Arcot Sowmya

Jianning Li, Zongwei Zhou, Jiancheng Yang et al.

Prior to the deep learning era, shape was commonly used to describe the objects. Nowadays, state-of-the-art (SOTA) algorithms in medical imaging are predominantly diverging from computer vision, where voxel grids, meshes, point clouds, and implicit surface models are used. This is seen from numerous shape-related publications in premier vision conferences as well as the growing popularity of ShapeNet (about 51,300 models) and Princeton ModelNet (127,915 models). For the medical domain, we present a large collection of anatomical shapes (e.g., bones, organs, vessels) and 3D models of surgical instrument, called MedShapeNet, created to facilitate the translation of data-driven vision algorithms to medical applications and to adapt SOTA vision algorithms to medical problems. As a unique feature, we directly model the majority of shapes on the imaging data of real patients. As of today, MedShapeNet includes 23 dataset with more than 100,000 shapes that are paired with annotations (ground truth). Our data is freely accessible via a web interface and a Python application programming interface (API) and can be used for discriminative, reconstructive, and variational benchmarks as well as various applications in virtual, augmented, or mixed reality, and 3D printing. Exemplary, we present use cases in the fields of classification of brain tumors, facial and skull reconstructions, multi-class anatomy completion, education, and 3D printing. In future, we will extend the data and improve the interfaces. The project pages are: https://medshapenet.ikim.nrw/ and https://github.com/Jianningli/medshapenet-feedback

Annette Spooner, Gelareh Mohammadi, Perminder S. Sachdev et al.

Healthcare datasets present many challenges to both machine learning and statistics as their data are typically heterogeneous, censored, high-dimensional and have missing information. Feature selection is often used to identify the important features but can produce unstable results when applied to high-dimensional data, selecting a different set of features on each iteration. The stability of feature selection can be improved with the use of feature selection ensembles, which aggregate the results of multiple base feature selectors. A threshold must be applied to the final aggregated feature set to separate the relevant features from the redundant ones. A fixed threshold, which is typically applied, offers no guarantee that the final set of selected features contains only relevant features. This work develops several data-driven thresholds to automatically identify the relevant features in an ensemble feature selector and evaluates their predictive accuracy and stability. To demonstrate the applicability of these methods to clinical data, they are applied to data from two real-world Alzheimer's disease (AD) studies. AD is a progressive neurodegenerative disease with no known cure, that begins at least 2-3 decades before overt symptoms appear, presenting an opportunity for researchers to identify early biomarkers that might identify patients at risk of developing AD. Features identified by applying these methods to both datasets reflect current findings in the AD literature.

Raktim Kumar Mondol, Ewan K. A. Millar, Peter H Graham et al.

Gene expression can be used to subtype breast cancer with improved prediction of risk of recurrence and treatment responsiveness over that obtained using routine immunohistochemistry (IHC). However, in the clinic, molecular profiling is primarily used for ER+ breast cancer, which is costly, tissue destructive, requires specialized platforms and takes several weeks to obtain a result. Deep learning algorithms can effectively extract morphological patterns in digital histopathology images to predict molecular phenotypes quickly and cost-effectively. We propose a new, computationally efficient approach called hist2RNA inspired by bulk RNA-sequencing techniques to predict the expression of 138 genes (incorporated from six commercially available molecular profiling tests), including luminal PAM50 subtype, from hematoxylin and eosin (H&E) stained whole slide images (WSIs). The training phase involves the aggregation of extracted features for each patient from a pretrained model to predict gene expression at the patient level using annotated H&E images from The Cancer Genome Atlas (TCGA, n=335). We demonstrate successful gene prediction on a held-out test set (n = 160, corr = 0.82 across patients, corr = 0.29 across genes) and perform exploratory analysis on an external tissue microarray (TMA) dataset (n = 498) with known IHC and survival information. Our model is able to predict gene expression and luminal PAM50 subtype (Luminal A versus Luminal B) on the TMA dataset with prognostic significance for overall survival in univariate analysis (c-index = 0.56, hazard ratio = 2.16 (95% CI 1.12-3.06), p < 5 x 10-3), and independent significance in multivariate analysis incorporating standard clinicopathological variables (c-index = 0.65, hazard ratio = 1.85 (95% CI 1.30-2.68), p < 5 x 10-3).

