Ilkin Isler

Zheyuan Zhang, Elif Keles, Gorkem Durak et al.

Automated volumetric segmentation of the pancreas on cross-sectional imaging is needed for diagnosis and follow-up of pancreatic diseases. While CT-based pancreatic segmentation is more established, MRI-based segmentation methods are understudied, largely due to a lack of publicly available datasets, benchmarking research efforts, and domain-specific deep learning methods. In this retrospective study, we collected a large dataset (767 scans from 499 participants) of T1-weighted (T1W) and T2-weighted (T2W) abdominal MRI series from five centers between March 2004 and November 2022. We also collected CT scans of 1,350 patients from publicly available sources for benchmarking purposes. We developed a new pancreas segmentation method, called PanSegNet, combining the strengths of nnUNet and a Transformer network with a new linear attention module enabling volumetric computation. We tested PanSegNet's accuracy in cross-modality (a total of 2,117 scans) and cross-center settings with Dice and Hausdorff distance (HD95) evaluation metrics. We used Cohen's kappa statistics for intra and inter-rater agreement evaluation and paired t-tests for volume and Dice comparisons, respectively. For segmentation accuracy, we achieved Dice coefficients of 88.3% (std: 7.2%, at case level) with CT, 85.0% (std: 7.9%) with T1W MRI, and 86.3% (std: 6.4%) with T2W MRI. There was a high correlation for pancreas volume prediction with R^2 of 0.91, 0.84, and 0.85 for CT, T1W, and T2W, respectively. We found moderate inter-observer (0.624 and 0.638 for T1W and T2W MRI, respectively) and high intra-observer agreement scores. All MRI data is made available at https://osf.io/kysnj/. Our source code is available at https://github.com/NUBagciLab/PaNSegNet.

Ilkin Sevgi Isler, David Mohaisen, Curtis Lisle et al.

Reliable tumor segmentation in thoracic computed tomography (CT) remains challenging due to boundary ambiguity, class imbalance, and anatomical variability. We propose an uncertainty-guided, coarse-to-fine segmentation framework that combines full-volume tumor localization with refined region-of-interest (ROI) segmentation, enhanced by anatomically aware post-processing. The first-stage model generates a coarse prediction, followed by anatomically informed filtering based on lung overlap, proximity to lung surfaces, and component size. The resulting ROIs are segmented by a second-stage model trained with uncertainty-aware loss functions to improve accuracy and boundary calibration in ambiguous regions. Experiments on private and public datasets demonstrate improvements in Dice and Hausdorff scores, with fewer false positives and enhanced spatial interpretability. These results highlight the value of combining uncertainty modeling and anatomical priors in cascaded segmentation pipelines for robust and clinically meaningful tumor delineation. On the Orlando dataset, our framework improved Swin UNETR Dice from 0.4690 to 0.6447. Reduction in spurious components was strongly correlated with segmentation gains, underscoring the value of anatomically informed post-processing.

Ilkin Isler, Debesh Jha, Curtis Lisle et al.

In this study, our goal is to show the impact of self-supervised pre-training of transformers for organ at risk (OAR) and tumor segmentation as compared to costly fully-supervised learning. The proposed algorithm is called Monte Carlo Transformer based U-Net (MC-Swin-U). Unlike many other available models, our approach presents uncertainty quantification with Monte Carlo dropout strategy while generating its voxel-wise prediction. We test and validate the proposed model on both public and one private datasets and evaluate the gross tumor volume (GTV) as well as nearby risky organs' boundaries. We show that self-supervised pre-training approach improves the segmentation scores significantly while providing additional benefits for avoiding large-scale annotation costs.

Ilkin Isler, Curtis Lisle, Justin Rineer et al.

Organ at risk (OAR) segmentation is a crucial step for treatment planning and outcome determination in radiotherapy treatments of cancer patients. Several deep learning based segmentation algorithms have been developed in recent years, however, U-Net remains the de facto algorithm designed specifically for biomedical image segmentation and has spawned many variants with known weaknesses. In this study, our goal is to present simple architectural changes in U-Net to improve its accuracy and generalization properties. Unlike many other available studies evaluating their algorithms on single center data, we thoroughly evaluate several variations of U-Net as well as our proposed enhanced architecture on multiple data sets for an extensive and reliable study of the OAR segmentation problem. Our enhanced segmentation model includes (a)architectural changes in the loss function, (b)optimization framework, and (c)convolution type. Testing on three publicly available multi-object segmentation data sets, we achieved an average of 80% dice score compared to the baseline U-Net performance of 63%.

Kamran Ali, Ilkin Isler, Charles Hughes

Facial expression recognition is a challenging task due to two major problems: the presence of inter-subject variations in facial expression recognition dataset and impure expressions posed by human subjects. In this paper we present a novel Human-to-Animation conditional Generative Adversarial Network (HA-GAN) to overcome these two problems by using many (human faces) to one (animated face) mapping. Specifically, for any given input human expression image, our HA-GAN transfers the expression information from the input image to a fixed animated identity. Stylized animated characters from the Facial Expression Research Group-Database (FERGDB) are used for the generation of fixed identity. By learning this many-to-one identity mapping function using our proposed HA-GAN, the effect of inter-subject variations can be reduced in Facial Expression Recognition(FER). We also argue that the expressions in the generated animated images are pure expressions and since FER is performed on these generated images, the performance of facial expression recognition is improved. Our initial experimental results on the state-of-the-art datasets show that facial expression recognition carried out on the generated animated images using our HA-GAN framework outperforms the baseline deep neural network and produces comparable or even better results than the state-of-the-art methods for facial expression recognition.