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  • Journal article
    Gionfrida L, Rusli W, Kedgley A, Bharath Aet al., 2022,

    A 3DCNN-LSTM multi-class temporal segmentation for hand gesture recognition

    , Electronics, Vol: 11, ISSN: 2079-9292

    This paper introduces a multi-class hand gesture recognition model developed to identify a set of hand gesture sequences from two-dimensional RGB video recordings, using both the appearance and spatiotemporal parameters of consecutive frames. The classifier utilizes a convolutional-based network combined with a long-short-term memory unit. To leverage the need for a large-scale dataset, the model deploys training on a public dataset, adopting a technique known as transfer learning to fine-tune the architecture on the hand gestures of relevance. Validation curves performed over a batch size of 64 indicate an accuracy of 93.95% (±0.37) with a mean Jaccard index of 0.812 (±0.105) for 22 participants. The fine-tuned architecture illustrates the possibility of refining a model with a small set of data (113,410 fully labelled image frames) to cover previously unknown hand gestures. The main contribution of this work includes a custom hand gesture recognition network driven by monocular RGB video sequences that outperform previous temporal segmentation models, embracing a small-sized architecture that facilitates wide adoption.

  • Journal article
    Lino M, Fotiadis S, Bharath AA, Cantwell CDet al., 2022,

    Multi-scale rotation-equivariant graph neural networks for unsteady Eulerian fluid dynamics

    , PHYSICS OF FLUIDS, Vol: 34, ISSN: 1070-6631
  • Journal article
    Atchison C, Moshe M, Brown J, Whitaker M, Wong N, Bharath A, Mckendry R, Darzi A, Ashby D, Donnelly C, Riley S, Elliott P, Barclay W, Cooke G, Ward Het al., 2022,

    Validity of self-testing at home with rapid SARS-CoV-2 antibody detection by lateral flow immunoassay

    , Clinical Infectious Diseases, ISSN: 1058-4838

    Background: We explore severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) antibody lateral flow immunoassay (LFIA) performance under field conditions compared to laboratory-based ELISA and live virus neutralisation. Methods: In July 2021, 3758 participants performed, at home, a self-administered LFIA on finger-prick blood, reported and submitted a photograph of the result, and provided a self-collected capillary blood sample for assessment of IgG antibodies using the Roche Elecsys® Anti-SARS-CoV-2 assay. We compared the self-reported LFIA result to the quantitative Roche assay and checked the reading of the LFIA result with an automated image analysis (ALFA). In a subsample of 250 participants, we compared the results to live virus neutralisation. Results: Almost all participants (3593/3758, 95.6%) had been vaccinated or reported prior infection. Overall, 2777/3758 (73.9%) were positive on self-reported LFIA, 2811/3457 (81.3%) positive by LFIA when ALFA-reported, and 3622/3758 (96.4%) positive on Roche (using the manufacturer reference standard threshold for positivity of 0.8 U ml−1). Live virus neutralisation was detected in 169 of 250 randomly selected samples (67.6%); 133/169 were positive with self-reported LFIA (sensitivity 78.7%; 95% CI 71.8, 84.6), 142/155 (91.6%; 86.1, 95.5) with ALFA, and 169 (100%; 97.8, 100.0) with Roche. There were 81 samples with no detectable virus neutralisation; 47/81 were negative with self-reported LFIA (specificity 58.0%; 95% CI 46.5, 68.9), 34/75 (45.3%; 33.8, 57.3) with ALFA, and 0/81 (0%; 0.0, 4.5) with Roche. Conclusions: Self-administered LFIA is less sensitive than a quantitative antibody test, but the positivity in LFIA correlates better than the quantitative ELISA with virus neutralisation.

