Displaying publications 81 - 100 of 133 in total

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  1. Characterization and classification of asthmatic wheeze sounds according to severity level using spectral integrated features
    Nabi FG, Sundaraj K, Lam CK, Palaniappan R
    Comput Biol Med, 2019 01;104:52-61.
    PMID: 30439599 DOI: 10.1016/j.compbiomed.2018.10.035
    OBJECTIVE: This study aimed to investigate and classify wheeze sounds of asthmatic patients according to their severity level (mild, moderate and severe) using spectral integrated (SI) features.

    METHOD: Segmented and validated wheeze sounds were obtained from auscultation recordings of the trachea and lower lung base of 55 asthmatic patients during tidal breathing manoeuvres. The segments were multi-labelled into 9 groups based on the auscultation location and/or breath phases. Bandwidths were selected based on the physiology, and a corresponding SI feature was computed for each segment. Univariate and multivariate statistical analyses were then performed to investigate the discriminatory behaviour of the features with respect to the severity levels in the various groups. The asthmatic severity levels in the groups were then classified using the ensemble (ENS), support vector machine (SVM) and k-nearest neighbour (KNN) methods.

    RESULTS AND CONCLUSION: All statistical comparisons exhibited a significant difference (p 

  2. Characterization of fibromyalgia using sleep EEG signals with nonlinear dynamical features
    Paul JK, Iype T, R D, Hagiwara Y, Koh JW, Acharya UR
    Comput Biol Med, 2019 08;111:103331.
    PMID: 31284155 DOI: 10.1016/j.compbiomed.2019.103331
    Fibromyalgia is an intense musculoskeletal pain causing sleep, fatigue, and mood problems. Sleep studies have suggested that 70%-80% of fibromyalgia patients complain of non-restorative sleep. The abnormalities in sleep have been implicated as both a cause and effect of the disease. In this paper, the electroencephalogram (EEG) signals of sleep stages 2 and 3 are used to classify the normal and fibromyalgia classes automatically. We have used various nonlinear parameters, namely sample entropy (SampEn), fractal dimension (FD), higher order spectra (HOS), largest Lyapunov exponent (LLE), Kolmogorov complexity (KC), Hurst exponent (HE), energy, and power in various frequency bands from the EEG signals. Then these features are subjected to Student's t-test to select the clinically significant features, and are classified using the support vector machine (SVM) classifier. Our proposed method can classify normal and fibromyalgia subjects using the stage 2 sleep EEG signals with an accuracy of 96.15%, sensitivity and specificity of 96.88% and 95.65%, respectively. Performance of the developed system can be improved further by adding more subjects in each class, and can be employed for clinical use.
  3. Machine learning-based coronary artery disease diagnosis: A comprehensive review
    Alizadehsani R, Abdar M, Roshanzamir M, Khosravi A, Kebria PM, Khozeimeh F, et al.
    Comput Biol Med, 2019 08;111:103346.
    PMID: 31288140 DOI: 10.1016/j.compbiomed.2019.103346
    Coronary artery disease (CAD) is the most common cardiovascular disease (CVD) and often leads to a heart attack. It annually causes millions of deaths and billions of dollars in financial losses worldwide. Angiography, which is invasive and risky, is the standard procedure for diagnosing CAD. Alternatively, machine learning (ML) techniques have been widely used in the literature as fast, affordable, and noninvasive approaches for CAD detection. The results that have been published on ML-based CAD diagnosis differ substantially in terms of the analyzed datasets, sample sizes, features, location of data collection, performance metrics, and applied ML techniques. Due to these fundamental differences, achievements in the literature cannot be generalized. This paper conducts a comprehensive and multifaceted review of all relevant studies that were published between 1992 and 2019 for ML-based CAD diagnosis. The impacts of various factors, such as dataset characteristics (geographical location, sample size, features, and the stenosis of each coronary artery) and applied ML techniques (feature selection, performance metrics, and method) are investigated in detail. Finally, the important challenges and shortcomings of ML-based CAD diagnosis are discussed.
