arXiv subjects

Sophia Bano

Publications and source records attributed to Sophia Bano.

At least 37 records · Page 2Linked to original sources

arXiv2024

PitVis-2023 Challenge: Workflow Recognition in videos of Endoscopic Pituitary Surgery

The field of computer vision applied to videos of minimally invasive surgery is ever-growing. Workflow recognition pertains to the automated recognition of various aspects of a surgery: including which surgical steps are performed; and which surgical instruments are used. This information can later be used to assist clinicians when learning the surgery; during live surgery; and when writing operation notes. The Pituitary Vision (PitVis) 2023 Challenge tasks the community to step and instrument recognition in videos of endoscopic pituitary surgery. This is a unique task when compared to other minimally invasive surgeries due to the smaller working space, which limits and distorts vision; and higher frequency of instrument and step switching, which requires more precise model predictions. Participants were provided with 25-videos, with results presented at the MICCAI-2023 conference as part of the Endoscopic Vision 2023 Challenge in Vancouver, Canada, on 08-Oct-2023. There were 18-submissions from 9-teams across 6-countries, using a variety of deep learning models. A commonality between the top performing models was incorporating spatio-temporal and multi-task methods, with greater than 50% and 10% macro-F1-score improvement over purely spacial single-task models in step and instrument recognition respectively. The PitVis-2023 Challenge therefore demonstrates state-of-the-art computer vision models in minimally invasive surgery are transferable to a new dataset, with surgery specific techniques used to enhance performance, progressing the field further. Benchmark results are provided in the paper, and the dataset is publicly available at: https://doi.org/10.5522/04/26531686.

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arXiv2024

Gaussian Pancakes: Geometrically-Regularized 3D Gaussian Splatting for Realistic Endoscopic Reconstruction

Within colorectal cancer diagnostics, conventional colonoscopy techniques face critical limitations, including a limited field of view and a lack of depth information, which can impede the detection of precancerous lesions. Current methods struggle to provide comprehensive and accurate 3D reconstructions of the colonic surface which can help minimize the missing regions and reinspection for pre-cancerous polyps. Addressing this, we introduce 'Gaussian Pancakes', a method that leverages 3D Gaussian Splatting (3D GS) combined with a Recurrent Neural Network-based Simultaneous Localization and Mapping (RNNSLAM) system. By introducing geometric and depth regularization into the 3D GS framework, our approach ensures more accurate alignment of Gaussians with the colon surface, resulting in smoother 3D reconstructions with novel viewing of detailed textures and structures. Evaluations across three diverse datasets show that Gaussian Pancakes enhances novel view synthesis quality, surpassing current leading methods with a 18% boost in PSNR and a 16% improvement in SSIM. It also delivers over 100X faster rendering and more than 10X shorter training times, making it a practical tool for real-time applications. Hence, this holds promise for achieving clinical translation for better detection and diagnosis of colorectal cancer.

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arXiv2024

SimCol3D -- 3D Reconstruction during Colonoscopy Challenge

Colorectal cancer is one of the most common cancers in the world. While colonoscopy is an effective screening technique, navigating an endoscope through the colon to detect polyps is challenging. A 3D map of the observed surfaces could enhance the identification of unscreened colon tissue and serve as a training platform. However, reconstructing the colon from video footage remains difficult. Learning-based approaches hold promise as robust alternatives, but necessitate extensive datasets. Establishing a benchmark dataset, the 2022 EndoVis sub-challenge SimCol3D aimed to facilitate data-driven depth and pose prediction during colonoscopy. The challenge was hosted as part of MICCAI 2022 in Singapore. Six teams from around the world and representatives from academia and industry participated in the three sub-challenges: synthetic depth prediction, synthetic pose prediction, and real pose prediction. This paper describes the challenge, the submitted methods, and their results. We show that depth prediction from synthetic colonoscopy images is robustly solvable, while pose estimation remains an open research question.

