Deep learning PET/CT-based radiomics integrates clinical data: A feasibility study to distinguish between tuberculosis nodules and lung cancer.

BACKGROUND: Radiomic diagnosis models generally consider only a single dimension of information, leading to limitations in their diagnostic accuracy and reliability. The integration of multiple dimensions of information into the deep learning model have the potential to improve its diagnostic capabilities. The purpose of study was to evaluate the performance of deep learning model in distinguishing tuberculosis (TB) nodules and lung cancer (LC) based on deep learning features, radiomic features, and clinical information. METHODS: Positron emission tomography (PET) and computed tomography (CT) image data from 97 patients with LC and 77 patients with TB nodules were collected. One hundred radiomic features were extracted from both PET and CT imaging using the pyradiomics platform, and 2048 deep learning features were obtained through a residual neural network approach. Four models included traditional machine learning model with radiomic features as input (traditional radiomics), a deep learning model with separate input of image features (deep convolutional neural networks [DCNN]), a deep learning model with two inputs of radiomic features and deep learning features (radiomics-DCNN) and a deep learning model with inputs of radiomic features and deep learning features and clinical information (integrated model). The models were evaluated using area under the curve (AUC), sensitivity, accuracy, specificity, and F1-score metrics. RESULTS: The results of the classification of TB nodules and LC showed that the integrated model achieved an AUC of 0.84 (0.82-0.88), sensitivity of 0.85 (0.80-0.88), and specificity of 0.84 (0.83-0.87), performing better than the other models. CONCLUSION: The integrated model was found to be the best classification model in the diagnosis of TB nodules and solid LC.

Effects of orthographic transparency on rhyme judgement.

This study investigated the influence of multiliteracy in opaque orthographies on phonological awareness. Using a visual rhyme judgement task in English, we assessed phonological processing in three multilingual and multiliterate populations who were distinguished by the transparency of the orthographies they can read in (N = 135; ages 18-40). The first group consisted of 45 multilinguals literate in English and a transparent Latin orthography like Malay; the second group consisted of 45 multilinguals literate in English and transparent orthographies like Malay and Arabic; and the third group consisted of 45 multilinguals literate in English, transparent orthographies, and Mandarin Chinese, an opaque orthography. Results showed that all groups had poorer performance in the two opaque conditions: rhyming pairs with different orthographic endings and non-rhyming pairs with similar orthographic endings, with the latter posing the greatest difficulty. Subjects whose languages consisted of half or more opaque orthographies performed significantly better than subjects who knew more transparent orthographies than opaque orthographies. The findings are consistent with past studies that used the visual rhyme judgement paradigm and suggest that literacy experience acquired over time relating to orthographic transparency may influence performance on phonological awareness tasks.

An Innovative Concept of a 3D-Coded Aperture Imaging System Proposed for Early Breast Cancer Detection.

Coded Aperture (CA) imaging has recently been used in nuclear medicine, but still, there is no commercial SPECT imaging camera based on CA for cancer detection. The literature is rich in examples of using the CA for planar and thin 3D imaging. However, thick 3D reconstruction is still challenging for small lesion detection. This paper presents the results of mosaic modified uniformly redundant array (MURA) mask/antimask CA combined with a maximum-likelihood expectation-maximization (MLEM) algorithm. The MLEM is an iterative algorithm applied to a mosaic MURA CA mask/antimask for 3D anthropomorphic breast phantom reconstruction, slice by slice. The difference between the mask and the antimask suppresses the background noise to enhance the quality of reconstructed images. Furthermore, all reconstructed slices are stacked to form a 3D breast phantom image from single-projection data. The results of phantom reconstruction with 8 mm, 6 mm, 4 mm, and 3 mm lesions are presented. Moreover, the proposed SPECT imaging camera can reconstruct a 3D breast phantom from single-projection data of the patient's scanning. To assess the quality of lesions in the reconstructed images, the contrast-to-background ratio (CBR), the peak signal-to-noise ratio (PSNR) and mean square error (MSE) were measured.

Towards efficient Monte Carlo N-Particle simulation of a positron emission tomography (PET) via source volume definition.