  4. Fulltext Application of deep learning technique to manage COVID-19 in routine clinical practice using CT images: Results of 10 convolutional neural networks
    Ardakani AA, Kanafi AR, Acharya UR, Khadem N, Mohammadi A
    Comput Biol Med, 2020 06;121:103795.
    PMID: 32568676 DOI: 10.1016/j.compbiomed.2020.103795
    Fast diagnostic methods can control and prevent the spread of pandemic diseases like coronavirus disease 2019 (COVID-19) and assist physicians to better manage patients in high workload conditions. Although a laboratory test is the current routine diagnostic tool, it is time-consuming, imposing a high cost and requiring a well-equipped laboratory for analysis. Computed tomography (CT) has thus far become a fast method to diagnose patients with COVID-19. However, the performance of radiologists in diagnosis of COVID-19 was moderate. Accordingly, additional investigations are needed to improve the performance in diagnosing COVID-19. In this study is suggested a rapid and valid method for COVID-19 diagnosis using an artificial intelligence technique based. 1020 CT slices from 108 patients with laboratory proven COVID-19 (the COVID-19 group) and 86 patients with other atypical and viral pneumonia diseases (the non-COVID-19 group) were included. Ten well-known convolutional neural networks were used to distinguish infection of COVID-19 from non-COVID-19 groups: AlexNet, VGG-16, VGG-19, SqueezeNet, GoogleNet, MobileNet-V2, ResNet-18, ResNet-50, ResNet-101, and Xception. Among all networks, the best performance was achieved by ResNet-101 and Xception. ResNet-101 could distinguish COVID-19 from non-COVID-19 cases with an AUC of 0.994 (sensitivity, 100%; specificity, 99.02%; accuracy, 99.51%). Xception achieved an AUC of 0.994 (sensitivity, 98.04%; specificity, 100%; accuracy, 99.02%). However, the performance of the radiologist was moderate with an AUC of 0.873 (sensitivity, 89.21%; specificity, 83.33%; accuracy, 86.27%). ResNet-101 can be considered as a high sensitivity model to characterize and diagnose COVID-19 infections, and can be used as an adjuvant tool in radiology departments.
  5. Fulltext A machine learning model for early detection of diabetic foot using thermogram images
    Khandakar A, Chowdhury MEH, Ibne Reaz MB, Md Ali SH, Hasan MA, Kiranyaz S, et al.
    Comput Biol Med, 2021 10;137:104838.
    PMID: 34534794 DOI: 10.1016/j.compbiomed.2021.104838
    Diabetes foot ulceration (DFU) and amputation are a cause of significant morbidity. The prevention of DFU may be achieved by the identification of patients at risk of DFU and the institution of preventative measures through education and offloading. Several studies have reported that thermogram images may help to detect an increase in plantar temperature prior to DFU. However, the distribution of plantar temperature may be heterogeneous, making it difficult to quantify and utilize to predict outcomes. We have compared a machine learning-based scoring technique with feature selection and optimization techniques and learning classifiers to several state-of-the-art Convolutional Neural Networks (CNNs) on foot thermogram images and propose a robust solution to identify the diabetic foot. A comparatively shallow CNN model, MobilenetV2 achieved an F1 score of ∼95% for a two-feet thermogram image-based classification and the AdaBoost Classifier used 10 features and achieved an F1 score of 97%. A comparison of the inference time for the best-performing networks confirmed that the proposed algorithm can be deployed as a smartphone application to allow the user to monitor the progression of the DFU in a home setting.
  6. Fulltext A systematic literature review on obesity: Understanding the causes & consequences of obesity and reviewing various machine learning approaches used to predict obesity
    Safaei M, Sundararajan EA, Driss M, Boulila W, Shapi'i A
    Comput Biol Med, 2021 09;136:104754.
