SwarmDeepSurv: swarm intelligence advances deep survival network for prognostic radiomics signatures in four solid cancers.

Survival models exist to study relationships between biomarkers and treatment effects. Deep learning-powered survival models supersede the classical Cox proportional hazards (CoxPH) model, but substantial performance drops were observed on high-dimensional features because of irrelevant/redundant information. To fill this gap, we proposed SwarmDeepSurv by integrating swarm intelligence algorithms with the deep survival model. Furthermore, four objective functions were designed to optimize prognostic prediction while regularizing selected feature numbers. When testing on multicenter sets (n = 1,058) of four different cancer types, SwarmDeepSurv was less prone to overfitting and achieved optimal patient risk stratification compared with popular survival modeling algorithms. Strikingly, SwarmDeepSurv selected different features compared with classical feature selection algorithms, including the least absolute shrinkage and selection operator (LASSO), with nearly no feature overlapping across these models. Taken together, SwarmDeepSurv offers an alternative approach to model relationships between radiomics features and survival endpoints, which can further extend to study other input data types including genomics.

Machine Learning Models for the Identification of Prognostic and Predictive Cancer Biomarkers: A Systematic Review.

The identification of biomarkers plays a crucial role in personalized medicine, both in the clinical and research settings. However, the contrast between predictive and prognostic biomarkers can be challenging due to the overlap between the two. A prognostic biomarker predicts the future outcome of cancer, regardless of treatment, and a predictive biomarker predicts the effectiveness of a therapeutic intervention. Misclassifying a prognostic biomarker as predictive (or vice versa) can have serious financial and personal consequences for patients. To address this issue, various statistical and machine learning approaches have been developed. The aim of this study is to present an in-depth analysis of recent advancements, trends, challenges, and future prospects in biomarker identification. A systematic search was conducted using PubMed to identify relevant studies published between 2017 and 2023. The selected studies were analyzed to better understand the concept of biomarker identification, evaluate machine learning methods, assess the level of research activity, and highlight the application of these methods in cancer research and treatment. Furthermore, existing obstacles and concerns are discussed to identify prospective research areas. We believe that this review will serve as a valuable resource for researchers, providing insights into the methods and approaches used in biomarker discovery and identifying future research opportunities.

Improved intelligent water drop-based hybrid feature selection method for microarray data processing.

Classifying microarray datasets, which usually contains many noise genes that degrade the performance of classifiers and decrease classification accuracy rate, is a competitive research topic. Feature selection (FS) is one of the most practical ways for finding the most optimal subset of genes that increases classification's accuracy for diagnostic and prognostic prediction of tumor cancer from the microarray datasets. This means that we always need to develop more efficient FS methods, that select only optimal or close-to-optimal subset of features to improve classification performance. In this paper, we propose a hybrid FS method for microarray data processing, that combines an ensemble filter with an Improved Intelligent Water Drop (IIWD) algorithm as a wrapper by adding one of three local search (LS) algorithms: Tabu search (TS), Novel LS algorithm (NLSA), or Hill Climbing (HC) in each iteration from IWD, and using a correlation coefficient filter as a heuristic undesirability (HUD) for next node selection in the original IWD algorithm. The effects of adding three different LS algorithms to the proposed IIWD algorithm have been evaluated through comparing the performance of the proposed ensemble filter-IIWD-based wrapper without adding any LS algorithms named (PHFS-IWD) FS method versus its performance when adding a specific LS algorithm from (TS, NLSA or HC) in FS methods named, (PHFS-IWDTS, PHFS-IWDNLSA, and PHFS-IWDHC), respectively. Naïve Bayes(NB) classifier with five microarray datasets have been deployed for evaluating and comparing the proposed hybrid FS methods. Results show that using LS algorithms in each iteration from the IWD algorithm improves F-score value with an average equal to 5% compared with PHFS-IWD. Also, PHFS-IWDNLSA improves the F-score value with an average of 4.15% over PHFS-IWDTS, and 5.67% over PHFS-IWDHC while PHFS-IWDTS outperformed PHFS-IWDHC with an average of increment equal to 1.6%. On the other hand, the proposed hybrid-based FS methods improve accuracy with an average equal to 8.92% in three out of five datasets and decrease the number of genes with a percentage of 58.5% in all five datasets compared with six of the most recent state-of-the-art FS methods.

