Search Results (28)

(1) Background: Emerging fungal infections associated with Scedosporium spp. and Lomentospora prolificans (S/L) are becoming more frequent and are very difficult to treat. Our objective was to analyze the frequency and management of S/L isolates in lung transplant (LTx) recipients, the patient outcomes and in vitro antifungal sensitivity. (2) Methods: We included all patients with S/L isolation during post-transplant follow-up. Data were collected from electronic medical records. All samples were cultivated on Sabouraud Chloramphenicol agar. Isolations of S/L were submitted to in vitro susceptibility tests. (3) Results: A total of 11 (2%) of the 576 LTx recipients included had at least one isolation of S/L. Classification for the 11 cases were colonization (4; 36%) and infection (7; 65%). Five infections were pulmonary (71%) and two were disseminated (29%). S. apiospermum complex was the most frequently occurring isolation in patients with pulmonary disease while L. prolificans was the most frequent in patients with disseminated disease. Ten patients were treated. The most frequent antifungal drugs used were voriconazole (n = 8) and terbinafine (n = 6). Seven patients (70%) received more than one drug. The mortality rate associated with L. prolificans isolation was 50% for colonization and 100% for disseminated disease. (4) Conclusions: Scedosporium spp. and L. prolificans infections are associated with high morbidity and mortality rates. New diagnostic and therapeutic tools are required to reduce the impact of these infections. Full article

The automated and precise classification of lung and colon cancer from histopathological photos continues to pose a significant challenge in medical diagnosis, as current computer-aided diagnosis (CAD) systems are frequently constrained by their dependence on singular deep learning architectures, elevated computational complexity, and their ineffectiveness in utilising multiscale features. To this end, the present research introduces a CAD system that integrates several lightweight convolutional neural networks (CNNs) with dual-layer feature extraction and feature selection to overcome the aforementioned constraints. Initially, it extracts deep attributes from two separate layers (pooling and fully connected) of three pre-trained CNNs (MobileNet, ResNet-18, and EfficientNetB0). Second, the system uses the benefits of canonical correlation analysis for dimensionality reduction in pooling layer attributes to reduce complexity. In addition, it integrates the dual-layer features to encapsulate both high- and low-level representations. Finally, to benefit from multiple deep network architectures while reducing classification complexity, the proposed CAD merges dual deep layer variables of the three CNNs and then applies the analysis of variance (ANOVA) and Chi-Squared for the selection of the most discriminative features from the integrated CNN architectures. The CAD is assessed on the LC25000 dataset leveraging eight distinct classifiers, encompassing various Support Vector Machine (SVM) variants, Decision Trees, Linear Discriminant Analysis, and k-nearest neighbours. The experimental results exhibited outstanding performance, attaining 99.8% classification accuracy with cubic SVM classifiers employing merely 50 ANOVA-selected features, exceeding the performance of individual CNNs while markedly diminishing computational complexity. The framework’s capacity to sustain exceptional accuracy with a limited feature set renders it especially advantageous for clinical applications where diagnostic precision and efficiency are critical. These findings confirm the efficacy of the multi-CNN, multi-layer methodology in enhancing cancer classification precision while mitigating the computational constraints of current systems. Full article

This study investigates the use of machine learning (ML) models combined with explainable artificial intelligence (XAI) techniques to identify the most influential genes in the classification of five recurrent cancer types in women: breast cancer (BRCA), lung adenocarcinoma (LUAD), thyroid cancer (THCA), ovarian cancer (OV), and colon adenocarcinoma (COAD). Gene expression data from RNA-seq, extracted from The Cancer Genome Atlas (TCGA), were used to train ML models, including decision trees (DTs), random forest (RF), and XGBoost (XGB), which achieved accuracies of 98.69%, 99.82%, and 99.37%, respectively. However, the challenges in this analysis included the high dimensionality of the dataset and the lack of transparency in the ML models. To mitigate these challenges, the SHAP (Shapley Additive Explanations) method was applied to generate a list of features, aiming to understand which characteristics influenced the models’ decision-making processes and, consequently, the prediction results for the five tumor types. The SHAP analysis identified 119, 80, and 10 genes for the RF, XGB, and DT models, respectively, totaling 209 genes, resulting in 172 unique genes. The new list, representing 0.8% of the original input features, is coherent and fully explainable, increasing confidence in the applied models. Additionally, the results suggest that the SHAP method can be effectively used as a feature selector in gene expression data. This approach not only enhances model transparency but also maintains high classification performance, highlighting its potential in identifying biologically relevant features that may serve as biomarkers for cancer diagnostics and treatment planning. Full article

