arXiv subjects

Ulas Bagci

Publications and source records attributed to Ulas Bagci.

At least 109 records · Page 6Linked to original sources

arXiv2024

A Novel Momentum-Based Deep Learning Techniques for Medical Image Classification and Segmentation

Accurately segmenting different organs from medical images is a critical prerequisite for computer-assisted diagnosis and intervention planning. This study proposes a deep learning-based approach for segmenting various organs from CT and MRI scans and classifying diseases. Our study introduces a novel technique integrating momentum within residual blocks for enhanced training dynamics in medical image analysis. We applied our method in two distinct tasks: segmenting liver, lung, & colon data and classifying abdominal pelvic CT and MRI scans. The proposed approach has shown promising results, outperforming state-of-the-art methods on publicly available benchmarking datasets. For instance, in the lung segmentation dataset, our approach yielded significant enhancements over the TransNetR model, including a 5.72% increase in dice score, a 5.04% improvement in mean Intersection over Union (mIoU), an 8.02% improvement in recall, and a 4.42% improvement in precision. Hence, incorporating momentum led to state-of-the-art performance in both segmentation and classification tasks, representing a significant advancement in the field of medical imaging.

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arXiv2024

Harmonized Spatial and Spectral Learning for Robust and Generalized Medical Image Segmentation

Deep learning has demonstrated remarkable achievements in medical image segmentation. However, prevailing deep learning models struggle with poor generalization due to (i) intra-class variations, where the same class appears differently in different samples, and (ii) inter-class independence, resulting in difficulties capturing intricate relationships between distinct objects, leading to higher false negative cases. This paper presents a novel approach that synergies spatial and spectral representations to enhance domain-generalized medical image segmentation. We introduce the innovative Spectral Correlation Coefficient objective to improve the model's capacity to capture middle-order features and contextual long-range dependencies. This objective complements traditional spatial objectives by incorporating valuable spectral information. Extensive experiments reveal that optimizing this objective with existing architectures like UNet and TransUNet significantly enhances generalization, interpretability, and noise robustness, producing more confident predictions. For instance, in cardiac segmentation, we observe a 0.81 pp and 1.63 pp (pp = percentage point) improvement in DSC over UNet and TransUNet, respectively. Our interpretability study demonstrates that, in most tasks, objectives optimized with UNet outperform even TransUNet by introducing global contextual information alongside local details. These findings underscore the versatility and effectiveness of our proposed method across diverse imaging modalities and medical domains.

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arXiv2024

Towards Synergistic Deep Learning Models for Volumetric Cirrhotic Liver Segmentation in MRIs

Liver cirrhosis, a leading cause of global mortality, requires precise segmentation of ROIs for effective disease monitoring and treatment planning. Existing segmentation models often fail to capture complex feature interactions and generalize across diverse datasets. To address these limitations, we propose a novel synergistic theory that leverages complementary latent spaces for enhanced feature interaction modeling. Our proposed architecture, nnSynergyNet3D integrates continuous and discrete latent spaces for 3D volumes and features auto-configured training. This approach captures both fine-grained and coarse features, enabling effective modeling of intricate feature interactions. We empirically validated nnSynergyNet3D on a private dataset of 628 high-resolution T1 abdominal MRI scans from 339 patients. Our model outperformed the baseline nnUNet3D by approximately 2%. Additionally, zero-shot testing on healthy liver CT scans from the public LiTS dataset demonstrated superior cross-modal generalization capabilities. These results highlight the potential of synergistic latent space models to improve segmentation accuracy and robustness, thereby enhancing clinical workflows by ensuring consistency across CT and MRI modalities.

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arXiv2024

Deformable Capsules for Object Detection

Capsule networks promise significant benefits over convolutional networks by storing stronger internal representations, and routing information based on the agreement between intermediate representations' projections. Despite this, their success has been limited to small-scale classification datasets due to their computationally expensive nature. Though memory efficient, convolutional capsules impose geometric constraints that fundamentally limit the ability of capsules to model the pose/deformation of objects. Further, they do not address the bigger memory concern of class-capsules scaling up to bigger tasks such as detection or large-scale classification. In this study, we introduce a new family of capsule networks, deformable capsules (\textit{DeformCaps}), to address a very important problem in computer vision: object detection. We propose two new algorithms associated with our \textit{DeformCaps}: a novel capsule structure (\textit{SplitCaps}), and a novel dynamic routing algorithm (\textit{SE-Routing}), which balance computational efficiency with the need for modeling a large number of objects and classes, which have never been achieved with capsule networks before. We demonstrate that the proposed methods efficiently scale up to create the first-ever capsule network for object detection in the literature. Our proposed architecture is a one-stage detection framework and it obtains results on MS COCO which are on par with state-of-the-art one-stage CNN-based methods, while producing fewer false positive detection, generalizing to unusual poses/viewpoints of objects.

