Ayse Ulgen
Current Organizations / Institutes
The organizations/institutes from the scholar's latest article
Previous Organizations / Institutes
The organizations / institutes from the scholar's other articles in the past ten years
Research Subjects
Research Interests
Ayse Ulgen has a total of 85 co-authors. Here are the top co-authors by number of shared publications:
- Wentian Li
Affiliations Department of Applied Mathematics and Statistics, Stony Brook University, Stony Brook, New York, United States of America, The Robert S. Boas Center for Genomics and Human Genetics, The Feinstein Institutes for Medical Research, Northwell Health, Manhasset, New York, United States of America
13 shared publications - Şirin Çetin
Department of Biostatistics, Faculty of Medicine, Amasya University, Amasya 05100, Turkey
7 shared publications Sirin Cetin
Affiliation Department of Biostatistics, Faculty of Medicine, Amasya University, Amasya, Türkiye
6 shared publicationsHakan Sivgin
Affiliation Department of Internal Medicine, Faculty of Medicine, Tokat Gaziosmanpaşa University, Tokat, Türkiye
5 shared publications- Meryem Cetin
Department of Microbiology, Faculty of Medicine, Amasya University, Amasya, TÜRKİYE
5 shared publications - Hakan Şivgin
Departmant of Internal Medicine, Tokat Gaziosmanpaşa University Faculty of Medicine, Tokat 60250, Türkiye
4 shared publications
Latest Publications
- Open Access
- 22 September 2026
- Published by Oxford University Press (OUP) in Skin Health and Disease
Neurological adverse events of ivermectin: a retrospective pharmacovigilance study using the FDA Adverse Event Reporting System (FAERS) database
Background: Ivermectin is a widely used antiparasitic agent administered in topical and systemic forms. Although ivermectin is generally deemed to be safe, data on rare central nervous system (CNS) adverse events (AEs) are limited. Objectives: To evaluate, using the FDA Adverse Event Reporting System (FAERS) database, the incidence, demographic characteristics and safety signals of CNS AEs associated with ivermectin use. Methods: AEs reported between April 2016 and April 2026 were retrieved from FAERS via the Public Dashboard and OpenVigil 2.1. Four Medical Dictionary for Regulatory Activities (MedDRA) System Organ Classes were analysed. Events with fewer than three reports were excluded. A total of 1749 cases (75 Preferred Terms) were included. Using proportional reporting ratios and the reporting odds ratios with 95% confidence intervals, according to the Evans criteria, disproportionality analysis was performed on reports where ivermectin was the primary suspected drug. Results: A total of 7571 ivermectin-related reports were entered into the FAERS database between 2016 and 2026. Of these, 1749 included CNS AEs. The majority of reports were in male individuals (n = 188/414; 45.4%) and in 18–64 years age group (n = 169/414; 40.8%). Disproportionality analysis identified 13 statistically significant AEs associated with ivermectin. Among these, the most frequently reported and statistically significant neurological AEs were ‘confusional state’, ‘neurotoxicity’ and ‘altered state of consciousness’. Severe AEs involving the CNS, such as coma and encephalopathy, were also reported. Conclusions: FAERS data suggest that ivermectin may be associated with rare but serious neurotoxicity. Specifically, this study adds quantitative real-world evidence that the strongest disproportionality signals cluster around neurotoxicity, encephalopathy and altered or depressed consciousness rather than around common, mild symptoms such as headache or dizziness. Although generally safe, neurological symptoms should be monitored, particularly in older and polymedicated patients.