  • Journal article
    Wong N, Meshkinfamfard S, Turbé V, Whitaker M, Moshe M, Bardanzellu A, Dai T, Pignatelli E, Barclay W, Darzi A, Elliott P, Ward H, Tanaka R, Cooke G, McKendry R, Atchison C, Bharath Aet al., 2022,

    Machine learning to support visual auditing of home-based lateral flow immunoassay self-test results for SARS-CoV-2 antibodies

    , Communications Medicine, Vol: 2, ISSN: 2730-664X

    Lateral flow immunoassays (LFIAs) are being used worldwide for COVID-19 mass testing and antibody prevalence studies. Relatively simple to use and low cost, these tests can be self-administered at home but rely on subjective interpretation of a test line by eye, risking false positives and negatives. Here we report the development of ALFA (Automated Lateral Flow Analysis) to improve reported sensitivity and specificity. Our computational pipeline uses machine learning, computer vision techniques and signal processing algorithms to analyse images of the Fortress LFIA SARS-CoV-2 antibody self-test, and subsequently classify results as invalid, IgG negative and IgG positive. A large image library of 595,339 participant-submitted test photographs was created as part of the REACT-2 community SARS-CoV-2 antibody prevalence study in England, UK. Automated analysis showed substantial agreement with human experts (Kappa 0.90-0.97) and performed consistently better than study participants, particularly for weak positive IgG results. Specificity (98.7-99.4%) and sensitivity (90.1-97.1%) were high compared with visual interpretation by human experts (ranges due to the varying prevalence of weak positive IgG tests in datasets). Alongside ALFA, we developed an analysis toolkit which could also detect device blood leakage issues. Given the potential for LFIAs to be used at scale in the COVID-19 response (for both antibody and antigen testing), even a small improvement in the accuracy of the algorithms could impact the lives of millions of people by reducing the risk of false positive and false negative result read-outs by members of the public. Our findings support the use of machine learning-enabled automated reading of at-home antibody lateral flow tests, to be a tool for improved accuracy for population-level community surveillance.

  • Conference paper
    Lino M, Fotiadis S, Bharath AA, Cantwell Cet al., 2022,

    Towards fast simulation of environmental fluid mechanics with multi-scale graph neural networks

    , AI for Earth and Space Science, Publisher: ICLR, Pages: 1-11

    Numerical simulators are essential tools in the study of naturalfluid-systems, but their performance often limits application in practice.Recent machine-learning approaches have demonstrated their ability toaccelerate spatio-temporal predictions, although, with only moderate accuracyin comparison. Here we introduce MultiScaleGNN, a novel multi-scale graphneural network model for learning to infer unsteady continuum mechanics inproblems encompassing a range of length scales and complex boundary geometries.We demonstrate this method on advection problems and incompressible fluiddynamics, both fundamental phenomena in oceanic and atmospheric processes. Ourresults show good extrapolation to new domain geometries and parameters forlong-term temporal simulations. Simulations obtained with MultiScaleGNN arebetween two and four orders of magnitude faster than those on which it wastrained.

  • Conference paper
    Lino M, Fotiadis S, Bharath AA, Cantwell Cet al., 2022,

    REMuS-GNN: A rotation-equivariant model for simulating continuum dynamics

    , ICLR 2022 workshop on ‘Geometrical and Topological Representation Learning’, Publisher: OpenReview.net

    Numerical simulation is an essential tool in many areas of science and engineering, but its performance often limits application in practice, or when used to explore large parameter spaces. On the other hand, surrogate deep learning models, while accelerating simulations, often exhibit poor accuracy and ability to generalise. In order to improve these two factors, we introduce REMuS-GNN, a rotation-equivariant multi-scale model for simulating continuum dynamical systems encompassing a range of length scales. REMuS-GNN is designed to predict an output vector field from an input vector field on a physical domain discredited into an unstructured set of nodes. Equivariance to rotations of the domain is a desirable inductive bias that allows the network to learn the underlying physics more efficiently, leading to improved accuracy and generalisation compared with similar architectures that lack such symmetry. We demonstrate and evaluate this method on the incompressible flow around elliptical cylinders.