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arXiv2024

SAM-EG: Segment Anything Model with Egde Guidance framework for efficient Polyp Segmentation

Polyp segmentation, a critical concern in medical imaging, has prompted numerous proposed methods aimed at enhancing the quality of segmented masks. While current state-of-the-art techniques produce impressive results, the size and computational cost of these models pose challenges for practical industry applications. Recently, the Segment Anything Model (SAM) has been proposed as a robust foundation model, showing promise for adaptation to medical image segmentation. Inspired by this concept, we propose SAM-EG, a framework that guides small segmentation models for polyp segmentation to address the computation cost challenge. Additionally, in this study, we introduce the Edge Guiding module, which integrates edge information into image features to assist the segmentation model in addressing boundary issues from current segmentation model in this task. Through extensive experiments, our small models showcase their efficacy by achieving competitive results with state-of-the-art methods, offering a promising approach to developing compact models with high accuracy for polyp segmentation and in the broader field of medical imaging.

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arXiv2024

Computation-Efficient Era: A Comprehensive Survey of State Space Models in Medical Image Analysis

Sequence modeling plays a vital role across various domains, with recurrent neural networks being historically the predominant method of performing these tasks. However, the emergence of transformers has altered this paradigm due to their superior performance. Built upon these advances, transformers have conjoined CNNs as two leading foundational models for learning visual representations. However, transformers are hindered by the $\mathcal{O}(N^2)$ complexity of their attention mechanisms, while CNNs lack global receptive fields and dynamic weight allocation. State Space Models (SSMs), specifically the \textit{\textbf{Mamba}} model with selection mechanisms and hardware-aware architecture, have garnered immense interest lately in sequential modeling and visual representation learning, challenging the dominance of transformers by providing infinite context lengths and offering substantial efficiency maintaining linear complexity in the input sequence. Capitalizing on the advances in computer vision, medical imaging has heralded a new epoch with Mamba models. Intending to help researchers navigate the surge, this survey seeks to offer an encyclopedic review of Mamba models in medical imaging. Specifically, we start with a comprehensive theoretical review forming the basis of SSMs, including Mamba architecture and its alternatives for sequence modeling paradigms in this context. Next, we offer a structured classification of Mamba models in the medical field and introduce a diverse categorization scheme based on their application, imaging modalities, and targeted organs. Finally, we summarize key challenges, discuss different future research directions of the SSMs in the medical domain, and propose several directions to fulfill the demands of this field. In addition, we have compiled the studies discussed in this paper along with their open-source implementations on our GitHub repository.

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arXiv2024

PGDS: Pose-Guidance Deep Supervision for Mitigating Clothes-Changing in Person Re-Identification

Person Re-Identification (Re-ID) task seeks to enhance the tracking of multiple individuals by surveillance cameras. It supports multimodal tasks, including text-based person retrieval and human matching. One of the most significant challenges faced in Re-ID is clothes-changing, where the same person may appear in different outfits. While previous methods have made notable progress in maintaining clothing data consistency and handling clothing change data, they still rely excessively on clothing information, which can limit performance due to the dynamic nature of human appearances. To mitigate this challenge, we propose the Pose-Guidance Deep Supervision (PGDS), an effective framework for learning pose guidance within the Re-ID task. It consists of three modules: a human encoder, a pose encoder, and a Pose-to-Human Projection module (PHP). Our framework guides the human encoder, i.e., the main re-identification model, with pose information from the pose encoder through multiple layers via the knowledge transfer mechanism from the PHP module, helping the human encoder learn body parts information without increasing computation resources in the inference stage. Through extensive experiments, our method surpasses the performance of current state-of-the-art methods, demonstrating its robustness and effectiveness for real-world applications. Our code is available at https://github.com/huyquoctrinh/PGDS.