    PMID: 34426171 DOI: 10.1016/j.compbiomed.2021.104754
    Obesity is considered a principal public health concern and ranked as the fifth foremost reason for death globally. Overweight and obesity are one of the main lifestyle illnesses that leads to further health concerns and contributes to numerous chronic diseases, including cancers, diabetes, metabolic syndrome, and cardiovascular diseases. The World Health Organization also predicted that 30% of death in the world will be initiated with lifestyle diseases in 2030 and can be stopped through the suitable identification and addressing of associated risk factors and behavioral involvement policies. Thus, detecting and diagnosing obesity as early as possible is crucial. Therefore, the machine learning approach is a promising solution to early predictions of obesity and the risk of overweight because it can offer quick, immediate, and accurate identification of risk factors and condition likelihoods. The present study conducted a systematic literature review to examine obesity research and machine learning techniques for the prevention and treatment of obesity from 2010 to 2020. Accordingly, 93 papers are identified from the review articles as primary studies from an initial pool of over 700 papers addressing obesity. Consequently, this study initially recognized the significant potential factors that influence and cause adult obesity. Next, the main diseases and health consequences of obesity and overweight are investigated. Ultimately, this study recognized the machine learning methods that can be used for the prediction of obesity. Finally, this study seeks to support decision-makers looking to understand the impact of obesity on health in the general population and identify outcomes that can be used to guide health authorities and public health to further mitigate threats and effectively guide obese people globally.
  7. EEG feature fusion for motor imagery: A new robust framework towards stroke patients rehabilitation
    Al-Qazzaz NK, Alyasseri ZAA, Abdulkareem KH, Ali NS, Al-Mhiqani MN, Guger C
    Comput Biol Med, 2021 10;137:104799.
    PMID: 34478922 DOI: 10.1016/j.compbiomed.2021.104799
    Stroke is the second foremost cause of death worldwide and is one of the most common causes of disability. Several approaches have been proposed to manage stroke patient rehabilitation such as robotic devices and virtual reality systems, and researchers have found that the brain-computer interfaces (BCI) approaches can provide better results. Therefore, the most challenging tasks with BCI applications involve identifying the best technique(s) that can reveal the neuron stimulus information from the patients' brains and extracting the most effective features from these signals as well. Accordingly, the main novelty of this paper is twofold: propose a new feature fusion method for motor imagery (MI)-based BCI and develop an automatic MI framework to detect the changes pre- and post-rehabilitation. This study investigated the electroencephalography (EEG) dataset from post-stroke patients with upper extremity hemiparesis. All patients performed 25 MI-based BCI sessions with follow up assessment visits to examine the functional changes before and after EEG neurorehabilitation. In the first stage, conventional filters and automatic independent component analysis with wavelet transform (AICA-WT) denoising technique were used. Next, attributes from time, entropy and frequency domains were computed, and the effective features were combined into time-entropy-frequency (TEF) attributes. Consequently, the AICA-WT and the TEF fusion set were utilised to develop an AICA-WT-TEF framework. Then, support vector machine (SVM), k-nearest neighbours (kNN) and random forest (RF) classification technique were tested for MI-based BCI rehabilitation. The proposed AICA-WT-TEF framework with RF classifier achieves the best results compared with other classifiers. Finally, the proposed framework and feature fusion set achieve a significant performance in terms of accuracy measures compared to the state-of-the-art. Therefore, the proposed methods could be crucial for improving the process of automatic MI rehabilitation and are recommended for implementation in real-time applications.
  8. Unidirectional ablation minimizes unwanted thermal damage and promotes better thermal ablation efficacy in time-based switching bipolar radiofrequency ablation
    Ooi EH, Ooi ET
    Comput Biol Med, 2021 10;137:104832.
    PMID: 34508975 DOI: 10.1016/j.compbiomed.2021.104832
    Switching bipolar radiofrequency ablation (bRFA) is a thermal treatment modality used for liver cancer treatment that is capable of producing larger, more confluent and more regular thermal coagulation. When implemented in the no-touch mode, switching bRFA can prevent tumour track seeding; a medical phenomenon defined by the deposition of cancer cells along the insertion track. Nevertheless, the no-touch mode was found to yield significant unwanted thermal damage as a result of the electrodes' position outside the tumour. It is postulated that the unwanted thermal damage can be minimized if ablation can be directed such that it focuses only within the tumour domain. As it turns out, this can be achieved by partially insulating the active tip of the RF electrodes such that electric current flows in and out of the tissue only through the non-insulated section of the electrode. This concept is known as unidirectional ablation and has been shown to produce the desired effect in monopolar RFA. In this paper, computational models based on a well-established mathematical framework for modelling RFA was developed to investigate if unidirectional ablation can minimize unwanted thermal damage during time-based switching bRFA. From the numerical results, unidirectional ablation was shown to produce treatment efficacy of nearly 100%, while at the same time, minimizing the amount of unwanted thermal damage. Nevertheless, this effect was observed only when the switch interval of the time-based protocol was set to 50 s. An extended switch interval negated the benefits of unidirectional ablation.
