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Guvenis, A.

Publications and source records attributed to Guvenis, A..

3 recordsLinked to original sources

A NOVEL DEEP LEARNING MODEL, RDBCYCYLEGAN-CBAM FOR LOW-DOSE CT IMAGE DENOISING

Computed Tomography (CT) is one of the largest contributors to radiation exposure from medical imaging, which can induce DNA damage and increase cancer risk. Reducing CT radiation dose to improve patient safety inherently increases image noise and artifacts. Generative adversarial networks (GANs) have shown promise for unsupervised low-dose CT (LDCT) denoising. Building on this, RDBCycleGAN-CBAM, a CycleGAN-based model that integrates residual dense blocks (RDBs) and convolutional block attention modules (CBAM), was developed to effectively denoise quarter-dose CT images while preserving structural detail. The model was trained on unpaired quarter-dose and full-dose CT scans from the NIH-AAPM-Mayo dataset using adversarial (LSGAN), cycle-consistency, and identity losses. Evaluation on held-out test slices was performed using PSNR and SSIM as the primary image-quality metrics. The results demonstrate that the proposed RDBCycleGAN-CBAM method not only achieves higher peak signal-to-noise ratio (PSNR) and structural similarity index (SSIM) values but also outperforms most existing deep learning-based methods, achieving mean improvements of +3.97 dB in PSNR and +0.053 in SSIM relative to quarter-dose inputs. Shapiro- Wilk tests for PSNR and SSIM motivated the use of the nonparametric Wilcoxon signed-rank test, by which highly significant improvements across both metrics (PSNR and SSIM) were demonstrated. The very large rank-biserial correlation values (1.0) indicate that nearly all test images experienced substantial quality improvement. Furthermore, the narrow bootstrap confidence intervals for the mean differences suggest that these improvements are consistent across the dataset. These advancements contribute to medical imaging by providing a viable, vendor-neutral tool for reducing patient radiation exposure without compromising diagnostic value.

bioengineering↗

Subregional Biomarkers in FDG PET for Alzheimer's Diagnosis and Staging: An Interpretable and Explainable model

ObjectiveTo investigate the radiomics features of the hippocampus and the amygdala subregions in FDG-PET images that can best differentiate Mild Cognitive Impairment (MCI), Alzheimers Disease (AD), and healthy patients. MethodsBaseline FDG-PET data from 555 participants in the ADNI dataset were analyzed, comprising 189 cognitively normal (CN) individuals, 201 with MCI, and 165 with AD. The hippocampus and amygdala were segmented based on the DKT-Atlas, with additional subdivisions guided by probabilistic atlases from Freesurfer. Then radiomic features (n=120) were extracted from 38 hippocampal subregions and 18 amygdala nuclei using PyRadiomics. Various feature selection techniques, including ANOVA, PCA, Chi-square, and LASSO, were applied alongside nine machine learning classifiers. ResultsThe Multi-Layer Perceptron (MLP) model combined with LASSO demonstrated excellent classification performance: ROC AUC of 0.957 for CN vs. AD, ROC AUC of 0.867 for MCI vs. AD, and ROC AUC of 0.782 for CN vs. MCI. Key regions, including the accessory basal nucleus, presubiculum head, and CA4 head, were identified as critical biomarkers. Features including GLRLM (Long Run Emphasis) and Small Dependence Emphasis (GLDM) showed strong diagnostic potential, reflecting subtle metabolic and microstructural changes often preceding anatomical alterations. ConclusionSpecific hippocampal and amygdala subregions and their four radiomic features were found to have a significant role in the early diagnosis of AD, its staging, and its severity assessment by capturing subtle shifts in metabolic patterns. Furthermore, these features offer potential insights into the diseases underlying mechanisms and model interpretability.

neuroscience↗

Hypoxia-related radiomics predict immunotherapy response: A multi-cohort study of NSCLC

Checkpoint blockade immunotherapy provides improved long-term survival in a subset of advanced stage non-small cell lung cancer (NSCLC) patients. However, highly predictive biomarkers of immunotherapy response are unmet clinical need. In this study, we utilized pre-treatment clinical factors and quantitative image-based biomarkers (radiomics) to identify a parsimonious model that predicts survival outcomes among NSCLC patients treated with immunotherapy. The NSCLC patients treated with single or double agent immunotherapy were included in three different cohorts: Training (N = 180), test (N = 90) and validation (N = 62) cohorts. The models were created based on overall survival (OS) and were additionally assessed for progression-free survival (PFS). Including most predictive radiomic features and clinical covariates, Classification and Regression Tree analysis was applied to stratify patients into survival risk-groups in the training cohort. The risk groups were later generated in the test and validation cohorts. Four independent NSCLC cohorts (total N = 446) were utilized for further validation of the radiomic signature. The biological underpinnings of the most informative radiomics were assessed using gene expression data from a radiogenomics dataset and validated by immunohistochemistry data (IHC). A parsimonious clinical-radiomics model was found to be significantly associated with OS and PFS after stratifying patients into groups of low-, moderate-, high-, and very-high risk of death and progression. This trained model was further tested and validated in two independent cohorts. When the extreme phenotypes were compared, the very-high risk group was found to be associated with extremely poor OS in both the test (hazard ratio [HR] = 5.35, 95% confidence interval [CI]: 2.14 - 13.36; 1-year OS = 11.1%) and validation (HR = 13.81, 95% CI: 2.58 - 73.93; 1-year OS = %47.6) cohorts when compared to the low risk group (HRs = 1.00; 1-year OS = 85.0% & 80.2%). Similar findings were observed for PFS. The final radiomic feature (GLCM inverse difference) was associated with OS in four independent NSCLC cohorts and was found to be positively associated with the hypoxia-related carbonic anhydrase, CAIX, by gene expression profiling and immunohistochemistry. We validated a novel clinical-radiomics model that is associated with OS and PFS among NSCLC patients treated with immunotherapy and identified a highly vulnerable subset of patients that are unlikely to respond to immunotherapy. The most informative radiomic feature was associated with CAIX, a marker of tumor hypoxia, tumor acidosis, and treatment resistance.

bioinformatics↗