Lung and colon cancers are among the leading causes of cancer-related mortality worldwide. Early and accurate detection of these cancers is crucial for effective treatment and improved patient outcomes. False or incorrect detection is harmful. Accurately detecting cancer in a patient’s tissue is crucial to their effective treatment. While analyzing tissue samples is complicated and time-consuming, deep learning techniques have made it possible to complete this process more efficiently and accurately. As a result, researchers can study more patients in a shorter amount of time and at a lower cost. Much research has been conducted to investigate deep learning models that require great computational ability and resources. However, none of these have had a $100\%$ accurate detection rate for these life-threatening malignancies. Misclassified or falsely detecting cancer can have very harmful consequences. This research proposes a new lightweight, parameter-efficient, and mobile-embedded deep learning model based on a 1D convolutional neural network with squeeze-and-excitation layers for efficient lung and colon cancer detection. This proposed model diagnoses and classifies lung squamous cell carcinomas and adenocarcinoma of the lung and colon from digital pathology images. Extensive experiment demonstrates that our proposed model achieves $100\%$ accuracy for detecting lung, colon, and lung and colon cancers from the histopathological (LC25000) lung and colon datasets, which is considered the best accuracy for around $0.35$ million trainable parameters and around $6.4$ million flops. Compared with the existing results, our proposed architecture shows state-of-the-art performance in lung, colon, and lung and colon cancer detection. Full article

Background: Lung and colon cancers are among the most prevalent and lethal malignancies worldwide, underscoring the urgent need for advanced diagnostic methodologies. This study aims to develop a hybrid deep learning and machine learning framework for the classification of Colon Adenocarcinoma, Colon Benign Tissue, Lung Adenocarcinoma, Lung Benign Tissue, and Lung Squamous Cell Carcinoma from histopathological images. Methods: Current approaches primarily rely on the LC25000 dataset, which, due to image augmentation, lacks the generalizability required for real-time clinical applications. To address this, Contrast Limited Adaptive Histogram Equalization (CLAHE) was applied to enhance image quality, and 1000 new images from the National Cancer Institute GDC Data Portal were introduced into the Colon Adenocarcinoma, Lung Adenocarcinoma, and Lung Squamous Cell Carcinoma classes, replacing augmented images to increase dataset diversity. A hybrid feature extraction model combining MobileNetV2 and EfficientNetB3 was optimized using the Grey Wolf Optimizer (GWO), resulting in the Lung and Colon histopathological classification technique (MEGWO-LCCHC). Cross-validation and hyperparameter tuning with Optuna were performed on various machine learning models, including XGBoost, LightGBM, and CatBoost. Results: The MEGWO-LCCHC technique achieved high classification accuracy, with the lightweight DNN model reaching 94.8%, LightGBM at 93.9%, XGBoost at 93.5%, and CatBoost at 93.3% on the test set. Conclusions: The findings suggest that our approach enhances classification performance and offers improved generalizability for real-world clinical applications. The proposed MEGWO-LCCHC framework shows promise as a robust tool in cancer diagnostics, advancing the application of AI in oncology. Full article

Background: The global healthcare system faces challenges in diagnosing and managing lung and colon cancers, which are significant health burdens. Traditional diagnostic methods are inefficient and prone to errors, while data privacy and security concerns persist. Objective: This study aims to develop a secure and transparent framework for remote consultation and classification of lung and colon cancer, leveraging blockchain technology and Microsoft Azure cloud services. Dataset and Features: The framework utilizes the LC25000 dataset, containing 25,000 histopathological images, for training and evaluating advanced machine learning models. Key features include secure data upload, anonymization, encryption, and controlled access via blockchain and Azure services. Methods: The proposed framework integrates Microsoft Azure’s cloud services with a permissioned blockchain network. Patients upload CT scans through a mobile app, which are then preprocessed, anonymized, and stored securely in Azure Blob Storage. Blockchain smart contracts manage data access, ensuring only authorized specialists can retrieve and analyze the scans. Azure Machine Learning is used to train and deploy state-of-the-art machine learning models for cancer classification. Evaluation Metrics: The framework’s performance is evaluated using metrics such as accuracy, precision, recall, and F1-score, demonstrating the effectiveness of the integrated approach in enhancing diagnostic accuracy and data security. Results: The proposed framework achieves an impressive accuracy of 100% for lung and colon cancer classification using DenseNet, ResNet50, and MobileNet models with different split ratios (70–30, 80–20, 90–10). The F1-score and k-fold cross-validation accuracy (5-fold and 10-fold) also demonstrate exceptional performance, with values exceeding 99.9%. Real-time notifications and secure remote consultations enhance the efficiency and transparency of the diagnostic process, contributing to better patient outcomes and streamlined cancer care management. Full article