  9. A deep CNN model for anomaly detection and localization in wireless capsule endoscopy images
    Jain S, Seal A, Ojha A, Yazidi A, Bures J, Tacheci I, et al.
    Comput Biol Med, 2021 10;137:104789.
    PMID: 34455302 DOI: 10.1016/j.compbiomed.2021.104789
    Wireless capsule endoscopy (WCE) is one of the most efficient methods for the examination of gastrointestinal tracts. Computer-aided intelligent diagnostic tools alleviate the challenges faced during manual inspection of long WCE videos. Several approaches have been proposed in the literature for the automatic detection and localization of anomalies in WCE images. Some of them focus on specific anomalies such as bleeding, polyp, lesion, etc. However, relatively fewer generic methods have been proposed to detect all those common anomalies simultaneously. In this paper, a deep convolutional neural network (CNN) based model 'WCENet' is proposed for anomaly detection and localization in WCE images. The model works in two phases. In the first phase, a simple and efficient attention-based CNN classifies an image into one of the four categories: polyp, vascular, inflammatory, or normal. If the image is classified in one of the abnormal categories, it is processed in the second phase for the anomaly localization. Fusion of Grad-CAM++ and a custom SegNet is used for anomalous region segmentation in the abnormal image. WCENet classifier attains accuracy and area under receiver operating characteristic of 98% and 99%. The WCENet segmentation model obtains a frequency weighted intersection over union of 81%, and an average dice score of 56% on the KID dataset. WCENet outperforms nine different state-of-the-art conventional machine learning and deep learning models on the KID dataset. The proposed model demonstrates potential for clinical applications.
  10. CASPIANET++: A multidimensional Channel-Spatial Asymmetric attention network with Noisy Student Curriculum Learning paradigm for brain tumor segmentation
    Liew A, Lee CC, Lan BL, Tan M
    Comput Biol Med, 2021 09;136:104690.
    PMID: 34352452 DOI: 10.1016/j.compbiomed.2021.104690
    Convolutional neural networks (CNNs) have been used quite successfully for semantic segmentation of brain tumors. However, current CNNs and attention mechanisms are stochastic in nature and neglect the morphological indicators used by radiologists to manually annotate regions of interest. In this paper, we introduce a channel and spatial wise asymmetric attention (CASPIAN) by leveraging the inherent structure of tumors to detect regions of saliency. To demonstrate the efficacy of our proposed layer, we integrate this into a well-established convolutional neural network (CNN) architecture to achieve higher Dice scores, with less GPU resources. Also, we investigate the inclusion of auxiliary multiscale and multiplanar attention branches to increase the spatial context crucial in semantic segmentation tasks. The resulting architecture is the new CASPIANET++, which achieves Dice Scores of 91.19%, 87.6% and 81.03% for whole tumor, tumor core and enhancing tumor respectively. Furthermore, driven by the scarcity of brain tumor data, we investigate the Noisy Student method for segmentation tasks. Our new Noisy Student Curriculum Learning paradigm, which infuses noise incrementally to increase the complexity of the training images exposed to the network, further boosts the enhancing tumor region to 81.53%. Additional validation performed on the BraTS2020 data shows that the Noisy Student Curriculum Learning method works well without any additional training or finetuning.
  11. Fulltext A numerical study to investigate the effects of tumour position on the treatment of bladder cancer in mice using gold nanorods assisted photothermal ablation
    Cheong JK, Popov V, Alchera E, Locatelli I, Alfano M, Menichetti L, et al.
    Comput Biol Med, 2021 11;138:104881.