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arXiv2024

PitVQA: Image-grounded Text Embedding LLM for Visual Question Answering in Pituitary Surgery

Visual Question Answering (VQA) within the surgical domain, utilizing Large Language Models (LLMs), offers a distinct opportunity to improve intra-operative decision-making and facilitate intuitive surgeon-AI interaction. However, the development of LLMs for surgical VQA is hindered by the scarcity of diverse and extensive datasets with complex reasoning tasks. Moreover, contextual fusion of the image and text modalities remains an open research challenge due to the inherent differences between these two types of information and the complexity involved in aligning them. This paper introduces PitVQA, a novel dataset specifically designed for VQA in endonasal pituitary surgery and PitVQA-Net, an adaptation of the GPT2 with a novel image-grounded text embedding for surgical VQA. PitVQA comprises 25 procedural videos and a rich collection of question-answer pairs spanning crucial surgical aspects such as phase and step recognition, context understanding, tool detection and localization, and tool-tissue interactions. PitVQA-Net consists of a novel image-grounded text embedding that projects image and text features into a shared embedding space and GPT2 Backbone with an excitation block classification head to generate contextually relevant answers within the complex domain of endonasal pituitary surgery. Our image-grounded text embedding leverages joint embedding, cross-attention and contextual representation to understand the contextual relationship between questions and surgical images. We demonstrate the effectiveness of PitVQA-Net on both the PitVQA and the publicly available EndoVis18-VQA dataset, achieving improvements in balanced accuracy of 8% and 9% over the most recent baselines, respectively. Our code and dataset is available at https://github.com/mobarakol/PitVQA.

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arXiv2024

Surgical-DeSAM: Decoupling SAM for Instrument Segmentation in Robotic Surgery

Purpose: The recent Segment Anything Model (SAM) has demonstrated impressive performance with point, text or bounding box prompts, in various applications. However, in safety-critical surgical tasks, prompting is not possible due to (i) the lack of per-frame prompts for supervised learning, (ii) it is unrealistic to prompt frame-by-frame in a real-time tracking application, and (iii) it is expensive to annotate prompts for offline applications. Methods: We develop Surgical-DeSAM to generate automatic bounding box prompts for decoupling SAM to obtain instrument segmentation in real-time robotic surgery. We utilise a commonly used detection architecture, DETR, and fine-tuned it to obtain bounding box prompt for the instruments. We then empolyed decoupling SAM (DeSAM) by replacing the image encoder with DETR encoder and fine-tune prompt encoder and mask decoder to obtain instance segmentation for the surgical instruments. To improve detection performance, we adopted the Swin-transformer to better feature representation. Results: The proposed method has been validated on two publicly available datasets from the MICCAI surgical instruments segmentation challenge EndoVis 2017 and 2018. The performance of our method is also compared with SOTA instrument segmentation methods and demonstrated significant improvements with dice metrics of 89.62 and 90.70 for the EndoVis 2017 and 2018. Conclusion: Our extensive experiments and validations demonstrate that Surgical-DeSAM enables real-time instrument segmentation without any additional prompting and outperforms other SOTA segmentation methods.

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arXiv2024

Investigation of Federated Learning Algorithms for Retinal Optical Coherence Tomography Image Classification with Statistical Heterogeneity

Purpose: We apply federated learning to train an OCT image classifier simulating a realistic scenario with multiple clients and statistical heterogeneous data distribution where data in the clients lack samples of some categories entirely. Methods: We investigate the effectiveness of FedAvg and FedProx to train an OCT image classification model in a decentralized fashion, addressing privacy concerns associated with centralizing data. We partitioned a publicly available OCT dataset across multiple clients under IID and Non-IID settings and conducted local training on the subsets for each client. We evaluated two federated learning methods, FedAvg and FedProx for these settings. Results: Our experiments on the dataset suggest that under IID settings, both methods perform on par with training on a central data pool. However, the performance of both algorithms declines as we increase the statistical heterogeneity across the client data, while FedProx consistently performs better than FedAvg in the increased heterogeneity settings. Conclusion: Despite the effectiveness of federated learning in the utilization of private data across multiple medical institutions, the large number of clients and heterogeneous distribution of labels deteriorate the performance of both algorithms. Notably, FedProx appears to be more robust to the increased heterogeneity.