Annette Spooner, Gelareh Mohammadi, Perminder S. Sachdev et al.

Healthcare datasets often contain groups of highly correlated features, such as features from the same biological system. When feature selection is applied to these datasets to identify the most important features, the biases inherent in some multivariate feature selectors due to correlated features make it difficult for these methods to distinguish between the important and irrelevant features and the results of the feature selection process can be unstable. Feature selection ensembles, which aggregate the results of multiple individual base feature selectors, have been investigated as a means of stabilising feature selection results, but do not address the problem of correlated features. We present a novel framework to create feature selection ensembles from multivariate feature selectors while taking into account the biases produced by groups of correlated features, using agglomerative hierarchical clustering in a pre-processing step. These methods were applied to two real-world datasets from studies of Alzheimer's disease (AD), a progressive neurodegenerative disease that has no cure and is not yet fully understood. Our results show a marked improvement in the stability of features selected over the models without clustering, and the features selected by these models are in keeping with the findings in the AD literature.

Louisa Canepa, Sonit Singh, Arcot Sowmya

Medical visual question answering (Med-VQA) is a machine learning task that aims to create a system that can answer natural language questions based on given medical images. Although there has been rapid progress on the general VQA task, less progress has been made on Med-VQA due to the lack of large-scale annotated datasets. In this paper, we present domain-specific pre-training strategies, including a novel contrastive learning pretraining method, to mitigate the problem of small datasets for the Med-VQA task. We find that the model benefits from components that use fewer parameters. We also evaluate and discuss the model's visual reasoning using evidence verification techniques. Our proposed model obtained an accuracy of 60% on the VQA-Med 2019 test set, giving comparable results to other state-of-the-art Med-VQA models.

Ramtin Gharleghi, Dona Adikari, Katy Ellenberger et al.

Computed Tomography Coronary Angiography (CTCA) is a non-invasive method to evaluate coronary artery anatomy and disease. CTCA is ideal for geometry reconstruction to create virtual models of coronary arteries. To our knowledge there is no public dataset that includes centrelines and segmentation of the full coronary tree. We provide anonymized CTCA images, voxel-wise annotations and associated data in the form of centrelines, calcification scores and meshes of the coronary lumen in 20 normal and 20 diseased cases. Images were obtained along with patient information with informed, written consent as part of Coronary Atlas (https://www.coronaryatlas.org/). Cases were classified as normal (zero calcium score with no signs of stenosis) or diseased (confirmed coronary artery disease). Manual voxel-wise segmentations by three experts were combined using majority voting to generate the final annotations. Provided data can be used for a variety of research purposes, such as 3D printing patient-specific models, development and validation of segmentation algorithms, education and training of medical personnel and in-silico analyses such as testing of medical devices.

Annette Spooner, Mohammad Karimi Moridani, Azadeh Safarchi et al.

The complementary information found in different modalities of patient data can aid in more accurate modelling of a patient's disease state and a better understanding of the underlying biological processes of a disease. However, the analysis of multi-modal, multi-omics data presents many challenges, including high dimensionality and varying size, statistical distribution, scale and signal strength between modalities. In this work we compare the performance of a variety of ensemble machine learning algorithms that are capable of late integration of multi-class data from different modalities. The ensemble methods and their variations tested were i) a voting ensemble, with hard and soft vote, ii) a meta learner, iii) a multi-modal Adaboost model using a hard vote, a soft vote and a meta learner to integrate the modalities on each boosting round, the PB-MVBoost model and a novel application of a mixture of experts model. These were compared to simple concatenation as a baseline. We examine these methods using data from an in-house study on hepatocellular carcinoma (HCC), along with four validation datasets on studies from breast cancer and irritable bowel disease (IBD). Using the area under the receiver operating curve as a measure of performance we develop models that achieve a performance value of up to 0.85 and find that two boosted methods, PB-MVBoost and Adaboost with a soft vote were the overall best performing models. We also examine the stability of features selected, and the size of the clinical signature determined. Finally, we provide recommendations for the integration of multi-modal multi-class data.

