Yazar "Alhussan, Amel Ali" seçeneğine göre listele

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    Identification of a Novel Lipidomic Biomarker for Hepatocyte Carcinoma Diagnosis: Advanced Boosting Machine Learning Techniques Integrated with Explainable Artificial Intelligence
    (Mdpi, 2025) Yagin, Fatma Hilal; Colak, Cemil; Al-Hashem, Fahaid; Alzakari, Sarah A.; Alhussan, Amel Ali; Aghaei, Mohammadreza
    Background: Hepatocellular carcinoma (HCC) is a leading cause of cancer-related mortality worldwide, often diagnosed at late stages due to the limited sensitivity of current screening tools. This study explores whether blood-based lipidomic profiling, combined with explainable artificial intelligence (XAI), can improve early and interpretable detection of HCC. Methods: We analyzed lipidomic data from 219 HCC patients and 219 matched healthy controls using liquid chromatography-mass spectrometry. An Explainable Boosting Machine (EBM) was employed to identify discriminatory lipid biomarkers and was compared against several standard machine learning algorithms. Results: The EBM model achieved superior performance with 87.0% accuracy, 87.7% sensitivity, 86.3% specificity, and an AUC of 91.8%, outperforming other models. Key lipid biomarkers identified included specific phosphatidylcholines (PC 38:2, PC 40:4), sphingomyelins (SM d40:2 B), and lysophosphatidylcholines (LPC 18:2), which exhibited significant alterations in HCC patients and highlighted disruptions in sphingolipid metabolism. Conclusions: Integration of lipidomics with explainable machine learning offers a powerful, transparent approach for HCC biomarker discovery, achieving high diagnostic accuracy while providing biological insights. This strategy holds promise for developing non-invasive, clinically interpretable screening tools to improve early detection of liver cancer.
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    Interpretable Machine Learning for Serum-Based Metabolomics in Breast Cancer Diagnostics: Insights from Multi-Objective Feature Selection-Driven LightGBM-SHAP Models
    (Mdpi, 2025) Guldogan, Emek; Yagin, Fatma Hilal; Ucuzal, Hasan; Alzakari, Sarah A.; Alhussan, Amel Ali; Ardigo, Luca Paolo
    Background and Objectives: Breast cancer accounts for 12.5% of all new cancer cases in women worldwide. Early detection significantly improves survival rates, but traditional biomarkers like CA 15-3 and HER2 lack sensitivity and specificity, particularly for early-stage disease. Advances in metabolomics and machine learning, particularly explainable artificial intelligence (XAI), offer new opportunities for identifying robust biomarkers and improving diagnostic accuracy. This study aimed to identify and validate serum-based metabolic biomarkers for breast cancer using advanced metabolomic profiling techniques and a Light Gradient Boosting Machine (LightGBM) model. Additionally, SHapley Additive exPlanations (SHAP) were applied to enhance model interpretability and biological insight. Materials and Methods: The study included 103 breast cancer patients and 31 healthy controls. Serum samples underwent liquid and gas chromatography-time-of-flight mass spectrometry (LC-TOFMS and GC-TOFMS). Mutual Information (MI), Sparse Partial Least Squares (sPLS), Boruta, and Multi-Objective Feature Selection (MOFS) approaches were applied to the data for biomarker discovery. LightGBM, AdaBoost, and Random Forest were employed for classification and to identify class imbalance with the Synthetic Minority Oversampling Technique (SMOTE). SHAP analysis ranked metabolites based on their contribution to model predictions. Results: Compared to other feature selection approaches, the MOFS approach was more robust in terms of predictive performance, and metabolites identified by this method were used in subsequent analyses for biomarker discovery. LightGBM outperformed the AdaBoost and Random Forest models, achieving 86.6% accuracy, 89.1% sensitivity, 84.2% specificity, and an F1-score of 87.0%. SHAP analysis identified 2-Aminobutyric acid, choline, and coproporphyrin as the most influential metabolites, with dysregulation of these markers associated with breast cancer risk. Conclusions: This study is among the first to integrate SHAP explainability with metabolomic profiling, bridging computational predictions and biological insights for improved clinical adoption. This study demonstrates the effectiveness of combining metabolomics with XAI-driven machine learning for breast cancer diagnostics. The identified biomarkers not only improve diagnostic accuracy but also reveal critical metabolic dysregulations associated with disease progression.