Background: In recent years, the healthcare field has experienced significant advancements. New diagnostic techniques, treatments, and insights into the causes of various diseases have emerged. Despite these progressions, cancer remains a major concern. It is a widespread illness affecting individuals of all ages and leads to one out of every six deaths. Lung and colon cancer alone account for nearly two million fatalities. Though it is rare for lung and colon cancers to co-occur, the spread of cancer cells between these two areas—known as metastasis—is notably high. Early detection of cancer greatly increases survival rates. Currently, histopathological image (HI) diagnosis and appropriate treatment are key methods for reducing cancer mortality and enhancing survival rates. Digital image processing (DIP) and deep learning (DL) algorithms can be employed to analyze the HIs of five different types of lung and colon tissues. Methods: Therefore, this paper proposes a refined DL model that integrates feature fusion for the multi-classification of lung and colon cancers. The proposed model incorporates three DL architectures: ResNet-101V2, NASNetMobile, and EfficientNet-B0. Each model has limitations concerning variations in the shape and texture of input images. To address this, the proposed model utilizes a concatenate layer to merge the pre-trained individual feature vectors from ResNet-101V2, NASNetMobile, and EfficientNet-B0 into a single feature vector, which is then fine-tuned. As a result, the proposed DL model achieves high success in multi-classification by leveraging the strengths of all three models to enhance overall accuracy. This model aims to assist pathologists in the early detection of lung and colon cancer with reduced effort, time, and cost. The proposed DL model was evaluated using the LC25000 dataset, which contains colon and lung HIs. The dataset was pre-processed using resizing and normalization techniques. Results: The model was tested and compared with recent DL models, achieving impressive results: 99.8% for precision, 99.8% for recall, 99.8% for F1-score, 99.96% for specificity, and 99.94% for accuracy. Conclusions: Thus, the proposed DL model demonstrates exceptional performance across all classification categories. Full article

Lung and colon cancer (LCC) is a dominant life-threatening disease that needs timely attention and precise diagnosis for efficient treatment. The conventional diagnostic techniques for LCC regularly encounter constraints in terms of efficiency and accuracy, thus causing challenges in primary recognition and treatment. Early diagnosis of the disease can immensely reduce the probability of death. In medical practice, the histopathological study of the tissue samples generally uses a classical model. Still, the automated devices that exploit artificial intelligence (AI) techniques produce efficient results in disease diagnosis. In histopathology, both machine learning (ML) and deep learning (DL) approaches can be deployed owing to their latent ability in analyzing and predicting physically accurate molecular phenotypes and microsatellite uncertainty. In this background, this study presents a novel technique called Lung and Colon Cancer using a Swin Transformer with an Ensemble Model on the Histopathological Images (LCCST-EMHI). The proposed LCCST-EMHI method focuses on designing a DL model for the diagnosis and classification of the LCC using histopathological images (HI). In order to achieve this, the LCCST-EMHI model utilizes the bilateral filtering (BF) technique to get rid of the noise. Further, the Swin Transformer (ST) model is also employed for the purpose of feature extraction. For the LCC detection and classification process, an ensemble deep learning classifier is used with three techniques: bidirectional long short-term memory with multi-head attention (BiLSTM-MHA), Double Deep Q-Network (DDQN), and sparse stacked autoencoder (SSAE). Eventually, the hyperparameter selection of the three DL models can be implemented utilizing the walrus optimization algorithm (WaOA) method. In order to illustrate the promising performance of the LCCST-EMHI approach, an extensive range of simulation analyses was conducted on a benchmark dataset. The experimentation results demonstrated the promising performance of the LCCST-EMHI approach over other recent methods. Full article