Deep feature selection using local search embedded social ski-driver optimization algorithm for breast cancer detection in mammograms.

Breast cancer has become a common malignancy in women. However, early detection and identification of this disease can save many lives. As computer-aided detection helps radiologists in detecting abnormalities efficiently, researchers across the world are striving to develop reliable models to deal with. One of the common approaches to identifying breast cancer is through breast mammograms. However, the identification of malignant breasts from mass lesions is a challenging research problem. In the current work, we propose a method for the classification of breast mass using mammograms which consists of two main stages. At first, we extract deep features from the input mammograms using the well-known VGG16 model while incorporating an attention mechanism into this model. Next, we apply a meta-heuristic called Social Ski-Driver (SSD) algorithm embedded with Adaptive Beta Hill Climbing based local search to obtain an optimal features subset. The optimal features subset is fed to the K-nearest neighbors (KNN) classifier for the classification. The proposed model is demonstrated to be very useful for identifying and differentiating malignant and healthy breasts successfully. For experimentation, we evaluate our model on the digital database for screening mammography (DDSM) database and achieve 96.07% accuracy using only 25% of features extracted by the attention-aided VGG16 model. The Python code of our research work is publicly available at: https://github.com/Ppayel/BreastLocalSearchSSD.

An Al-Biruni Earth Radius Optimization-Based Deep Convolutional Neural Network for Classifying Monkeypox Disease.

Human skin diseases have become increasingly prevalent in recent decades, with millions of individuals in developed countries experiencing monkeypox. Such conditions often carry less obvious but no less devastating risks, including increased vulnerability to monkeypox, cancer, and low self-esteem. Due to the low visual resolution of monkeypox disease images, medical specialists with high-level tools are typically required for a proper diagnosis. The manual diagnosis of monkeypox disease is subjective, time-consuming, and labor-intensive. Therefore, it is necessary to create a computer-aided approach for the automated diagnosis of monkeypox disease. Most research articles on monkeypox disease relied on convolutional neural networks (CNNs) and using classical loss functions, allowing them to pick up discriminative elements in monkeypox images. To enhance this, a novel framework using Al-Biruni Earth radius (BER) optimization-based stochastic fractal search (BERSFS) is proposed to fine-tune the deep CNN layers for classifying monkeypox disease from images. As a first step in the proposed approach, we use deep CNN-based models to learn the embedding of input images in Euclidean space. In the second step, we use an optimized classification model based on the triplet loss function to calculate the distance between pairs of images in Euclidean space and learn features that may be used to distinguish between different cases, including monkeypox cases. The proposed approach uses images of human skin diseases obtained from an African hospital. The experimental results of the study demonstrate the proposed framework's efficacy, as it outperforms numerous examples of prior research on skin disease problems. On the other hand, statistical experiments with Wilcoxon and analysis of variance (ANOVA) tests are conducted to evaluate the proposed approach in terms of effectiveness and stability. The recorded results confirm the superiority of the proposed method when compared with other optimization algorithms and machine learning models.

Abnormality classification and localization using dual-branch whole-region-based CNN model with histopathological images.

The task of classification and localization with detecting abnormalities in medical images is considered very challenging. Computer-aided systems have been widely employed to address this issue, and the proliferation of deep learning network architectures is proof of the outstanding performance reported in the literature. However, localizing abnormalities in regions of images that can support the confidence of classification continues to attract research interest. The difficulty of using digital histopathology images for this task is another drawback, which needs high-level deep learning models to address the situation. Successful pathology localization automation will support automatic acquisition planning and post-imaging analysis. In this paper, we address issues related to the combination of classification with image localization and detection through a dual branch deep learning framework that uses two different configurations of convolutional neural networks (CNN) architectures. Whole-image based CNN (WCNN) and region-based CNN (RCNN) architectures are systematically combined to classify and localize abnormalities in samples. A multi-class classification and localization of abnormalities are achieved using the method with no annotation-dependent images. In addition, seamless confidence and explanation mechanism is provided so that outcomes from WCNN and RCNN are mapped together for further analysis. Using images from both BACH and BreakHis databases, an exhaustive set of experiments was carried out to validate the performance of the proposed method in achieving classification and localization simultaneously. Obtained results showed that the system achieved a classification accuracy of 97.08%, a localization accuracy of 94%, and an area under the curve (AUC) of 0.10 for classification. Further findings from this study revealed that a multi-neural network approach could provide a suitable method for addressing the combinatorial problem of classification and localization anomalies in digital medical images. Lastly, the study's outcome offers means for automating the annotation of histopathology images and the support for human pathologists in locating abnormalities.

