Improving accuracy of vascular access quality classification in hemodialysis patients using deep learning with K highest score feature selection.

OBJECTIVE: To develop and evaluate a novel feature selection technique, using photoplethysmography (PPG) sensors, for enhancing the performance of deep learning models in classifying vascular access quality in hemodialysis patients. METHODS: This cross-sectional study involved creating a novel feature selection method based on SelectKBest principles, specifically designed to optimize deep learning models for PPG sensor data, in hemodialysis patients. The method effectiveness was assessed by comparing the performance of multiple deep learning models using the feature selection approach versus complete feature set. The model with the highest accuracy was then trained and tested using a 70:30 approach, respectively, with the full dataset and the SelectKBest dataset. Performance results were compared using Student's paired t-test. RESULTS: Data from 398 hemodialysis patients were included. The 1-dimensional convolutional neural network (CNN1D) displayed the highest accuracy among different models. Implementation of the SelectKBest-based feature selection technique resulted in a statistically significant improvement in the CNN1D model's performance, achieving an accuracy of 92.05% (with feature selection) versus 90.79% (with full feature set). CONCLUSION: These findings suggest that the newly developed feature selection approach might aid in accurately predicting vascular access quality in hemodialysis patients. This advancement may contribute to the development of reliable diagnostic tools for identifying vascular complications, such as stenosis, potentially improving patient outcomes and their quality of life.

DeepVAQ : an adaptive deep learning for prediction of vascular access quality in hemodialysis patients.

BACKGROUND: Chronic kidney disease is a prevalent global health issue, particularly in advanced stages requiring dialysis. Vascular access (VA) quality is crucial for the well-being of hemodialysis (HD) patients, ensuring optimal blood transfer through a dialyzer machine. The ultrasound dilution technique (UDT) is used as the gold standard for assessing VA quality; however, its limited availability due to high costs impedes its widespread adoption. We aimed to develop a novel deep learning model specifically designed to predict VA quality from Photoplethysmography (PPG) sensors. METHODS: Clinical data were retrospectively gathered from 398 HD patients, spanning from February 2021 to February 2022. The DeepVAQ model leverages a convolutional neural network (CNN) to process PPG sensor data, pinpointing specific frequencies and patterns that are indicative of VA quality. Meticulous training and fine-tuning were applied to ensure the model's accuracy and reliability. Validation of the DeepVAQ model was carried out against established diagnostic standards using key performance metrics, including accuracy, specificity, precision, F-score, and area under the receiver operating characteristic curve (AUC). RESULT: DeepVAQ demonstrated superior performance, achieving an accuracy of 0.9213 and a specificity of 0.9614. Its precision and F-score stood at 0.8762 and 0.8364, respectively, with an AUC of 0.8605. In contrast, traditional models like Decision Tree, Naive Bayes, and kNN demonstrated significantly lower performance across these metrics. This comparison underscores DeepVAQ's enhanced capability in accurately predicting VA quality compared to existing methodologies. CONCLUSION: Exemplifying the potential of artificial intelligence in healthcare, particularly in the realm of deep learning, DeepVAQ represents a significant advancement in non-invasive diagnostics. Its precise multi-class classification ability for VA quality in hemodialysis patients holds substantial promise for improving patient outcomes, potentially leading to a reduction in mortality rates.

MSTAC: A Multi-Stage Automated Classification of COVID-19 Chest X-ray Images Using Stacked CNN Models.

This study introduces a Multi-Stage Automated Classification (MSTAC) system for COVID-19 chest X-ray (CXR) images, utilizing stacked Convolutional Neural Network (CNN) models. Suspected COVID-19 patients often undergo CXR imaging, making it valuable for disease classification. The study collected CXR images from public datasets and aimed to differentiate between COVID-19, non-COVID-19, and healthy cases. MSTAC employs two classification stages: the first distinguishes healthy from unhealthy cases, and the second further classifies COVID-19 and non-COVID-19 cases. Compared to a single CNN-Multiclass model, MSTAC demonstrated superior classification performance, achieving 97.30% accuracy and sensitivity. In contrast, the CNN-Multiclass model showed 94.76% accuracy and sensitivity. MSTAC's effectiveness is highlighted in its promising results over the CNN-Multiclass model, suggesting its potential to assist healthcare professionals in efficiently diagnosing COVID-19 cases. The system outperformed similar techniques, emphasizing its accuracy and efficiency in COVID-19 diagnosis. This research underscores MSTAC as a valuable tool in medical image analysis for enhanced disease classification.

DisVar: an R library for identifying variants associated with diseases using large-scale personal genetic information.

Background: Genetic variants may potentially play a contributing factor in the development of diseases. Several genetic disease databases are used in medical research and diagnosis but the web applications used to search these databases for disease-associated variants have limitations. The application may not be able to search for large-scale genetic variants, the results of searches may be difficult to interpret and variants mapped from the latest reference genome (GRCH38/hg38) may not be supported. Methods: In this study, we developed a novel R library called "DisVar" to identify disease-associated genetic variants in large-scale individual genomic data. This R library is compatible with variants from the latest reference genome version. DisVar uses five databases of disease-associated variants. Over 100 million variants can be simultaneously searched for specific associated diseases. Results: The package was evaluated using 24 Variant Call Format (VCF) files (215,054 to 11,346,899 sites) from the 1000 Genomes Project. Disease-associated variants were detected in 298,227 hits across all the VCF files, taking a total of 63.58 m to complete. The package was also tested on ClinVar's VCF file (2,120,558 variants), where 20,657 hits associated with diseases were identified with an estimated elapsed time of 45.98 s. Conclusions: DisVar can overcome the limitations of existing tools and is a fast and effective diagnostic and preventive tool that identifies disease-associated variations from large-scale genetic variants against the latest reference genome.

