arXiv subjects

Aleksandar Vakanski

Publications and source records attributed to Aleksandar Vakanski.

30 records · Page 2Linked to original sources

arXiv2023

Enhanced Sharp-GAN For Histopathology Image Synthesis

Histopathology image synthesis aims to address the data shortage issue in training deep learning approaches for accurate cancer detection. However, existing methods struggle to produce realistic images that have accurate nuclei boundaries and less artifacts, which limits the application in downstream tasks. To address the challenges, we propose a novel approach that enhances the quality of synthetic images by using nuclei topology and contour regularization. The proposed approach uses the skeleton map of nuclei to integrate nuclei topology and separate touching nuclei. In the loss function, we propose two new contour regularization terms that enhance the contrast between contour and non-contour pixels and increase the similarity between contour pixels. We evaluate the proposed approach on the two datasets using image quality metrics and a downstream task (nuclei segmentation). The proposed approach outperforms Sharp-GAN in all four image quality metrics on two datasets. By integrating 6k synthetic images from the proposed approach into training, a nuclei segmentation model achieves the state-of-the-art segmentation performance on TNBC dataset and its detection quality (DQ), segmentation quality (SQ), panoptic quality (PQ), and aggregated Jaccard index (AJI) is 0.855, 0.863, 0.691, and 0.683, respectively.

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arXiv2022

MIRST-DM: Multi-Instance RST with Drop-Max Layer for Robust Classification of Breast Cancer

Robust self-training (RST) can augment the adversarial robustness of image classification models without significantly sacrificing models' generalizability. However, RST and other state-of-the-art defense approaches failed to preserve the generalizability and reproduce their good adversarial robustness on small medical image sets. In this work, we propose the Multi-instance RST with a drop-max layer, namely MIRST-DM, which involves a sequence of iteratively generated adversarial instances during training to learn smoother decision boundaries on small datasets. The proposed drop-max layer eliminates unstable features and helps learn representations that are robust to image perturbations. The proposed approach was validated using a small breast ultrasound dataset with 1,190 images. The results demonstrate that the proposed approach achieves state-of-the-art adversarial robustness against three prevalent attacks.

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arXiv2022

EMT-NET: Efficient multitask network for computer-aided diagnosis of breast cancer

Deep learning-based computer-aided diagnosis has achieved unprecedented performance in breast cancer detection. However, most approaches are computationally intensive, which impedes their broader dissemination in real-world applications. In this work, we propose an efficient and light-weighted multitask learning architecture to classify and segment breast tumors simultaneously. We incorporate a segmentation task into a tumor classification network, which makes the backbone network learn representations focused on tumor regions. Moreover, we propose a new numerically stable loss function that easily controls the balance between the sensitivity and specificity of cancer detection. The proposed approach is evaluated using a breast ultrasound dataset with 1,511 images. The accuracy, sensitivity, and specificity of tumor classification is 88.6%, 94.1%, and 85.3%, respectively. We validate the model using a virtual mobile device, and the average inference time is 0.35 seconds per image.

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arXiv2021

Potato Crop Stress Identification in Aerial Images using Deep Learning-based Object Detection

Recent research on the application of remote sensing and deep learning-based analysis in precision agriculture demonstrated a potential for improved crop management and reduced environmental impacts of agricultural production. Despite the promising results, the practical relevance of these technologies for field deployment requires novel algorithms that are customized for analysis of agricultural images and robust to implementation on natural field imagery. The paper presents an approach for analyzing aerial images of a potato (Solanum tuberosum L.) crop using deep neural networks. The main objective is to demonstrate automated spatial recognition of healthy vs. stressed crop at a plant level. Specifically, we examine premature plant senescence resulting in drought stress on Russet Burbank potato plants. We propose a novel deep learning (DL) model for detecting crop stress, named Retina-UNet-Ag. The proposed architecture is a variant of Retina-UNet and includes connections from low-level semantic representation maps to the feature pyramid network. The paper also introduces a dataset of aerial field images acquired with a Parrot Sequoia camera. The dataset includes manually annotated bounding boxes of healthy and stressed plant regions. Experimental validation demonstrated the ability for distinguishing healthy and stressed plants in field images, achieving an average dice score coefficient (DSC) of 0.74. A comparison to related state-of-the-art DL models for object detection revealed that the presented approach is effective for this task. The proposed method is conducive toward the assessment and recognition of potato crop stress in aerial field images collected under natural conditions.