- 22 September 2026
- Published by Oxford University Press (OUP) in Skin Health and Disease
Open AccessNeurological adverse events of ivermectin: a retrospective pharmacovigilance study using the FDA Adverse Event Reporting System (FAERS) database
Background: Ivermectin is a widely used antiparasitic agent administered in topical and systemic forms. Although ivermectin is generally deemed to be safe, data on rare central nervous system (CNS) adverse events (AEs) are limited. Objectives: To evaluate, using the FDA Adverse Event Reporting System (FAERS) database, the incidence, demographic characteristics and safety signals of CNS AEs associated with ivermectin use. Methods: AEs reported between April 2016 and April 2026 were retrieved from FAERS via the Public Dashboard and OpenVigil 2.1. Four Medical Dictionary for Regulatory Activities (MedDRA) System Organ Classes were analysed. Events with fewer than three reports were excluded. A total of 1749 cases (75 Preferred Terms) were included. Using proportional reporting ratios and the reporting odds ratios with 95% confidence intervals, according to the Evans criteria, disproportionality analysis was performed on reports where ivermectin was the primary suspected drug. Results: A total of 7571 ivermectin-related reports were entered into the FAERS database between 2016 and 2026. Of these, 1749 included CNS AEs. The majority of reports were in male individuals (n = 188/414; 45.4%) and in 18–64 years age group (n = 169/414; 40.8%). Disproportionality analysis identified 13 statistically significant AEs associated with ivermectin. Among these, the most frequently reported and statistically significant neurological AEs were ‘confusional state’, ‘neurotoxicity’ and ‘altered state of consciousness’. Severe AEs involving the CNS, such as coma and encephalopathy, were also reported. Conclusions: FAERS data suggest that ivermectin may be associated with rare but serious neurotoxicity. Specifically, this study adds quantitative real-world evidence that the strongest disproportionality signals cluster around neurotoxicity, encephalopathy and altered or depressed consciousness rather than around common, mild symptoms such as headache or dizziness. Although generally safe, neurological symptoms should be monitored, particularly in older and polymedicated patients.
- Top Cited PapersOpen Access
- 24 August 2026
- Published by Wiley in AI Magazine
- Vol. 47 (3)
Privacy‐preserving multi‐agent systems for human‐centred inclusive healthcare AI
Healthcare environments present uniquely demanding constraints for the deployment of artificial intelligence (AI). Clinical decisions of significant consequence are rarely the product of a single isolated computation; rather, safe and effective patient care relies on the continuous collaboration of distributed entities, including clinicians, hospital networks, laboratory systems, monitoring devices, and patients themselves. As generative models and large language models are increasingly deployed in clinical settings, the transition from monolithic AI models to Multi‐Agent Systems (MAS) offers unprecedented capabilities for distributed monitoring, coordinated decision support, and service integration. However, multi‐agent collaboration simultaneously introduces severe novel vulnerabilities, including topological contamination, privacy leakage, cascading systemic failures, and the socio‐psychological risks of undue algorithmic persuasion. This work introduces a comprehensive, privacy‐preserving, explainable, and human‐centred MAS framework explicitly designed for collaborative clinical decision support. Rejecting the paradigm of a single, omniscient AI model with unrestricted data access, the proposed architecture operationalises clinical AI as a heavily regulated team of specialised, interacting agents. The framework defines six distinct agent classes: Data Stewardship, Modality, Explanation, Consensus, Safety Monitor, and Clinician Interface agents. Furthermore, the implementation is governed by six foundational design principles grounded in classic Autonomous Agents and MAS theory, adapted for modern generative systems. By enforcing minimum‐necessary data exchange, verifiable team‐level explainability, explicit hierarchical escalation, secure communication topologies, and human‐centred safety protocols, this framework provides both a domain‐grounded blueprint and a transferable set of robust design principles for deploying trustworthy MAS in high‐stakes environments.
- 24 August 2026
- Published by Wiley in AI Magazine
- Vol. 47 (3)
Top Cited PapersOpen AccessPrivacy‐preserving multi‐agent systems for human‐centred inclusive healthcare AI
Healthcare environments present uniquely demanding constraints for the deployment of artificial intelligence (AI). Clinical decisions of significant consequence are rarely the product of a single isolated computation; rather, safe and effective patient care relies on the continuous collaboration of distributed entities, including clinicians, hospital networks, laboratory systems, monitoring devices, and patients themselves. As generative models and large language models are increasingly deployed in clinical settings, the transition from monolithic AI models to Multi‐Agent Systems (MAS) offers unprecedented capabilities for distributed monitoring, coordinated decision support, and service integration. However, multi‐agent collaboration simultaneously introduces severe novel vulnerabilities, including topological contamination, privacy leakage, cascading systemic failures, and the socio‐psychological risks of undue algorithmic persuasion. This work introduces a comprehensive, privacy‐preserving, explainable, and human‐centred MAS framework explicitly designed for collaborative clinical decision support. Rejecting the paradigm of a single, omniscient AI model with unrestricted data access, the proposed architecture operationalises clinical AI as a heavily regulated team of specialised, interacting agents. The framework defines six distinct agent classes: Data Stewardship, Modality, Explanation, Consensus, Safety Monitor, and Clinician Interface agents. Furthermore, the implementation is governed by six foundational design principles grounded in classic Autonomous Agents and MAS theory, adapted for modern generative systems. By enforcing minimum‐necessary data exchange, verifiable team‐level explainability, explicit hierarchical escalation, secure communication topologies, and human‐centred safety protocols, this framework provides both a domain‐grounded blueprint and a transferable set of robust design principles for deploying trustworthy MAS in high‐stakes environments.