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arXiv2023

Biomedical image analysis competitions: The state of current participation practice

The number of international benchmarking competitions is steadily increasing in various fields of machine learning (ML) research and practice. So far, however, little is known about the common practice as well as bottlenecks faced by the community in tackling the research questions posed. To shed light on the status quo of algorithm development in the specific field of biomedical imaging analysis, we designed an international survey that was issued to all participants of challenges conducted in conjunction with the IEEE ISBI 2021 and MICCAI 2021 conferences (80 competitions in total). The survey covered participants' expertise and working environments, their chosen strategies, as well as algorithm characteristics. A median of 72% challenge participants took part in the survey. According to our results, knowledge exchange was the primary incentive (70%) for participation, while the reception of prize money played only a minor role (16%). While a median of 80 working hours was spent on method development, a large portion of participants stated that they did not have enough time for method development (32%). 25% perceived the infrastructure to be a bottleneck. Overall, 94% of all solutions were deep learning-based. Of these, 84% were based on standard architectures. 43% of the respondents reported that the data samples (e.g., images) were too large to be processed at once. This was most commonly addressed by patch-based training (69%), downsampling (37%), and solving 3D analysis tasks as a series of 2D tasks. K-fold cross-validation on the training set was performed by only 37% of the participants and only 50% of the participants performed ensembling based on multiple identical models (61%) or heterogeneous models (39%). 48% of the respondents applied postprocessing steps.

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arXiv2023

SurgT challenge: Benchmark of Soft-Tissue Trackers for Robotic Surgery

This paper introduces the ``SurgT: Surgical Tracking" challenge which was organised in conjunction with MICCAI 2022. There were two purposes for the creation of this challenge: (1) the establishment of the first standardised benchmark for the research community to assess soft-tissue trackers; and (2) to encourage the development of unsupervised deep learning methods, given the lack of annotated data in surgery. A dataset of 157 stereo endoscopic videos from 20 clinical cases, along with stereo camera calibration parameters, have been provided. Participants were assigned the task of developing algorithms to track the movement of soft tissues, represented by bounding boxes, in stereo endoscopic videos. At the end of the challenge, the developed methods were assessed on a previously hidden test subset. This assessment uses benchmarking metrics that were purposely developed for this challenge, to verify the efficacy of unsupervised deep learning algorithms in tracking soft-tissue. The metric used for ranking the methods was the Expected Average Overlap (EAO) score, which measures the average overlap between a tracker's and the ground truth bounding boxes. Coming first in the challenge was the deep learning submission by ICVS-2Ai with a superior EAO score of 0.617. This method employs ARFlow to estimate unsupervised dense optical flow from cropped images, using photometric and regularization losses. Second, Jmees with an EAO of 0.583, uses deep learning for surgical tool segmentation on top of a non-deep learning baseline method: CSRT. CSRT by itself scores a similar EAO of 0.563. The results from this challenge show that currently, non-deep learning methods are still competitive. The dataset and benchmarking tool created for this challenge have been made publicly available at https://surgt.grand-challenge.org/.

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arXiv2023

Why is the winner the best?

International benchmarking competitions have become fundamental for the comparative performance assessment of image analysis methods. However, little attention has been given to investigating what can be learnt from these competitions. Do they really generate scientific progress? What are common and successful participation strategies? What makes a solution superior to a competing method? To address this gap in the literature, we performed a multi-center study with all 80 competitions that were conducted in the scope of IEEE ISBI 2021 and MICCAI 2021. Statistical analyses performed based on comprehensive descriptions of the submitted algorithms linked to their rank as well as the underlying participation strategies revealed common characteristics of winning solutions. These typically include the use of multi-task learning (63%) and/or multi-stage pipelines (61%), and a focus on augmentation (100%), image preprocessing (97%), data curation (79%), and postprocessing (66%). The "typical" lead of a winning team is a computer scientist with a doctoral degree, five years of experience in biomedical image analysis, and four years of experience in deep learning. Two core general development strategies stood out for highly-ranked teams: the reflection of the metrics in the method design and the focus on analyzing and handling failure cases. According to the organizers, 43% of the winning algorithms exceeded the state of the art but only 11% completely solved the respective domain problem. The insights of our study could help researchers (1) improve algorithm development strategies when approaching new problems, and (2) focus on open research questions revealed by this work.