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arXiv2024

Rethinking Intermediate Layers design in Knowledge Distillation for Kidney and Liver Tumor Segmentation

Knowledge distillation (KD) has demonstrated remarkable success across various domains, but its application to medical imaging tasks, such as kidney and liver tumor segmentation, has encountered challenges. Many existing KD methods are not specifically tailored for these tasks. Moreover, prevalent KD methods often lack a careful consideration of `what' and `from where' to distill knowledge from the teacher to the student. This oversight may lead to issues like the accumulation of training bias within shallower student layers, potentially compromising the effectiveness of KD. To address these challenges, we propose Hierarchical Layer-selective Feedback Distillation (HLFD). HLFD strategically distills knowledge from a combination of middle layers to earlier layers and transfers final layer knowledge to intermediate layers at both the feature and pixel levels. This design allows the model to learn higher-quality representations from earlier layers, resulting in a robust and compact student model. Extensive quantitative evaluations reveal that HLFD outperforms existing methods by a significant margin. For example, in the kidney segmentation task, HLFD surpasses the student model (without KD) by over 10\%, significantly improving its focus on tumor-specific features. From a qualitative standpoint, the student model trained using HLFD excels at suppressing irrelevant information and can focus sharply on tumor-specific details, which opens a new pathway for more efficient and accurate diagnostic tools. Code is available \href{https://github.com/vangorade/RethinkingKD_ISBI24}{here}.

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arXiv2024

PP-SAM: Perturbed Prompts for Robust Adaptation of Segment Anything Model for Polyp Segmentation

The Segment Anything Model (SAM), originally designed for general-purpose segmentation tasks, has been used recently for polyp segmentation. Nonetheless, fine-tuning SAM with data from new imaging centers or clinics poses significant challenges. This is because this necessitates the creation of an expensive and time-intensive annotated dataset, along with the potential for variability in user prompts during inference. To address these issues, we propose a robust fine-tuning technique, PP-SAM, that allows SAM to adapt to the polyp segmentation task with limited images. To this end, we utilize variable perturbed bounding box prompts (BBP) to enrich the learning context and enhance the model's robustness to BBP perturbations during inference. Rigorous experiments on polyp segmentation benchmarks reveal that our variable BBP perturbation significantly improves model resilience. Notably, on Kvasir, 1-shot fine-tuning boosts the DICE score by 20% and 37% with 50 and 100-pixel BBP perturbations during inference, respectively. Moreover, our experiments show that 1-shot, 5-shot, and 10-shot PP-SAM with 50-pixel perturbations during inference outperform a recent state-of-the-art (SOTA) polyp segmentation method by 26%, 7%, and 5% DICE scores, respectively. Our results motivate the broader applicability of our PP-SAM for other medical imaging tasks with limited samples. Our implementation is available at https://github.com/SLDGroup/PP-SAM.

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arXiv2024

Segmentation Quality and Volumetric Accuracy in Medical Imaging

Current medical image segmentation relies on the region-based (Dice, F1-score) and boundary-based (Hausdorff distance, surface distance) metrics as the de-facto standard. While these metrics are widely used, they lack a unified interpretation, particularly regarding volume agreement. Clinicians often lack clear benchmarks to gauge the "goodness" of segmentation results based on these metrics. Recognizing the clinical relevance of volumetry, we utilize relative volume prediction error (vpe) to directly assess the accuracy of volume predictions derived from segmentation tasks. Our work integrates theoretical analysis and empirical validation across diverse datasets. We delve into the often-ambiguous relationship between segmentation quality (measured by Dice) and volumetric accuracy in clinical practice. Our findings highlight the critical role of incorporating volumetric prediction accuracy into segmentation evaluation. This approach empowers clinicians with a more nuanced understanding of segmentation performance, ultimately improving the interpretation and utility of these metrics in real-world healthcare settings.

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arXiv2024

MDNet: Multi-Decoder Network for Abdominal CT Organs Segmentation

Accurate segmentation of organs from abdominal CT scans is essential for clinical applications such as diagnosis, treatment planning, and patient monitoring. To handle challenges of heterogeneity in organ shapes, sizes, and complex anatomical relationships, we propose a \textbf{\textit{\ac{MDNet}}}, an encoder-decoder network that uses the pre-trained \textit{MiT-B2} as the encoder and multiple different decoder networks. Each decoder network is connected to a different part of the encoder via a multi-scale feature enhancement dilated block. With each decoder, we increase the depth of the network iteratively and refine segmentation masks, enriching feature maps by integrating previous decoders' feature maps. To refine the feature map further, we also utilize the predicted masks from the previous decoder to the current decoder to provide spatial attention across foreground and background regions. MDNet effectively refines the segmentation mask with a high dice similarity coefficient (DSC) of 0.9013 and 0.9169 on the Liver Tumor segmentation (LiTS) and MSD Spleen datasets. Additionally, it reduces Hausdorff distance (HD) to 3.79 for the LiTS dataset and 2.26 for the spleen segmentation dataset, underscoring the precision of MDNet in capturing the complex contours. Moreover, \textit{\ac{MDNet}} is more interpretable and robust compared to the other baseline models.

