoded using a set of conditional probability distributions, which can be estimated by the fragment weighting function, a function of the frequencies of the fragments in the molecule or the reference structure as well as throughout the collection. The weighting function combines one or more fragment weighting schemes. In this paper, we have investigated five different weighting functions and present a new fragment weighting scheme. Later on, these functions were modified to combine the new weighting scheme. Simulated virtual screening experiments with the MDL Drug Data Report (23) and maximum unbiased validation data sets show that the use of new weighting scheme can provide significantly more effective screening when compared with the use of current weighting schemes.

Matched MeSH terms: Bayes Theorem
Fulltext Investigating cultural evolution using phylogenetic analysis: the origins and descent of the southeast Asian tradition of warp ikat weaving

Buckley CD

PLoS One, 2012;7(12):e52064.
PMID: 23272211 DOI: 10.1371/journal.pone.0052064

The warp ikat method of making decorated textiles is one of the most geographically widespread in southeast Asia, being used by Austronesian peoples in Indonesia, Malaysia and the Philippines, and Daic peoples on the Asian mainland. In this study a dataset consisting of the decorative characters of 36 of these warp ikat weaving traditions is investigated using Bayesian and Neighbornet techniques, and the results are used to construct a phylogenetic tree and taxonomy for warp ikat weaving in southeast Asia. The results and analysis show that these diverse traditions have a common ancestor amongst neolithic cultures the Asian mainland, and parallels exist between the patterns of textile weaving descent and linguistic phylogeny for the Austronesian group. Ancestral state analysis is used to reconstruct some of the features of the ancestral weaving tradition. The widely held theory that weaving motifs originated in the late Bronze Age Dong-Son culture is shown to be inconsistent with the data.

Matched MeSH terms: Bayes Theorem
Fulltext Dormant phages of Helicobacter pylori reveal distinct populations in Europe

Vale FF, Vadivelu J, Oleastro M, Breurec S, Engstrand L, Perets TT, et al.

Sci Rep, 2015;5:14333.
PMID: 26387443 DOI: 10.1038/srep14333

Prophages of Helicobacter pylori, a bacterium known to co-evolve in the stomach of its human host, were recently identified. However, their role in the diversity of H. pylori strains is unknown. We demonstrate here and for the first time that the diversity of the prophage genes offers the ability to distinguish between European populations, and that H. pylori prophages and their host bacteria share a complex evolutionary history. By comparing the phylogenetic trees of two prophage genes (integrase and holin) and the multilocus sequence typing (MLST)-based data obtained for seven housekeeping genes, we observed that the majority of the strains belong to the same phylogeographic group in both trees. Furthermore, we found that the Bayesian analysis of the population structure of the prophage genes identified two H. pylori European populations, hpNEurope and hpSWEurope, while the MLST sequences identified one European population, hpEurope. The population structure analysis of H. pylori prophages was even more discriminative than the traditional MLST-based method for the European population. Prophages are new players to be considered not only to show the diversity of H. pylori strains but also to more sharply define human populations.

Matched MeSH terms: Bayes Theorem
Fulltext Modelling the longevity of dental restorations by means of a CBR system

Aliaga IJ, Vera V, De Paz JF, García AE, Mohamad MS

Biomed Res Int, 2015;2015:540306.
PMID: 25866792 DOI: 10.1155/2015/540306

The lifespan of dental restorations is limited. Longevity depends on the material used and the different characteristics of the dental piece. However, it is not always the case that the best and longest lasting material is used since patients may prefer different treatments according to how noticeable the material is. Over the last 100 years, the most commonly used material has been silver amalgam, which, while very durable, is somewhat aesthetically displeasing. Our study is based on the collection of data from the charts, notes, and radiographic information of restorative treatments performed by Dr. Vera in 1993, the analysis of the information by computer artificial intelligence to determine the most appropriate restoration, and the monitoring of the evolution of the dental restoration. The data will be treated confidentially according to the Organic Law 15/1999 on 13 December on the Protection of Personal Data. This paper also presents a clustering technique capable of identifying the most significant cases with which to instantiate the case-base. In order to classify the cases, a mixture of experts is used which incorporates a Bayesian network and a multilayer perceptron; the combination of both classifiers is performed with a neural network.