- 13 August 2026
- Published by Oxford University Press (OUP) in Significance
- Vol. 23 (5) , 18-21
The thrill of the new
Exciting modern statistical methods can bring about huge leaps forward in science. Elizabeth Eisenhauer, Maria Nareklishvili, Ayse Ulgen, Andrej Srakar and Dean Bodenham, members of the RSS Emerging Applications Section committee, describe some recent applications of three of these methods: natural experiments, citizen science and changepoint detection
- 13 August 2026
- Published by Oxford University Press (OUP) in Significance
- Vol. 23 (5) , 18-21
The thrill of the new
Exciting modern statistical methods can bring about huge leaps forward in science. Elizabeth Eisenhauer, Maria Nareklishvili, Ayse Ulgen, Andrej Srakar and Dean Bodenham, members of the RSS Emerging Applications Section committee, describe some recent applications of three of these methods: natural experiments, citizen science and changepoint detection
- Open Access
- 16 September 2025
- Published by Public Library of Science (PLoS) in PLOS ONE
- Vol. 20 (9) , e0331344
Osmolality as a strong predictor of COVID-19 mortality and its possible links to other biomarkers
Osmolality, concentration of solute particles, was rarely used for prognosis for COVID-19. By analyzing blood samples of more than 1300 COVID-19 patients from Tokat, Turkey (including 100 surviving and 30 deceased inpatients), we found calculated osmolality to be an excellent prognostic biomarker for mortality and significantly associated with hospitalization, independent from gender and age. Although calculated osmolality is defined as a weighted sum of sodium, glucose, and urea, the three are not necessarily independent. Other blood test biomarkers, ferritin, creatine, and chloride are also correlated with osmolality after conditioning on age. By applying a combination of collider analysis and mediation analysis, we design a pipeline to construct a causal model among all these variables in their relationship to osmolality. We confirm that while glucose and sodium are independent contributors of osmolality, glucose and urea, urea and sodium are correlated. We also conclude that ferritin and creatine are associated with osmolality through urea, and chloride’s association to osmolality is through sodium.
- 16 September 2025
- Published by Public Library of Science (PLoS) in PLOS ONE
- Vol. 20 (9) , e0331344
Open AccessOsmolality as a strong predictor of COVID-19 mortality and its possible links to other biomarkers
Osmolality, concentration of solute particles, was rarely used for prognosis for COVID-19. By analyzing blood samples of more than 1300 COVID-19 patients from Tokat, Turkey (including 100 surviving and 30 deceased inpatients), we found calculated osmolality to be an excellent prognostic biomarker for mortality and significantly associated with hospitalization, independent from gender and age. Although calculated osmolality is defined as a weighted sum of sodium, glucose, and urea, the three are not necessarily independent. Other blood test biomarkers, ferritin, creatine, and chloride are also correlated with osmolality after conditioning on age. By applying a combination of collider analysis and mediation analysis, we design a pipeline to construct a causal model among all these variables in their relationship to osmolality. We confirm that while glucose and sodium are independent contributors of osmolality, glucose and urea, urea and sodium are correlated. We also conclude that ferritin and creatine are associated with osmolality through urea, and chloride’s association to osmolality is through sodium.