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arXiv2024

Validating polyp and instrument segmentation methods in colonoscopy through Medico 2020 and MedAI 2021 Challenges

Automatic analysis of colonoscopy images has been an active field of research motivated by the importance of early detection of precancerous polyps. However, detecting polyps during the live examination can be challenging due to various factors such as variation of skills and experience among the endoscopists, lack of attentiveness, and fatigue leading to a high polyp miss-rate. Deep learning has emerged as a promising solution to this challenge as it can assist endoscopists in detecting and classifying overlooked polyps and abnormalities in real time. In addition to the algorithm's accuracy, transparency and interpretability are crucial to explaining the whys and hows of the algorithm's prediction. Further, most algorithms are developed in private data, closed source, or proprietary software, and methods lack reproducibility. Therefore, to promote the development of efficient and transparent methods, we have organized the "Medico automatic polyp segmentation (Medico 2020)" and "MedAI: Transparency in Medical Image Segmentation (MedAI 2021)" competitions. We present a comprehensive summary and analyze each contribution, highlight the strength of the best-performing methods, and discuss the possibility of clinical translations of such methods into the clinic. For the transparency task, a multi-disciplinary team, including expert gastroenterologists, accessed each submission and evaluated the team based on open-source practices, failure case analysis, ablation studies, usability and understandability of evaluations to gain a deeper understanding of the models' credibility for clinical deployment. Through the comprehensive analysis of the challenge, we not only highlight the advancements in polyp and surgical instrument segmentation but also encourage qualitative evaluation for building more transparent and understandable AI-based colonoscopy systems.

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arXiv2024

PAM-UNet: Shifting Attention on Region of Interest in Medical Images

Computer-aided segmentation methods can assist medical personnel in improving diagnostic outcomes. While recent advancements like UNet and its variants have shown promise, they face a critical challenge: balancing accuracy with computational efficiency. Shallow encoder architectures in UNets often struggle to capture crucial spatial features, leading in inaccurate and sparse segmentation. To address this limitation, we propose a novel \underline{P}rogressive \underline{A}ttention based \underline{M}obile \underline{UNet} (\underline{PAM-UNet}) architecture. The inverted residual (IR) blocks in PAM-UNet help maintain a lightweight framework, while layerwise \textit{Progressive Luong Attention} ($\mathcal{PLA}$) promotes precise segmentation by directing attention toward regions of interest during synthesis. Our approach prioritizes both accuracy and speed, achieving a commendable balance with a mean IoU of 74.65 and a dice score of 82.87, while requiring only 1.32 floating-point operations per second (FLOPS) on the Liver Tumor Segmentation Benchmark (LiTS) 2017 dataset. These results highlight the importance of developing efficient segmentation models to accelerate the adoption of AI in clinical practice.

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arXiv2024

TransRUPNet for Improved Polyp Segmentation

Colorectal cancer is among the most common cause of cancer worldwide. Removal of precancerous polyps through early detection is essential to prevent them from progressing to colon cancer. We develop an advanced deep learning-based architecture, Transformer based Residual Upsampling Network (TransRUPNet) for automatic and real-time polyp segmentation. The proposed architecture, TransRUPNet, is an encoder-decoder network consisting of three encoder and decoder blocks with additional upsampling blocks at the end of the network. With the image size of $256\times256$, the proposed method achieves an excellent real-time operation speed of 47.07 frames per second with an average mean dice coefficient score of 0.7786 and mean Intersection over Union of 0.7210 on the out-of-distribution polyp datasets. The results on the publicly available PolypGen dataset suggest that TransRUPNet can give real-time feedback while retaining high accuracy for in-distribution datasets. Furthermore, we demonstrate the generalizability of the proposed method by showing that it significantly improves performance on out-of-distribution datasets compared to the existing methods. The source code of our network is available at https://github.com/DebeshJha/TransRUPNet.