Matched MeSH terms: Bayes Theorem
Fulltext Geographical structure, narrow species ranges, and Cenozoic diversification in a pantropical clade of epiphyllous leafy liverworts

Bechteler J, Schäfer-Verwimp A, Lee GE, Feldberg K, Pérez-Escobar OA, Pócs T, et al.

Ecol Evol, 2017 01;7(2):638-653.
PMID: 28116059 DOI: 10.1002/ece3.2656

The evolutionary history and classification of epiphyllous cryptogams are still poorly known. Leptolejeunea is a largely epiphyllous pantropical liverwort genus with about 25 species characterized by deeply bilobed underleaves, elliptic to narrowly obovate leaf lobes, the presence of ocelli, and vegetative reproduction by cladia. Sequences of three chloroplast regions (rbcL, trnL-F, psbA) and the nuclear ribosomal ITS region were obtained for 66 accessions of Leptolejeunea and six outgroup species to explore the phylogeny, divergence times, and ancestral areas of this genus. The phylogeny was estimated using maximum-likelihood and Bayesian inference approaches, and divergence times were estimated with a Bayesian relaxed clock method. Leptolejeunea likely originated in Asia or the Neotropics within a time interval from the Early Eocene to the Late Cretaceous (67.9 Ma, 95% highest posterior density [HPD]: 47.9-93.7). Diversification of the crown group initiated in the Eocene or early Oligocene (38.4 Ma, 95% HPD: 27.2-52.6). Most species clades were established in the Miocene. Leptolejeunea epiphylla and L. schiffneri originated in Asia and colonized African islands during the Plio-Pleistocene. Accessions of supposedly pantropical species are placed in different main clades. Several monophyletic morphospecies exhibit considerable sequence variation related to a geographical pattern. The clear geographic structure of the Leptolejeunea crown group points to evolutionary processes including rare long-distance dispersal and subsequent speciation. Leptolejeunea may have benefitted from the large-scale distribution of humid tropical angiosperm forests in the Eocene.

Matched MeSH terms: Bayes Theorem
Modelling Asthma Cases by Count Analysis Approach: Poisson INGARCH and Negative Binomial INGARCH

'Aaishah Radziah Jamaludin, Fadhilah Yusof, Suhartono

MATEMATIKA, 2020;36(1):15-30.
MyJurnal

Johor Bahru with its rapid development where pollution is an issue that needs to be considered because it has contributed to the number of asthma cases in this area. Therefore, the goal of this study is to investigate the behaviour of asthma disease in Johor Bahru by count analysis approach namely; Poisson Integer Generalized Autoregressive Conditional Heteroscedasticity (Poisson-INGARCH) and Negative Binomial INGARCH (NB-INGARCH) with identity and log link function. Intervention analysis was conducted since the outbreak in the asthma data for the period of July 2012 to July 2013. This occurs perhaps due to the extremely bad haze in Johor Bahru from Indonesian fires. The estimation of the parameter will be done by quasi-maximum likelihood estimation. Model assessment was evaluated from the Pearson residuals, cumulative periodogram, the probability integral transform (PIT) histogram, log-likelihood value, Akaike’s Information Criterion (AIC) and Bayesian information criterion (BIC). Our result shows that NB-INGARCH with identity and log link function is adequate in representing the asthma data with uncorrelated Pearson residuals, higher in log likelihood, the PIT exhibits normality yet the lowest AIC and BIC. However, in terms of forecasting accuracy, NB-INGARCH with identity link function performed better with the smaller RMSE (8.54) for the sample data. Therefore, NB-INGARCH with identity link function can be applied as the prediction model for asthma disease in Johor Bahru. Ideally, this outcome can assist the Department of Health in executing counteractive action and early planning to curb asthma diseases in Johor Bahru.