- Open Access
- 28 August 2025
- Published by MDPI AG in Journal of Clinical Medicine
- Vol. 14 (17) , 6091
Determination of Malignancy Risk Factors Using Gallstone Data and Comparing Machine Learning Methods to Predict Malignancy
Background/Objectives: Gallstone disease, a prevalent and costly digestive system disorder, is influenced by multifactorial risk factors, some of which may predispose to malignancy. This study aims to evaluate the association between gallstone disease and malignancy using advanced machine learning (ML) algorithms. Methods: A dataset comprising approximately 1000 patients was analyzed, employing six ML methods: random forests (RFs), support vector machines (SVMs), multi-layer perceptron (MLP), MLP with PyTorch 2.3.1 (MLP_PT), naive Bayes (NB), and Tabular Prior-data Fitted Network (TabPFN). Comparative performance was assessed using Pearson correlation, sensitivity, specificity, Kappa, receiver operating characteristic (ROC), area under curve (AUC), and accuracy metrics. Results: Our results revealed that age, body mass index (BMI), and history of HRT were the most significant predictors of malignancy. Among the ML models, TabPFN emerged as the most effective, achieving superior performance across multiple evaluation criteria. Conclusions: This study highlights the potential of leveraging cutting-edge ML methodologies to uncover complex relationships in clinical datasets, offering a novel perspective on gallstone-related malignancy. By identifying critical risk factors and demonstrating the efficacy of TabPFN, this research provides actionable insights for predictive modeling and personalized patient management in clinical practice.
- 28 August 2025
- Published by MDPI AG in Journal of Clinical Medicine
- Vol. 14 (17) , 6091
Open AccessDetermination of Malignancy Risk Factors Using Gallstone Data and Comparing Machine Learning Methods to Predict Malignancy
Background/Objectives: Gallstone disease, a prevalent and costly digestive system disorder, is influenced by multifactorial risk factors, some of which may predispose to malignancy. This study aims to evaluate the association between gallstone disease and malignancy using advanced machine learning (ML) algorithms. Methods: A dataset comprising approximately 1000 patients was analyzed, employing six ML methods: random forests (RFs), support vector machines (SVMs), multi-layer perceptron (MLP), MLP with PyTorch 2.3.1 (MLP_PT), naive Bayes (NB), and Tabular Prior-data Fitted Network (TabPFN). Comparative performance was assessed using Pearson correlation, sensitivity, specificity, Kappa, receiver operating characteristic (ROC), area under curve (AUC), and accuracy metrics. Results: Our results revealed that age, body mass index (BMI), and history of HRT were the most significant predictors of malignancy. Among the ML models, TabPFN emerged as the most effective, achieving superior performance across multiple evaluation criteria. Conclusions: This study highlights the potential of leveraging cutting-edge ML methodologies to uncover complex relationships in clinical datasets, offering a novel perspective on gallstone-related malignancy. By identifying critical risk factors and demonstrating the efficacy of TabPFN, this research provides actionable insights for predictive modeling and personalized patient management in clinical practice.
- Open Access
- 11 August 2025
- Published by Frontiers Media SA in Frontiers in Medicine
- Vol. 12, 1604286
Two sides of the coin: coagulation and inflammation in deep vein thrombosis – a prospective study on D-dimer and SIRI
Background: Deep vein thrombosis (DVT) is a major cause of morbidity and mortality, including pulmonary embolism and post-thrombotic syndrome. This study aimed to assess the effectiveness of inflammatory indices, derived from routine laboratory parameters, in predicting DVT. Method: In this prospectively designed study, patients diagnosed with DVT through Doppler ultrasound at a tertiary healthcare center between December 2024 and February 2025, along with a control group confirmed to be DVT-free by Doppler ultrasound, were analyzed. Blood markers such as D-dimer, CRP, IL-6, and inflammatory indices (SIRI, MHR, PLR) were compared between groups. Statistical tests included chi-square, t -tests, logistic regression, and ROC curve analysis. Diagnostic performance was measured using odds ratios (ORs) with 95% confidence intervals (CIs). Result: Inflammatory markers (SIRI, MHR, D-dimer, CRP, IL-6) were significantly elevated in DVT cases. SIRI demonstrated high diagnostic accuracy (AUC: 0.934) with a threshold of 0.97. Combined SIRI and D-dimer analyses yielded 93% positive and 100% negative predictive accuracy. Conclusion: This study demonstrated that inflammatory markers, particularly SIRI, were elevated in patients with deep vein thrombosis (DVT) and carried high predictive value in this patient group. The combined use of SIRI and D-dimer provided high diagnostic accuracy for DVT. SIRI, a low-cost index calculable through routine blood tests, was shown to be more effective than other inflammatory markers in predicting DVT. Additionally, the combination of SIRI and D-dimer yielded high positive and negative predictive values for DVT diagnosis.
