Moona Mazher

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19ranked-venue papers
1as first author
19since 2021 · last 2026
0000-0003-4444-5776ORCID · verified

Domains — the database's venue-derived domains; a paper can count in several

Applied, interdisciplinary, general and emerging computing · 16 · 16 since 2021Artificial intelligence and machine learning · 3 · 1 first-author · 3 since 2021Computer networks · 1 · 1 since 2021Databases, data management, data science and information retrieval · 1 · 1 since 2021Graphics, computer vision, multimedia, augmented reality and games · 1 · 1 since 2021
YearPublicationVenuePosition
2026 SegRap2025: A benchmark of gross tumor volume and lymph node clinical target volume Segmentation for Radiotherapy Planning of nasopharyngeal carcinoma
Litingyu Wang, Chenyuan Bian, Zijun Gao, Chunbin Gu, Xin Weng, Jianghao Wu 0001, Yicheng Wu 0001, Jin Ye 0002, Linhao Li, Yiwen Ye, Yong Xia 0001, Elias Tappeiner, Abdul Qayyum 0002, Moona Mazher, Steven A. Niederer, Junqiang Chen, Chuanyi Huang, Lisheng Wang, Zhaohu Xing, Hongqiu Wang, Lei Zhu 0003, Shichuan Zhang, Shaoting Zhang 0001, Wenjun Liao, Guotai Wang
Medical Image Anal.19
2026 Multi-class segmentation of aortic branches and zones in computed tomography angiography: The AortaSeg24 challenge
Muhammad Imran 0013, Jonathan R. Krebs, Vishal Balaji Sivaraman, Amarjeet Kumar, Walker R. Ueland, Michael J. Fassler, Lisheng Wang, Maximilian Rokuss, Michael Baumgartner 0001, Yannick Kirchhof, Klaus H. Maier-Hein, Fabian Isensee, Shuolin Liu, Bong Thanh Nguyen, Dong-jin Shin, Park Ji-Woo, Matthew Choi, Kwang-Hyun Uhm, Sung-Jea Ko, Chanwoong Lee, Jaehee Chun, Yun Gu, Zhaohong Pan, Xiaokun Liang, Markus Tiefenthaler, Enrique Almar-Munoz, Matthias Schwab, Mikhail Kotyushev, Rostislav Epifanov, Marek Wodzinski, Henning Müller, Abdul Qayyum 0002, Moona Mazher, Steven A. Niederer, Zhiwei Wang 0002, Kaixiang Yang 0004, Jintao Ren, Stine Sofia Korreman, Yuchong Gao, Hongye Zeng, Jinghua Yue, Fugen Zhou, Alexander Cosman, Muxuan Liang, Gilbert R. Upchurch Jr., Yuyin Zhou, Michol A. Cooper, Wei Shao 0008
Medical Image Anal.44
2026 Extreme cardiac MRI analysis under respiratory motion: Results of the CMRxMotion challenge
Kang Wang 0017, Chen Qin, Zhang Shi, Haoran Wang 0009, Chen Chen 0042, Cheng Ouyang, Chengliang Dai, Yuanhan Mo, Chenchen Dai, Xutong Kuang, Ruizhe Li 0005, Xin Chen 0003, Xiuzheng Yue, Song Tian, Alejandro Mora-Rubio, Kumaradevan Punithakumar, Shizhan Gong, Qi Dou 0001, Sina Amirrajab, Yasmina Alkhalil, Cian M. Scannell, Lexiaozi Fan, Huili Yang, Xiaowu Sun, Rob J. van der Geest, Tewodros Weldebirhan Arega, Fabrice Mériaudeau, Caner Ozer, Amin Ranem, John Kalkhof, Ilkay Öksüz, Anirban Mukhopadhyay 0003, Abdul Qayyum 0002, Moona Mazher, Steven A. Niederer, Carles García-Cabrera, Eric Arazo Sanchez, Michal K. Grzeszczyk, Szymon Plotka, Wanqin Ma, Xiaomeng Li 0001, Rongjun Ge, Yongqing Kou, Xinrong Chen, He Wang 0016, Chengyan Wang, Wenjia Bai, Shuo Wang 0011
Medical Image Anal.35
2026 MBAS2024: A large-scale benchmark for multi-class bi-atrial segmentation in multi-center contrast-enhanced MRIs
abstract
Atrial fibrillation (AF), the most common cardiac arrhythmia, affects one in three adults over 45 years of age. Improving its treatment requires a better understanding of bi-atrial anatomy. Existing benchmarks have focused on the left atrial (LA) cavity, overlooking the fundamental challenges posed by bi-atrial anatomy, most notably the thin atrial walls, which are critical for substrate-guided ablation planning in patients with atrial fibrillation. To address these limitations, the Multi-class Bi-Atrial Segmentation 2024 Challenge (MBAS2024) introduced the first large-scale, multi-class benchmark for simultaneous segmentation of the LA cavity, right atrial (RA) cavity, and bi-atrial walls from late gadolinium-enhanced (LGE) MRI. We systematically evaluated 13 state-of-the-art methods on the world's largest curated bi-atrial dataset, comprising 175 3D multi-center scans with