Matched MeSH terms: Bayes Theorem
Fulltext Smart Helmet 5.0 for Industrial Internet of Things Using Artificial Intelligence

Campero-Jurado I, Márquez-Sánchez S, Quintanar-Gómez J, Rodríguez S, Corchado JM

Sensors (Basel), 2020 Nov 01;20(21).
PMID: 33139608 DOI: 10.3390/s20216241

Information and communication technologies (ICTs) have contributed to advances in Occupational Health and Safety, improving the security of workers. The use of Personal Protective Equipment (PPE) based on ICTs reduces the risk of accidents in the workplace, thanks to the capacity of the equipment to make decisions on the basis of environmental factors. Paradigms such as the Industrial Internet of Things (IIoT) and Artificial Intelligence (AI) make it possible to generate PPE models feasibly and create devices with more advanced characteristics such as monitoring, sensing the environment and risk detection between others. The working environment is monitored continuously by these models and they notify the employees and their supervisors of any anomalies and threats. This paper presents a smart helmet prototype that monitors the conditions in the workers' environment and performs a near real-time evaluation of risks. The data collected by sensors is sent to an AI-driven platform for analysis. The training dataset consisted of 11,755 samples and 12 different scenarios. As part of this research, a comparative study of the state-of-the-art models of supervised learning is carried out. Moreover, the use of a Deep Convolutional Neural Network (ConvNet/CNN) is proposed for the detection of possible occupational risks. The data are processed to make them suitable for the CNN and the results are compared against a Static Neural Network (NN), Naive Bayes Classifier (NB) and Support Vector Machine (SVM), where the CNN had an accuracy of 92.05% in cross-validation.

Matched MeSH terms: Bayes Theorem
Fulltext The classification of motor imagery response: an accuracy enhancement through the ensemble of random subspace k-NN

Rashid M, Bari BS, Hasan MJ, Razman MAM, Musa RM, Ab Nasir AF, et al.

PeerJ Comput Sci, 2021;7:e374.
PMID: 33817022 DOI: 10.7717/peerj-cs.374

Brain-computer interface (BCI) is a viable alternative communication strategy for patients of neurological disorders as it facilitates the translation of human intent into device commands. The performance of BCIs primarily depends on the efficacy of the feature extraction and feature selection techniques, as well as the classification algorithms employed. More often than not, high dimensional feature set contains redundant features that may degrade a given classifier's performance. In the present investigation, an ensemble learning-based classification algorithm, namely random subspace k-nearest neighbour (k-NN) has been proposed to classify the motor imagery (MI) data. The common spatial pattern (CSP) has been applied to extract the features from the MI response, and the effectiveness of random forest (RF)-based feature selection algorithm has also been investigated. In order to evaluate the efficacy of the proposed method, an experimental study has been implemented using four publicly available MI dataset (BCI Competition III dataset 1 (data-1), dataset IIIA (data-2), dataset IVA (data-3) and BCI Competition IV dataset II (data-4)). It was shown that the ensemble-based random subspace k-NN approach achieved the superior classification accuracy (CA) of 99.21%, 93.19%, 93.57% and 90.32% for data-1, data-2, data-3 and data-4, respectively against other models evaluated, namely linear discriminant analysis, support vector machine, random forest, Naïve Bayes and the conventional k-NN. In comparison with other classification approaches reported in the recent studies, the proposed method enhanced the accuracy by 2.09% for data-1, 1.29% for data-2, 4.95% for data-3 and 5.71% for data-4, respectively. Moreover, it is worth highlighting that the RF feature selection technique employed in the present study was able to significantly reduce the feature dimension without compromising the overall CA. The outcome from the present study implies that the proposed method may significantly enhance the accuracy of MI data classification.

Matched MeSH terms: Bayes Theorem
Fulltext Effective Connectivity of a Default Mode Network In Human Brain: In Search of a Dominant Node Using Spectral Dynamic Causal Modeling

Mohd Nawi, N. S. A., Rahmad, A. A., Abdul Hamid, K., Rahman, S., Osman, S. S., Surat, S., et al.

