The most common approaches to discovering genes associated with specific diseases are based on machine learning and use a variety of feature selection techniques to identify significant genes that can serve as biomarkers for a given disease. More recently, the integration in this process of prior knowledge-based approaches has shown significant promise in the discovery of new biomarkers with potential translational applications. In this study, we developed a novel approach, GediNET, that integrates prior biological knowledge to gene Groups that are shown to be associated with a specific disease such as a cancer. The novelty of GediNET is that it then also allows the discovery of significant associations between that specific disease and other diseases. The initial step in this process involves the identification of gene Groups. The Groups are then subjected to a Scoring component to identify the top performing classification Groups. The top-ranked gene Groups are then used to train a Machine Learning Model. The process of Grouping, Scoring and Modelling (G-S-M) is used by GediNET to identify other diseases that are similarly associated with this signature. GediNET identifies these relationships through Disease–Disease Association (DDA) based machine learning. DDA explores novel associations between diseases and identifies relationships which could be used to further improve approaches to diagnosis, prognosis, and treatment. The GediNET KNIME workflow can be downloaded from: https://github.com/malikyousef/GediNET.git or https://kni.me/w/3kH1SQV_mMUsMTS.

In the broad and complex field of biological data analysis, researchers frequently gather information from a single source or database. Despite being a widespread practice, this has disadvantages. Relying exclusively on a single source can limit our comprehension as it may omit various perspectives that could be obtained by combining multiple knowledge bases. Acknowledging this shortcoming, we report on miRGediNET, a novel approach combining information from three biological databases. Our investigation focuses on microRNAs (miRNAs), small non-coding RNA molecules that regulate gene expression post-transcriptionally. We delve deeply into the knowledge of these miRNA's interactions with genes and the possible effects these interactions may have on different diseases. The scientific community has long recognized a direct correlation between the progression of specific diseases and miRNAs, as well as the genes they target. By using miRGediNET, we go beyond simply acknowledging this relationship. Rather, we actively look for the critical genes that could act as links between the actions of miRNAs and the mechanisms underlying disease. Our methodology, which carefully identifies and investigates these important genes, is supported by a strategic framework that may open up new possibilities for comprehending diseases and creating treatments. We have developed a tool on the Knime platform as a concrete application of our research. This tool serves as both a validation of our study and an invitation to the larger community to interact with, investigate, and build upon our findings. miRGediNET is publicly accessible on GitHub at https://github.com/malikyousef/miRGediNET, providing a collaborative environment for additional research and innovation for enthusiasts and fellow researchers.

Over the past few years, phishing has evolved into an increasingly prevalent form of cybercrime, as more people use the Internet and its applications. Phishing is a type of social engineering that targets users' sensitive or personal information. This paper seeks to achieve two main objectives: first, to identify the most effective classifier for detecting phishing among 40 classifiers representing six learning strategies. Secondly, it aims to determine which feature selection method performs best on websites with phishing datasets. By analyzing three unique datasets on phishing and evaluating eight metrics, this study found that Random Forest and Random Tree were superior at identifying phishing websites compared with other approaches. Similarly, GainRatioAttributeEval, along with InfoGainAttributeEval, performed better than the five alternative feature selection methods considered in this study.

The development of sequencing technology and the increase in biological data repositories have allowed for a more thorough understanding of the complex molecular aspects of diseases like cancer. This paper evaluates GediNET, an integrative machine learning approach that employs a Grouping-Scoring-Modeling (GSM) approach to classify different molecular subtypes of breast cancer using the BRCA LumAB_Her2Basal dataset against different feature selection approaches and machine learning classifiers. GediNET distinguishes itself from traditional feature selection methods by analyzing groups of genes to identify relevant disease-disease associations and potential biomarkers. The results of our study show that GediNET performs better than traditional approaches in terms of accuracy and Area Under the Curve (AUC) metrics. This demonstrates that GediNET is effective in understanding the genetic intricacies of breast cancer. This approach improves the identification of molecular subtypes and promotes the development of targeted medicines and customized medicine.

Background: Heart disease remains one of the leading causes of mortality worldwide, highlighting the need for early and accurate diagnosis to support effective prevention and treatment strategies. Methods: This study presents a machine-learning-based approach for predicting heart disease using clinical and demographic data from a publicly available dataset. Four widely used classification algorithms—Logistic Regression, Random Forest, K-Nearest Neighbors (KNN), and Decision Trees—were evaluated to identify the most effective predictive model. The dataset underwent comprehensive preprocessing, including handling missing values, categorical encoding, and feature normalization, to enhance data quality and model robustness. Model performance was assessed using accuracy, precision, recall, and AUC-ROC metrics. Results: Findings show that hyperparameter-optimized models, particularly Random Forest and KNN, demonstrated strong predictive performance. Explainability techniques, specifically SHapley Additive exPlanations (SHAP), were incorporated to improve interpretability, transparency, and clinical trust. SHAP values were used to analyze feature importance and provide explanations for individual predictions. Conclusion: The results underscore the potential of interpretable machine-learning models as valuable tools for early diagnosis, risk stratification, and clinical decision support. Future research should employ larger datasets and investigate real-time predictive applications further to enhance the generalizability and clinical utility of these models.