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    Leveraging Explainable Automated Machine Learning (AutoML) and Metabolomics for Robust Diagnosis and Pathophysiological Insights in Myalgic Encephalomyelitis/Chronic Fatigue Syndrome (ME/CFS)
    (Mdpi, 2025) Yagin, Fatma Hilal; Colak, Cemil; Al-Hashem, Fahaid; Alzakari, Sarah A.; Alhussan, Amel Ali; Aghaei, Mohammadreza
    Background/Objectives: Myalgic Encephalomyelitis/Chronic Fatigue Syndrome (ME/CFS) is a debilitating complex disease with an elusive etiology, lacking objective diagnostic biomarkers. This study leverages advanced Automated Machine Learning (AutoML) to analyze plasma metabolomic and lipidomic profiles for the purpose of ME/CFS detection. Methods: We utilized a publicly available dataset comprising 888 metabolic features from 106 ME/CFS patients and 91 matched controls. Three AutoML frameworks-TPOT, Auto-Sklearn, and H2O AutoML-were benchmarked under identical time constraints. Univariate ROC and PLS-DA analyses with cross-validation, permutation testing, and VIP-based feature selection were applied to standardized, log-transformed omics data to identify significant discriminatory metabolites/lipids and assess their intercorrelations. Results: TPOT significantly outperformed its counterparts, achieving an area under the curve (AUC) of 92.1%, accuracy of 87.3%, sensitivity of 85.8%, and specificity of 89.0%. The PLS-DA model revealed a moderate but statistically significant discrimination between ME/CFS and controls. Explainable artificial intelligence (XAI) via SHAP analysis of the optimal TPOT model identified key metabolites implicating dysregulated pathways in mitochondrial energy metabolism (succinic acid, pyruvic acid, leucine), chronic inflammation (prostaglandin D2, 11,12-EET), gut-brain axis communication (glycocholic acid), and cell membrane integrity (pc(35:2)a). Conclusions: Our results demonstrate that TPOT-derived models not only provide a highly accurate and robust diagnostic tool but also yield biologically interpretable insights into the pathophysiology of ME/CFS, highlighting its potential for clinical decision support and elucidating novel therapeutic targets.
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    Machine Learning Classification of Cognitive Status in Community-Dwelling Sarcopenic Women: A SHAP-Based Analysis of Physical Activity and Anthropometric Factors
    (Mdpi, 2025) Gormez, Yasin; Yagin, Fatma Hilal; Aygun, Yalin; Alzakari, Sarah A.; Alhussan, Amel Ali; Aghaei, Mohammadreza
    Background and Objectives: Sarcopenia, characterized by progressive loss of skeletal muscle mass and function, has increasingly been recognized not only as a physical health concern but also as a potential risk factor for cognitive decline. This study investigates the application of machine learning algorithms to classify cognitive status based on Mini-Mental State Examination (MMSE) scores in community-dwelling sarcopenic women. Materials and Methods: A dataset of 67 participants was analyzed, with MMSE scores categorized into severe (<= 17) and mild (>17) cognitive impairment. Eight classification models-MLP, CatBoost, LightGBM, XGBoost, Random Forest (RF), Gradient Boosting (GB), Logistic Regression (LR), and AdaBoost-were evaluated using a repeated holdout strategy over 100 iterations. Hyperparameter optimization was performed via Bayesian optimization, and model performance was assessed using metrics including weighted F1-score (w_f1), accuracy, precision, recall, PR-AUC, and ROC-AUC. Results: Among the models, CatBoost achieved the highest w_f1 (87.05 +/- 2.85%) and ROC-AUC (90 +/- 5.65%), while AdaBoost and GB showed superior PR-AUC scores (92.49% and 91.88%, respectively), indicating strong performance in handling class imbalance and threshold sensitivity. SHAP (SHapley Additive exPlanations) analysis revealed that moderate physical activity (moderatePA minutes), walking days, and sitting time were among the most influential features, with higher physical activity associated with reduced risk of cognitive impairment. Anthropometric factors such as age, BMI, and weight also contributed significantly. Conclusions: The results highlight the effectiveness of boosting-based models in capturing complex patterns in clinical data and provide interpretable evidence supporting the role of modifiable lifestyle factors in cognitive health. These findings suggest that machine learning, combined with explainable AI, can enhance risk assessment and inform targeted interventions for cognitive decline in older women.