Yazar "Algarni, Abdulmohsen" seçeneğine göre listele

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    Explainable Boosting Machines Identify Key Metabolomic Biomarkers in Rheumatoid Arthritis
    (Mdpi, 2025) Yagin, Fatma Hilal; Colak, Cemil; Algarni, Abdulmohsen; Algarni, Ali; Al-Hashem, Fahaid; Ardigo, Luca Paolo
    Background and Objectives: Rheumatoid arthritis (RA) is a chronic autoimmune disease characterised by joint inflammation and pain. Metabolomics approaches, which are high-throughput profiling of small molecule metabolites in plasma or serum in RA patients, have so far provided biomarker discovery in the literature for clinical subgroups, risk factors, and predictors of treatment response using classical statistical approaches or machine learning models. Despite these recent developments, an explainable artificial intelligence (XAI)-based methodology has not been used to identify RA metabolomic biomarkers and distinguish patients with RA. This study constructed a XAI-based EBM model using global plasma metabolomics profiling to identify metabolites predictive of RA patients and to develop a classification model that can distinguish RA patients from healthy controls. Materials and Methods: Global plasma metabolomics data were analysed from RA patients (49 samples) and healthy individuals (10 samples). SMOTE technique was used for class imbalance in data preprocessing. EBM, LightGBM, and AdaBoost algorithms were applied to generate a discriminatory model between RA and controls. Comprehensive performance metrics were calculated, and the interpretability of the optimal model was assessed using global and local feature descriptions. Results: A total of 59 samples were analysed, 49 from RA patients, and 10 from healthy subjects. The EBM generated better results than LightGBM and AdaBoost by attaining an AUC of 0.901 (95% CI: 0.847-0.955) with 87.8% sensitivity which helps prevent false negative early RA diagnosis. The primary biomarkers EBM-based XAI identified were N-acetyleucine, pyruvic acid, and glycerol-3-phosphate. EBM global explanation analysis indicated that elevated pyruvic acid levels were significantly correlated with RA, whereas N-acetyleucine exhibited a nonlinear relationship, implying possible protective effects at specific concentrations. Conclusions: This study underscores the promise of XAI and evidence-based medicine methodology in developing biomarkers for RA through metabolomics. The discovered metabolites offer significant insights into RA pathophysiology and may function as diagnostic biomarkers or therapeutic targets. Incorporating EBM methodologies integrated with XAI improves model transparency and increases the therapeutic applicability of predictive models for RA diagnosis/management. Furthermore, the transparent structure of the EBM model empowers clinicians to understand and verify the reasoning behind each prediction, thereby fostering trust in AI-assisted decision-making and facilitating the integration of metabolomic insights into routine clinical practice.
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    HearteXplain: explainable prediction of acute heart failure and identification of hematologic biomarkers using EBMs and Morris sensitivity analysis
    (Nature Portfolio, 2025) Yagin, Fatma Hilal; Gormez, Yasin; Algarni, Abdulmohsen; Al-Hashem, Fahaid; Dutta, Ashit Kumar; Aghaei, Mohammadreza
    Hematological biomarkers have emerged as powerful tools in diagnosing Acute Heart Failure (AHF). This study introduces a novel diagnostic framework that integrates Explainable Artificial Intelligence (XAI) with Morris Sensitivity Analysis (MSA) to enhance both the interpretability and performance of machine learning models in AHF detection. A dataset consisting of 425 AHF patients and 430 controls was analyzed using eight machine learning models, including XGBoost, Histogram-based Gradient Boosting (histGB), Explainable Boosting Machine (EBM), and Random Forest. Model performance was evaluated through metrics such as AUC, accuracy, precision, recall, and Brier score. Hyperparameters were optimized via Bayesian optimization. Feature importance was assessed using MSA to identify variables with the highest predictive influence. The histGB model achieved the highest performance with an AUC of 87.93%. Both MSA and EBM consistently identified PDW, RDW-CV, NEU, NEU/LY ratio, age, and WBC as top predictive features across multiple models. These hematological markers demonstrated strong potential for early diagnosis and risk stratification in AHF patients. This study presents a clinically relevant, interpretable, and cost-effective diagnostic strategy that combines XAI with MSA for AHF prediction. The framework enhances clinical trust and provides a pathway toward personalized treatment by identifying accessible hematological biomarkers. The integration of explainability into AI models improves their transparency and applicability in real-world clinical settings.
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    Precision Enhanced Bioactivity Prediction of Tyrosine Kinase Inhibitors by Integrating Deep Learning and Molecular Fingerprints Towards Cost-Effective and Targeted Cancer Therapy
    (Mdpi, 2025) Yagin, Fatma Hilal; Gormez, Yasin; Colak, Cemil; Algarni, Abdulmohsen; Al-Hashem, Fahaid; Ardigo, Luca Paolo
    Background and Objective: Dysregulated tyrosine kinase signaling is a central driver of tumorigenesis, metastasis, and therapeutic resistance. While tyrosine kinase inhibitors (TKIs) have revolutionized targeted cancer treatment, identifying compounds with optimal bioactivity remains a critical bottleneck. This study presents a robust machine learning framework-leveraging deep artificial neural networks (dANNs), convolutional neural networks (CNNs), and structural molecular fingerprints-to accurately predict TKI bioactivity, ultimately accelerating the preclinical phase of drug development. Methods: A curated dataset of 28,314 small molecules from the ChEMBL database targeting 11 tyrosine kinases was analyzed. Using Morgan fingerprints and physicochemical descriptors (e.g., molecular weight, LogP, hydrogen bonding), ten supervised models, including dANN, SVM, CatBoost, and CNN, were trained and optimized through a randomized hyperparameter search. Model performance was evaluated using F1-score, ROC-AUC, precision-recall curves, and log loss. Results: SVM achieved the highest F1-score (87.9%) and accuracy (85.1%), while dANNs yielded the lowest log loss (0.25096), indicating superior probabilistic reliability. CatBoost excelled in ROC-AUC and precision-recall metrics. The integration of Morgan fingerprints significantly improved bioactivity prediction across all models by enhancing structural feature recognition. Conclusions: This work highlights the transformative role of machine learning-particularly dANNs and SVM-in rational drug discovery. By enabling accurate bioactivity prediction, our model pipeline can effectively reduce experimental burden, optimize compound selection, and support personalized cancer treatment design. The proposed framework advances kinase inhibitor screening pipelines and provides a scalable foundation for translational applications in precision oncology. By enabling early identification of bioactive compounds with favorable pharmacological profiles, the results of this study may support more efficient candidate selection for clinical drug development, particularly in regards to cancer therapy and kinase-associated disorders.