Syed Javed, Tariq M. Khan, Abdul Qayyum et al.

Retinal imaging has emerged as a promising method of addressing this challenge, taking advantage of the unique structure of the retina. The retina is an embryonic extension of the central nervous system, providing a direct in vivo window into neurological health. Recent studies have shown that specific structural changes in retinal vessels can not only serve as early indicators of various diseases but also help to understand disease progression. In this work, we present a lightweight retinal vessel segmentation network based on the encoder-decoder mechanism with region-guided attention. We introduce inverse addition attention blocks with region guided attention to focus on the foreground regions and improve the segmentation of regions of interest. To further boost the model's performance on retinal vessel segmentation, we employ a weighted dice loss. This choice is particularly effective in addressing the class imbalance issues frequently encountered in retinal vessel segmentation tasks. Dice loss penalises false positives and false negatives equally, encouraging the model to generate more accurate segmentation with improved object boundary delineation and reduced fragmentation. Extensive experiments on a benchmark dataset show better performance (0.8285, 0.8098, 0.9677, and 0.8166 recall, precision, accuracy and F1 score respectively) compared to state-of-the-art methods.

Shisheng Zhang, Ramtin Gharleghi, Sonit Singh et al.

Coronary artery diseases are among the leading causes of mortality worldwide. Timely and accurate diagnosis, facilitated by precise coronary artery segmentation, is pivotal in changing patient outcomes. In the realm of biomedical imaging, convolutional neural networks, especially the U-Net architecture, have revolutionised segmentation processes. However, one of the primary challenges remains the lack of benchmarking datasets specific to coronary arteries. However through the use of the recently published public dataset ASOCA, the potential of deep learning for accurate coronary segmentation can be improved. This paper delves deep into examining the performance of 25 distinct encoder-decoder combinations. Through analysis of the 40 cases provided to ASOCA participants, it is revealed that the EfficientNet-LinkNet combination, serving as encoder and decoder, stands out. It achieves a Dice coefficient of 0.882 and a 95th percentile Hausdorff distance of 4.753. These findings not only underscore the superiority of our model in comparison to those presented at the MICCAI 2020 challenge but also set the stage for future advancements in coronary artery segmentation, opening doors to enhanced diagnostic and treatment strategies.

Md Akizur Rahman, Sonit Singh, Kuruparan Shanmugalingam et al.

Segmentation of the sigmoid colon is a crucial aspect of treating diverticulitis. It enables accurate identification and localisation of inflammation, which in turn helps healthcare professionals make informed decisions about the most appropriate treatment options. This research presents a novel deep learning architecture for segmenting the sigmoid colon from Computed Tomography (CT) images using a modified 3D U-Net architecture. Several variations of the 3D U-Net model with modified hyper-parameters were examined in this study. Pyramid pooling (PyP) and channel-spatial Squeeze and Excitation (csSE) were also used to improve the model performance. The networks were trained using manually annotated sigmoid colon. A five-fold cross-validation procedure was used on a test dataset to evaluate the network's performance. As indicated by the maximum Dice similarity coefficient (DSC) of 56.92+/-1.42%, the application of PyP and csSE techniques improves segmentation precision. We explored ensemble methods including averaging, weighted averaging, majority voting, and max ensemble. The results show that average and majority voting approaches with a threshold value of 0.5 and consistent weight distribution among the top three models produced comparable and optimal results with DSC of 88.11+/-3.52%. The results indicate that the application of a modified 3D U-Net architecture is effective for segmenting the sigmoid colon in Computed Tomography (CT) images. In addition, the study highlights the potential benefits of integrating ensemble methods to improve segmentation precision.