Monte Carlo N-Particle (MCNP) simulation has been extensively proven in nuclear medicine imaging systems, most notably in designing and optimizing new medical imaging tools. It enables more complicated geometries and the simulation of particles passing through and interacting with materials. However, a relatively long simulation time is a drawback of Monte Carlo simulation, mainly when complex geometry exists. The current study presents an alternative variance reduction technique for a modeled positron emission tomography (PET) camera by reducing the height of the source volume definition while maintaining the geometry of the simulated model. The National Electrical Manufacturers Association (NEMA) of the International Electrotechnical Commission (IEC) PET's phantom was used with a 1 cm diameter and 7 cm height of line source placed in the middle. The first geometry was fully filled the line source with 0.50 mCi radioactivity. In contrast, the second geometry decreased the source definition to 2.4 cm in height, covering 1 cm above and below the sub-block detector level. The source volume definition approach led to a 71% reduction in the total photons to be simulated. Results showed that the proposed variance reduction strategy could produce spatial resolution as precise as fully filled geometry and sped up the simulation time by approximately 65%. Hence, this strategy can be utilized for further PET optimizing simulation studies.

Task-State EEG Signal Classification for Spatial Cognitive Evaluation Based on Multiscale High-Density Convolutional Neural Network.

In this study, a multi-scale high-density convolutional neural network (MHCNN) classification method for spatial cognitive ability assessment was proposed, aiming at achieving the binary classification of task-state EEG signals before and after spatial cognitive training. Besides, the multi-dimensional conditional mutual information method was used to extract the frequency band features of the EEG data. And the coupling features under the combination of multi-frequency bands were transformed into multi-spectral images. At the same time, the idea of Densenet was introduced to improve the multi-scale convolutional neural network. Firstly, according to the discreteness of multispectral EEG image features, two-scale convolution kernels were used to calculate and learn useful channel and frequency band feature information in multispectral image data. Secondly, to enhance feature propagation and reduce the number of parameters, the dense network was connected after the multi-scale convolutional network, and the learning rate change function of the stochastic gradient descent algorithm was optimized to objectively evaluate the training effect. The experimental results showed that compared with the classical convolution neural network (CNN) and multi-scale convolution neural network, the proposed MHCNN had better classification performance in the six frequency band combinations with the highest accuracy of 98%: Theta-Alpha2-Gamma, Alpha2-Beta2-Gamma, Beta1-Beta2-Gamma, Theta-Beta2-Gamma, Theta- Alpha1-Gamma, and Alpha1-Alpha2-Gamma. By comparing the classification results of six frequency band combinations, it was found that the combination of the Theta-Beta2-Gamma band had the best classification effect. The MHCNN classification method proposed in this research could be used as an effective biological indicator of spatial cognitive training effect and could be extended to other brain function evaluations.

Multi-dimensional conditional mutual information with application on the EEG signal analysis for spatial cognitive ability evaluation.

This study aims to explore an effective method to evaluate spatial cognitive ability, which can effectively extract and classify the feature of EEG signals collected from subjects participating in the virtual reality (VR) environment; and evaluate the training effect objectively and quantitatively to ensure the objectivity and accuracy of spatial cognition evaluation, according to the classification results. Therefore, a multi-dimensional conditional mutual information (MCMI) method is proposed, which could calculate the coupling strength of two channels considering the influence of other channels. The coupled characteristics of the multi-frequency combination were transformed into multi-spectral images, and the image data were classified employing the convolutional neural networks (CNN) model. The experimental results showed that the multi-spectral image transform features based on MCMI are better in classification than other methods, and among the classification results of six band combinations, the best classification accuracy of Beta1-Beta2-Gamma combination is 98.3%. The MCMI characteristics on the Beta1-Beta2-Gamma band combination can be a biological marker for the evaluation of spatial cognition. The proposed feature extraction method based on MCMI provides a new perspective for spatial cognitive ability assessment and analysis.

Hyperparameter Tuning and Pipeline Optimization via Grid Search Method and Tree-Based AutoML in Breast Cancer Prediction.