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arXiv2023

Placental Vessel Segmentation and Registration in Fetoscopy: Literature Review and MICCAI FetReg2021 Challenge Findings

Fetoscopy laser photocoagulation is a widely adopted procedure for treating Twin-to-Twin Transfusion Syndrome (TTTS). The procedure involves photocoagulation pathological anastomoses to regulate blood exchange among twins. The procedure is particularly challenging due to the limited field of view, poor manoeuvrability of the fetoscope, poor visibility, and variability in illumination. These challenges may lead to increased surgery time and incomplete ablation. Computer-assisted intervention (CAI) can provide surgeons with decision support and context awareness by identifying key structures in the scene and expanding the fetoscopic field of view through video mosaicking. Research in this domain has been hampered by the lack of high-quality data to design, develop and test CAI algorithms. Through the Fetoscopic Placental Vessel Segmentation and Registration (FetReg2021) challenge, which was organized as part of the MICCAI2021 Endoscopic Vision challenge, we released the first largescale multicentre TTTS dataset for the development of generalized and robust semantic segmentation and video mosaicking algorithms. For this challenge, we released a dataset of 2060 images, pixel-annotated for vessels, tool, fetus and background classes, from 18 in-vivo TTTS fetoscopy procedures and 18 short video clips. Seven teams participated in this challenge and their model performance was assessed on an unseen test dataset of 658 pixel-annotated images from 6 fetoscopic procedures and 6 short clips. The challenge provided an opportunity for creating generalized solutions for fetoscopic scene understanding and mosaicking. In this paper, we present the findings of the FetReg2021 challenge alongside reporting a detailed literature review for CAI in TTTS fetoscopy. Through this challenge, its analysis and the release of multi-centre fetoscopic data, we provide a benchmark for future research in this field.

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arXiv2022

Retrieval of surgical phase transitions using reinforcement learning

In minimally invasive surgery, surgical workflow segmentation from video analysis is a well studied topic. The conventional approach defines it as a multi-class classification problem, where individual video frames are attributed a surgical phase label. We introduce a novel reinforcement learning formulation for offline phase transition retrieval. Instead of attempting to classify every video frame, we identify the timestamp of each phase transition. By construction, our model does not produce spurious and noisy phase transitions, but contiguous phase blocks. We investigate two different configurations of this model. The first does not require processing all frames in a video (only <60% and <20% of frames in 2 different applications), while producing results slightly under the state-of-the-art accuracy. The second configuration processes all video frames, and outperforms the state-of-the art at a comparable computational cost. We compare our method against the recent top-performing frame-based approaches TeCNO and Trans-SVNet on the public dataset Cholec80 and also on an in-house dataset of laparoscopic sacrocolpopexy. We perform both a frame-based (accuracy, precision, recall and F1-score) and an event-based (event ratio) evaluation of our algorithms.

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arXiv2022

Learning-Based Keypoint Registration for Fetoscopic Mosaicking

In Twin-to-Twin Transfusion Syndrome (TTTS), abnormal vascular anastomoses in the monochorionic placenta can produce uneven blood flow between the two fetuses. In the current practice, TTTS is treated surgically by closing abnormal anastomoses using laser ablation. This surgery is minimally invasive and relies on fetoscopy. Limited field of view makes anastomosis identification a challenging task for the surgeon. To tackle this challenge, we propose a learning-based framework for in-vivo fetoscopy frame registration for field-of-view expansion. The novelties of this framework relies on a learning-based keypoint proposal network and an encoding strategy to filter (i) irrelevant keypoints based on fetoscopic image segmentation and (ii) inconsistent homographies. We validate of our framework on a dataset of 6 intraoperative sequences from 6 TTTS surgeries from 6 different women against the most recent state of the art algorithm, which relies on the segmentation of placenta vessels. The proposed framework achieves higher performance compared to the state of the art, paving the way for robust mosaicking to provide surgeons with context awareness during TTTS surgery.

