arXiv subjects

Vicente Grau

Publications and source records attributed to Vicente Grau.

At least 37 records · Page 2Linked to original sources

arXiv2024

Medical Graph RAG: Towards Safe Medical Large Language Model via Graph Retrieval-Augmented Generation

We introduce a novel graph-based Retrieval-Augmented Generation (RAG) framework specifically designed for the medical domain, called \textbf{MedGraphRAG}, aimed at enhancing Large Language Model (LLM) capabilities for generating evidence-based medical responses, thereby improving safety and reliability when handling private medical data. Graph-based RAG (GraphRAG) leverages LLMs to organize RAG data into graphs, showing strong potential for gaining holistic insights from long-form documents. However, its standard implementation is overly complex for general use and lacks the ability to generate evidence-based responses, limiting its effectiveness in the medical field. To extend the capabilities of GraphRAG to the medical domain, we propose unique Triple Graph Construction and U-Retrieval techniques over it. In our graph construction, we create a triple-linked structure that connects user documents to credible medical sources and controlled vocabularies. In the retrieval process, we propose U-Retrieval which combines Top-down Precise Retrieval with Bottom-up Response Refinement to balance global context awareness with precise indexing. These effort enable both source information retrieval and comprehensive response generation. Our approach is validated on 9 medical Q\&A benchmarks, 2 health fact-checking benchmarks, and one collected dataset testing long-form generation. The results show that MedGraphRAG consistently outperforms state-of-the-art models across all benchmarks, while also ensuring that responses include credible source documentation and definitions. Our code is released at: https://github.com/MedicineToken/Medical-Graph-RAG.

cs.CV↗

arXiv2024

Transesophageal Echocardiography Generation using Anatomical Models

Through automation, deep learning (DL) can enhance the analysis of transesophageal echocardiography (TEE) images. However, DL methods require large amounts of high-quality data to produce accurate results, which is difficult to satisfy. Data augmentation is commonly used to tackle this issue. In this work, we develop a pipeline to generate synthetic TEE images and corresponding semantic labels. The proposed data generation pipeline expands on an existing pipeline that generates synthetic transthoracic echocardiography images by transforming slices from anatomical models into synthetic images. We also demonstrate that such images can improve DL network performance through a left-ventricle semantic segmentation task. For the pipeline's unpaired image-to-image (I2I) translation section, we explore two generative methods: CycleGAN and contrastive unpaired translation. Next, we evaluate the synthetic images quantitatively using the Fréchet Inception Distance (FID) Score and qualitatively through a human perception quiz involving expert cardiologists and the average researcher. In this study, we achieve a dice score improvement of up to 10% when we augment datasets with our synthetic images. Furthermore, we compare established methods of assessing unpaired I2I translation and observe a disagreement when evaluating the synthetic images. Finally, we see which metric better predicts the generated data's efficacy when used for data augmentation.

eess.IV↗

arXiv2024

Solving the Inverse Problem of Electrocardiography for Cardiac Digital Twins: A Survey

Cardiac digital twins (CDTs) are personalized virtual representations used to understand complex cardiac mechanisms. A critical component of CDT development is solving the ECG inverse problem, which enables the reconstruction of cardiac sources and the estimation of patient-specific electrophysiology (EP) parameters from surface ECG data. Despite challenges from complex cardiac anatomy, noisy ECG data, and the ill-posed nature of the inverse problem, recent advances in computational methods have greatly improved the accuracy and efficiency of ECG inverse inference, strengthening the fidelity of CDTs. This paper aims to provide a comprehensive review of the methods of solving ECG inverse problem, the validation strategies, the clinical applications, and future perspectives. For the methodologies, we broadly classify state-of-the-art approaches into two categories: deterministic and probabilistic methods, including both conventional and deep learning-based techniques. Integrating physics laws with deep learning models holds promise, but challenges such as capturing dynamic electrophysiology accurately, accessing accurate domain knowledge, and quantifying prediction uncertainty persist. Integrating models into clinical workflows while ensuring interpretability and usability for healthcare professionals is essential. Overcoming these challenges will drive further research in CDTs.

cs.CV↗

arXiv2024

Large Language Model-informed ECG Dual Attention Network for Heart Failure Risk Prediction