expert-validated annotations, providing a comprehensive assessment of current methodological capabilities and limitations. Key findings include: segmentation of the LA and RA cavities is generally robust to image quality, whereas atrial wall delineation is highly sensitive to image degradation. Performance varies across centers, indicating limited generalization of atrial wall segmentation across different acquisition protocols. Model architecture, rather than hyperparameter tuning, is the primary driver of performance, with U-Net-based models and emerging state-space models (e.g., UMambaBot) achieving higher accuracy at modest computational cost. Segmentation accuracy also varies along the slice dimension, with central slices segmented more reliably. Finally, hybrid labeling strategies-separating LA and RA cavities while merging bi-atrial walls into a single class-consistently improve performance. The MBAS2024 challenge establishes a foundational benchmark for bi-atrial segmentation, providing validated baselines and actionable insights to guide the development of clinically relevant, efficient, and anatomically aware segmentation algorithms to improve targeted ablation in patients with AF.
Fangqiang Xu, James Kennelly, Alexander M. Zolotarev, Caroline H. Roney, Michal Nohel, Constantin Ulrich, Bryan Anenberg, Peter Chang, Yu Hon On, Marta Varela, Claas Thesing, Abhirup Banerjee, Enrique Almar-Munoz, Markus Tiefenthaler, Susana Merino-Caviedes, Emmanuel C. Nnadozie, Abdul Qayyum 0002, Moona Mazher, Waqas Anwaar, Wufeng Xue, Jingsu Kang, Lucas Beveridge, Malitha Gunawardhana, Kunihiko Kiuchi, Martin K. Stiles, Jichao Zhao
Medical Image Anal.18
2026 Advances in automated fetal brain MRI segmentation and biometry: Insights from the FeTA 2024 challenge
abstract
Accurate fetal brain tissue segmentation and biometric measurement are essential for monitoring neurodevelopment and detecting abnormalities in utero. The Fetal Tissue Annotation (FeTA) Challenges have established robust multi-center benchmarks for evaluating state-of-the-art segmentation methods. This paper presents the results of the 2024 challenge edition, which introduced three key innovations. First, we introduced a topology-aware metric based on the Euler characteristic difference (ED) to overcome the performance plateau observed with traditional metrics like Dice or Hausdorff distance (HD), as the performance of the best models in segmentation surpassed the inter-rater variability. While the best teams reached similar scores in Dice (0.81-0.82) and HD95 (2.1-2.3 mm), ED provided greater discriminative power: the winning method achieved an ED of 20.9, representing roughly a 50% improvement over the second- and third-ranked teams despite comparable Dice scores. Second, we introduced a new 0.55T low-field MRI test set, which, when paired with high-quality super-resolution reconstruction, achieved the highest segmentation performance across all test cohorts (Dice=0.86, HD95=1.69, ED=6.26). This provides the first quantitative evidence that low-cost, low-field MRI can match or surpass high-field systems in automated fetal brain segmentation. Third, the new biometry estimation task exposed a clear performance gap: although the best model reached a mean average percentage error (MAPE) of 7.72%, most submissions failed to outperform a simple gestational-age-based linear regression model (MAPE=9.56%), and all remained above inter-rater variability with a MAPE of 5.38%. Finally, by analyzing the top-performing models from FeTA 2024 alongside those from previous challenge editions, we identify ensembles of 3D nnU-Net trained on both real and synthetic data with both image- and anatomy-level augmentations as the most effective approaches for fetal brain segmentation. Our quantitative analysis reveals that acquisition site, super-resolution strategy, and image quality are the primary sources of domain shift, informing recommendations to enhance the robustness and generalizability of automated fetal brain analysis methods.