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arXiv2022

BiometryNet: Landmark-based Fetal Biometry Estimation from Standard Ultrasound Planes

Fetal growth assessment from ultrasound is based on a few biometric measurements that are performed manually and assessed relative to the expected gestational age. Reliable biometry estimation depends on the precise detection of landmarks in standard ultrasound planes. Manual annotation can be time-consuming and operator dependent task, and may results in high measurements variability. Existing methods for automatic fetal biometry rely on initial automatic fetal structure segmentation followed by geometric landmark detection. However, segmentation annotations are time-consuming and may be inaccurate, and landmark detection requires developing measurement-specific geometric methods. This paper describes BiometryNet, an end-to-end landmark regression framework for fetal biometry estimation that overcomes these limitations. It includes a novel Dynamic Orientation Determination (DOD) method for enforcing measurement-specific orientation consistency during network training. DOD reduces variabilities in network training, increases landmark localization accuracy, thus yields accurate and robust biometric measurements. To validate our method, we assembled a dataset of 3,398 ultrasound images from 1,829 subjects acquired in three clinical sites with seven different ultrasound devices. Comparison and cross-validation of three different biometric measurements on two independent datasets shows that BiometryNet is robust and yields accurate measurements whose errors are lower than the clinically permissible errors, outperforming other existing automated biometry estimation methods. Code is available at https://github.com/netanellavisdris/fetalbiometry.

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arXiv2022

Fluorescence angiography classification in colorectal surgery -- A preliminary report

Background: Fluorescence angiography has shown very promising results in reducing anastomotic leaks by allowing the surgeon to select optimally perfused tissue. However, subjective interpretation of the fluorescent signal still hinders broad application of the technique, as significant variation between different surgeons exists. Our aim is to develop an artificial intelligence algorithm to classify colonic tissue as 'perfused' or 'not perfused' based on intraoperative fluorescence angiography data. Methods: A classification model with a Resnet architecture was trained on a dataset of fluorescence angiography videos of colorectal resections at a tertiary referral centre. Frames corresponding to fluorescent and non-fluorescent segments of colon were used to train a classification algorithm. Validation using frames from patients not used in the training set was performed, including both data collected using the same equipment and data collected using a different camera. Performance metrics were calculated, and saliency maps used to further analyse the output. A decision boundary was identified based on the tissue classification. Results: A convolutional neural network was successfully trained on 1790 frames from 7 patients and validated in 24 frames from 14 patients. The accuracy on the training set was 100%, on the validation set was 80%. Recall and precision were respectively 100% and 100% on the training set and 68.8% and 91.7% on the validation set. Conclusion: Automated classification of intraoperative fluorescence angiography with a high degree of accuracy is possible and allows automated decision boundary identification. This will enable surgeons to standardise the technique of fluorescence angiography. A web based app was made available to deploy the algorithm.

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arXiv2022

2020 CATARACTS Semantic Segmentation Challenge

Surgical scene segmentation is essential for anatomy and instrument localization which can be further used to assess tissue-instrument interactions during a surgical procedure. In 2017, the Challenge on Automatic Tool Annotation for cataRACT Surgery (CATARACTS) released 50 cataract surgery videos accompanied by instrument usage annotations. These annotations included frame-level instrument presence information. In 2020, we released pixel-wise semantic annotations for anatomy and instruments for 4670 images sampled from 25 videos of the CATARACTS training set. The 2020 CATARACTS Semantic Segmentation Challenge, which was a sub-challenge of the 2020 MICCAI Endoscopic Vision (EndoVis) Challenge, presented three sub-tasks to assess participating solutions on anatomical structure and instrument segmentation. Their performance was assessed on a hidden test set of 531 images from 10 videos of the CATARACTS test set.

