A Novel Patch-Based TDA Approach for Computed Tomography
Authors:
Dashti A. Ali,
Aras T. Asaad,
Jacob J. Peoples,
Mohammad Hamghalam,
Alex Robins,
Mane Piliposyan,
Richard K. G. Do,
Natalie Gangai,
Yun S. Chun,
Ahmad Bashir Barekzai,
Jayasree Chakraborty,
Hala Khasawneh,
Camila Vilela,
Natally Horvat,
João Miranda,
Alice C. Wei,
Amber L. Simpson
Abstract:
The development of machine learning (ML) models based on computed tomography (CT) imaging modality has been a major focus of recent research in the medical imaging domain. Incorporating robust feature engineering approach can highly improve the performance of these models. Topological data analysis (TDA), a recent development based on the mathematical field of algebraic topology, mainly focuses on…
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The development of machine learning (ML) models based on computed tomography (CT) imaging modality has been a major focus of recent research in the medical imaging domain. Incorporating robust feature engineering approach can highly improve the performance of these models. Topological data analysis (TDA), a recent development based on the mathematical field of algebraic topology, mainly focuses on the data from a topological perspective, extracting deeper insight and higher dimensional structures from the data. Persistent homology (PH), a fundamental tool in the area of TDA, can extract topological features such as connected components, cycles and voids from the data. A popular approach to construct PH from 3D CT images is to utilize the 3D cubical complex filtration, a method adapted for grid-structured data. However, this approach may not always yield the best performance and can suffer from computational complexity with higher resolution CT images. This study introduces a novel patch-based PH construction approach tailored for volumetric medical imaging data, in particular CT modality. A wide range of experiments has been conducted on several datasets of 3D CT images to comprehensively analyze the performance of the proposed method with various parameters and benchmark it against the 3D cubical complex algorithm. Our results highlight the dominance of the patch-based TDA approach in terms of both classification performance and time-efficiency. The proposed approach outperformed the cubical complex method, achieving average improvement of 10.38%, 6.94%, 2.06%, 11.58%, and 8.51% in accuracy, AUC, sensitivity, specificity, and F1 score, respectively, across all datasets. Finally, we provide a convenient python package, Patch-TDA, to facilitate the utilization of the proposed approach.
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Submitted 12 December, 2025;
originally announced December 2025.
Deep Learning Methods for Retinal Blood Vessel Segmentation: Evaluation on Images with Retinopathy of Prematurity
Authors:
Gorana Gojić,
Veljko Petrović,
Radovan Turović,
Dinu Dragan,
Ana Oros,
Dušan Gajić,
Nebojša Horvat
Abstract:
Automatic blood vessel segmentation from retinal images plays an important role in the diagnosis of many systemic and eye diseases, including retinopathy of prematurity. Current state-of-the-art research in blood vessel segmentation from retinal images is based on convolutional neural networks. The solutions proposed so far are trained and tested on images from a few available retinal blood vessel…
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Automatic blood vessel segmentation from retinal images plays an important role in the diagnosis of many systemic and eye diseases, including retinopathy of prematurity. Current state-of-the-art research in blood vessel segmentation from retinal images is based on convolutional neural networks. The solutions proposed so far are trained and tested on images from a few available retinal blood vessel segmentation datasets, which might limit their performance when given an image with retinopathy of prematurity signs. In this paper, we evaluate the performance of three high-performing convolutional neural networks for retinal blood vessel segmentation in the context of blood vessel segmentation on retinopathy of prematurity retinal images. The main motive behind the study is to test if existing public datasets suffice to develop a high-performing predictor that could assist an ophthalmologist in retinopathy of prematurity diagnosis. To do so, we create a dataset consisting solely of retinopathy of prematurity images with retinal blood vessel annotations manually labeled by two observers, where one is the ophthalmologist experienced in retinopathy of prematurity treatment. Experimental results show that all three solutions have difficulties in detecting the retinal blood vessels of infants due to a lower contrast compared to images from public datasets as demonstrated by a significant drop in classification sensitivity. All three solutions segment alongside retinal also choroidal blood vessels which are not used to diagnose retinopathy of prematurity, but instead represent noise and are confused with retinal blood vessels. By visual and numerical observations, we observe that existing solutions for retinal blood vessel segmentation need improvement toward more detailed datasets or deeper models in order to assist the ophthalmologist in retinopathy of prematurity diagnosis.
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Submitted 20 June, 2023;
originally announced June 2023.