    PMID: 34583149 DOI: 10.1016/j.compbiomed.2021.104881
    Gold nanorods assisted photothermal therapy (GNR-PTT) is a new cancer treatment technique that has shown promising potential for bladder cancer treatment. The position of the bladder cancer at different locations along the bladder wall lining can potentially affect the treatment efficacy since laser is irradiated externally from the skin surface. The present study investigates the efficacy of GNR-PTT in the treatment of bladder cancer in mice for tumours growing at three different locations on the bladder, i.e., Case 1: closest to skin surface, Case 2: at the bottom half of the bladder, and Case 3: at the side of the bladder. Investigations were carried out numerically using an experimentally validated framework for optical-thermal simulations. An in-silico approach was adopted due to the flexibility in placing the tumour at a desired location along the bladder lining. Results indicate that for the treatment parameters considered (laser power 0.3 W, GNR volume fraction 0.01% v/v), only Case 1 can be used for an effective GNR-PTT. No damage to the tumour was observed in Cases 2 and 3. Analysis of the thermo-physiological responses showed that the effectiveness of GNR-PTT in treating bladder cancer depends not only on the depth of the tumour from the skin surface, but also on the type of tissue that the laser must pass through before reaching the tumour. In addition, the results are reliant on GNRs with a diameter of 10 nm and an aspect ratio of 3.8 - tuned to exhibit peak absorption for the chosen laser wavelength. Results from the present study can be used to highlight the potential for using GNR-PTT for treatment of human bladder cancer. It appears that Cases 2 and 3 suggest that GNR-PTT, where the laser passes through the skin to reach the bladder, may be unfeasible in humans. While this study shows the feasibility of using GNRs for photothermal ablation of bladder cancer, it also identifies the current limitations needed to be overcome for an effective clinical application in the bladder cancer patients.
  12. Structural probing of HapR to identify potent phytochemicals to control Vibrio cholera through integrated computational approaches
    Tahir Ul Qamar M, Ahmad S, Khan A, Mirza MU, Ahmad S, Abro A, et al.
    Comput Biol Med, 2021 11;138:104929.
    PMID: 34655900 DOI: 10.1016/j.compbiomed.2021.104929
    Cholera is a severe small intestine bacterial disease caused by consumption of water and food contaminated with Vibrio cholera. The disease causes watery diarrhea leading to severe dehydration and even death if left untreated. In the past few decades, V. cholerae has emerged as multidrug-resistant enteric pathogen due to its rapid ability to adapt in detrimental environmental conditions. This research study aimed to design inhibitors of a master virulence gene expression regulator, HapR. HapR is critical in regulating the expression of several set of V. cholera virulence genes, quorum-sensing circuits and biofilm formation. A blind docking strategy was employed to infer the natural binding tendency of diverse phytochemicals extracted from medicinal plants by exposing the whole HapR structure to the screening library. Scoring function criteria was applied to prioritize molecules with strong binding affinity (binding energy 
  13. An investigation to study the effects of Tai Chi on human gait dynamics using classical machine learning
    Faisal MAA, Chowdhury MEH, Khandakar A, Hossain MS, Alhatou M, Mahmud S, et al.
    Comput Biol Med, 2022 Mar;142:105184.
    PMID: 35016098 DOI: 10.1016/j.compbiomed.2021.105184
    Tai Chi has been proven effective in preventing falls in older adults, improving the joint function of knee osteoarthritis patients, and improving the balance of stroke survivors. However, the effect of Tai Chi on human gait dynamics is still less understood. Studies conducted in this domain only relied on statistical and clinical measurements on the time-series gait data. In recent years machine learning has proven its ability in recognizing complex patterns from time-series data. In this research work, we have evaluated the performance of several machine learning algorithms in classifying the walking gait of Tai Chi masters (people expert on Tai Chi) from the normal subjects. The study is designed in a longitudinal manner where the Tai Chi naive subjects received 6 months of Tai Chi training and the data was recorded during the initial and follow-up sessions. A total of 57 subjects participated in the experiment among which 27 were Tai Chi masters. We have introduced a gender, BMI-based scaling of the features to mitigate their effects from the gait parameters. A hybrid feature ranking technique has also been proposed for selecting the best features for classification. The research reports 88.17% accuracy and 93.10% ROC AUC values from subject-wise 5-fold cross-validation for the Tai Chi masters' vs normal subjects' walking gait classification for the "Single-task" walking scenarios. We have also got fairly good accuracy for the "Dual-task" walking scenarios (82.62% accuracy and 84.11% ROC AUC values). The results indicate that Tai Chi clearly has an effect on the walking gait dynamics. The findings and methodology of this study could provide preliminary guidance for applying machine learning-based approaches to similar gait kinematics analyses.
