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Researcher profile

Amirreza Mahbod

Amirreza Mahbod contributes to research discovery and scholarly infrastructure.

ResearcherAffiliation not importedOpen to collaborate
Computer Visioneess.IVMachine Learning

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Published work

7 published item(s)

preprint2026arXiv

Developing Predictive and Robust Radiomics Models for Chemotherapy Response in High-Grade Serous Ovarian Carcinoma

Objectives: High-grade serous ovarian carcinoma (HGSOC) is typically diagnosed at an advanced stage with extensive peritoneal metastases, making treatment challenging. Neoadjuvant chemotherapy (NACT) is often used to reduce tumor burden before surgery, but about 40% of patients show limited response. Radiomics, combined with machine learning (ML), offers a promising non-invasive method for predicting NACT response by analyzing computed tomography (CT) imaging data. This study aimed to improve response prediction in HGSOC patients undergoing NACT by integration different feature selection methods. Materials and methods: A framework for selecting robust radiomics features was introduced by employing an automated randomisation algorithm to mimic inter-observer variability, ensuring a balance between feature robustness and prediction accuracy. Four response metrics were used: chemotherapy response score (CRS), RECIST, volume reduction (VolR), and diameter reduction (DiaR). Lesions in different anatomical sites were studied. Pre- and post-NACT CT scans were used for feature extraction and model training on one cohort, and an independent cohort was used for external testing. Results: The best prediction performance was achieved using all lesions combined for VolR prediction, with an AUC of 0.83. Omental lesions provided the best results for CRS prediction (AUC 0.77), while pelvic lesions performed best for DiaR (AUC 0.76). Conclusion: The integration of robustness into the feature selection processes ensures the development of reliable models and thus facilitates the implementation of the radiomics models in clinical applications for HGSOC patients. Future work should explore further applications of radiomics in ovarian cancer, particularly in real-time clinical settings.

0 citations0 reviewsNo code linkedOpen access
preprint2026arXiv

NucEval: A Robust Evaluation Framework for Nuclear Instance Segmentation

In computational pathology, nuclear instance segmentation is a fundamental task with many downstream clinical applications. With the advent of deep learning, many approaches, including convolutional neural networks (CNNs) and vision transformers (ViTs), have been proposed for this task, along with both machine learning-based and non-machine learning-based pre- and post-processing techniques to further boost performance. However, one fundamental aspect that has received less attention is the evaluation pipeline. In this study, we identify four key issues associated with nuclear instance segmentation evaluation and propose corresponding solutions. Our proposed modifications, namely handling vague regions, score normalization, overlapping instances, and border uncertainty, are integrated into a unified framework called NucEval, which enables robust evaluation of nuclear instance segmentation. We evaluate this pipeline using the NuInsSeg dataset, which provides unique characteristics that make it particularly suitable for this study, as well as two additional external datasets, with three CNN- and ViT-based nuclear instance segmentation models, to demonstrate the impact of these modifications on instance segmentation metrics. The code, along with complete guidelines and illustrative examples, is publicly available at: https://github.com/masih4/nuc_eval.

0 citations0 reviewsNo code linkedOpen access
preprint2024arXiv

Improving Generalization Capability of Deep Learning-Based Nuclei Instance Segmentation by Non-deterministic Train Time and Deterministic Test Time Stain Normalization

With the advent of digital pathology and microscopic systems that can scan and save whole slide histological images automatically, there is a growing trend to use computerized methods to analyze acquired images. Among different histopathological image analysis tasks, nuclei instance segmentation plays a fundamental role in a wide range of clinical and research applications. While many semi- and fully-automatic computerized methods have been proposed for nuclei instance segmentation, deep learning (DL)-based approaches have been shown to deliver the best performances. However, the performance of such approaches usually degrades when tested on unseen datasets. In this work, we propose a novel method to improve the generalization capability of a DL-based automatic segmentation approach. Besides utilizing one of the state-of-the-art DL-based models as a baseline, our method incorporates non-deterministic train time and deterministic test time stain normalization, and ensembling to boost the segmentation performance. We trained the model with one single training set and evaluated its segmentation performance on seven test datasets. Our results show that the proposed method provides up to 4.9%, 5.4%, and 5.9% better average performance in segmenting nuclei based on Dice score, aggregated Jaccard index, and panoptic quality score, respectively, compared to the baseline segmentation model.