Vladyslav Zalevskyi, Thomas Sanchez, Misha P. T. Kaandorp, Margaux Roulet, Diego Fajardo-Rojas, Liu Li 0001, Jana Hutter, Hongwei Li 0004, Matthew J. Barkovich, Luca Wilhelmi, Aline Dändliker, Céline Steger, Mériam Koob, Yvan Gomez, Anton Jakovcic, Melita Klaic, Ana Adzic, Pavel Markovic, Gracia Grabaric, Milan Rados, Jordina Aviles Verdera, Gregor Kasprian, Gregor Dovjak, Raphael Gaubert-Rachmühl, Maurice Aschwanden, Davood Karimi, Denis Peruzzo, Tommaso Ciceri, Giorgio Longari, Rachika E. Hamadache, Amina Bouzid, Xavier Lladó, Simone Chiarella, Gerard Martí-Juan, Miguel Ángel González Ballester, Marco Castellaro, Marco Pinamonti, Valentina Visani, Robin Cremese, Keïn Sam, Fleur Gaudfernau, Param Ahir, Mehul Parikh, Maximilian Zenk, Michael Baumgartner 0001, Klaus H. Maier-Hein, Li Tianhong, Zhao Longfei, Domen Preloznik, Ziga Spiclin, Jae Won Choi, Guotai Wang, Lyuyang Tong, Bo Du 0001, Andrea Gondova, Sungmin You, Kiho Im, Abdul Qayyum 0002, Moona Mazher, Steven A. Niederer, András Jakab, Roxane Licandro, Kelly Payette, Meritxell Bach Cuadra
Medical Image Anal.65
2026 Two-Stage Self-Supervised Contrastive Learning Aided Transformer for Real-Time Medical Image Segmentation
abstract
The availability of large, high-quality annotated datasets in the medical domain poses a substantial challenge in segmentation tasks. To mitigate the reliance on annotated training data, self-supervised pre-training strategies have emerged, particularly employing contrastive learning methods on dense pixel-level representations. In this work, we proposed to capitalize on intrinsic anatomical similarities within medical image data and develop a semantic segmentation framework through a self-supervised fusion network, where the availability of annotated volumes is limited. In a unified training phase, we combine segmentation loss with contrastive loss, enhancing the distinction between significant anatomical regions that adhere to the available annotations. To further improve the segmentation performance, we introduce an efficient parallel transformer module that leverages Multiview multiscale feature fusion and depth-wise features. The proposed transformer architecture, based on multiple encoders, is trained in a self-supervised manner using contrastive loss. Initially, the transformer is trained using an unlabeled dataset. We then fine-tune one encoder using data from the first stage and another encoder using a small set of annotated segmentation masks. These encoder features are subsequently concatenated for the purpose of brain tumor segmentation. The multiencoder-based transformer model yields significantly better outcomes across three medical image segmentation tasks. We validated our proposed solution by fusing images across diverse medical image segmentation challenge datasets, demonstrating its efficacy by outperforming state-of-the-art methodologies.
Abdul Qayyum 0002, Muhammad Imran Razzak, Moona Mazher, Tariq Mahmood Khan, Weiping Ding 0001, Steven A. Niederer
IEEE J. Biomed. Health Informatics3
2025 PitVis-2023 challenge: Workflow recognition in videos of endoscopic pituitary surgery
abstract
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 or during live surgery. The Pituitary Vision (PitVis) 2023 Challenge tasks the community to step and instrument recognition in videos of endoscopic pituitary surgery. This is a particularly challenging 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. The top performing model for step recognition utilised a transformer based architecture, uniquely using an autoregressive decoder with a positional encoding input. The top performing model for instrument recognition utilised a spatial encoder followed by a temporal encoder, which uniquely used a 2-layer temporal architecture. In both cases, these models outperformed purely spatial based models, illustrating the importance of sequential and temporal information. This PitVis-2023 therefore demonstrates state-of-the-art computer vision models in minimally invasive surgery are transferable to a new dataset. Benchmark results are provided in the paper, and the dataset is publicly available at: https://doi.org/10.5522/04/26531686.