Lung and colon cancers are common types of cancer with significant fatality rates. Early identification considerably improves the odds of survival for those suffering from these diseases. Histopathological image analysis is crucial for detecting cancer by identifying morphological anomalies in tissue samples. Regulations such as the HIPAA and GDPR impose considerable restrictions on the sharing of sensitive patient data, mostly because of privacy concerns. Federated learning (FL) is a promising technique that allows the training of strong models while maintaining data privacy. The use of a federated learning strategy has been suggested in this study to address privacy concerns in cancer categorization. To classify histopathological images of lung and colon cancers, this methodology uses local models with an Inception-V3 backbone. The global model is then updated on the basis of the local weights. The images were obtained from the LC25000 dataset, which consists of five separate classes. Separate analyses were performed for lung cancer, colon cancer, and their combined classification. The implemented model successfully classified lung cancer images into three separate classes with a classification accuracy of 99.867%. The classification of colon cancer images was achieved with 100% accuracy. More significantly, for the lung and colon cancers combined, the accuracy reached an impressive 99.720%. Compared with other current approaches, the proposed framework showed an improved performance. A heatmap, visual saliency map, and GradCAM were generated to pinpoint the crucial areas in the histopathology pictures of the test set where the models focused in particular during cancer class predictions. This approach demonstrates the potential of federated learning to enhance collaborative efforts in automated disease diagnosis through medical image analysis while ensuring patient data privacy. Full article

Advancements in the field of next generation sequencing (NGS) have generated vast amounts of data for the same set of subjects. The challenge that arises is how to combine and reconcile results from different omics studies, such as epigenome and transcriptome, to improve the classification of disease subtypes. In this study, we introduce sCClust (sparse canonical correlation analysis with clustering), a technique to combine high-dimensional omics data using sparse canonical correlation analysis (sCCA), such that the correlation between datasets is maximized. This stage is followed by clustering the integrated data in a lower-dimensional space. We apply sCClust to gene expression and DNA methylation data for three cancer genomics datasets from the Cancer Genome Atlas (TCGA) to distinguish between underlying subtypes. We evaluate the identified subtypes using Kaplan–Meier plots and hazard ratio analysis on the three types of cancer—GBM (glioblastoma multiform), lung cancer and colon cancer. Comparison with subtypes identified by both single- and multi-omics studies implies improved clinical association. We also perform pathway over-representation analysis in order to identify up-regulated and down-regulated genes as tentative drug targets. The main goal of the paper is twofold: the integration of epigenomic and transcriptomic datasets followed by elucidating subtypes in the latent space. The significance of this study lies in the enhanced categorization of cancer data, which is crucial to precision medicine. Full article

To effectively treat lung and colon cancer and save lives, early and accurate identification is essential. Conventional diagnosis takes a long time and requires the manual expertise of radiologists. The rising number of new cancer cases makes it challenging to process massive volumes of data quickly. Different machine learning approaches to the classification and detection of lung and colon cancer have been proposed by multiple research studies. However, when it comes to self-learning classification and detection tasks, deep learning (DL) excels. This paper suggests a novel DL convolutional neural network (CNN) model for detecting lung and colon cancer. The proposed model is lightweight and multi-scale since it uses only 1.1 million parameters, making it appropriate for real-time applications as it provides an end-to-end solution. By incorporating features extracted at multiple scales, the model can effectively capture both local and global patterns within the input data. The explainability tools such as gradient-weighted class activation mapping and Shapley additive explanation can identify potential problems by highlighting the specific input data areas that have an impact on the model’s choice. The experimental findings demonstrate that for lung and colon cancer detection, the proposed model was outperformed by the competition and accuracy rates of 99.20% have been achieved for multi-class (containing five classes) predictions. Full article

Cancer, a genetic disease, is considered one of the leading causes of death globally and affects people of all ages. Ribonucleic acid sequencing (RNA-Seq) is a technique used to quantify the expression of genes of interest and can be used to classify cancer tumor types. This paper describes a machine learning technique to classify cancer tissue samples by tumor type, such as breast cancer, lung cancer, colon cancer, and others. More than 60,000 RNA-Seq features were analyzed using six different machine learning classification algorithms, both individually and as an ensemble. Numerous dimensionality reduction techniques addressed the challenges of working with enormous amounts of genetic data. In particular, we were able to reduce the number of features from over 60,000 to 660 in the random forest feature selection and to 68 factor features using factor analysis with an accuracy of 99% in classifying tumor types. Full article