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arXiv2021

AutoFB: Automating Fetal Biometry Estimation from Standard Ultrasound Planes

During pregnancy, ultrasound examination in the second trimester can assess fetal size according to standardized charts. To achieve a reproducible and accurate measurement, a sonographer needs to identify three standard 2D planes of the fetal anatomy (head, abdomen, femur) and manually mark the key anatomical landmarks on the image for accurate biometry and fetal weight estimation. This can be a time-consuming operator-dependent task, especially for a trainee sonographer. Computer-assisted techniques can help in automating the fetal biometry computation process. In this paper, we present a unified automated framework for estimating all measurements needed for the fetal weight assessment. The proposed framework semantically segments the key fetal anatomies using state-of-the-art segmentation models, followed by region fitting and scale recovery for the biometry estimation. We present an ablation study of segmentation algorithms to show their robustness through 4-fold cross-validation on a dataset of 349 ultrasound standard plane images from 42 pregnancies. Moreover, we show that the network with the best segmentation performance tends to be more accurate for biometry estimation. Furthermore, we demonstrate that the error between clinically measured and predicted fetal biometry is lower than the permissible error during routine clinical measurements.

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arXiv2021

FetReg: Placental Vessel Segmentation and Registration in Fetoscopy Challenge Dataset

Fetoscopy laser photocoagulation is a widely used procedure for the treatment of Twin-to-Twin Transfusion Syndrome (TTTS), that occur in mono-chorionic multiple pregnancies due to placental vascular anastomoses. This procedure is particularly challenging due to limited field of view, poor manoeuvrability of the fetoscope, poor visibility due to fluid turbidity, variability in light source, and unusual position of the placenta. This may lead to increased procedural time and incomplete ablation, resulting in persistent TTTS. Computer-assisted intervention may help overcome these challenges by expanding the fetoscopic field of view through video mosaicking and providing better visualization of the vessel network. However, the research and development in this domain remain limited due to unavailability of high-quality data to encode the intra- and inter-procedure variability. Through the \textit{Fetoscopic Placental Vessel Segmentation and Registration (FetReg)} challenge, we present a large-scale multi-centre dataset for the development of generalized and robust semantic segmentation and video mosaicking algorithms for the fetal environment with a focus on creating drift-free mosaics from long duration fetoscopy videos. In this paper, we provide an overview of the FetReg dataset, challenge tasks, evaluation metrics and baseline methods for both segmentation and registration. Baseline methods results on the FetReg dataset shows that our dataset poses interesting challenges, offering large opportunity for the creation of novel methods and models through a community effort initiative guided by the FetReg challenge.

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arXiv2021

Deep learning for detection and segmentation of artefact and disease instances in gastrointestinal endoscopy

The Endoscopy Computer Vision Challenge (EndoCV) is a crowd-sourcing initiative to address eminent problems in developing reliable computer aided detection and diagnosis endoscopy systems and suggest a pathway for clinical translation of technologies. Whilst endoscopy is a widely used diagnostic and treatment tool for hollow-organs, there are several core challenges often faced by endoscopists, mainly: 1) presence of multi-class artefacts that hinder their visual interpretation, and 2) difficulty in identifying subtle precancerous precursors and cancer abnormalities. Artefacts often affect the robustness of deep learning methods applied to the gastrointestinal tract organs as they can be confused with tissue of interest. EndoCV2020 challenges are designed to address research questions in these remits. In this paper, we present a summary of methods developed by the top 17 teams and provide an objective comparison of state-of-the-art methods and methods designed by the participants for two sub-challenges: i) artefact detection and segmentation (EAD2020), and ii) disease detection and segmentation (EDD2020). Multi-center, multi-organ, multi-class, and multi-modal clinical endoscopy datasets were compiled for both EAD2020 and EDD2020 sub-challenges. The out-of-sample generalization ability of detection algorithms was also evaluated. Whilst most teams focused on accuracy improvements, only a few methods hold credibility for clinical usability. The best performing teams provided solutions to tackle class imbalance, and variabilities in size, origin, modality and occurrences by exploring data augmentation, data fusion, and optimal class thresholding techniques.

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