Adrito Das, Danyal Z. Khan, Dimitris Psychogyios, John G. Hanrahan, Francisco Vasconcelos 0001, You Pang, Zhen Chen 0018, Jinlin Wu, Xiaoyang Zou, Guoyan Zheng, Abdul Qayyum 0002, Moona Mazher, Muhammad Imran Razzak, Tianbin Li, Jin Ye 0002, Junjun He, Szymon Plotka, Joanna Kaleta, Amine Yamlahi, Antoine Jund, Patrick Godau, Satoshi Kondo, Satoshi Kasai, Kousuke Hirasawa, Dominik Rivoir, Stefanie Speidel, Alejandra Pérez, Santiago Rodríguez, Pablo Andrés Arbeláez, Danail Stoyanov, Hani J. Marcus, Sophia Bano
Medical Image Anal.13
2025 Multi-Center Fetal Brain Tissue Annotation (FeTA) Challenge 2022 Results
abstract
Segmentation is a critical step in analyzing the developing human fetal brain. There have been vast improvements in automatic segmentation methods in the past several years, and the Fetal Brain Tissue Annotation (FeTA) Challenge 2021 helped to establish an excellent standard of fetal brain segmentation. However, FeTA 2021 was a single center study, limiting real-world clinical applicability and acceptance. The multi-center FeTA Challenge 2022 focused on advancing the generalizability of fetal brain segmentation algorithms for magnetic resonance imaging (MRI). In FeTA 2022, the training dataset contained images and corresponding manually annotated multi-class labels from two imaging centers, and the testing data contained images from these two centers as well as two additional unseen centers. The multi-center data included different MR scanners, imaging parameters, and fetal brain super-resolution algorithms applied. 16 teams participated and 17 algorithms were evaluated. Here, the challenge results are presented, focusing on the generalizability of the submissions. Both in- and out-of-domain, the white matter and ventricles were segmented with the highest accuracy (Top Dice scores: 0.89, 0.87 respectively), while the most challenging structure remains the grey matter (Top Dice score: 0.75) due to anatomical complexity. The top 5 average Dices scores ranged from 0.81-0.82, the top 5 average percentile Hausdorff distance values ranged from 2.3-2.5mm, and the top 5 volumetric similarity scores ranged from 0.90-0.92. The FeTA Challenge 2022 was able to successfully evaluate and advance generalizability of multi-class fetal brain tissue segmentation algorithms for MRI and it continues to benchmark new algorithms.
Kelly Payette, Céline Steger, Roxane Licandro, Priscille de Dumast, Hongwei Li 0004, Matthew J. Barkovich, Liu Li 0001, Maik Dannecker, Chen Chen 0042, Cheng Ouyang, Niccolò McConnell, Alina Dana Miron, Yongmin Li 0001, Alena Uus, Irina Grigorescu, Paula Ramirez Gilliland, Md Mahfuzur Rahman Siddiquee, Daguang Xu, Andriy Myronenko, Haoyu Wang 0010, Ziyan Huang, Jin Ye 0002, Mireia Alenyà, Valentin Comte, Oscar Camara 0001, Jean-Baptiste Masson, Astrid Nilsson, Charlotte Godard, Moona Mazher, Abdul Qayyum 0002, Yibo Gao, Hangqi Zhou, Shangqi Gao, Guiming Dong, Guotai Wang, ZunHyan Rieu, HyeonSik Yang, Szymon Plotka, Michal K. Grzeszczyk, Arkadiusz Sitek, Luisa Vargas Daza, Santiago Usma, Pablo Andrés Arbeláez, Wenying Lu, Romain Valabrègue, Anand A. Joshi, Krishna N. Nayak, Richard M. Leahy, Luca Wilhelmi, Aline Dändliker, Antonio G. Gennari, Anton Jakovcic, Melita Klaic, Ana Adzic, Pavel Markovic, Gracia Grabaric, Gregor Kasprian, Gregor Dovjak, Milan Rados, Lana Vasung, Meritxell Bach Cuadra, András Jakab
IEEE Trans. Medical Imaging29
2024 Federated Focal Modulated UNet for Cardiovascular Image Segmentation
abstract
Federated learning facilitates collaborative training of machine learning models on data distributed across multiple locations, effectively addressing the privacy concerns by eliminating the need for data centralization—a critical consideration in medical image analysis. In healthcare applications like cardiovascular segmentation, datasets from individual sites often feature annotations for specific heart regions, leading to partial overlaps. To address this challenge, we present a two-step partial annotation framework for federated learning, featuring a hybrid 3D multi-encoding UNet enhanced with focal modulation layers in the second stage. This architecture enables specialized subnetworks to act as experts, extracting features tailored to specific regions of interest based on each client’s data. To further improve feature extraction and differentiation, we incorporate focal modulation blocks and apply regularization by introducing an auxiliary generic decoder during training. Comprehensive experiments on diverse cardiac MRI datasets demonstrate that our approach significantly outperforms centralized learning models.