  • Journal article
    Bharath A, Uslu F, Varela Anjari M, Boniface G, Mahenthran T, Chubb Het al., 2022,

    LA-Net: A multi-task deep network for the segmentation of the left atrium

    , IEEE Transactions on Medical Imaging, Vol: 41, Pages: 456-464, ISSN: 0278-0062

    Although atrial fibrillation (AF) is the most common sustained atrial arrhythmia, treatment success for this condition remains suboptimal. Information from magnetic resonance imaging (MRI) has the potential to improve treatment efficacy, but there are currently few automatic tools for the segmentation of the atria in MR images. In the study, we propose a LA-Net, a multi-task network optimised to simultaneously generate left atrial segmentation and edge masks from MRI. LA-Net includes cross attention modules (CAMs) and enhanced decoder modules (EDMs) to purposefully select the most meaningful edge information for segmentation and smoothly incorporate it into segmentation masks at multiple-scales. We evaluate the performance of LA-Net on two MR sequences: late gadolinium enhanced (LGE) atrial MRI and atrial short axis balanced steady state free precession (bSSFP) MRI. LA-Net gives Hausdorff distances of 12.43 mm and Dice scores of 0.92 on the LGE (STACOM 2018) dataset and Hausdorff distances of 17.41 mm and Dice scores of 0.90 on the bSSFP (in-house) dataset without any post-processing, surpassing previously proposed segmentation networks, including U-Net and SEGANet. Our method allows automatic extraction of information about the LA from MR images, which can play an important role in the management of AF patients.

  • Journal article
    Dai T, Du Y, Fang M, Bharath Aet al., 2022,

    Diversity-augmented intrinsic motivation for deep reinforcement learning

    , Neurocomputing, Vol: 468, Pages: 396-406, ISSN: 0925-2312

    In many real-world problems, reward signals received by agents are delayed or sparse, which makes it challenging to train a reinforcement learning (RL) agent. An intrinsic reward signal can help an agent to explore such environments in the quest for novel states. In this work, we propose a general end-to-end diversity-augmented intrinsic motivation for deep reinforcement learning which encourages the agent to explore new states and automatically provides denser rewards. Specifically, we measure the diversity of adjacent states under a model of state sequences based on determinantal point process (DPP); this is coupled with a straight-through gradient estimator to enable end-to-end differentiability. The proposed approach is comprehensively evaluated on the MuJoCo and the Arcade Learning Environments (Atari and SuperMarioBros). The experiments show that an intrinsic reward based on the diversity measure derived from the DPP model accelerates the early stages of training in Atari games and SuperMarioBros. In MuJoCo, the approach improves on prior techniques for tasks using the standard reward setting, and achieves the state-of-the-art performance on 12 out of 15 tasks containing delayed rewards.

  • Journal article
    Zaman S, Petri C, Vimalesvaran K, Howard J, Bharath A, Francis D, Peters N, Cole GD, Linton Net al., 2022,

    Automatic diagnosis labeling of cardiovascular MRI by using semisupervised natural language processing of text reports

    , Radiology: Artificial Intelligence, Vol: 4, ISSN: 2638-6100

    A semisupervised natural language processing (NLP) algorithm, based on bidirectional transformers, accurately categorized diagnoses from cardiac MRI text of radiology reports for the labeling of MR images; the model had a higher accuracy than traditional NLP models and performed faster labeling than clinicians.

  • Conference paper
    Galazis C, Wu H, Li Z, Petri C, Bharath AA, Varela Met al., 2022,

    Tempera: Spatial Transformer Feature Pyramid Network for Cardiac MRI Segmentation

    , Pages: 268-276, ISSN: 0302-9743

    Assessing the structure and function of the right ventricle (RV) is important in the diagnosis of several cardiac pathologies. However, it remains more challenging to segment the RV than the left ventricle (LV). In this paper, we focus on segmenting the RV in both short (SA) and long-axis (LA) cardiac MR images simultaneously. For this task, we propose a new multi-input/output architecture, hybrid 2D/3D geometric spatial TransformEr Multi-Pass fEature pyRAmid (Tempera). Our feature pyramid extends current designs by allowing not only a multi-scale feature output but multi-scale SA and LA input images as well. Tempera transfers learned features between SA and LA images via layer weight sharing and incorporates a geometric target transformer to map the predicted SA segmentation to LA space. Our model achieves an average Dice score of 0.836 and 0.798 for the SA and LA, respectively, and 26.31 mm and 31.19 mm Hausdorff distances. This opens up the potential for the incorporation of RV segmentation models into clinical workflows.

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