Physics and Technology in Medicine, 2020;1(1):1-14.
MyJurnal

The connectivity patterns among the DMN nodes when the brain is resting are still in great debate. Among the unknowns is whether a dominant node exists in the network and if any, how does it influences the other nodes. Resting state functional magnetic resonance imaging (rsfMRI) was utilized in data acquisition on 25 healthy male and female participants. The DMN nodes selected were posterior cingulate cortex (PCC), bilateral inferior parietal cortex (IPL) and medial prefrontal cortex (mPFC). Fully connected causal models were constructed comprising four DMN nodes. The time invariant covariance of the random fluctuations between nodes was then estimated to obtain the effective connectivity (EC) between the DMN nodes. The EC values among the DMN nodes were averaged over the participants using Bayesian Parameter Averaging (BPA). All the DMN nodes have self-inhibitory dynamics. All connections between nodes were significant (P > 0.9) with a condition for any of the two nodes, one node inhibited the others. The PCC which exhibited the highest signal intensity was in fact inhibited by others. Inter-hemispheric RIPC to LIPC connections acted the same way, with excitatory LIPC to RIPC and inhibitory RIPC to LIPC connections. The results also showed a stronger mPFC to RIPC connection in the right hemisphere (as compared to mPFC to LIPC connection in the left hemisphere) and a weaker PCC to RIPC connection in the right hemisphere (as compared to PCC to LIPC connection in the left hemisphere). PCC can be regarded as a dominant node among the four nodes, being connected to all other nodes in different ways. All the four nodes were significantly activated and connected to each other even though the brain was in a state of resting.

Matched MeSH terms: Bayes Theorem
Fulltext New Insights on the Evolution of the Sweet Taste Receptor of Primates Adapted to Harsh Environments

Tamrin NAM, Zainudin R, Esa Y, Alias H, Isa MNM, Croft L, et al.

Animals (Basel), 2020 Dec 10;10(12).
PMID: 33321745 DOI: 10.3390/ani10122359

Taste perception is an essential function that provides valuable dietary and sensory information, which is crucial for the survival of animals. Studies into the evolution of the sweet taste receptor gene (TAS1R2) are scarce, especially for Bornean endemic primates such as Nasalis larvatus (proboscis monkey), Pongo pygmaeus (Bornean orangutan), and Hylobates muelleri (Muller's Bornean gibbon). Primates are the perfect taxa to study as they are diverse dietary feeders, comprising specialist folivores, frugivores, gummivores, herbivores, and omnivores. We constructed phylogenetic trees of the TAS1R2 gene for 20 species of anthropoid primates using four different methods (neighbor-joining, maximum parsimony, maximum-likelihood, and Bayesian) and also established the time divergence of the phylogeny. The phylogeny successfully separated the primates into their taxonomic groups as well as by their dietary preferences. Of note, the reviewed time of divergence estimation for the primate speciation pattern in this study was more recent than the previously published estimates. It is believed that this difference may be due to environmental changes, such as food scarcity and climate change, during the late Miocene epoch, which forced primates to change their dietary preferences. These findings provide a starting point for further investigation.

Matched MeSH terms: Bayes Theorem
The utility of the Laplace effect size prior distribution in Bayesian fine-mapping studies

Walters K, Cox A, Yaacob H

Genet Epidemiol, 2021 Jun;45(4):386-401.
PMID: 33410201 DOI: 10.1002/gepi.22375

The Gaussian distribution is usually the default causal single-nucleotide polymorphism (SNP) effect size prior in Bayesian population-based fine-mapping association studies, but a recent study showed that the heavier-tailed Laplace prior distribution provided a better fit to breast cancer top hits identified in genome-wide association studies. We investigate the utility of the Laplace prior as an effect size prior in univariate fine-mapping studies. We consider ranking SNPs using Bayes factors and other summaries of the effect size posterior distribution, the effect of prior choice on credible set size based on the posterior probability of causality, and on the noteworthiness of SNPs in univariate analyses. Across a wide range of fine-mapping scenarios the Laplace prior generally leads to larger 90% credible sets than the Gaussian prior. These larger credible sets for the Laplace prior are due to relatively high prior mass around zero which can yield many noncausal SNPs with relatively large Bayes factors. If using conventional credible sets, the Gaussian prior generally yields a better trade off between including the causal SNP with high probability and keeping the set size reasonable. Interestingly when using the less well utilised measure of noteworthiness, the Laplace prior performs well, leading to causal SNPs being declared noteworthy with high probability, whilst generally declaring fewer than 5% of noncausal SNPs as being noteworthy. In contrast, the Gaussian prior leads to the causal SNP being declared noteworthy with very low probability.