Mohammad Asjad, Abdul Qayyum 0002, Moona Mazher, Usman Naseem, Tariq Mahmood Khan, Steven A. Niederer, Muhammad Imran Razzak
IEEE Big Data3
2024 Placental vessel segmentation and registration in fetoscopy: Literature review and MICCAI FetReg2021 challenge findings
abstract
Fetoscopy laser photocoagulation is a widely adopted procedure for treating Twin-to-Twin Transfusion Syndrome (TTTS). The procedure involves photocoagulation pathological anastomoses to restore a physiological blood exchange among twins. The procedure is particularly challenging, from the surgeon's side, due to the limited field of view, poor manoeuvrability of the fetoscope, poor visibility due to amniotic fluid turbidity, and variability in illumination. These challenges may lead to increased surgery time and incomplete ablation of pathological anastomoses, resulting in persistent TTTS. Computer-assisted intervention (CAI) can provide TTTS 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 (EndoVis) challenge, we released the first large-scale multi-center TTTS dataset for the development of generalized and robust semantic segmentation and video mosaicking algorithms with a focus on creating drift-free mosaics from long duration fetoscopy videos. 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 of an average length of 411 frames for developing placental scene segmentation and frame registration for mosaicking techniques. 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. For the segmentation task, overall baseline performed was the top performing (aggregated mIoU of 0.6763) and was the best on the vessel class (mIoU of 0.5817) while team RREB was the best on the tool (mIoU of 0.6335) and fetus (mIoU of 0.5178) classes. For the registration task, overall the baseline performed better than team SANO with an overall mean 5-frame SSIM of 0.9348. Qualitatively, it was observed that team SANO performed better in planar scenarios, while baseline was better in non-planner scenarios. The detailed analysis showed that no single team outperformed on all 6 test fetoscopic videos. The challenge provided an opportunity to create 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-center fetoscopic data, we provide a benchmark for future research in this field.
