Automated analysis of small intestinal lamina propria to distinguish normal, Celiac Disease, and Non-Celiac Duodenitis biopsy images.

BACKGROUND AND OBJECTIVE: Celiac Disease (CD) is characterized by gluten intolerance in genetically predisposed individuals. High disease prevalence, absence of a cure, and low diagnosis rates make this disease a public health problem. The diagnosis of CD predominantly relies on recognizing characteristic mucosal alterations of the small intestine, such as villous atrophy, crypt hyperplasia, and intraepithelial lymphocytosis. However, these changes are not entirely specific to CD and overlap with Non-Celiac Duodenitis (NCD) due to various etiologies. We investigated whether Artificial Intelligence (AI) models could assist in distinguishing normal, CD, and NCD (and unaffected individuals) based on the characteristics of small intestinal lamina propria (LP). METHODS: Our method was developed using a dataset comprising high magnification biopsy images of the duodenal LP compartment of CD patients with different clinical stages of CD, those with NCD, and individuals lacking an intestinal inflammatory disorder (controls). A pre-processing step was used to standardize and enhance the acquired images. RESULTS: For the normal controls versus CD use case, a Support Vector Machine (SVM) achieved an Accuracy (ACC) of 98.53%. For a second use case, we investigated the ability of the classification algorithm to differentiate between normal controls and NCD. In this use case, the SVM algorithm with linear kernel outperformed all the tested classifiers by achieving 98.55% ACC. CONCLUSIONS: To the best of our knowledge, this is the first study that documents automated differentiation between normal, NCD, and CD biopsy images. These findings are a stepping stone toward automated biopsy image analysis that can significantly benefit patients and healthcare providers.

CCPNet136: automated detection of schizophrenia using carbon chain pattern and iterative TQWT technique with EEG signals.

Objective.Schizophrenia (SZ) is a severe, chronic psychiatric-cognitive disorder. The primary objective of this work is to present a handcrafted model using state-of-the-art technique to detect SZ accurately with EEG signals.Approach.In our proposed work, the features are generated using a histogram-based generator and an iterative decomposition model. The graph-based molecular structure of the carbon chain is employed to generate low-level features. Hence, the developed feature generation model is called the carbon chain pattern (CCP). An iterative tunable q-factor wavelet transform (ITQWT) technique is implemented in the feature extraction phase to generate various sub-bands of the EEG signal. The CCP was applied to the generated sub-bands to obtain several feature vectors. The clinically significant features were selected using iterative neighborhood component analysis (INCA). The selected features were then classified using the k nearest neighbor (kNN) with a 10-fold cross-validation strategy. Finally, the iterative weighted majority method was used to obtain the results in multiple channels.Main results.The presented CCP-ITQWT and INCA-based automated model achieved an accuracy of 95.84% and 99.20% using a single channel and majority voting method, respectively with kNN classifier.Significance.Our results highlight the success of the proposed CCP-ITQWT and INCA-based model in the automated detection of SZ using EEG signals.

Hamlet-Pattern-Based Automated COVID-19 and Influenza Detection Model Using Protein Sequences.

SARS-CoV-2 and Influenza-A can present similar symptoms. Computer-aided diagnosis can help facilitate screening for the two conditions, and may be especially relevant and useful in the current COVID-19 pandemic because seasonal Influenza-A infection can still occur. We have developed a novel text-based classification model for discriminating between the two conditions using protein sequences of varying lengths. We downloaded viral protein sequences of SARS-CoV-2 and Influenza-A with varying lengths (all 100 or greater) from the NCBI database and randomly selected 16,901 SARS-CoV-2 and 19,523 Influenza-A sequences to form a two-class study dataset. We used a new feature extraction function based on a unique pattern, HamletPat, generated from the text of Shakespeare's Hamlet, and a signum function to extract local binary pattern-like bits from overlapping fixed-length (27) blocks of the protein sequences. The bits were converted to decimal map signals from which histograms were extracted and concatenated to form a final feature vector of length 1280. The iterative Chi-square function selected the 340 most discriminative features to feed to an SVM with a Gaussian kernel for classification. The model attained 99.92% and 99.87% classification accuracy rates using hold-out (75:25 split ratio) and five-fold cross-validations, respectively. The excellent performance of the lightweight, handcrafted HamletPat-based classification model suggests that it can be a valuable tool for screening protein sequences to discriminate between SARS-CoV-2 and Influenza-A infections.

Novel Radiomics Features for Automated Detection of Cardiac Abnormality in Patients with Pacemaker.