Heart failure (HF) poses a significant public health challenge, with a rising global mortality rate. Early detection and prevention of HF could significantly reduce its impact. We introduce a novel methodology for predicting HF risk using 12-lead electrocardiograms (ECGs). We present a novel, lightweight dual-attention ECG network designed to capture complex ECG features essential for early HF risk prediction, despite the notable imbalance between low and high-risk groups. This network incorporates a cross-lead attention module and twelve lead-specific temporal attention modules, focusing on cross-lead interactions and each lead's local dynamics. To further alleviate model overfitting, we leverage a large language model (LLM) with a public ECG-Report dataset for pretraining on an ECG-report alignment task. The network is then fine-tuned for HF risk prediction using two specific cohorts from the UK Biobank study, focusing on patients with hypertension (UKB-HYP) and those who have had a myocardial infarction (UKB-MI).The results reveal that LLM-informed pre-training substantially enhances HF risk prediction in these cohorts. The dual-attention design not only improves interpretability but also predictive accuracy, outperforming existing competitive methods with C-index scores of 0.6349 for UKB-HYP and 0.5805 for UKB-MI. This demonstrates our method's potential in advancing HF risk assessment with clinical complex ECG data.

q-bio.QM↗

arXiv2024

Towards Enabling Cardiac Digital Twins of Myocardial Infarction Using Deep Computational Models for Inverse Inference

Cardiac digital twins (CDTs) have the potential to offer individualized evaluation of cardiac function in a non-invasive manner, making them a promising approach for personalized diagnosis and treatment planning of my-ocardial infarction (MI). The inference of accurate myocardial tissue properties is crucial in creating a reliable CDT of MI. In this work, we investigate the feasibility of inferring myocardial tissue properties from the electrocardiogram (ECG) within a CDT platform. The platform integrates multi-modal data, such as cardiac MRI and ECG, to enhance the accuracy and reliability of the inferred tissue properties. We perform a sensitivity analysis based on computer simulations, systematically exploring the effects of infarct location, size, degree of transmurality, and electrical ac-tivity alteration on the simulated QRS complex of ECG, to establish the limits of the approach. We subsequently present a novel deep computational model, comprising a dual-branch variational autoencoder and an inference model, to infer infarct location and distribution from the simulated QRS. The proposed model achieves mean Dice scores of 0.457 \pm 0.317 and 0.302 \pm 0.273 for the inference of left ventricle scars and border zone, respectively. The sensitivity analysis enhances our understanding of the complex relationship between infarct characteristics and electrophysiological features. The in silico experimental results show that the model can effectively capture the relationship for the inverse inference, with promising potential for clinical application in the future. The code will be released publicly once the manuscript is accepted for publication.

eess.SP↗

arXiv2024

Segment Anything Model for Medical Images?

The Segment Anything Model (SAM) is the first foundation model for general image segmentation. It has achieved impressive results on various natural image segmentation tasks. However, medical image segmentation (MIS) is more challenging because of the complex modalities, fine anatomical structures, uncertain and complex object boundaries, and wide-range object scales. To fully validate SAM's performance on medical data, we collected and sorted 53 open-source datasets and built a large medical segmentation dataset with 18 modalities, 84 objects, 125 object-modality paired targets, 1050K 2D images, and 6033K masks. We comprehensively analyzed different models and strategies on the so-called COSMOS 1050K dataset. Our findings mainly include the following: 1) SAM showed remarkable performance in some specific objects but was unstable, imperfect, or even totally failed in other situations. 2) SAM with the large ViT-H showed better overall performance than that with the small ViT-B. 3) SAM performed better with manual hints, especially box, than the Everything mode. 4) SAM could help human annotation with high labeling quality and less time. 5) SAM was sensitive to the randomness in the center point and tight box prompts, and may suffer from a serious performance drop. 6) SAM performed better than interactive methods with one or a few points, but will be outpaced as the number of points increases. 7) SAM's performance correlated to different factors, including boundary complexity, intensity differences, etc. 8) Finetuning the SAM on specific medical tasks could improve its average DICE performance by 4.39% and 6.68% for ViT-B and ViT-H, respectively. We hope that this comprehensive report can help researchers explore the potential of SAM applications in MIS, and guide how to appropriately use and develop SAM.

eess.IV↗

arXiv2023

Modeling 3D cardiac contraction and relaxation with point cloud deformation networks