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arXiv2021

TA-Net: Topology-Aware Network for Gland Segmentation

Gland segmentation is a critical step to quantitatively assess the morphology of glands in histopathology image analysis. However, it is challenging to separate densely clustered glands accurately. Existing deep learning-based approaches attempted to use contour-based techniques to alleviate this issue but only achieved limited success. To address this challenge, we propose a novel topology-aware network (TA-Net) to accurately separate densely clustered and severely deformed glands. The proposed TA-Net has a multitask learning architecture and enhances the generalization of gland segmentation by learning shared representation from two tasks: instance segmentation and gland topology estimation. The proposed topology loss computes gland topology using gland skeletons and markers. It drives the network to generate segmentation results that comply with the true gland topology. We validate the proposed approach on the GlaS and CRAG datasets using three quantitative metrics, F1-score, object-level Dice coefficient, and object-level Hausdorff distance. Extensive experiments demonstrate that TA-Net achieves state-of-the-art performance on the two datasets. TA-Net outperforms other approaches in the presence of densely clustered glands.

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arXiv2021

Sharp-GAN: Sharpness Loss Regularized GAN for Histopathology Image Synthesis

Existing deep learning-based approaches for histopathology image analysis require large annotated training sets to achieve good performance; but annotating histopathology images is slow and resource-intensive. Conditional generative adversarial networks have been applied to generate synthetic histopathology images to alleviate this issue, but current approaches fail to generate clear contours for overlapped and touching nuclei. In this study, We propose a sharpness loss regularized generative adversarial network to synthesize realistic histopathology images. The proposed network uses normalized nucleus distance map rather than the binary mask to encode nuclei contour information. The proposed sharpness loss enhances the contrast of nuclei contour pixels. The proposed method is evaluated using four image quality metrics and segmentation results on two public datasets. Both quantitative and qualitative results demonstrate that the proposed approach can generate realistic histopathology images with clear nuclei contours.

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arXiv2021

BI-RADS-Net: An Explainable Multitask Learning Approach for Cancer Diagnosis in Breast Ultrasound Images

In healthcare, it is essential to explain the decision-making process of machine learning models to establish the trustworthiness of clinicians. This paper introduces BI-RADS-Net, a novel explainable deep learning approach for cancer detection in breast ultrasound images. The proposed approach incorporates tasks for explaining and classifying breast tumors, by learning feature representations relevant to clinical diagnosis. Explanations of the predictions (benign or malignant) are provided in terms of morphological features that are used by clinicians for diagnosis and reporting in medical practice. The employed features include the BI-RADS descriptors of shape, orientation, margin, echo pattern, and posterior features. Additionally, our approach predicts the likelihood of malignancy of the findings, which relates to the BI-RADS assessment category reported by clinicians. Experimental validation on a dataset consisting of 1,192 images indicates improved model accuracy, supported by explanations in clinical terms using the BI-RADS lexicon.

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arXiv2021

Bend-Net: Bending Loss Regularized Multitask Learning Network for Nuclei Segmentation in Histopathology Images

Separating overlapped nuclei is a major challenge in histopathology image analysis. Recently published approaches have achieved promising overall performance on nuclei segmentation; however, their performance on separating overlapped nuclei is quite limited. To address the issue, we propose a novel multitask learning network with a bending loss regularizer to separate overlapped nuclei accurately. The newly proposed multitask learning architecture enhances the generalization by learning shared representation from three tasks: instance segmentation, nuclei distance map prediction, and overlapped nuclei distance map prediction. The proposed bending loss defines high penalties to concave contour points with large curvatures, and applies small penalties to convex contour points with small curvatures. Minimizing the bending loss avoids generating contours that encompass multiple nuclei. In addition, two new quantitative metrics, Aggregated Jaccard Index of overlapped nuclei (AJIO) and Accuracy of overlapped nuclei (ACCO), are designed for the evaluation of overlapped nuclei segmentation. We validate the proposed approach on the CoNSeP and MoNuSegv1 datasets using seven quantitative metrics: Aggregate Jaccard Index, Dice, Segmentation Quality, Recognition Quality, Panoptic Quality, AJIO, and ACCO. Extensive experiments demonstrate that the proposed Bend-Net outperforms eight state-of-the-art approaches.