Cardiac pacemakers are used in the treatment of patients with symptomatic bradycardia. The pacemaker paces the heart at the predetermined rate to maintain uninterrupted cardiac activity. Usually, pacemaker lead will be connected to the right atrium (RA) and right ventricle (RV) in dual-chamber pacemaker implantation and RV alone in single-chamber pacemaker implantation. This alters the route of proper conduction across the myocardial cells. The cell-to-cell conduction transmission in pacing delays the activation of selected intraventricular myocardial activation. Pacing-induced cardiomyopathy (PICM) is most commonly defined as a drop in left ventricle ejection fraction (LVEF) in the setting of chronic, high-burden right ventricle (RV) pacing. Currently, very few effective treatments are standard for PICM which rely on the detection of the RV pacing. Such treatments have primarily focused on upgrading to cardiac resynchronization therapy (CRT) when LVEF has dropped. However, the early and accurate detection of these stress factors is challenging. Cardiac desynchrony and interventricular desynchrony can be determined by various echocardiographic techniques, including M-mode, Doppler method, tissue Doppler method, and speckle tracking echocardiography which is subjective measures and shows a significant difference between RV and LV preejection period where the activation of LV is delayed considerably. Computer-aided diagnosis (CAD) is a noninvasive technique that can classify the ultrasound images of the heart in pacemaker-implanted patients and healthy patients with normal left ventricular systolic function and further detect the variations in pacemaker functions in its early stage using heart ultrasound images. Developing such a system requires a vast and diverse database to reach optimum performance. This paper proposes a novel CAD tool for the accurate detection of pacemaker variations using machine learning models of decision tree, SVM, random forest, and AdaBoost. The models have been used to extract radiomics features in terms of textures and then screened by their Relief-F scores for selection and ranking to be classified into nine groups consisting of up to 250 radiomics features. Ten best features were fed to the machine learning models. The R-wave dataset achieved a maximum test performance accuracy of 97.73% with four features in the random forest model. The T-wave dataset achieved a maximum test performance accuracy of 96.59% with three features in the SVM model. Our experimental results demonstrate the system's robustness, which can be developed as an early and accurate detection system for pacing-induced cardiomyopathy.

Machine Learning Optimization of the Collocation Point Set for Solving the Kohn-Sham Equation.

The rectangular collocation approach makes it possible to solve the Schrödinger equation with basis functions that do not have amplitude in all regions in which wave functions have significant amplitude. Collocation points can be restricted to a small region of space. As no integrals are computed, there are no problems due to discontinuities in the potential, and there is no need to use integrable basis functions. In this paper, we show, for the Kohn-Sham equation, that machine learning can be used to drastically reduce the size of the collocation point set. This is demonstrated by solving the Kohn-Sham equations for CO and H2O. We solve the Kohn-Sham equation on a given effective potential which is a critical part of all DFT calculations, and monitor orbital energies and orbital shapes. We use a combination of Gaussian process regression and a genetic algorithm to reduce the collocation point set size by more than an order of magnitude (from about 51 000 points to 2000 points) while retaining mhartree accuracy.

Neural networks vs Gaussian process regression for representing potential energy surfaces: A comparative study of fit quality and vibrational spectrum accuracy.

For molecules with more than three atoms, it is difficult to fit or interpolate a potential energy surface (PES) from a small number of (usually ab initio) energies at points. Many methods have been proposed in recent decades, each claiming a set of advantages. Unfortunately, there are few comparative studies. In this paper, we compare neural networks (NNs) with Gaussian process (GP) regression. We re-fit an accurate PES of formaldehyde and compare PES errors on the entire point set used to solve the vibrational Schrödinger equation, i.e., the only error that matters in quantum dynamics calculations. We also compare the vibrational spectra computed on the underlying reference PES and the NN and GP potential surfaces. The NN and GP surfaces are constructed with exactly the same points, and the corresponding spectra are computed with the same points and the same basis. The GP fitting error is lower, and the GP spectrum is more accurate. The best NN fits to 625/1250/2500 symmetry unique potential energy points have global PES root mean square errors (RMSEs) of 6.53/2.54/0.86 cm-1, whereas the best GP surfaces have RMSE values of 3.87/1.13/0.62 cm-1, respectively. When fitting 625 symmetry unique points, the error in the first 100 vibrational levels is only 0.06 cm-1 with the best GP fit, whereas the spectrum on the best NN PES has an error of 0.22 cm-1, with respect to the spectrum computed on the reference PES. This error is reduced to about 0.01 cm-1 when fitting 2500 points with either the NN or GP. We also find that the GP surface produces a relatively accurate spectrum when obtained based on as few as 313 points.