Automated machine learning (AutoML) has been recognized as a powerful tool to build a system that automates the design and optimizes the model selection machine learning (ML) pipelines. In this study, we present a tree-based pipeline optimization tool (TPOT) as a method for determining ML models with significant performance and less complex breast cancer diagnostic pipelines. Some features of pre-processors and ML models are defined as expression trees and optimal gene programming (GP) pipelines, a stochastic search system. Features of radiomics have been presented as a guide for the ML pipeline selection from the breast cancer data set based on TPOT. Breast cancer data were used in a comparative analysis of the TPOT-generated ML pipelines with the selected ML classifiers, optimized by a grid search approach. The principal component analysis (PCA) random forest (RF) classification was proven to be the most reliable pipeline with the lowest complexity. The TPOT model selection technique exceeded the performance of grid search (GS) optimization. The RF classifier showed an outstanding outcome amongst the models in combination with only two pre-processors, with a precision of 0.83. The grid search optimized for support vector machine (SVM) classifiers generated a difference of 12% in comparison, while the other two classifiers, naïve Bayes (NB) and artificial neural network-multilayer perceptron (ANN-MLP), generated a difference of almost 39%. The method's performance was based on sensitivity, specificity, accuracy, precision, and receiver operating curve (ROC) analysis.

Stability and Reproducibility of Radiomic Features Based Various Segmentation Technique on MR Images of Hepatocellular Carcinoma (HCC).

Hepatocellular carcinoma (HCC) is considered as a complex liver disease and ranked as the eighth-highest mortality rate with a prevalence of 2.4% in Malaysia. Magnetic resonance imaging (MRI) has been acknowledged for its advantages, a gold technique for diagnosing HCC, and yet the false-negative diagnosis from the examinations is inevitable. In this study, 30 MR images from patients diagnosed with HCC is used to evaluate the robustness of semi-automatic segmentation using the flood fill algorithm for quantitative features extraction. The relevant features were extracted from the segmented MR images of HCC. Four types of features extraction were used for this study, which are tumour intensity, shape feature, textural feature and wavelet feature. A total of 662 radiomic features were extracted from manual and semi-automatic segmentation and compared using intra-class relation coefficient (ICC). Radiomic features extracted using semi-automatic segmentation utilized flood filling algorithm from 3D-slicer had significantly higher reproducibility (average ICC = 0.952 ± 0.009, p < 0.05) compared with features extracted from manual segmentation (average ICC = 0.897 ± 0.011, p > 0.05). Moreover, features extracted from semi-automatic segmentation were more robust compared to manual segmentation. This study shows that semi-automatic segmentation from 3D-Slicer is a better alternative to the manual segmentation, as they can produce more robust and reproducible radiomic features.

Classification of ERP signal from amnestic mild cognitive impairment with type 2 diabetes mellitus using single-scale multi-input convolution neural network.

BACKGROUND: The application of deep learning models to electroencephalogram (EEG) signal classification has recently become a popular research topic. Several deep learning models have been proposed to classify EEG signals in patients with various neurological diseases. However, no effective deep learning model for event-related potential (ERP) signal classification is yet available for amnestic mild cognitive impairment (aMCI) with type 2 diabetes mellitus (T2DM). METHOD: This study proposed a single-scale multi-input convolutional neural network (SSMICNN) method to classify ERP signals between aMCI patients with T2DM and the control group. Firstly, the 18-electrode ERP signal on alpha, beta, and theta frequency bands was extracted by using the fast Fourier transform, and then the mean, sum of squares, and absolute value feature of each frequency band were calculated. Finally, these three features are converted into multispectral images respectively and used as the input of the SSMICNN network to realize the classification task. RESULTS: The results show that the SSMICNN can fuse MSI formed by different features, SSMICNN enriches the feature quantity of the neural network input layer and has excellent robustness, and the errors of SSMICNN can be simultaneously transmitted to the three convolution channels in the back-propagation phase. Comparison with Existing Method(s): SSMICNN could more effectively identify ERP signals from aMCI with T2DM from the control group compared to existing classification methods, including convolution neural network, support vector machine, and logistic regression. CONCLUSIONS: The combination of SSMICNN and MSI can be used as an effective biological marker to distinguish aMCI patients with T2DM from the control group.