Global single-valued biomarkers of cardiac function typically used in clinical practice, such as ejection fraction, provide limited insight on the true 3D cardiac deformation process and hence, limit the understanding of both healthy and pathological cardiac mechanics. In this work, we propose the Point Cloud Deformation Network (PCD-Net) as a novel geometric deep learning approach to model 3D cardiac contraction and relaxation between the extreme ends of the cardiac cycle. It employs the recent advances in point cloud-based deep learning into an encoder-decoder structure, in order to enable efficient multi-scale feature learning directly on multi-class 3D point cloud representations of the cardiac anatomy. We evaluate our approach on a large dataset of over 10,000 cases from the UK Biobank study and find average Chamfer distances between the predicted and ground truth anatomies below the pixel resolution of the underlying image acquisition. Furthermore, we observe similar clinical metrics between predicted and ground truth populations and show that the PCD-Net can successfully capture subpopulation-specific differences between normal subjects and myocardial infarction (MI) patients. We then demonstrate that the learned 3D deformation patterns outperform multiple clinical benchmarks by 13% and 7% in terms of area under the receiver operating characteristic curve for the tasks of prevalent MI detection and incident MI prediction and by 7% in terms of Harrell's concordance index for MI survival analysis.

eess.IV↗

arXiv2023

Multi-objective point cloud autoencoders for explainable myocardial infarction prediction

Myocardial infarction (MI) is one of the most common causes of death in the world. Image-based biomarkers commonly used in the clinic, such as ejection fraction, fail to capture more complex patterns in the heart's 3D anatomy and thus limit diagnostic accuracy. In this work, we present the multi-objective point cloud autoencoder as a novel geometric deep learning approach for explainable infarction prediction, based on multi-class 3D point cloud representations of cardiac anatomy and function. Its architecture consists of multiple task-specific branches connected by a low-dimensional latent space to allow for effective multi-objective learning of both reconstruction and MI prediction, while capturing pathology-specific 3D shape information in an interpretable latent space. Furthermore, its hierarchical branch design with point cloud-based deep learning operations enables efficient multi-scale feature learning directly on high-resolution anatomy point clouds. In our experiments on a large UK Biobank dataset, the multi-objective point cloud autoencoder is able to accurately reconstruct multi-temporal 3D shapes with Chamfer distances between predicted and input anatomies below the underlying images' pixel resolution. Our method outperforms multiple machine learning and deep learning benchmarks for the task of incident MI prediction by 19% in terms of Area Under the Receiver Operating Characteristic curve. In addition, its task-specific compact latent space exhibits easily separable control and MI clusters with clinically plausible associations between subject encodings and corresponding 3D shapes, thus demonstrating the explainability of the prediction.

cs.CV↗

arXiv2023

Multi-class point cloud completion networks for 3D cardiac anatomy reconstruction from cine magnetic resonance images

Cine magnetic resonance imaging (MRI) is the current gold standard for the assessment of cardiac anatomy and function. However, it typically only acquires a set of two-dimensional (2D) slices of the underlying three-dimensional (3D) anatomy of the heart, thus limiting the understanding and analysis of both healthy and pathological cardiac morphology and physiology. In this paper, we propose a novel fully automatic surface reconstruction pipeline capable of reconstructing multi-class 3D cardiac anatomy meshes from raw cine MRI acquisitions. Its key component is a multi-class point cloud completion network (PCCN) capable of correcting both the sparsity and misalignment issues of the 3D reconstruction task in a unified model. We first evaluate the PCCN on a large synthetic dataset of biventricular anatomies and observe Chamfer distances between reconstructed and gold standard anatomies below or similar to the underlying image resolution for multiple levels of slice misalignment. Furthermore, we find a reduction in reconstruction error compared to a benchmark 3D U-Net by 32% and 24% in terms of Hausdorff distance and mean surface distance, respectively. We then apply the PCCN as part of our automated reconstruction pipeline to 1000 subjects from the UK Biobank study in a cross-domain transfer setting and demonstrate its ability to reconstruct accurate and topologically plausible biventricular heart meshes with clinical metrics comparable to the previous literature. Finally, we investigate the robustness of our proposed approach and observe its capacity to successfully handle multiple common outlier conditions.