- 11 August 2025
- Published by Frontiers Media SA in Frontiers in Medicine
- Vol. 12, 1604286
Open AccessTwo sides of the coin: coagulation and inflammation in deep vein thrombosis – a prospective study on D-dimer and SIRI
Background: Deep vein thrombosis (DVT) is a major cause of morbidity and mortality, including pulmonary embolism and post-thrombotic syndrome. This study aimed to assess the effectiveness of inflammatory indices, derived from routine laboratory parameters, in predicting DVT. Method: In this prospectively designed study, patients diagnosed with DVT through Doppler ultrasound at a tertiary healthcare center between December 2024 and February 2025, along with a control group confirmed to be DVT-free by Doppler ultrasound, were analyzed. Blood markers such as D-dimer, CRP, IL-6, and inflammatory indices (SIRI, MHR, PLR) were compared between groups. Statistical tests included chi-square, t -tests, logistic regression, and ROC curve analysis. Diagnostic performance was measured using odds ratios (ORs) with 95% confidence intervals (CIs). Result: Inflammatory markers (SIRI, MHR, D-dimer, CRP, IL-6) were significantly elevated in DVT cases. SIRI demonstrated high diagnostic accuracy (AUC: 0.934) with a threshold of 0.97. Combined SIRI and D-dimer analyses yielded 93% positive and 100% negative predictive accuracy. Conclusion: This study demonstrated that inflammatory markers, particularly SIRI, were elevated in patients with deep vein thrombosis (DVT) and carried high predictive value in this patient group. The combined use of SIRI and D-dimer provided high diagnostic accuracy for DVT. SIRI, a low-cost index calculable through routine blood tests, was shown to be more effective than other inflammatory markers in predicting DVT. Additionally, the combination of SIRI and D-dimer yielded high positive and negative predictive values for DVT diagnosis.
- Open Access
- 1 November 2023
- Published by Frontiers Media SA in Frontiers in Medicine
- Vol. 10, 1231641
Diabetes and bacterial co-infection are two independent risk factors for respiratory syncytial virus disease severity
Diabetes mellitus (DM) is common among older adults hospitalized with lower respiratory tract infection, yet information on the impact of DM on disease severity is limited. This study retrospectively analyzed 46 Turkish patients infected with respiratory syncytial virus (RSV), with information on their comorbidities, co-infection status, and symptoms. Patients are grouped into four severity levels from mild to severe, according to lung parenchymal infiltration status and oxygen level. Similar to previously published studies, we found that comorbidities of diabetes, heart failure, hypertension, co-infection of any type, bacterial co-infection, and age are associated with the disease severity. Cough is the most common symptom (89%) followed by fever (26%) and myalgia, dyspnea, and weakness (around 20%). Using a second-order analysis (two-variable regression), we identified two independent risks for disease severity, the first is represented by diabetes, and the second is represented by bacterial co-infection. We observed two patients whose more severe symptoms were not associated with an older age, but associated with a combination of diabetes and bacterial co-infection. To confirm the true causality from the statistical correlation, further studies are needed.
- 1 November 2023
- Published by Frontiers Media SA in Frontiers in Medicine
- Vol. 10, 1231641
Open AccessDiabetes and bacterial co-infection are two independent risk factors for respiratory syncytial virus disease severity
Diabetes mellitus (DM) is common among older adults hospitalized with lower respiratory tract infection, yet information on the impact of DM on disease severity is limited. This study retrospectively analyzed 46 Turkish patients infected with respiratory syncytial virus (RSV), with information on their comorbidities, co-infection status, and symptoms. Patients are grouped into four severity levels from mild to severe, according to lung parenchymal infiltration status and oxygen level. Similar to previously published studies, we found that comorbidities of diabetes, heart failure, hypertension, co-infection of any type, bacterial co-infection, and age are associated with the disease severity. Cough is the most common symptom (89%) followed by fever (26%) and myalgia, dyspnea, and weakness (around 20%). Using a second-order analysis (two-variable regression), we identified two independent risks for disease severity, the first is represented by diabetes, and the second is represented by bacterial co-infection. We observed two patients whose more severe symptoms were not associated with an older age, but associated with a combination of diabetes and bacterial co-infection. To confirm the true causality from the statistical correlation, further studies are needed.