Matched MeSH terms: Bayes Theorem
Fulltext SENTIMENT ANALYSIS OF PEOPLE’S ACCEPTANCE TOWARDS THE NEW MALAYSIAN GOVERNMENT USING NAÏVE BAYES METHOD

R.U GOBITHAASAN, NUR FARHANA SYAHIRA CHE HAMID

UMT Journal of Undergraduate Research, 2020;2(3):93-102.
MyJurnal

Sentiment analysis is a field of research that has a significant impact on today’s nations, politics and businesses. It is an algorithmic process to comprehend the opinions of a given subject based on the Natural Language Processing (NLP) methodologies. It has received much attention in recent years and is proven vital in various fields, e.g., online product reviews and social media analysis (Twitter, Facebook, etc.). This paper reports the outcome of sentiment analysis to investigate people’s acceptance of Pakatan Harapan, as the new Malaysian government, spearheaded by Tun Dr. Mahathir Mohamad and Dr. Wan Azizah, with an influence of Dato Seri Anwar Ibrahim. The objective is to classify tweets into three types of sentiments; positive, neutral and negative using Naïve Bayes method which is readily available in Python. The first step is tweets extraction for a month (March to April 2019) using search queries: {Pakatan Harapan, Mahathir, Anwar Ibrahim, Wan Azizah}. It is followed by tweets wrangling using NLP library and lastly output visualization in the form of a word cloud. A word cloud is a visual representation of text data with various font sizes depending on its probabilities. Final results showed that the tweets related to new government consist of neutral sentiment (41%) followed by positive sentiment (30%) and negative sentiment (29%). Malaysians do prefer the new government. However careful mitigation steps must be crafted to overcome controversial issues such as the ‘Rome Statute’ to avoid negative digital footprint, hence winning the Malaysians’ heart.

Matched MeSH terms: Bayes Theorem
Fulltext Molecular Phylogenesis and Spatiotemporal Spread of SARS-CoV-2 in Southeast Asia

Zhu M, Shen J, Zeng Q, Tan JW, Kleepbua J, Chew I, et al.

Front Public Health, 2021 07 30;9:685315.
PMID: 34395364 DOI: 10.3389/fpubh.2021.685315

Background: The ongoing coronavirus disease 2019 (COVID-19) pandemic has posed an unprecedented challenge to public health in Southeast Asia, a tropical region with limited resources. This study aimed to investigate the evolutionary dynamics and spatiotemporal patterns of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in the region. Materials and Methods: A total of 1491 complete SARS-CoV-2 genome sequences from 10 Southeast Asian countries were downloaded from the Global Initiative on Sharing Avian Influenza Data (GISAID) database on November 17, 2020. The evolutionary relationships were assessed using maximum likelihood (ML) and time-scaled Bayesian phylogenetic analyses, and the phylogenetic clustering was tested using principal component analysis (PCA). The spatial patterns of SARS-CoV-2 spread within Southeast Asia were inferred using the Bayesian stochastic search variable selection (BSSVS) model. The effective population size (Ne) trajectory was inferred using the Bayesian Skygrid model. Results: Four major clades (including one potentially endemic) were identified based on the maximum clade credibility (MCC) tree. Similar clustering was yielded by PCA; the first three PCs explained 46.9% of the total genomic variations among the samples. The time to the most recent common ancestor (tMRCA) and the evolutionary rate of SARS-CoV-2 circulating in Southeast Asia were estimated to be November 28, 2019 (September 7, 2019 to January 4, 2020) and 1.446 × 10-3 (1.292 × 10-3 to 1.613 × 10-3) substitutions per site per year, respectively. Singapore and Thailand were the two most probable root positions, with posterior probabilities of 0.549 and 0.413, respectively. There were high-support transmission links (Bayes factors exceeding 1,000) in Singapore, Malaysia, and Indonesia; Malaysia involved the highest number (7) of inferred transmission links within the region. A twice-accelerated viral population expansion, followed by a temporary setback, was inferred during the early stages of the pandemic in Southeast Asia. Conclusions: With available genomic data, we illustrate the phylogeography and phylodynamics of SARS-CoV-2 circulating in Southeast Asia. Continuous genomic surveillance and enhanced strategic collaboration should be listed as priorities to curb the pandemic, especially for regional communities dominated by developing countries.

Matched MeSH terms: Bayes Theorem
Fulltext Using Machine Learning Algorithms to Develop a Clinical Decision-Making Tool for COVID-19 Inpatients

Vepa A, Saleem A, Rakhshan K, Daneshkhah A, Sedighi T, Shohaimi S, et al.