eess.IV↗

arXiv2023

3D Shape-Based Myocardial Infarction Prediction Using Point Cloud Classification Networks

Myocardial infarction (MI) is one of the most prevalent cardiovascular diseases with associated clinical decision-making typically based on single-valued imaging biomarkers. However, such metrics only approximate the complex 3D structure and physiology of the heart and hence hinder a better understanding and prediction of MI outcomes. In this work, we investigate the utility of complete 3D cardiac shapes in the form of point clouds for an improved detection of MI events. To this end, we propose a fully automatic multi-step pipeline consisting of a 3D cardiac surface reconstruction step followed by a point cloud classification network. Our method utilizes recent advances in geometric deep learning on point clouds to enable direct and efficient multi-scale learning on high-resolution surface models of the cardiac anatomy. We evaluate our approach on 1068 UK Biobank subjects for the tasks of prevalent MI detection and incident MI prediction and find improvements of ~13% and ~5% respectively over clinical benchmarks. Furthermore, we analyze the role of each ventricle and cardiac phase for 3D shape-based MI detection and conduct a visual analysis of the morphological and physiological patterns typically associated with MI outcomes.

cs.CV↗

arXiv2023

Digital Twinning of the Human Ventricular Activation Sequence to Clinical 12-lead ECGs and Magnetic Resonance Imaging Using Realistic Purkinje Networks for in Silico Clinical Trials

Cardiac in silico clinical trials can virtually assess the safety and efficacy of therapies using human-based modelling and simulation. These technologies can provide mechanistic explanations for clinically observed pathological behaviour. Designing virtual cohorts for in silico trials requires exploiting clinical data to capture the physiological variability in the human population. The clinical characterisation of ventricular activation and the Purkinje network is challenging, especially non-invasively. Our study aims to present a novel digital twinning pipeline that can efficiently generate and integrate Purkinje networks into human multiscale biventricular models based on subject-specific clinical 12-lead electrocardiogram and magnetic resonance recordings. Essential novel features of the pipeline are the human-based Purkinje network generation method, personalisation considering ECG R wave progression as well as QRS morphology, and translation from reduced-order Eikonal models to equivalent biophysically-detailed monodomain ones. We demonstrate ECG simulations in line with clinical data with clinical image-based multiscale models with Purkinje in four control subjects and two hypertrophic cardiomyopathy patients (simulated and clinical QRS complexes with Pearson's correlation coefficients > 0.7). Our methods also considered possible differences in the density of Purkinje myocardial junctions in the Eikonal-based inference as regional conduction velocities. These differences translated into regional coupling effects between Purkinje and myocardial models in the monodomain formulation. In summary, we demonstrate a digital twin pipeline enabling simulations yielding clinically-consistent ECGs with clinical CMR image-based biventricular multiscale models, including personalised Purkinje in healthy and cardiac disease conditions.

physics.med-ph↗

arXiv2023

Influence of Myocardial Infarction on QRS Properties: A Simulation Study

The interplay between structural and electrical changes in the heart after myocardial infarction (MI) plays a key role in the initiation and maintenance of arrhythmia. The anatomical and electrophysiological properties of scar, border zone, and normal myocardium modify the electrocardiographic morphology, which is routinely analysed in clinical settings. However, the influence of various MI properties on the QRS is not intuitively predictable.In this work, we have systematically investigated the effects of 17 post-MI scenarios, varying the location, size, transmural extent, and conductive level of scarring and border zone area, on the forward-calculated QRS. Additionally, we have compared the contributions of different QRS score criteria for quantifying post-MI pathophysiology.The propagation of electrical activity in the ventricles is simulated via a Eikonal model on a unified coordinate system.The analysis has been performed on 49 subjects, and the results imply that the QRS is capable of identifying MI, suggesting the feasibility of inversely reconstructing infarct regions from QRS.There exist sensitivity variations of different QRS criteria for identifying 17 MI scenarios, which is informative for solving the inverse problem.