Sophia Bano, Alessandro Casella, Francisco Vasconcelos 0001, Abdul Qayyum 0002, Abdessalam Benzinou, Moona Mazher, Fabrice Mériaudeau, Chiara Lena, Ilaria A. Cintorrino, Gaia Romana De Paolis, Jessica Biagioli, Daria Grechishnikova, Jing Jiao, Bizhe Bai, Yanyan Qiao, Binod Bhattarai, Rebati Raman Gaire, Ronast Subedi, Eduard Vazquez, Szymon Plotka, Aneta Lisowska, Arkadiusz Sitek, George Attilakos, Ruwan Wimalasundera, Anna L. David, Dario Paladini, Jan Deprest, Elena De Momi, Leonardo S. Mattos, Sara Moccia, Danail Stoyanov
Medical Image Anal.6
2024 Hunting imaging biomarkers in pulmonary fibrosis: Benchmarks of the AIIB23 challenge
abstract
• This paper investigates the capacity of AI models for airway modelling on national datasets with paired clinical metadata. • We evaluated AI models against unharmonised, noisy, and out-of-distribution data, as well as the prognostication for FLD. • We found a new biomarker for mortality prediction, outperforming existing clinical measurements (FVC% and fibrosis scores). • In-depth analysis of AI models on airway modelling and prognosis, highlighting challenges and future research directions. Airway-related quantitative imaging biomarkers are crucial for examination, diagnosis, and prognosis in pulmonary diseases. However, the manual delineation of airway structures remains prohibitively time-consuming. While significant efforts have been made towards enhancing automatic airway modelling, current public-available datasets predominantly concentrate on lung diseases with moderate morphological variations. The intricate honeycombing patterns present in the lung tissues of fibrotic lung disease patients exacerbate the challenges, often leading to various prediction errors. To address this issue, the 'Airway-Informed Quantitative CT Imaging Biomarker for Fibrotic Lung Disease 2023′ (AIIB23) competition was organized in conjunction with the official 2023 International Conference on Medical Image Computing and Computer Assisted Intervention (MICCAI). The airway structures were meticulously annotated by three experienced radiologists. Competitors were encouraged to develop automatic airway segmentation models with high robustness and generalization abilities, followed by exploring the most correlated QIB of mortality prediction. A training set of 120 high-resolution computerised tomography (HRCT) scans were publicly released with expert annotations and mortality status. The online validation set incorporated 52 HRCT scans from patients with fibrotic lung disease and the offline test set included 140 cases from fibrosis and COVID-19 patients. The results have shown that the capacity of extracting airway trees from patients with fibrotic lung disease could be enhanced by introducing voxel-wise weighted general union loss and continuity loss. In addition to the competitive image biomarkers for mortality prediction, a strong airway-derived biomarker (Hazard ratio>1.5, p < 0.0001) was revealed for survival prognostication compared with existing clinical measurements, clinician assessment and AI-based biomarkers.
Yang Nan 0002, Xiaodan Xing, Zeyu Tang 0001, Federico Felder, Sheng Zhang 0024, Roberta Eufrasia Ledda, Xiaoliu Ding, Feng Shi 0001, Tianyang Sun, Zehong Cao, Yun Gu, Pingyu Wang, Wen Tang 0005, Pengxin Yu, Han Kang, Junqiang Chen, Michail Mamalakis, Francesco Prinzi, Gianluca Carlini, Lisa Cuneo, Abhirup Banerjee, Zhaohu Xing, Lei Zhu 0003, Zacharia Mesbah, Dhruv Jain, Tsiry Mayet, Hongyu Yuan, Qing Lyu 0009, Abdul Qayyum 0002, Moona Mazher, Athol Wells, Simon Walsh, Guang Yang 0006
Medical Image Anal.38
2024 3D-IncNet: Head and Neck (H&N) Primary Tumors Segmentation and Survival Prediction
abstract
Cancer begins when healthy cells change and grow out of control, forming a mass called a tumor. Head and neck (H&N) cancers usually develop in or around the head and neck, including the mouth (oral cavity), nose and sinuses, throat (pharynx), and voice box (larynx). 4% of all cancers are H&N cancers with a very low survival rate (a five-year survival rate of 64.7%). FDG-PET/CT imaging is often used for early diagnosis and staging of H&N tumors, thus improving these patients' survival rates. This work presents a novel 3D-Inception-Residual aided with 3D depth-wise convolution and squeeze and excitation block. We introduce a 3D depth-wise convolution-inception encoder consisting of an additional 3D squeeze and excitation block and a 3D depth-wise convolution-based residual learning decoder (3D-IncNet), which not only helps to recalibrate the channel-wise features but adaptively through explicit inter-dependencies modeling but also integrate the coarse and fine features resulting in accurate tumor segmentation. We further demonstrate the effectiveness of inception-residual encoder-decoder architecture in achieving better dice scores and the impact of depth-wise convolution in lowering the computational cost. We applied random forest for survival prediction on deep, clinical, and radiomics features. Experiments are conducted on the benchmark HECKTOR21 challenge, which showed significantly better performance by surpassing the state-of-the-artwork and achieved 0.836 and 0.811 concordance index and dice scores, respectively. We made the model and code publicly available.