Int J Environ Res Public Health, 2021 06 09;18(12).
PMID: 34207560 DOI: 10.3390/ijerph18126228

BACKGROUND: Within the UK, COVID-19 has contributed towards over 103,000 deaths. Although multiple risk factors for COVID-19 have been identified, using this data to improve clinical care has proven challenging. The main aim of this study is to develop a reliable, multivariable predictive model for COVID-19 in-patient outcomes, thus enabling risk-stratification and earlier clinical decision-making.
METHODS: Anonymised data consisting of 44 independent predictor variables from 355 adults diagnosed with COVID-19, at a UK hospital, was manually extracted from electronic patient records for retrospective, case-control analysis. Primary outcomes included inpatient mortality, required ventilatory support, and duration of inpatient treatment. Pulmonary embolism sequala was the only secondary outcome. After balancing data, key variables were feature selected for each outcome using random forests. Predictive models were then learned and constructed using Bayesian networks.
RESULTS: The proposed probabilistic models were able to predict, using feature selected risk factors, the probability of the mentioned outcomes. Overall, our findings demonstrate reliable, multivariable, quantitative predictive models for four outcomes, which utilise readily available clinical information for COVID-19 adult inpatients. Further research is required to externally validate our models and demonstrate their utility as risk stratification and clinical decision-making tools.

Matched MeSH terms: Bayes Theorem
Fulltext Bayesian network classification of gastrointestinal bleeding

Nazziwa Aisha, Mohd Bakri Adam, Shamarina Shohaimi, Aida Mustapha

Pertanika Journal of Science & Technology, 2014;22(2):567-575.
MyJurnal

The source of gastrointestinal bleeding (GIB) remains uncertain in patients presenting without hematemesis. This paper aims at studying the accuracy, specificity and sensitivity of the Naive Bayesian Classifier (NBC) in identifying the source of GIB in the absence of hematemesis. Data of 325 patients admitted via the emergency department (ED) for GIB without hematemesis and who underwent confirmatory testing were analysed. Six attributes related to demography and their presenting signs were chosen. NBC was used to calculate the conditional probability of an individual being assigned to Upper Gastrointestinal bleeding (UGIB) or Lower Gastrointestinal bleeding (LGIB). High classification accuracy (87.3 %), specificity (0.85) and sensitivity (0.88) were achieved. NBC is a useful tool to support the identification of the source of gastrointestinal bleeding in patients without hematemesis.

Matched MeSH terms: Bayes Theorem
Fulltext Correlation analysis of air pollutant index levels and dengue cases across five different zones in Selangor, Malaysia

Thiruchelvam L, Dass SC, Zaki R, Yahya A, Asirvadam VS

Geospat Health, 2018 05 07;13(1):613.
PMID: 29772882 DOI: 10.4081/gh.2018.613

This study investigated the potential relationship between dengue cases and air quality - as measured by the Air Pollution Index (API) for five zones in the state of Selangor, Malaysia. Dengue case patterns can be learned using prediction models based on feedback (lagged terms). However, the question whether air quality affects dengue cases is still not thoroughly investigated based on such feedback models. This work developed dengue prediction models using the autoregressive integrated moving average (ARIMA) and ARIMA with an exogeneous variable (ARIMAX) time series methodologies with API as the exogeneous variable. The Box Jenkins approach based on maximum likelihood was used for analysis as it gives effective model estimates and prediction. Three stages of model comparison were carried out for each zone: first with ARIMA models without API, then ARIMAX models with API data from the API station for that zone and finally, ARIMAX models with API data from the zone and spatially neighbouring zones. Bayesian Information Criterion (BIC) gives goodness-of-fit versus parsimony comparisons between all elicited models. Our study found that ARIMA models, with the lowest BIC value, outperformed the rest in all five zones. The BIC values for the zone of Kuala Selangor were -800.66, -796.22, and -790.5229, respectively, for ARIMA only, ARIMAX with single API component and ARIMAX with API components from its zone and spatially neighbouring zones. Therefore, we concluded that API levels, either temporally for each zone or spatio- temporally based on neighbouring zones, do not have a significant effect on dengue cases.