Hongyan Xu, Dadong Wang, Arcot Sowmya

Coronavirus Disease 2019 (COVID-19) has spread globally and become a health crisis faced by humanity since first reported. Radiology imaging technologies such as computer tomography (CT) and chest X-ray imaging (CXR) are effective tools for diagnosing COVID-19. However, in CT and CXR images, the infected area occupies only a small part of the image. Some common deep learning methods that integrate large-scale receptive fields may cause the loss of image detail, resulting in the omission of the region of interest (ROI) in COVID-19 images and are therefore not suitable for further processing. To this end, we propose a deep spatial pyramid pooling (D-SPP) module to integrate contextual information over different resolutions, aiming to extract information under different scales of COVID-19 images effectively. Besides, we propose a COVID-19 infection detection (CID) module to draw attention to the lesion area and remove interference from irrelevant information. Extensive experiments on four CT and CXR datasets have shown that our method produces higher accuracy of detecting COVID-19 lesions in CT and CXR images. It can be used as a computer-aided diagnosis tool to help doctors effectively diagnose and screen for COVID-19.

Huma Hafeez, Matthew Garratt, Jo Plested et al.

The processing of omnidirectional 360-degree images poses significant challenges for object detection due to inherent spatial distortions, wide fields of view, and ultra-high-resolution inputs. Conventional detectors such as YOLO are optimised for standard image sizes (for example, 640x640 pixels) and often struggle with the computational demands of 4K or higher-resolution imagery typical of 360-degree vision. To address these limitations, we introduce YOLO11-4K, an efficient real-time detection framework tailored for 4K panoramic images. The architecture incorporates a novel multi-scale detection head with a P2 layer to improve sensitivity to small objects often missed at coarser scales, and a GhostConv-based backbone to reduce computational complexity without sacrificing representational power. To enable evaluation, we manually annotated the CVIP360 dataset, generating 6,876 frame-level bounding boxes and producing a publicly available, detection-ready benchmark for 4K panoramic scenes. YOLO11-4K achieves 0.95 mAP at 0.50 IoU with 28.3 milliseconds inference per frame, representing a 75 percent latency reduction compared to YOLO11 (112.3 milliseconds), while also improving accuracy (mAP at 0.50 of 0.95 versus 0.908). This balance of efficiency and precision enables robust object detection in expansive 360-degree environments, making the framework suitable for real-world high-resolution panoramic applications. While this work focuses on 4K omnidirectional images, the approach is broadly applicable to high-resolution detection tasks in autonomous navigation, surveillance, and augmented reality.

Lachlan Nguyen, Aidan Cousins, Arcot Sowmya et al.

Cardiovascular disease causes high rates of mortality worldwide. Coronary artery calcium (CAC) scoring is a powerful tool to stratify the risk of atherosclerotic cardiovascular disease. Current scoring practices require time-intensive semiautomatic analysis of cardiac computed tomography by radiologists and trained radiographers. The purpose of this study is to develop a deep learning convolutional neural networks (CNN) model to classify the calcium score in cardiac, non-contrast computed tomography images into one of six clinical categories. A total of 68 patient scans were retrospectively obtained together with their respective reported semiautomatic calcium score using an ECG-gated GE Discovery 570 Cardiac SPECT/CT camera. The dataset was divided into training, validation and test sets. Using the semiautomatic CAC score as the reference label, the model demonstrated high performance on a six-class CAC scoring categorisation task. Of the scans analysed, the model misclassified 32 cases, tending towards overestimating the CAC in 26 out of 32 misclassifications. Overall, the model showed high agreement (Cohen's kappa of 0.962), an overall accuracy of 96.5% and high generalisability. The results suggest that the model outputs were accurate and consistent with current semiautomatic practice, with good generalisability to test data. The model demonstrates the viability of a CNN model to stratify the calcium score into an expanded set of six clinical categories.

Annette Spooner, Gelareh Mohammadi, Perminder S. Sachdev et al.

A novel framework is proposed for handling the complex task of modelling and analysis of longitudinal, multivariate, heterogeneous clinical data. This method uses temporal abstraction to convert the data into a more appropriate form for modelling, temporal pattern mining, to discover patterns in the complex, longitudinal data and machine learning models of survival analysis to select the discovered patterns. The method is applied to a real-world study of Alzheimer's disease (AD), a progressive neurodegenerative disease that has no cure. The patterns discovered were predictive of AD in survival analysis models with a Concordance index of up to 0.8. This is the first work that performs survival analysis of AD data using temporal data collections for AD. A visualisation module also provides a clear picture of the discovered patterns for ease of interpretability.