Multiparametric MRI for the improved diagnostic accuracy of Alzheimer's disease and mild cognitive impairment: Research protocol of a case-control study design.

BACKGROUND: Alzheimer's disease (AD) is a major neurocognitive disorder identified by memory loss and a significant cognitive decline based on previous level of performance in one or more cognitive domains that interferes in the independence of everyday activities. The accuracy of imaging helps to identify the neuropathological features that differentiate AD from its common precursor, mild cognitive impairment (MCI). Identification of early signs will aid in risk stratification of disease and ensures proper management is instituted to reduce the morbidity and mortality associated with AD. Magnetic resonance imaging (MRI) using structural MRI (sMRI), functional MRI (fMRI), diffusion tensor imaging (DTI), and magnetic resonance spectroscopy (1H-MRS) performed alone is inadequate. Thus, the combination of multiparametric MRI is proposed to increase the accuracy of diagnosing MCI and AD when compared to elderly healthy controls. METHODS: This protocol describes a non-interventional case control study. The AD and MCI patients and the healthy elderly controls will undergo multi-parametric MRI. The protocol consists of sMRI, fMRI, DTI, and single-voxel proton MRS sequences. An eco-planar imaging (EPI) will be used to perform resting-state fMRI sequence. The structural images will be analysed using Computational Anatomy Toolbox-12, functional images will be analysed using Statistical Parametric Mapping-12, DPABI (Data Processing & Analysis for Brain Imaging), and Conn software, while DTI and 1H-MRS will be analysed using the FSL (FMRIB's Software Library) and Tarquin respectively. Correlation of the MRI results and the data acquired from the APOE genotyping, neuropsychological evaluations (i.e. Montreal Cognitive Assessment [MoCA], and Mini-Mental State Examination [MMSE] scores) will be performed. The imaging results will also be correlated with the sociodemographic factors. The diagnosis of AD and MCI will be standardized and based on the DSM-5 criteria and the neuropsychological scores. DISCUSSION: The combination of sMRI, fMRI, DTI, and MRS sequences can provide information on the anatomical and functional changes in the brain such as regional grey matter volume atrophy, impaired functional connectivity among brain regions, and decreased metabolite levels specifically at the posterior cingulate cortex/precuneus. The combination of multiparametric MRI sequences can be used to stratify the management of MCI and AD patients. Accurate imaging can decide on the frequency of follow-up at memory clinics and select classifiers for machine learning that may aid in the disease identification and prognostication. Reliable and consistent quantification, using standardised protocols, are crucial to establish an optimal diagnostic capability in the early detection of Alzheimer's disease.

Correlation between 18F-FDG dosage and SNR on various BMI patient groups tested in NEMA IEC PET phantom.

The present study was conducted to determine quantitatively the correlation between injected radiotracer and signal-to-noise ratio (SNR) based on differences in physiques and stages of cancer. Eight different activities were evaluated with modelled National Electrical Manufacturers Association (NEMA) of the International Electrotechnical Commission (IEC) PET's phantom with nine different tumour-to-background ratio (TBR). The findings suggest that the optimal value of dosage is required for all categories of patients in the early stages of cancer diagnosis.

Diagnostic power of resting-state fMRI for detection of network connectivity in Alzheimer's disease and mild cognitive impairment: A systematic review.

Resting-state fMRI (rs-fMRI) detects functional connectivity (FC) abnormalities that occur in the brains of patients with Alzheimer's disease (AD) and mild cognitive impairment (MCI). FC of the default mode network (DMN) is commonly impaired in AD and MCI. We conducted a systematic review aimed at determining the diagnostic power of rs-fMRI to identify FC abnormalities in the DMN of patients with AD or MCI compared with healthy controls (HCs) using machine learning (ML) methods. Multimodal support vector machine (SVM) algorithm was the commonest form of ML method utilized. Multiple kernel approach can be utilized to aid in the classification by incorporating various discriminating features, such as FC graphs based on "nodes" and "edges" together with structural MRI-based regional cortical thickness and gray matter volume. Other multimodal features include neuropsychiatric testing scores, DTI features, and regional cerebral blood flow. Among AD patients, the posterior cingulate cortex (PCC)/Precuneus was noted to be a highly affected hub of the DMN that demonstrated overall reduced FC. Whereas reduced DMN FC between the PCC and anterior cingulate cortex (ACC) was observed in MCI patients. Evidence indicates that the nodes of the DMN can offer moderate to high diagnostic power to distinguish AD and MCI patients. Nevertheless, various concerns over the homogeneity of data based on patient selection, scanner effects, and the variable usage of classifiers and algorithms pose a challenge for ML-based image interpretation of rs-fMRI datasets to become a mainstream option for diagnosing AD and predicting the conversion of HC/MCI to AD.