Abdul Qayyum 0002, Abdessalam Benzinou, Muhammad Imran Razzak, Moona Mazher, Thanh Thi Nguyen 0001, Domenec Puig, Fatemeh Vafaee
IEEE J. Biomed. Health Informatics4
2024 Spontaneous Facial Behavior Analysis Using Deep Transformer-based Framework for Child-computer Interaction
abstract
A fascinating challenge in robotics-human interaction is imitating the emotion recognition capability of humans to robots with the aim to make human-robotics interaction natural, genuine and intuitive. To achieve the natural interaction in affective robots, human-machine interfaces, and autonomous vehicles, understanding our attitudes and opinions is very important, and it provides a practical and feasible path to realize the connection between machine and human. Multimodal interface that includes voice along with facial expression can manifest a large range of nuanced emotions compared to purely textual interfaces and provide a great value to improve the intelligence level of effective communication. Interfaces that fail to manifest or ignore user emotions may significantly impact the performance and risk being perceived as cold, socially inept, untrustworthy, and incompetent. To equip a child well for life, we need to help our children identify their feelings, manage them well, and express their needs in healthy, respectful, and direct ways. Early identification of emotional deficits can help to prevent low social functioning in children. In this work, we analyzed the child’s spontaneous behavior using multimodal facial expression and voice signal presenting multimodal transformer-based last feature fusion for facial behavior analysis in children to extract contextualized representations from RGB video sequence and Hematoxylin and eosin video sequence and then using these representations followed by pairwise concatenations of contextualized representations using cross-feature fusion technique to predict users emotions. To validate the performance of the proposed framework, we have performed experiments with the different pairwise concatenations of contextualized representations that showed significantly better performance than state-of-the-art method. Besides, we perform t-distributed stochastic neighbor embedding visualization to visualize the discriminative feature in lower dimension space and probability density estimation to visualize the prediction capability of our proposed model.
Abdul Qayyum 0002, Muhammad Imran Razzak, Muhammad Tanveer 0001, Moona Mazher
ACM Trans. Multim. Comput. Commun. Appl.4
2023 Fetal brain tissue annotation and segmentation challenge results
abstract
In-utero fetal MRI is emerging as an important tool in the diagnosis and analysis of the developing human brain. Automatic segmentation of the developing fetal brain is a vital step in the quantitative analysis of prenatal neurodevelopment both in the research and clinical context. However, manual segmentation of cerebral structures is time-consuming and prone to error and inter-observer variability. Therefore, we organized the Fetal Tissue Annotation (FeTA) Challenge in 2021 in order to encourage the development of automatic segmentation algorithms on an international level. The challenge utilized FeTA Dataset, an open dataset of fetal brain MRI reconstructions segmented into seven different tissues (external cerebrospinal fluid, gray matter, white matter, ventricles, cerebellum, brainstem, deep gray matter). 20 international teams participated in this challenge, submitting a total of 21 algorithms for evaluation. In this paper, we provide a detailed analysis of the results from both a technical and clinical perspective. All participants relied on deep learning methods, mainly U-Nets, with some variability present in the network architecture, optimization, and image pre- and post-processing. The majority of teams used existing medical imaging deep learning frameworks. The main differences between the submissions were the fine tuning done during training, and the specific pre- and post-processing steps performed. The challenge results showed that almost all submissions performed similarly. Four of the top five teams used ensemble learning methods. However, one team's algorithm performed significantly superior to the other submissions, and consisted of an asymmetrical U-Net network architecture. This paper provides a first of its kind benchmark for future automatic multi-tissue segmentation algorithms for the developing human brain in utero.