cs.CV↗

arXiv2022

Multi-Modality Cardiac Image Computing: A Survey

Multi-modality cardiac imaging plays a key role in the management of patients with cardiovascular diseases. It allows a combination of complementary anatomical, morphological and functional information, increases diagnosis accuracy, and improves the efficacy of cardiovascular interventions and clinical outcomes. Fully-automated processing and quantitative analysis of multi-modality cardiac images could have a direct impact on clinical research and evidence-based patient management. However, these require overcoming significant challenges including inter-modality misalignment and finding optimal methods to integrate information from different modalities. This paper aims to provide a comprehensive review of multi-modality imaging in cardiology, the computing methods, the validation strategies, the related clinical workflows and future perspectives. For the computing methodologies, we have a favored focus on the three tasks, i.e., registration, fusion and segmentation, which generally involve multi-modality imaging data, \textit{either combining information from different modalities or transferring information across modalities}. The review highlights that multi-modality cardiac imaging data has the potential of wide applicability in the clinic, such as trans-aortic valve implantation guidance, myocardial viability assessment, and catheter ablation therapy and its patient selection. Nevertheless, many challenges remain unsolved, such as missing modality, combination of imaging and non-imaging data, and uniform analysis and representation of different modalities. There is also work to do in defining how the well-developed techniques fit in clinical workflows and how much additional and relevant information they introduce. These problems are likely to continue to be an active field of research and the questions to be answered in the future.

eess.IV↗

arXiv2022

Deep Computational Model for the Inference of Ventricular Activation Properties

Patient-specific cardiac computational models are essential for the efficient realization of precision medicine and in-silico clinical trials using digital twins. Cardiac digital twins can provide non-invasive characterizations of cardiac functions for individual patients, and therefore are promising for the patient-specific diagnosis and therapy stratification. However, current workflows for both the anatomical and functional twinning phases, referring to the inference of model anatomy and parameter from clinical data, are not sufficiently efficient, robust, and accurate. In this work, we propose a deep learning based patient-specific computational model, which can fuse both anatomical and electrophysiological information for the inference of ventricular activation properties, i.e., conduction velocities and root nodes. The activation properties can provide a quantitative assessment of cardiac electrophysiological function for the guidance of interventional procedures. We employ the Eikonal model to generate simulated electrocardiogram (ECG) with ground truth properties to train the inference model, where specific patient information has also been considered. For evaluation, we test the model on the simulated data and obtain generally promising results with fast computational time.

cs.CV↗

arXiv2020

Inference of ventricular activation properties from non-invasive electrocardiography

The realisation of precision cardiology requires novel techniques for the non-invasive characterisation of individual patients' cardiac function to inform therapeutic and diagnostic decision-making. The electrocardiogram (ECG) is the most widely used clinical tool for cardiac diagnosis. Its interpretation is, however, confounded by functional and anatomical variability in heart and torso. In this study, we develop new computational techniques to estimate key ventricular activation properties for individual subjects by exploiting the synergy between non-invasive electrocardiography and image-based torso-biventricular modelling and simulation. More precisely, we present an efficient sequential Monte Carlo approximate Bayesian computation-based inference method, integrated with Eikonal simulations and torso-biventricular models constructed based on clinical cardiac magnetic resonance (CMR) imaging. The method also includes a novel strategy to treat combined continuous (conduction speeds) and discrete (earliest activation sites) parameter spaces, and an efficient dynamic time warping-based ECG comparison algorithm. We demonstrate results from our inference method on a cohort of twenty virtual subjects with cardiac volumes ranging from 74 cm3 to 171 cm3 and considering low versus high resolution for the endocardial discretisation (which determines possible locations of the earliest activation sites). Results show that our method can successfully infer the ventricular activation properties from non-invasive data, with higher accuracy for earliest activation sites, endocardial speed, and sheet (transmural) speed in sinus rhythm, rather than the fibre or sheet-normal speeds.

q-bio.TO↗

arXiv2020

A Deep learning Approach to Generate Contrast-Enhanced Computerised Tomography Angiography without the Use of Intravenous Contrast Agents