Multi-view secondary input collaborative deep learning for lung nodule 3D segmentation.

BACKGROUND: Convolutional neural networks (CNNs) have been extensively applied to two-dimensional (2D) medical image segmentation, yielding excellent performance. However, their application to three-dimensional (3D) nodule segmentation remains a challenge. METHODS: In this study, we propose a multi-view secondary input residual (MV-SIR) convolutional neural network model for 3D lung nodule segmentation using the Lung Image Database Consortium and Image Database Resource Initiative (LIDC-IDRI) dataset of chest computed tomography (CT) images. Lung nodule cubes are prepared from the sample CT images. Further, from the axial, coronal, and sagittal perspectives, multi-view patches are generated with randomly selected voxels in the lung nodule cubes as centers. Our model consists of six submodels, which enable learning of 3D lung nodules sliced into three views of features; each submodel extracts voxel heterogeneity and shape heterogeneity features. We convert the segmentation of 3D lung nodules into voxel classification by inputting the multi-view patches into the model and determine whether the voxel points belong to the nodule. The structure of the secondary input residual submodel comprises a residual block followed by a secondary input module. We integrate the six submodels to classify whether voxel points belong to nodules, and then reconstruct the segmentation image. RESULTS: The results of tests conducted using our model and comparison with other existing CNN models indicate that the MV-SIR model achieves excellent results in the 3D segmentation of pulmonary nodules, with a Dice coefficient of 0.926 and an average surface distance of 0.072. CONCLUSION: our MV-SIR model can accurately perform 3D segmentation of lung nodules with the same segmentation accuracy as the U-net model.

Assessing Ethoshunt as a Gamification-Based Mobile App in Ethics Education: Pilot Mixed-Methods Study.

BACKGROUND: Gamification has remarkable potential in the learning space. The process of creating a gamified system and its influence on human behavior reflect the interaction between educators and machines. OBJECTIVE: The purpose of this pilot study was to present Ethoshunt as a gamification-based mobile app that can be used in teaching and learning ethics. METHODS: This study involved a mixed-methods research design. The researchers surveyed 39 undergraduate students who were introduced to Ethoshunt in order to examine the relationships between mobile app usability and positive emotions, ethical competency, and user experience. Affinity diagramming was used as a tool to organize the opinions and experiences of participants using featured gamification elements. RESULTS: Game dynamics and game mechanics explained the functionality of Ethoshunt. In addition, the learning flow through Ethoshunt was discussed. Overall, the findings were positive, and mobile app usability had the strongest relationship with positive emotions (r=0.744, P<.001), followed by ethical competency (r=0.686, P<.001) and user experience (r=0.614, P<.001). CONCLUSIONS: Positive emotions could be perceived as an important dimension in the development and usability of Ethoshunt. The researchers suggest that the gamification-based mobile app advocated in this study may provide ideas for ethics educators who wish to develop a technology-mediated learning environment.

Older age and duration of exposure to type 2 diabetes in selective screening of asymptomatic carotid artery stenosis for primary stroke prevention-A single institution experience.