Kelly Payette, Hongwei Li 0004, Priscille de Dumast, Roxane Licandro, Md Mahfuzur Rahman Siddiquee, Daguang Xu, Andriy Myronenko, Yuchen Pei, Lisheng Wang, Juanying Xie, Huiquan Zhang, Guiming Dong, Hao Fu 0014, Guotai Wang, ZunHyan Rieu, Hyun Gi Kim, Davood Karimi, Ali Gholipour, Helena R. Torres, Bruno Oliveira 0002, João L. Vilaça, Netanell Avisdris, Ori Ben-Zvi, Dafna Ben-Bashat, Lucas Fidon, Michael Aertsen, Tom Vercauteren, Daniel Sobotka, Georg Langs, Mireia Alenyà, Maria Inmaculada Villanueva, Oscar Camara 0001, Bella Specktor-Fadida, Leo Joskowicz, Liao Weibin, Lv Yi, Xuesong Li 0003, Moona Mazher, Abdul Qayyum 0002, Domenec Puig, Hamza Kebiri, KuanLun Liao, YiXuan Wu, JinTai Chen, Yunzhi Xu, Lana Vasung, Bjoern Menze, Meritxell Bach Cuadra, András Jakab
Medical Image Anal.43
2023 Multi-site, Multi-domain Airway Tree Modeling
Yangqian Wu, Yulei Qin, Hao Zheng 0008, Wen Tang 0005, Corey W. Arnold, Chenhao Pei, Pengxin Yu, Yang Nan 0002, Guang Yang 0006, Simon Walsh, Dominic C. Marshall, Matthieu Komorowski, Puyang Wang, Dazhou Guo, Dakai Jin, Shuiqing Zhao, Runsheng Chang, Abdul Qayyum 0002, Moona Mazher, Yonghuang Wu, Ying'ao Liu, Jiancheng Yang, Ashkan Pakzad, Bojidar Rangelov, Raúl San José Estépar, Carlos Cano-Espinosa, Jiayuan Sun, Guang-Zhong Yang, Yun Gu
Medical Image Anal.24
2023 High-Density Electroencephalography and Speech Signal Based Deep Framework for Clinical Depression Diagnosis
abstract
Depression is a mental disorder characterized by persistent depressed mood or loss of interest in performing activities, causing significant impairment in daily routine. Possible causes include psychological, biological, and social sources of distress. Clinical depression is the more-severe form of depression, also known as major depression or major depressive disorder. Recently, electroencephalography and speech signals have been used for early diagnosis of depression; however, they focus on moderate or severe depression. We have combined audio spectrogram and multiple frequencies of EEG signals to improve diagnostic performance. To do so, we have fused different levels of speech and EEG features to generate descriptive features and applied vision transformers and various pre-trained networks on the speech and EEG spectrum. We have conducted extensive experiments on Multimodal Open Dataset for Mental-disorder Analysis (MODMA) dataset, which showed significant improvement in performance in depression diagnosis (0.972,0.973and0.973precision, recall and F1 score respectively) for patients at the mild stage. Besides, we provided a web-based framework using Flask and provided the source code publicly.1
Abdul Qayyum 0002, Muhammad Imran Razzak, Muhammad Tanveer 0001, Moona Mazher, Bandar Alhaqbani
IEEE ACM Trans. Comput. Biol. Bioinform.4
2023 Deep Learning Segmentation of the Right Ventricle in Cardiac MRI: The M&Ms Challenge
abstract
In recent years, several deep learning models have been proposed to accurately quantify and diagnose cardiac pathologies. These automated tools heavily rely on the accurate segmentation of cardiac structures in MRI images. However, segmentation of the right ventricle is challenging due to its highly complex shape and ill-defined borders. Hence, there is a need for new methods to handle such structure's geometrical and textural complexities, notably in the presence of pathologies such as Dilated Right Ventricle, Tricuspid Regurgitation, Arrhythmogenesis, Tetralogy of Fallot, and Inter-atrial Communication. The last MICCAI challenge on right ventricle segmentation was held in 2012 and included only 48 cases from a single clinical center. As part of the 12th Workshop on Statistical Atlases and Computational Models of the Heart (STACOM 2021), the M&Ms-2 challenge was organized to promote the interest of the research community around right ventricle segmentation in multi-disease, multi-view, and multi-center cardiac MRI. Three hundred sixty CMR cases, including short-axis and long-axis 4-chamber views, were collected from three Spanish hospitals using nine different scanners from three different vendors, and included a diverse set of right and left ventricle pathologies. The solutions provided by the participants show that nnU-Net achieved the best results overall. However, multi-view approaches were able to capture additional information, highlighting the need to integrate multiple cardiac diseases, views, scanners, and acquisition protocols to produce reliable automatic cardiac segmentation algorithms.
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IEEE J. Biomed. Health Informatics18
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