Contrast-enhanced computed tomography angiograms (CTAs) are widely used in cardiovascular imaging to obtain a non-invasive view of arterial structures. However, contrast agents are associated with complications at the injection site as well as renal toxicity leading to contrast-induced nephropathy (CIN) and renal failure. We hypothesised that the raw data acquired from a non-contrast CT contains sufficient information to differentiate blood and other soft tissue components. We utilised deep learning methods to define the subtleties between soft tissue components in order to simulate contrast enhanced CTAs without contrast agents. Twenty-six patients with paired non-contrast and CTA images were randomly selected from an approved clinical study. Non-contrast axial slices within the AAA from 10 patients (n = 100) were sampled for the underlying Hounsfield unit (HU) distribution at the lumen, intra-luminal thrombus and interface locations. Sampling of HUs in these regions revealed significant differences between all regions (p<0.001 for all comparisons), confirming the intrinsic differences in the radiomic signatures between these regions. To generate a large training dataset, paired axial slices from the training set (n=13) were augmented to produce a total of 23,551 2-D images. We trained a 2-D Cycle Generative Adversarial Network (cycleGAN) for this non-contrast to contrast (NC2C) transformation task. The accuracy of the cycleGAN output was assessed by comparison to the contrast image. This pipeline is able to differentiate between visually incoherent soft tissue regions in non-contrast CT images. The CTAs generated from the non-contrast images bear strong resemblance to the ground truth. Here we describe a novel application of Generative Adversarial Network for CT image processing. This is poised to disrupt clinical pathways requiring contrast enhanced CT imaging.

eess.IV↗

arXiv2020

A Deep Learning Approach to Automate High-Resolution Blood Vessel Reconstruction on Computerized Tomography Images With or Without the Use of Contrast Agent

Existing methods to reconstruct vascular structures from a computed tomography (CT) angiogram rely on injection of intravenous contrast to enhance the radio-density within the vessel lumen. However, pathological changes can be present in the blood lumen, vessel wall or a combination of both that prevent accurate reconstruction. In the example of aortic aneurysmal disease, a blood clot or thrombus adherent to the aortic wall within the expanding aneurysmal sac is present in 70-80% of cases. These deformations prevent the automatic extraction of vital clinically relevant information by current methods. In this study, we implemented a modified U-Net architecture with attention-gating to establish a high-throughput and automated segmentation pipeline of pathological blood vessels in CT images acquired with or without the use of a contrast agent. Twenty-six patients with paired non-contrast and contrast-enhanced CT images within the ongoing Oxford Abdominal Aortic Aneurysm (OxAAA) study were randomly selected, manually annotated and used for model training and evaluation (13/13). Data augmentation methods were implemented to diversify the training data set in a ratio of 10:1. The performance of our Attention-based U-Net in extracting both the inner lumen and the outer wall of the aortic aneurysm from CT angiograms (CTA) was compared against a generic 3-D U-Net and displayed superior results. Subsequent implementation of this network architecture within the aortic segmentation pipeline from both contrast-enhanced CTA and non-contrast CT images has allowed for accurate and efficient extraction of the entire aortic volume. This extracted volume can be used to standardize current methods of aneurysmal disease management and sets the foundation for subsequent complex geometric and morphological analysis. Furthermore, the proposed pipeline can be extended to other vascular pathologies.

eess.IV↗

arXiv2019

Efficient 3D Fully Convolutional Networks for Pulmonary Lobe Segmentation in CT Images

The human lung is a complex respiratory organ, consisting of five distinct anatomic compartments called lobes. Accurate and automatic segmentation of these pulmonary lobes from computed tomography (CT) images is of clinical importance for lung disease assessment and treatment planning. However, this task is challenging due to ambiguous lobar boundaries, anatomical variations and pathological deformations. In this paper, we propose a high-resolution and efficient 3D fully convolutional network to automatically segment the lobes. We refer to the network as Pulmonary Lobe Segmentation Network (PLS-Net), which is designed to efficiently exploit 3D spatial and contextual information from high-resolution volumetric CT images for effective volume-to-volume learning and inference. The PLS-Net is based on an asymmetric encoder-decoder architecture with three novel components: (i) 3D depthwise separable convolutions to improve the network efficiency by factorising each regular 3D convolution into two simpler operations; (ii) dilated residual dense blocks to efficiently expand the receptive field of the network and aggregate multi-scale contextual information for segmentation; and (iii) input reinforcement at each downsampled resolution to compensate for the loss of spatial information due to convolutional and downsampling operations. We evaluated the proposed PLS-Net on a multi-institutional dataset that consists of 210 CT images acquired from patients with a wide range of lung abnormalities. Experimental results show that our PLS-Net achieves state-of-the-art performance with better computational efficiency. Further experiments confirm the effectiveness of each novel component of the PLS-Net.

eess.IV↗