AIMS: To evaluate the incidence and risk factors for carotid artery stenosis amongst asymptomatic type 2 diabetes from a single Malaysian tertiary institution. METHODS: This is a prospective cross-sectional study of asymptomatic type 2 diabetics selected from the outpatient ophthalmology and endocrine clinics for carotid duplex ultrasound scanning performed by a single radiologist. The duplex ultrasound criteria were based on the North American Symptomatic Carotid Endarterectomy Trial (NASCET) classification of carotid artery stenosis. Univariate and multivariate analysis was performed to identify possible risk factors of carotid artery stenosis. RESULTS: Amongst the 200 patients, the majority were males (56%) and Malay predominance (58.5%). There were 12/200 patients (6%) with mean age of 69.2 years identified to have carotid artery stenosis. Univariate analysis of patients with asymptomatic carotid artery stenosis identified older age of 69.2 years (p=0.027) and duration of exposure to diabetes of 17.9 years (p=0.024) as significant risk factors. CONCLUSION: Patients with longer exposure of diabetes and older age were risk factors of carotid artery stenosis in asymptomatic type 2 diabetics. These patients should be considered for selective screening of carotid artery stenosis during primary care visit for early identification and closer surveillance for stroke prevention.

Methods and Challenges in Shot Boundary Detection: A Review.

The recent increase in the number of videos available in cyberspace is due to the availability of multimedia devices, highly developed communication technologies, and low-cost storage devices. These videos are simply stored in databases through text annotation. Content-based video browsing and retrieval are inefficient due to the method used to store videos in databases. Video databases are large in size and contain voluminous information, and these characteristics emphasize the need for automated video structure analyses. Shot boundary detection (SBD) is considered a substantial process of video browsing and retrieval. SBD aims to detect transition and their boundaries between consecutive shots; hence, shots with rich information are used in the content-based video indexing and retrieval. This paper presents a review of an extensive set for SBD approaches and their development. The advantages and disadvantages of each approach are comprehensively explored. The developed algorithms are discussed, and challenges and recommendations are presented.

Supervised retinal vessel segmentation from color fundus images based on matched filtering and AdaBoost classifier.

The structure and appearance of the blood vessel network in retinal fundus images is an essential part of diagnosing various problems associated with the eyes, such as diabetes and hypertension. In this paper, an automatic retinal vessel segmentation method utilizing matched filter techniques coupled with an AdaBoost classifier is proposed. The fundus image is enhanced using morphological operations, the contrast is increased using contrast limited adaptive histogram equalization (CLAHE) method and the inhomogeneity is corrected using Retinex approach. Then, the blood vessels are enhanced using a combination of B-COSFIRE and Frangi matched filters. From this preprocessed image, different statistical features are computed on a pixel-wise basis and used in an AdaBoost classifier to extract the blood vessel network inside the image. Finally, the segmented images are postprocessed to remove the misclassified pixels and regions. The proposed method was validated using publicly accessible Digital Retinal Images for Vessel Extraction (DRIVE), Structured Analysis of the Retina (STARE) and Child Heart and Health Study in England (CHASE_DB1) datasets commonly used for determining the accuracy of retinal vessel segmentation methods. The accuracy of the proposed segmentation method was comparable to other state of the art methods while being very close to the manual segmentation provided by the second human observer with an average accuracy of 0.972, 0.951 and 0.948 in DRIVE, STARE and CHASE_DB1 datasets, respectively.

Foundation and methodologies in computer-aided diagnosis systems for breast cancer detection.

Breast cancer is the most prevalent cancer that affects women all over the world. Early detection and treatment of breast cancer could decline the mortality rate. Some issues such as technical reasons, which related to imaging quality and human error, increase misdiagnosis of breast cancer by radiologists. Computer-aided detection systems (CADs) are developed to overcome these restrictions and have been studied in many imaging modalities for breast cancer detection in recent years. The CAD systems improve radiologists' performance in finding and discriminating between the normal and abnormal tissues. These procedures are performed only as a double reader but the absolute decisions are still made by the radiologist. In this study, the recent CAD systems for breast cancer detection on different modalities such as mammography, ultrasound, MRI, and biopsy histopathological images are introduced. The foundation of CAD systems generally consist of four stages: Pre-processing, Segmentation, Feature extraction, and Classification. The approaches which applied to design different stages of CAD system are summarised. Advantages and disadvantages of different segmentation, feature extraction and classification techniques are listed. In addition, the impact of imbalanced datasets in classification outcomes and appropriate methods to solve these issues are discussed. As well as, performance evaluation metrics for various stages of breast cancer detection CAD systems are reviewed.