Raktim Kumar Mondol, Ewan K. A. Millar, Arcot Sowmya et al.

Breast cancer is a significant health concern affecting millions of women worldwide. Accurate survival risk stratification plays a crucial role in guiding personalised treatment decisions and improving patient outcomes. Here we present BioFusionNet, a deep learning framework that fuses image-derived features with genetic and clinical data to obtain a holistic profile and achieve survival risk stratification of ER+ breast cancer patients. We employ multiple self-supervised feature extractors (DINO and MoCoV3) pretrained on histopathological patches to capture detailed image features. These features are then fused by a variational autoencoder and fed to a self-attention network generating patient-level features. A co-dual-cross-attention mechanism combines the histopathological features with genetic data, enabling the model to capture the interplay between them. Additionally, clinical data is incorporated using a feed-forward network, further enhancing predictive performance and achieving comprehensive multimodal feature integration. Furthermore, we introduce a weighted Cox loss function, specifically designed to handle imbalanced survival data, which is a common challenge. Our model achieves a mean concordance index of 0.77 and a time-dependent area under the curve of 0.84, outperforming state-of-the-art methods. It predicts risk (high versus low) with prognostic significance for overall survival in univariate analysis (HR=2.99, 95% CI: 1.88--4.78, p<0.005), and maintains independent significance in multivariate analysis incorporating standard clinicopathological variables (HR=2.91, 95\% CI: 1.80--4.68, p<0.005).

Raktim Kumar Mondol, Ewan K. A. Millar, Arcot Sowmya et al.

Survival risk stratification is an important step in clinical decision making for breast cancer management. We propose a novel deep learning approach for this purpose by integrating histopathological imaging, genetic and clinical data. It employs vision transformers, specifically the MaxViT model, for image feature extraction, and self-attention to capture intricate image relationships at the patient level. A dual cross-attention mechanism fuses these features with genetic data, while clinical data is incorporated at the final layer to enhance predictive accuracy. Experiments on the public TCGA-BRCA dataset show that our model, trained using the negative log likelihood loss function, can achieve superior performance with a mean C-index of 0.64, surpassing existing methods. This advancement facilitates tailored treatment strategies, potentially leading to improved patient outcomes.

Raktim Kumar Mondol, Ewan K. A. Millar, Peter H. Graham et al.

Explainable AI (XAI) in medical histopathology is essential for enhancing the interpretability and clinical trustworthiness of deep learning models in cancer diagnosis. However, the black-box nature of these models often limits their clinical adoption. We introduce GRAPHITE (Graph-based Interpretable Tissue Examination), a post-hoc explainable framework designed for breast cancer tissue microarray (TMA) analysis. GRAPHITE employs a multiscale approach, extracting patches at various magnification levels, constructing an hierarchical graph, and utilising graph attention networks (GAT) with scalewise attention (SAN) to capture scale-dependent features. We trained the model on 140 tumour TMA cores and four benign whole slide images from which 140 benign samples were created, and tested it on 53 pathologist-annotated TMA samples. GRAPHITE outperformed traditional XAI methods, achieving a mean average precision (mAP) of 0.56, an area under the receiver operating characteristic curve (AUROC) of 0.94, and a threshold robustness (ThR) of 0.70, indicating that the model maintains high performance across a wide range of thresholds. In clinical utility, GRAPHITE achieved the highest area under the decision curve (AUDC) of 4.17e+5, indicating reliable decision support across thresholds. These results highlight GRAPHITE's potential as a clinically valuable tool in computational pathology, providing interpretable visualisations that align with the pathologists' diagnostic reasoning and support precision medicine.

Sonit Singh, Gordon Stevenson, Brendan Mein et al.