- 3 April 2023
- Published by Walter de Gruyter GmbH in The International Journal of Biostatistics
- Vol. 20 (1) , 43-56
Approximate reciprocal relationship between two cause-specific hazard ratios in COVID-19 data with mutually exclusive events
COVID-19 survival data presents a special situation where not only the time-to-event period is short, but also the two events or outcome types, death and release from hospital, are mutually exclusive, leading to two cause-specific hazard ratios (csHR d and csHR r ). The eventual mortality/release outcome is also analyzed by logistic regression to obtain odds-ratio (OR). We have the following three empirical observations: (1) The magnitude of OR is an upper limit of the csHR d : |log(OR)| ≥ |log(csHR d )|. This relationship between OR and HR might be understood from the definition of the two quantities; (2) csHR d and csHR r point in opposite directions: log(csHR d ) ⋅ log(csHR r ) < 0; This relation is a direct consequence of the nature of the two events; and (3) there is a tendency for a reciprocal relation between csHR d and csHR r : csHR d ∼ 1/csHR r . Though an approximate reciprocal trend between the two hazard ratios is in indication that the same factor causing faster death also lead to slow recovery by a similar mechanism, and vice versa, a quantitative relation between csHR d and csHR r in this context is not obvious. These results may help future analyses of data from COVID-19 or other similar diseases, in particular if the deceased patients are lacking, whereas surviving patients are abundant.
- 3 April 2023
- Published by Walter de Gruyter GmbH in The International Journal of Biostatistics
- Vol. 20 (1) , 43-56
Approximate reciprocal relationship between two cause-specific hazard ratios in COVID-19 data with mutually exclusive events
COVID-19 survival data presents a special situation where not only the time-to-event period is short, but also the two events or outcome types, death and release from hospital, are mutually exclusive, leading to two cause-specific hazard ratios (csHR d and csHR r ). The eventual mortality/release outcome is also analyzed by logistic regression to obtain odds-ratio (OR). We have the following three empirical observations: (1) The magnitude of OR is an upper limit of the csHR d : |log(OR)| ≥ |log(csHR d )|. This relationship between OR and HR might be understood from the definition of the two quantities; (2) csHR d and csHR r point in opposite directions: log(csHR d ) ⋅ log(csHR r ) < 0; This relation is a direct consequence of the nature of the two events; and (3) there is a tendency for a reciprocal relation between csHR d and csHR r : csHR d ∼ 1/csHR r . Though an approximate reciprocal trend between the two hazard ratios is in indication that the same factor causing faster death also lead to slow recovery by a similar mechanism, and vice versa, a quantitative relation between csHR d and csHR r in this context is not obvious. These results may help future analyses of data from COVID-19 or other similar diseases, in particular if the deceased patients are lacking, whereas surviving patients are abundant.
- 13 October 2022
- Published by Elsevier in Transfusion Clinique et Biologique
- Vol. 30 (1) , 116-122
Blood-Type-A is a COVID-19 infection and hospitalization risk in a Turkish cohort
- 13 October 2022
- Published by Elsevier in Transfusion Clinique et Biologique
- Vol. 30 (1) , 116-122
Blood-Type-A is a COVID-19 infection and hospitalization risk in a Turkish cohort
- 22 September 2022
- Published by Galenos Yayinevi in Cyprus Journal of Medical Sciences
- Vol. 7 (4) , 438-443
Magnitude of Antibody Response and Risk Factors for Reduced Immunogenicity after Two Doses of an Inactivated Whole-Virion COVID-19 Vaccine (CoronaVac®)
- 22 September 2022
- Published by Galenos Yayinevi in Cyprus Journal of Medical Sciences
- Vol. 7 (4) , 438-443
Magnitude of Antibody Response and Risk Factors for Reduced Immunogenicity after Two Doses of an Inactivated Whole-Virion COVID-19 Vaccine (CoronaVac®)