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arXiv2020

Attention Enriched Deep Learning Model for Breast Tumor Segmentation in Ultrasound Images

Incorporating human domain knowledge for breast tumor diagnosis is challenging, since shape, boundary, curvature, intensity, or other common medical priors vary significantly across patients and cannot be employed. This work proposes a new approach for integrating visual saliency into a deep learning model for breast tumor segmentation in ultrasound images. Visual saliency refers to image maps containing regions that are more likely to attract radiologists visual attention. The proposed approach introduces attention blocks into a U-Net architecture, and learns feature representations that prioritize spatial regions with high saliency levels. The validation results demonstrate increased accuracy for tumor segmentation relative to models without salient attention layers. The approach achieved a Dice similarity coefficient of 90.5 percent on a dataset of 510 images. The salient attention model has potential to enhance accuracy and robustness in processing medical images of other organs, by providing a means to incorporate task-specific knowledge into deep learning architectures.

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arXiv2020

A Review of Computational Approaches for Evaluation of Rehabilitation Exercises

Recent advances in data analytics and computer-aided diagnostics stimulate the vision of patient-centric precision healthcare, where treatment plans are customized based on the health records and needs of every patient. In physical rehabilitation, the progress in machine learning and the advent of affordable and reliable motion capture sensors have been conducive to the development of approaches for automated assessment of patient performance and progress toward functional recovery. The presented study reviews computational approaches for evaluating patient performance in rehabilitation programs using motion capture systems. Such approaches will play an important role in supplementing traditional rehabilitation assessment performed by trained clinicians, and in assisting patients participating in home-based rehabilitation. The reviewed computational methods for exercise evaluation are grouped into three main categories: discrete movement score, rule-based, and template-based approaches. The review places an emphasis on the application of machine learning methods for movement evaluation in rehabilitation. Related work in the literature on data representation, feature engineering, movement segmentation, and scoring functions is presented. The study also reviews existing sensors for capturing rehabilitation movements and provides an informative listing of pertinent benchmark datasets. The significance of this paper is in being the first to provide a comprehensive review of computational methods for evaluation of patient performance in rehabilitation programs.

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arXiv2020

Bending Loss Regularized Network for Nuclei Segmentation in Histopathology Images

Separating overlapped nuclei is a major challenge in histopathology image analysis. Recently published approaches have achieved promising overall performance on public datasets; however, their performance in segmenting overlapped nuclei are limited. To address the issue, we propose the bending loss regularized network for nuclei segmentation. The proposed bending loss defines high penalties to contour points with large curvatures, and applies small penalties to contour points with small curvature. Minimizing the bending loss can avoid generating contours that encompass multiple nuclei. The proposed approach is validated on the MoNuSeg dataset using five quantitative metrics. It outperforms six state-of-the-art approaches on the following metrics: Aggregate Jaccard Index, Dice, Recognition Quality, and Pan-optic Quality.

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arXiv2020

Stan: Small tumor-aware network for breast ultrasound image segmentation

Breast tumor segmentation provides accurate tumor boundary, and serves as a key step toward further cancer quantification. Although deep learning-based approaches have been proposed and achieved promising results, existing approaches have difficulty in detecting small breast tumors. The capacity to detecting small tumors is particularly important in finding early stage cancers using computer-aided diagnosis (CAD) systems. In this paper, we propose a novel deep learning architecture called Small Tumor-Aware Network (STAN), to improve the performance of segmenting tumors with different size. The new architecture integrates both rich context information and high-resolution image features. We validate the proposed approach using seven quantitative metrics on two public breast ultrasound datasets. The proposed approach outperformed the state-of-the-art approaches in segmenting small breast tumors. Index

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