  14. Robust biometric system using session invariant multimodal EEG and keystroke dynamics by the ensemble of self-ONNs
    Rahman A, Chowdhury MEH, Khandakar A, Tahir AM, Ibtehaz N, Hossain MS, et al.
    Comput Biol Med, 2022 Mar;142:105238.
    PMID: 35077938 DOI: 10.1016/j.compbiomed.2022.105238
    Harnessing the inherent anti-spoofing quality from electroencephalogram (EEG) signals has become a potential field of research in recent years. Although several studies have been conducted, still there are some vital challenges present in the deployment of EEG-based biometrics, which is stable and capable of handling the real-world scenario. One of the key challenges is the large signal variability of EEG when recorded on different days or sessions which impedes the performance of biometric systems significantly. To address this issue, a session invariant multimodal Self-organized Operational Neural Network (Self-ONN) based ensemble model combining EEG and keystroke dynamics is proposed in this paper. Our model is tested successfully on a large number of sessions (10 recording days) with many challenging noisy and variable environments for the identification and authentication tasks. In most of the previous studies, training and testing were performed either over a single recording session (same day) only or without ensuring appropriate splitting of the data on multiple recording days. Unlike those studies, in our work, we have rigorously split the data so that train and test sets do not share the data of the same recording day. The proposed multimodal Self-ONN based ensemble model has achieved identification accuracy of 98% in rigorous validation cases and outperformed the equivalent ensemble of deep CNN models. A novel Self-ONN Siamese network has also been proposed to measure the similarity of templates during the authentication task instead of the commonly used simple distance measure techniques. The multimodal Siamese network reduces the Equal Error Rate (EER) to 1.56% in rigorous authentication. The obtained results indicate that the proposed multimodal Self-ONN model can automatically extract session invariant unique non-linear features to identify and authenticate users with high accuracy.
  15. Discrete flower pollination algorithm for patient admission scheduling problem
    Abdalkareem ZA, Al-Betar MA, Amir A, Ehkan P, Hammouri AI, Salman OH
    Comput Biol Med, 2022 Feb;141:105007.
    PMID: 34785077 DOI: 10.1016/j.compbiomed.2021.105007
    This paper aims to tackle the Patient Admission Scheduling Problem (PASP) using the Discrete Flower Pollination Algorithm (DFPA), a new, meta-heuristic optimization method based on plant pollination. PASP is one of the most important problems in the field of health care. It is a highly constrained and combinatorial optimization problem of assigning patients to medical resources in a hospital, subject to predefined constraints, while maximizing patient comfort. While the flower pollination algorithm was designed for continuous optimization domains, a discretization of the algorithm has been carried out for application to the PASP. Various neighborhood structures have been employed to enhance the method, and to explore more solutions in the search space. The proposed method has been tested on six instances of benchmark datasets for comparison against another algorithm using the same dataset. The prospective method is shown to be very efficient in solving any scheduling problem.
  16. A nomogram-based diabetic sensorimotor polyneuropathy severity prediction using Michigan neuropathy screening instrumentations
    Haque F, Ibne Reaz MB, Chowdhury MEH, Md Ali SH, Ashrif A Bakar A, Rahman T, et al.
    Comput Biol Med, 2021 12;139:104954.
    PMID: 34715551 DOI: 10.1016/j.compbiomed.2021.104954
    BACKGROUND: Diabetic Sensorimotor polyneuropathy (DSPN) is one of the major indelible complications in diabetic patients. Michigan neuropathy screening instrumentation (MNSI) is one of the most common screening techniques used for DSPN, however, it does not provide any direct severity grading system.