Lung and colon cancers are among the leading causes of human mortality and morbidity. Early diagnostic work up of these diseases include radiography, ultrasound, magnetic resonance imaging, and computed tomography. Certain blood tumor markers for carcinoma lung and colon also aid in the diagnosis. Despite the lab and diagnostic imaging, histopathology remains the gold standard, which provides cell-level images of tissue under examination. To read these images, a histopathologist spends a large amount of time. Furthermore, using conventional diagnostic methods involve high-end equipment as well. This leads to limited number of patients getting final diagnosis and early treatment. In addition, there are chances of inter-observer errors. In recent years, deep learning has shown promising results in the medical field. This has helped in early diagnosis and treatment according to severity of disease. With the help of EffcientNetV2 models that have been cross-validated and tested fivefold, we propose an automated method for detecting lung (lung adenocarcinoma, lung benign, and lung squamous cell carcinoma) and colon (colon adenocarcinoma and colon benign) cancer subtypes from LC25000 histopathology images. A state-of-the-art deep learning architecture based on the principles of compound scaling and progressive learning, EffcientNetV2 large, medium, and small models. An accuracy of 99.97%, AUC of 99.99%, F1-score of 99.97%, balanced accuracy of 99.97%, and Matthew’s correlation coefficient of 99.96% were obtained on the test set using the EffcientNetV2-L model for the 5-class classification of lung and colon cancers, outperforming the existing methods. Using gradCAM, we created visual saliency maps to precisely locate the vital regions in the histopathology images from the test set where the models put more attention during cancer subtype predictions. This visual saliency maps may potentially assist pathologists to design better treatment strategies. Therefore, it is possible to use the proposed pipeline in clinical settings for fully automated lung and colon cancer detection from histopathology images with explainability. Full article

Pancreatic cancer is projected to become the second leading cause of cancer-related mortality in the United States by 2030. This is in part due to the paucity of reliable screening and diagnostic options for early detection. Amongst known pre-malignant pancreatic lesions, pancreatic intraepithelial neoplasia (PanIN) and intraductal papillary mucinous neoplasms (IPMNs) are the most prevalent. The current standard of care for the diagnosis and classification of pancreatic cystic lesions (PCLs) involves cross-sectional imaging studies and endoscopic ultrasound (EUS) and, when indicated, EUS-guided fine needle aspiration and cyst fluid analysis. However, this is suboptimal for the identification and risk stratification of PCLs, with accuracy of only 65–75% for detecting mucinous PCLs. Artificial intelligence (AI) is a promising tool that has been applied to improve accuracy in screening for solid tumors, including breast, lung, cervical, and colon cancer. More recently, it has shown promise in diagnosing pancreatic cancer by identifying high-risk populations, risk-stratifying premalignant lesions, and predicting the progression of IPMNs to adenocarcinoma. This review summarizes the available literature on artificial intelligence in the screening and prognostication of precancerous lesions in the pancreas, and streamlining the diagnosis of pancreatic cancer. Full article

Deep learning (DL) and convolutional neural networks (CNNs) have achieved state-of-the-art performance in many medical image analysis tasks. Histopathological images contain valuable information that can be used to diagnose diseases and create treatment plans. Therefore, the application of DL for the classification of histological images is a rapidly expanding field of research. The popularity of CNNs has led to a rapid growth in the number of works related to CNNs in histopathology. This paper aims to provide a clear overview for better navigation. In this paper, recent DL-based classification studies in histopathology using strongly annotated data have been reviewed. All the works have been categorized from two points of view. First, the studies have been categorized into three groups according to the training approach and model construction: 1. fine-tuning of pre-trained networks for one-stage classification, 2. training networks from scratch for one-stage classification, and 3. multi-stage classification. Second, the papers summarized in this study cover a wide range of applications (e.g., breast, lung, colon, brain, kidney). To help navigate through the studies, the classification of reviewed works into tissue classification, tissue grading, and biomarker identification was used. Full article