Matched MeSH terms: Bayes Theorem
Examining the relationship between local extinction risk and position in range

Boakes EH, Isaac NJB, Fuller RA, Mace GM, McGowan PJK

Conserv Biol, 2018 02;32(1):229-239.
PMID: 28678438 DOI: 10.1111/cobi.12979

Over half of globally threatened animal species have experienced rapid geographic range loss. Identifying the parts of species' distributions most vulnerable to local extinction would benefit conservation planning. However, previous studies give little consensus on whether ranges decline to the core or edge. We built on previous work by using empirical data to examine the position of recent local extinctions within species' geographic ranges, address range position as a continuum, and explore the influence of environmental factors. We aggregated point-locality data for 125 Galliform species from across the Palearctic and Indo-Malaya into equal-area half-degree grid cells and used a multispecies dynamic Bayesian occupancy model to estimate rates of local extinctions. Our model provides a novel approach to identify loss of populations from within species ranges. We investigated the relationship between extinction rates and distance from range edge by examining whether patterns were consistent across biogeographic realm and different categories of land use. In the Palearctic, local extinctions occurred closer to the range edge than range core in both unconverted and human-dominated landscapes. In Indo-Malaya, no pattern was found for unconverted landscapes, but in human-dominated landscapes extinctions tended to occur closer to the core than the edge. Our results suggest that local and regional factors override general spatial patterns of recent local extinction within species' ranges and highlight the difficulty of predicting the parts of a species' distribution most vulnerable to threat.

Matched MeSH terms: Bayes Theorem
Fulltext Automatic Annotation of Unlabeled Data from Smartphone-Based Motion and Location Sensors

Pius Owoh N, Mahinderjit Singh M, Zaaba ZF

Sensors (Basel), 2018 Jul 03;18(7).
PMID: 29970823 DOI: 10.3390/s18072134

Automatic data annotation eliminates most of the challenges we faced due to the manual methods of annotating sensor data. It significantly improves users’ experience during sensing activities since their active involvement in the labeling process is reduced. An unsupervised learning technique such as clustering can be used to automatically annotate sensor data. However, the lingering issue with clustering is the validation of generated clusters. In this paper, we adopted the k-means clustering algorithm for annotating unlabeled sensor data for the purpose of detecting sensitive location information of mobile crowd sensing users. Furthermore, we proposed a cluster validation index for the k-means algorithm, which is based on Multiple Pair-Frequency. Thereafter, we trained three classifiers (Support Vector Machine, K-Nearest Neighbor, and Naïve Bayes) using cluster labels generated from the k-means clustering algorithm. The accuracy, precision, and recall of these classifiers were evaluated during the classification of “non-sensitive” and “sensitive” data from motion and location sensors. Very high accuracy scores were recorded from Support Vector Machine and K-Nearest Neighbor classifiers while a fairly high accuracy score was recorded from the Naïve Bayes classifier. With the hybridized machine learning (unsupervised and supervised) technique presented in this paper, unlabeled sensor data was automatically annotated and then classified.

Matched MeSH terms: Bayes Theorem
Modeling flood susceptibility using data-driven approaches of naïve Bayes tree, alternating decision tree, and random forest methods

Chen W, Li Y, Xue W, Shahabi H, Li S, Hong H, et al.

Sci Total Environ, 2020 Jan 20;701:134979.
PMID: 31733400 DOI: 10.1016/j.scitotenv.2019.134979

Floods are one of the most devastating types of disasters that cause loss of lives and property worldwide each year. This study aimed to evaluate and compare the prediction capability of the naïve Bayes tree (NBTree), alternating decision tree (ADTree), and random forest (RF) methods for the spatial prediction of flood occurrence in the Quannan area, China. A flood inventory map with 363 flood locations was produced and partitioned into training and validation datasets through random selection with a ratio of 70/30. The spatial flood database was constructed using thirteen flood explanatory factors. The probability certainty factor (PCF) method was used to analyze the correlation between the factors and flood occurrences. Consequently, three flood susceptibility maps were produced using the NBTree, ADTree, and RF methods. Finally, the area under the curve (AUC) and statistical measures were used to validate the flood susceptibility models. The results indicated that the RF method is an efficient and reliable model in flood susceptibility assessment, with the highest AUC values, positive predictive rate, negative predictive rate, sensitivity, specificity, and accuracy for the training (0.951, 0.892, 0.941, 0.945, 0.886, and 0.915, respectively) and validation (0.925, 0.851, 0.938, 0.945, 0.835, and 0.890, respectively) datasets.

Matched MeSH terms: Bayes Theorem

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