    METHOD: For designing and modeling the DSPN severity grading systems for MNSI, 19 years of data from Epidemiology of Diabetes Interventions and Complications (EDIC) clinical trials were used. Different Machine learning-based feature ranking techniques were investigated to identify the important MNSI features associated with DSPN diagnosis. A multivariable logistic regression-based nomogram was generated and validated for DSPN severity grading using the best performing top-ranked MNSI features.

    RESULTS: Top-10 ranked features from MNSI features: Appearance of Feet (R), Ankle Reflexes (R), Vibration perception (L), Vibration perception (R), Appearance of Feet (L), 10-gm filament (L), Ankle Reflexes (L), 10-gm filament (R), Bed Cover Touch, and Ulceration (R) were identified as important features for identifying DSPN by Multi-Tree Extreme Gradient Boost model. The nomogram-based prediction model exhibited an accuracy of 97.95% and 98.84% for the EDIC test set and an independent test set, respectively. A DSPN severity score technique was generated for MNSI from the DSPN severity prediction model. DSPN patients were stratified into four severity levels: absent, mild, moderate, and severe using the cut-off values of 17.6, 19.1, 20.5 for the DSPN probability less than 50%, 75%-90%, and above 90%, respectively.

    CONCLUSIONS: The findings of this work provide a machine learning-based MNSI severity grading system which has the potential to be used as a secondary decision support system by health professionals in clinical applications and large clinical trials to identify high-risk DSPN patients.

  17. A review on omics-based biomarkers discovery for Alzheimer's disease from the bioinformatics perspectives: Statistical approach vs machine learning approach
    Tan MS, Cheah PL, Chin AV, Looi LM, Chang SW
    Comput Biol Med, 2021 12;139:104947.
    PMID: 34678481 DOI: 10.1016/j.compbiomed.2021.104947
    Alzheimer's Disease (AD) is a neurodegenerative disease that affects cognition and is the most common cause of dementia in the elderly. As the number of elderly individuals increases globally, the incidence and prevalence of AD are expected to increase. At present, AD is diagnosed clinically, according to accepted criteria. The essential elements in the diagnosis of AD include a patients history, a physical examination and neuropsychological testing, in addition to appropriate investigations such as neuroimaging. The omics-based approach is an emerging field of study that may not only aid in the diagnosis of AD but also facilitate the exploration of factors that influence the development of the disease. Omics techniques, including genomics, transcriptomics, proteomics and metabolomics, may reveal the pathways that lead to neuronal death and identify biomolecular markers associated with AD. This will further facilitate an understanding of AD neuropathology. In this review, omics-based approaches that were implemented in studies on AD were assessed from a bioinformatics perspective. Current state-of-the-art statistical and machine learning approaches used in the single omics analysis of AD were compared based on correlations of variants, differential expression, functional analysis and network analysis. This was followed by a review of the approaches used in the integration and analysis of multi-omics of AD. The strengths and limitations of multi-omics analysis methods were explored and the issues and challenges associated with omics studies of AD were highlighted. Lastly, future studies in this area of research were justified.
  18. Explainable deep learning ensemble for food image analysis on edge devices
    Tahir GA, Loo CK
    Comput Biol Med, 2021 12;139:104972.
    PMID: 34749093 DOI: 10.1016/j.compbiomed.2021.104972
    Food recognition systems recently garnered much research attention in the relevant field due to their ability to obtain objective measurements for dietary intake. This feature contributes to the management of various chronic conditions. Challenges such as inter and intraclass variations alongside the practical applications of smart glasses, wearable cameras, and mobile devices require resource-efficient food recognition models with high classification performance. Furthermore, explainable AI is also crucial in health-related domains as it characterizes model performance, enhancing its transparency and objectivity. Our proposed architecture attempts to address these challenges by drawing on the strengths of the transfer learning technique upon initializing MobiletNetV3 with weights from a pre-trained model of ImageNet. The MobileNetV3 achieves superior performance using the squeeze and excitation strategy, providing unequal weight to different input channels and contrasting equal weights in other variants. Despite being fast and efficient, there is a high possibility for it to be stuck in the local optima like other deep neural networks, reducing the desired classification performance of the model. Thus, we overcome this issue by applying the snapshot ensemble approach as it enables the M model in a single training process without any increase in the required training time. As a result, each snapshot in the ensemble visits different local minima before converging to the final solution which enhances recognition performance. On overcoming the challenge of explainability, we argue that explanations cannot be monolithic, since each stakeholder perceive the results', explanations based on different objectives and aims. Thus, we proposed a user-centered explainable artificial intelligence (AI) framework to increase the trust of the involved parties by inferencing and rationalizing the results according to needs and user profile. Our framework is comprehensive in terms of a dietary assessment app as it detects Food/Non-Food, food categories, and ingredients. Experimental results on the standard food benchmarks and newly contributed Malaysian food dataset for ingredient detection demonstrated superior performance on an integrated set of measures over other methodologies.