0 citations0 reviewsNo code linkedOpen access
preprint2022arXiv

Automatic Foot Ulcer Segmentation Using an Ensemble of Convolutional Neural Networks

Foot ulcer is a common complication of diabetes mellitus and, associated with substantial morbidity and mortality, remains a major risk factor for lower leg amputations. Extracting accurate morphological features from foot wounds is crucial for appropriate treatment. Although visual inspection by a medical professional is the common approach for diagnosis, this is subjective and error-prone, and computer-aided approaches thus provide an interesting alternative. Deep learning-based methods, and in particular convolutional neural networks (CNNs), have shown excellent performance for various tasks in medical image analysis including medical image segmentation. In this paper, we propose an ensemble approach based on two encoder-decoder-based CNN models, namely LinkNet and U-Net, to perform foot ulcer segmentation. To deal with a limited number of available training samples, we use pre-trained weights (EfficientNetB1 for the LinkNet model and EfficientNetB2 for the U-Net model) and perform further pre-training using the Medetec dataset while also applying a number of morphological-based and colour-based augmentation techniques. To boost the segmentation performance, we incorporate five-fold cross-validation, test time augmentation and result fusion. Applied on the publicly available chronic wound dataset and the MICCAI 2021 Foot Ulcer Segmentation (FUSeg) Challenge, our method achieves state-of-the-art performance with data-based Dice scores of 92.07% and 88.80%, respectively, and is the top ranked method in the FUSeg challenge leaderboard. The Dockerised guidelines, inference codes and saved trained models are publicly available at https://github.com/masih4/Foot_Ulcer_Segmentation.

0 citations0 reviewsNo code linkedOpen access
preprint2022arXiv

Deep Neural Network Pruning for Nuclei Instance Segmentation in Hematoxylin & Eosin-Stained Histological Images

Recently, pruning deep neural networks (DNNs) has received a lot of attention for improving accuracy and generalization power, reducing network size, and increasing inference speed on specialized hardwares. Although pruning was mainly tested on computer vision tasks, its application in the context of medical image analysis has hardly been explored. This work investigates the impact of well-known pruning techniques, namely layer-wise and network-wide magnitude pruning, on the nuclei instance segmentation performance in histological images. Our utilized instance segmentation model consists of two main branches: (1) a semantic segmentation branch, and (2) a deep regression branch. We investigate the impact of weight pruning on the performance of both branches separately and on the final nuclei instance segmentation result. Evaluated on two publicly available datasets, our results show that layer-wise pruning delivers slightly better performance than networkwide pruning for small compression ratios (CRs) while for large CRs, network-wide pruning yields superior performance. For semantic segmentation, deep regression and final instance segmentation, 93.75 %, 95 %, and 80 % of the model weights can be pruned by layer-wise pruning with less than 2 % reduction in the performance of respective models.

0 citations0 reviewsNo code linkedOpen access
preprint2022arXiv

FUSeg: The Foot Ulcer Segmentation Challenge

Acute and chronic wounds with varying etiologies burden the healthcare systems economically. The advanced wound care market is estimated to reach $22 billion by 2024. Wound care professionals provide proper diagnosis and treatment with heavy reliance on images and image documentation. Segmentation of wound boundaries in images is a key component of the care and diagnosis protocol since it is important to estimate the area of the wound and provide quantitative measurement for the treatment. Unfortunately, this process is very time-consuming and requires a high level of expertise. Recently automatic wound segmentation methods based on deep learning have shown promising performance but require large datasets for training and it is unclear which methods perform better. To address these issues, we propose the Foot Ulcer Segmentation challenge (FUSeg) organized in conjunction with the 2021 International Conference on Medical Image Computing and Computer Assisted Intervention (MICCAI). We built a wound image dataset containing 1,210 foot ulcer images collected over 2 years from 889 patients. It is pixel-wise annotated by wound care experts and split into a training set with 1010 images and a testing set with 200 images for evaluation. Teams around the world developed automated methods to predict wound segmentations on the testing set of which annotations were kept private. The predictions were evaluated and ranked based on the average Dice coefficient. The FUSeg challenge remains an open challenge as a benchmark for wound segmentation after the conference.

0 citations0 reviewsNo code linkedOpen access
preprint2020arXiv

Investigating and Exploiting Image Resolution for Transfer Learning-based Skin Lesion Classification

Skin cancer is among the most common cancer types. Dermoscopic image analysis improves the diagnostic accuracy for detection of malignant melanoma and other pigmented skin lesions when compared to unaided visual inspection. Hence, computer-based methods to support medical experts in the diagnostic procedure are of great interest. Fine-tuning pre-trained convolutional neural networks (CNNs) has been shown to work well for skin lesion classification. Pre-trained CNNs are usually trained with natural images of a fixed image size which is typically significantly smaller than captured skin lesion images and consequently dermoscopic images are downsampled for fine-tuning. However, useful medical information may be lost during this transformation. In this paper, we explore the effect of input image size on skin lesion classification performance of fine-tuned CNNs. For this, we resize dermoscopic images to different resolutions, ranging from 64x64 to 768x768 pixels and investigate the resulting classification performance of three well-established CNNs, namely DenseNet-121, ResNet-18, and ResNet-50. Our results show that using very small images (of size 64x64 pixels) degrades the classification performance, while images of size 128x128 pixels and above support good performance with larger image sizes leading to slightly improved classification. We further propose a novel fusion approach based on a three-level ensemble strategy that exploits multiple fine-tuned networks trained with dermoscopic images at various sizes. When applied on the ISIC 2017 skin lesion classification challenge, our fusion approach yields an area under the receiver operating characteristic curve of 89.2% and 96.6% for melanoma classification and seborrheic keratosis classification, respectively, outperforming state-of-the-art algorithms.

0 citations0 reviewsNo code linkedOpen access