Purpose: Ultrasound is the most commonly used medical imaging modality for diagnosis and screening in clinical practice. Due to its safety profile, noninvasive nature and portability, ultrasound is the primary imaging modality for fetal assessment in pregnancy. Current ultrasound processing methods are either manual or semi-automatic and are therefore laborious, time-consuming and prone to errors, and automation would go a long way in addressing these challenges. Automated identification of placental changes at earlier gestation could facilitate potential therapies for conditions such as fetal growth restriction and pre-eclampsia that are currently detected only at late gestational age, potentially preventing perinatal morbidity and mortality. Methods: We propose an automatic three-dimensional multi-modal (B-mode and power Doppler) ultrasound segmentation of the human placenta using deep learning combined with different fusion strategies.We collected data containing Bmode and power Doppler ultrasound scans for 400 studies. Results: We evaluated different fusion strategies and state-of-the-art image segmentation networks for placenta segmentation based on standard overlap- and boundary-based metrics. We found that multimodal information in the form of B-mode and power Doppler scans outperform any single modality. Furthermore, we found that B-mode and power Doppler input scans fused at the data level provide the best results with a mean Dice Similarity Coefficient (DSC) of 0.849. Conclusion: We conclude that the multi-modal approach of combining B-mode and power Doppler scans is effective in segmenting the placenta from 3D ultrasound scans in a fully automated manner and is robust to quality variation of the datasets.

Ryan Anthony Jalova de Belen, Gelareh Mohammadi, Arcot Sowmya

Gaze communication plays a crucial role in daily social interactions. Quantifying this behavior can help in human-computer interaction and digital phenotyping. While end-to-end models exist for gaze target detection, they only utilize a single decoder to simultaneously localize human heads and predict their corresponding gaze (e.g., 2D points or heatmap) in a scene. This multitask learning approach generates a unified and entangled representation for human head localization and gaze location prediction. Herein, we propose GazeDETR, a novel end-to-end architecture with two disentangled decoders that individually learn unique representations and effectively utilize coherent attentive fields for each subtask. More specifically, we demonstrate that its human head predictor utilizes local information, while its gaze decoder incorporates both local and global information. Our proposed architecture achieves state-of-the-art results on the GazeFollow, VideoAttentionTarget and ChildPlay datasets. It outperforms existing end-to-end models with a notable margin.

Shisheng Zhang, Ramtin Gharleghi, Sonit Singh et al.

Coronary artery disease (CAD) remains the leading cause of death globally, with computed tomography coronary angiography (CTCA) serving as a key diagnostic tool. However, coronary arterial analysis using CTCA, such as identifying artery-specific features from computational modelling, is labour-intensive and time-consuming. Automated anatomical labelling of coronary arteries offers a potential solution, yet the inherent anatomical variability of coronary trees presents a significant challenge. Traditional knowledge-based labelling methods fall short in leveraging data-driven insights, while recent deep-learning approaches often demand substantial computational resources and overlook critical clinical knowledge. To address these limitations, we propose a lightweight method that integrates anatomical knowledge with rule-based topology constraints for effective coronary artery labelling. Our approach achieves state-of-the-art performance on benchmark datasets, providing a promising alternative for automated coronary artery labelling.

Sankaran Iyer, Alan Blair, Laughlin Dawes et al.

Computer aided diagnostics often requires analysis of a region of interest (ROI) within a radiology scan, and the ROI may be an organ or a suborgan. Although deep learning algorithms have the ability to outperform other methods, they rely on the availability of a large amount of annotated data. Motivated by the need to address this limitation, an approach to localisation and detection of multiple organs based on supervised and semi-supervised learning is presented here. It draws upon previous work by the authors on localising the thoracic and lumbar spine region in CT images. The method generates six bounding boxes of organs of interest, which are then fused to a single bounding box. The results of experiments on localisation of the Spleen, Left and Right Kidneys in CT Images using supervised and semi supervised learning (SSL) demonstrate the ability to address data limitations with a much smaller data set and fewer annotations, compared to other state-of-the-art methods. The SSL performance was evaluated using three different mixes of labelled and unlabelled data (i.e.30:70,35:65,40:60) for each of lumbar spine, spleen left and right kidneys respectively. The results indicate that SSL provides a workable alternative especially in medical imaging where it is difficult to obtain annotated data.