  19. Fulltext Computational modelling of potentially emerging SARS-CoV-2 spike protein RBDs mutations with higher binding affinity towards ACE2: A structural modelling study
    Khan A, Hussain S, Ahmad S, Suleman M, Bukhari I, Khan T, et al.
    Comput Biol Med, 2022 02;141:105163.
    PMID: 34979405 DOI: 10.1016/j.compbiomed.2021.105163
    The spike protein of SARS-CoV-2 and the host ACE2 receptor plays a vital role in the entry to the cell. Among which the hotspot residue 501 is continuously subjected to positive selection pressure and induces unusual virulence. Keeping in view the importance of the hot spot residue 501, we predicted the potentially emerging structural variants of 501 residue. We analyzed the binding pattern of wild type and mutants (Spike RBD) to the ACE2 receptor by deciphering variations in the amino acids' interaction networks by graph kernels along with evolutionary, network metrics, and energetic information. Our analysis revealed that N501I, N501T, and N501V increase the binding affinity and alter the intra and inter-residue bonding networks. The N501T has shown strong positive selection and fitness in other animals. Docking results and repeated simulations (three times) confirmed the structural stability and tighter binding of these three variants, correlated with the previous results following the global stability trend. Consequently, we reported three variants N501I, N501T, and N501V could worsen the situation further if they emerged. The relations between the viral fitness and binding affinity is a complicated game thus the emergence of high affinity mutations in the SARS-CoV-2 RBD brings up the question of whether or not positive selection favours these mutations or not?
  20. Automated characterization of fatty liver disease and cirrhosis using curvelet transform and entropy features extracted from ultrasound images
    Acharya UR, Raghavendra U, Fujita H, Hagiwara Y, Koh JE, Jen Hong T, et al.
    Comput Biol Med, 2016 12 01;79:250-258.
    PMID: 27825038 DOI: 10.1016/j.compbiomed.2016.10.022
    Fatty liver disease (FLD) is reversible disease and can be treated, if it is identified at an early stage. However, if diagnosed at the later stage, it can progress to an advanced liver disease such as cirrhosis which may ultimately lead to death. Therefore, it is essential to detect it at an early stage before the disease progresses to an irreversible stage. Several non-invasive computer-aided techniques are proposed to assist in the early detection of FLD and cirrhosis using ultrasound images. In this work, we are proposing an algorithm to discriminate automatically the normal, FLD and cirrhosis ultrasound images using curvelet transform (CT) method. Higher order spectra (HOS) bispectrum, HOS phase, fuzzy, Kapoor, max, Renyi, Shannon, Vajda and Yager entropies are extracted from CT coefficients. These extracted features are subjected to locality sensitive discriminant analysis (LSDA) feature reduction method. Then these LSDA coefficients ranked based on F-value are fed to different classifiers to choose the best performing classifier using minimum number of features. Our proposed technique can characterize normal, FLD and cirrhosis using probabilistic neural network (PNN) classifier with an accuracy of 97.33%, specificity of 100.00% and sensitivity of 96.00% using only six features. In addition, these chosen features are used to develop a liver disease index (LDI) to differentiate the normal, FLD and cirrhosis classes using a single number. This can significantly help the radiologists to discriminate FLD and cirrhosis in their routine liver screening.
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