HGSORF: Henry Gas Solubility Optimization-based Random Forest for C-Section prediction and XAI-based cause analysis.

A stable predictive model is essential for forecasting the chances of cesarean or C-section (CS) delivery, as unnecessary CS delivery can adversely affect neonatal, maternal, and pediatric morbidity and mortality, and can incur significant financial burdens. Limited state-of-the-art machine learning models have been applied in this area in recent years, and the current models are insufficient to correctly predict the probability of CS delivery. To alleviate this drawback, we have proposed a Henry gas solubility optimization (HGSO)-based random forest (RF), with an improved objective function, called HGSORF, for the classification of CS and non-CS classes. Real-world CS datasets can be noisy, such as the Pakistan Demographic and Health Survey (PDHS) dataset used in this study. The HGSO can provide fine-tuned hyperparameters of RF by avoiding local minima points. To compare performance, Gaussian Naive Bayes (GNB), linear discriminant analysis (LDA), K-nearest neighbors (KNN), gradient boosting classifier (GBC), and logistic regression (LR) have been considered in this research. The ADAptive SYNthetic (ADASYN) algorithm has been used to balance the model, and the proposed HGSORF has been compared with other classifiers as well as with other studies. The superior performance was achieved by HGSORF with an accuracy of 98.33% for the PDHS dataset. The hyperparameters of RF have also been optimized by using commonly used hyperparameter-optimization algorithms, and the proposed HGSORF provided comparatively better performance. Additionally, to analyze the causes of CS and their significance, the HGSORF is explained locally and globally using eXplainable artificial intelligence (XAI)-based tools such as SHapely Additive exPlanation (SHAP) and Local Interpretable Model-Agnostic Explanations (LIME). A decision support system has been developed as a potential application to support clinical staffs. All pre-trained models and relevant codes are available on: https://github.com/MIrazul29/HGSORF_CSection.

Machine Learning-Based Research for COVID-19 Detection, Diagnosis, and Prediction: A Survey.

The year 2020 experienced an unprecedented pandemic called COVID-19, which impacted the whole world. The absence of treatment has motivated research in all fields to deal with it. In Computer Science, contributions mainly include the development of methods for the diagnosis, detection, and prediction of COVID-19 cases. Data science and Machine Learning (ML) are the most widely used techniques in this area. This paper presents an overview of more than 160 ML-based approaches developed to combat COVID-19. They come from various sources like Elsevier, Springer, ArXiv, MedRxiv, and IEEE Xplore. They are analyzed and classified into two categories: Supervised Learning-based approaches and Deep Learning-based ones. In each category, the employed ML algorithm is specified and a number of used parameters is given. The parameters set for each of the algorithms are gathered in different tables. They include the type of the addressed problem (detection, diagnosis, or detection), the type of the analyzed data (Text data, X-ray images, CT images, Time series, Clinical data,...) and the evaluated metrics (accuracy, precision, sensitivity, specificity, F1-Score, and AUC). The study discusses the collected information and provides a number of statistics drawing a picture about the state of the art. Results show that Deep Learning is used in 79% of cases where 65% of them are based on the Convolutional Neural Network (CNN) and 17% use Specialized CNN. On his side, supervised learning is found in only 16% of the reviewed approaches and only Random Forest, Support Vector Machine (SVM) and Regression algorithms are employed.

Feature selection methods on gene expression microarray data for cancer classification: A systematic review.

This systematic review provides researchers interested in feature selection (FS) for processing microarray data with comprehensive information about the main research directions for gene expression classification conducted during the recent seven years. A set of 132 researches published by three different publishers is reviewed. The studied papers are categorized into nine directions based on their objectives. The FS directions that received various levels of attention were then summarized. The review revealed that 'propose hybrid FS methods' represented the most interesting research direction with a percentage of 34.9%, while the other directions have lower percentages that ranged from 13.6% down to 3%. This guides researchers to select the most competitive research direction. Papers in each category are thoroughly reviewed based on six perspectives, mainly: method(s), classifier(s), dataset(s), dataset dimension(s) range, performance metric(s), and result(s) achieved.