Nuha Aldausari, Arcot Sowmya, Nadine Marcus et al.

With the increasing interest in the content creation field in multiple sectors such as media, education, and entertainment, there is an increasing trend in the papers that uses AI algorithms to generate content such as images, videos, audio, and text. Generative Adversarial Networks (GANs) in one of the promising models that synthesizes data samples that are similar to real data samples. While the variations of GANs models, in general, have been covered to some extent in several survey papers, to the best of our knowledge, this is among the first survey papers that reviews the state-of-the-art video GANs models. This paper first categorized GANs review papers into general GANs review papers, image GANs review papers, and special field GANs review papers such as anomaly detection, medical imaging, or cybersecurity. The paper then summarizes the main improvements in GANs frameworks that are not initially developed for the video domain but have been adopted in multiple video GANs variations. Then, a comprehensive review of video GANs models is provided under two main divisions according to the presence or non-presence of a condition. The conditional models then further grouped according to the type of condition into audio, text, video, and image. The paper is concluded by highlighting the main challenges and limitations of the current video GANs models. A comprehensive list of datasets, applied loss functions, and evaluation metrics is provided in the supplementary material.

Mina Ghaffari, Arcot Sowmya, Ruth Oliver

Accurate brain tumour segmentation is a crucial step towards improving disease diagnosis and proper treatment planning. In this paper, we propose a deep-learning based method to segment a brain tumour into its subregions: whole tumour, tumour core and enhancing tumour. The proposed architecture is a 3D convolutional neural network based on a variant of the U-Net architecture of Ronneberger et al. [17] with three main modifications: (i) a heavy encoder, light decoder structure using residual blocks (ii) employment of dense blocks instead of skip connections, and (iii) utilization of self-ensembling in the decoder part of the network. The network was trained and tested using two different approaches: a multitask framework to segment all tumour subregions at the same time and a three-stage cascaded framework to segment one sub-region at a time. An ensemble of the results from both frameworks was also computed. To address the class imbalance issue, appropriate patch extraction was employed in a pre-processing step. The connected component analysis was utilized in the post-processing step to reduce false positive predictions. Experimental results on the BraTS20 validation dataset demonstrates that the proposed model achieved average Dice Scores of 0.90, 0.82, and 0.78 for whole tumour, tumour core and enhancing tumour respectively.

Feng Zhou, Zhidong Li, Xuhui Fan et al.

In this paper, we consider the sigmoid Gaussian Hawkes process model: the baseline intensity and triggering kernel of Hawkes process are both modeled as the sigmoid transformation of random trajectories drawn from Gaussian processes (GP). By introducing auxiliary latent random variables (branching structure, Pólya-Gamma random variables and latent marked Poisson processes), the likelihood is converted to two decoupled components with a Gaussian form which allows for an efficient conjugate analytical inference. Using the augmented likelihood, we derive an expectation-maximization (EM) algorithm to obtain the maximum a posteriori (MAP) estimate. Furthermore, we extend the EM algorithm to an efficient approximate Bayesian inference algorithm: mean-field variational inference. We demonstrate the performance of two algorithms on simulated fictitious data. Experiments on real data show that our proposed inference algorithms can recover well the underlying prompting characteristics efficiently.

Feng Zhou, Zhidong Li, Xuhui Fan et al.

In classical Hawkes process, the baseline intensity and triggering kernel are assumed to be a constant and parametric function respectively, which limits the model flexibility. To generalize it, we present a fully Bayesian nonparametric model, namely Gaussian process modulated Hawkes process and propose an EM-variational inference scheme. In this model, a transformation of Gaussian process is used as a prior on the baseline intensity and triggering kernel. By introducing a latent branching structure, the inference of baseline intensity and triggering kernel is decoupled and the variational inference scheme is embedded into an EM framework naturally. We also provide a series of schemes to accelerate the inference. Results of synthetic and real data experiments show that the underlying baseline intensity and triggering kernel can be recovered without parametric restriction and our Bayesian nonparametric estimation is superior to other state of the arts.