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arXiv2024

Detection of Peri-Pancreatic Edema using Deep Learning and Radiomics Techniques

Identifying peri-pancreatic edema is a pivotal indicator for identifying disease progression and prognosis, emphasizing the critical need for accurate detection and assessment in pancreatitis diagnosis and management. This study \textit{introduces a novel CT dataset sourced from 255 patients with pancreatic diseases, featuring annotated pancreas segmentation masks and corresponding diagnostic labels for peri-pancreatic edema condition}. With the novel dataset, we first evaluate the efficacy of the \textit{LinTransUNet} model, a linear Transformer based segmentation algorithm, to segment the pancreas accurately from CT imaging data. Then, we use segmented pancreas regions with two distinctive machine learning classifiers to identify existence of peri-pancreatic edema: deep learning-based models and a radiomics-based eXtreme Gradient Boosting (XGBoost). The LinTransUNet achieved promising results, with a dice coefficient of 80.85\%, and mIoU of 68.73\%. Among the nine benchmarked classification models for peri-pancreatic edema detection, \textit{Swin-Tiny} transformer model demonstrated the highest recall of $98.85 \pm 0.42$ and precision of $98.38\pm 0.17$. Comparatively, the radiomics-based XGBoost model achieved an accuracy of $79.61\pm4.04$ and recall of $91.05\pm3.28$, showcasing its potential as a supplementary diagnostic tool given its rapid processing speed and reduced training time. Our code is available \url{https://github.com/NUBagciLab/Peri-Pancreatic-Edema-Detection}.

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arXiv2024

CT Liver Segmentation via PVT-based Encoding and Refined Decoding

Accurate liver segmentation from CT scans is essential for effective diagnosis and treatment planning. Computer-aided diagnosis systems promise to improve the precision of liver disease diagnosis, disease progression, and treatment planning. In response to the need, we propose a novel deep learning approach, \textit{\textbf{PVTFormer}}, that is built upon a pretrained pyramid vision transformer (PVT v2) combined with advanced residual upsampling and decoder block. By integrating a refined feature channel approach with a hierarchical decoding strategy, PVTFormer generates high quality segmentation masks by enhancing semantic features. Rigorous evaluation of the proposed method on Liver Tumor Segmentation Benchmark (LiTS) 2017 demonstrates that our proposed architecture not only achieves a high dice coefficient of 86.78\%, mIoU of 78.46\%, but also obtains a low HD of 3.50. The results underscore PVTFormer's efficacy in setting a new benchmark for state-of-the-art liver segmentation methods. The source code of the proposed PVTFormer is available at \url{https://github.com/DebeshJha/PVTFormer}.

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arXiv2024

Explainable Transformer Prototypes for Medical Diagnoses

Deployments of artificial intelligence in medical diagnostics mandate not just accuracy and efficacy but also trust, emphasizing the need for explainability in machine decisions. The recent trend in automated medical image diagnostics leans towards the deployment of Transformer-based architectures, credited to their impressive capabilities. Since the self-attention feature of transformers contributes towards identifying crucial regions during the classification process, they enhance the trustability of the methods. However, the complex intricacies of these attention mechanisms may fall short of effectively pinpointing the regions of interest directly influencing AI decisions. Our research endeavors to innovate a unique attention block that underscores the correlation between 'regions' rather than 'pixels'. To address this challenge, we introduce an innovative system grounded in prototype learning, featuring an advanced self-attention mechanism that goes beyond conventional ad-hoc visual explanation techniques by offering comprehensible visual insights. A combined quantitative and qualitative methodological approach was used to demonstrate the effectiveness of the proposed method on the large-scale NIH chest X-ray dataset. Experimental results showed that our proposed method offers a promising direction for explainability, which can lead to the development of more trustable systems, which can facilitate easier and rapid adoption of such technology into routine clinics. The code is available at www.github.com/NUBagcilab/r2r_proto.

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arXiv2023

AI Powered Road Network Prediction with Multi-Modal Data

This study presents an innovative approach for automatic road detection with deep learning, by employing fusion strategies for utilizing both lower-resolution satellite imagery and GPS trajectory data, a concept never explored before. We rigorously investigate both early and late fusion strategies, and assess deep learning based road detection performance using different fusion settings. Our extensive ablation studies assess the efficacy of our framework under diverse model architectures, loss functions, and geographic domains (Istanbul and Montreal). For an unbiased and complete evaluation of road detection results, we use both region-based and boundary-based evaluation metrics for road segmentation. The outcomes reveal that the ResUnet model outperforms U-Net and D-Linknet in road extraction tasks, achieving superior results over the benchmark study using low-resolution Sentinel-2 data. This research not only contributes to the field of automatic road detection but also offers novel insights into the utilization of data fusion methods in diverse applications.

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