Classifying COVID-19 Patients From Chest X-ray Images Using Hybrid Machine Learning Techniques: Development and Evaluation.

BACKGROUND: The COVID-19 pandemic has raised global concern, with moderate to severe cases displaying lung inflammation and respiratory failure. Chest x-ray (CXR) imaging is crucial for diagnosis and is usually interpreted by experienced medical specialists. Machine learning has been applied with acceptable accuracy, but computational efficiency has received less attention. OBJECTIVE: We introduced a novel hybrid machine learning model to accurately classify COVID-19, non-COVID-19, and healthy patients from CXR images with reduced computational time and promising results. Our proposed model was thoroughly evaluated and compared with existing models. METHODS: A retrospective study was conducted to analyze 5 public data sets containing 4200 CXR images using machine learning techniques including decision trees, support vector machines, and neural networks. The images were preprocessed to undergo image segmentation, enhancement, and feature extraction. The best performing machine learning technique was selected and combined into a multilayer hybrid classification model for COVID-19 (MLHC-COVID-19). The model consisted of 2 layers. The first layer was designed to differentiate healthy individuals from infected patients, while the second layer aimed to classify COVID-19 and non-COVID-19 patients. RESULTS: The MLHC-COVID-19 model was trained and evaluated on unseen COVID-19 CXR images, achieving reasonably high accuracy and F measures of 0.962 and 0.962, respectively. These results show the effectiveness of the MLHC-COVID-19 in classifying COVID-19 CXR images, with improved accuracy and a reduction in interpretation time. The model was also embedded into a web-based MLHC-COVID-19 computer-aided diagnosis system, which was made publicly available. CONCLUSIONS: The study found that the MLHC-COVID-19 model effectively differentiated CXR images of COVID-19 patients from those of healthy and non-COVID-19 individuals. It outperformed other state-of-the-art deep learning techniques and showed promising results. These results suggest that the MLHC-COVID-19 model could have been instrumental in early detection and diagnosis of COVID-19 patients, thus playing a significant role in controlling and managing the pandemic. Although the pandemic has slowed down, this model can be adapted and utilized for future similar situations. The model was also integrated into a publicly accessible web-based computer-aided diagnosis system.

Binary semantic segmentation for detection of prostate adenocarcinoma using an ensemble with attention and residual U-Net architectures.

An accurate determination of the Gleason Score (GS) or Gleason Pattern (GP) is crucial in the diagnosis of prostate cancer (PCa) because it is one of the criterion used to guide treatment decisions for prognostic-risk groups. However, the manually designation of GP by a pathologist using a microscope is prone to error and subject to significant inter-observer variability. Deep learning has been used to automatically differentiate GP on digitized slides, aiding pathologists and reducing inter-observer variability, especially in the early GP of cancer. This article presents a binary semantic segmentation for the GP of prostate adenocarcinoma. The segmentation separates benign and malignant tissues, with the malignant class consisting of adenocarcinoma GP3 and GP4 tissues annotated from 50 unique digitized whole slide images (WSIs) of prostate needle core biopsy specimens stained with hematoxylin and eosin. The pyramidal digitized WSIs were extracted into image patches with a size of 256 × 256 pixels at a magnification of 20×. An ensemble approach is proposed combining U-Net-based architectures, including traditional U-Net, attention-based U-Net, and residual attention-based U-Net. This work initially considers a PCa tissue analysis using a combination of attention gate units with residual convolution units. The performance evaluation revealed a mean Intersection-over-Union of 0.79 for the two classes, 0.88 for the benign class, and 0.70 for the malignant class. The proposed method was then used to produce pixel-level segmentation maps of PCa adenocarcinoma tissue slides in the testing set. We developed a screening tool to discriminate between benign and malignant prostate tissue in digitized images of needle biopsy samples using an AI approach. We aimed to identify malignant adenocarcinoma tissues from our own collected, annotated, and organized dataset. Our approach returned the performance which was accepted by the pathologists.

Integrated Automatic Workflow for Phylogenetic Tree Analysis Using Public Access and Local Web Services.

At the present, coding sequence (CDS) has been discovered and larger CDS is being revealed frequently. Approaches and related tools have also been developed and upgraded concurrently, especially for phylogenetic tree analysis. This paper proposes an integrated automatic Taverna workflow for the phylogenetic tree inferring analysis using public access web services at European Bioinformatics Institute (EMBL-EBI) and Swiss Institute of Bioinformatics (SIB), and our own deployed local web services. The workflow input is a set of CDS in the Fasta format. The workflow supports 1,000 to 20,000 numbers in bootstrapping replication. The workflow performs the tree inferring such as Parsimony (PARS), Distance Matrix - Neighbor Joining (DIST-NJ), and Maximum Likelihood (ML) algorithms of EMBOSS PHYLIPNEW package based on our proposed Multiple Sequence Alignment (MSA) similarity score. The local web services are implemented and deployed into two types using the Soaplab2 and Apache Axis2 deployment. There are SOAP and Java Web Service (JWS) providing WSDL endpoints to Taverna Workbench, a workflow manager. The workflow has been validated, the performance has been measured, and its results have been verified. Our workflow's execution time is less than ten minutes for inferring a tree with 10,000 replicates of the bootstrapping numbers. This paper proposes a new integrated automatic workflow which will be beneficial to the bioinformaticians with an intermediate level of knowledge and experiences. All local services have been deployed at our portal http://bioservices.sci.psu.ac.th.