Alejandro F Frangi
@manchester.ac.uk
University of Manchester
RESEARCH, TEACHING, or OTHER INTERESTS
Multidisciplinary, Computer Vision and Pattern Recognition, Biomedical Engineering, Management Science and Operations Research
Scopus Publications
Scholar Citations
Scholar h-index
Scholar i10-index
Scopus Publications
Rodrigo Bonazzola, Enzo Ferrante, Nishant Ravikumar, Yan Xia, Bernard Keavney, Sven Plein, Tanveer Syeda-Mahmood, and Alejandro F. Frangi
Springer Science and Business Media LLC
AbstractRecent genome-wide association studies have successfully identified associations between genetic variants and simple cardiac morphological parameters derived from cardiac magnetic resonance images. However, the emergence of large databases, including genetic data linked to cardiac magnetic resonance facilitates the investigation of more nuanced patterns of cardiac shape variability than those studied so far. Here we propose a framework for gene discovery coined unsupervised phenotype ensembles. The unsupervised phenotype ensemble builds a redundant yet highly expressive representation by pooling a set of phenotypes learnt in an unsupervised manner, using deep learning models trained with different hyperparameters. These phenotypes are then analysed via genome-wide association studies, retaining only highly confident and stable associations across the ensemble. We applied our approach to the UK Biobank database to extract geometric features of the left ventricle from image-derived three-dimensional meshes. We demonstrate that our approach greatly improves the discoverability of genes that influence left ventricle shape, identifying 49 loci with study-wide significance and 25 with suggestive significance. We argue that our approach would enable more extensive discovery of gene associations with image-derived phenotypes for other organs or image modalities.
Michael MacRaild, Ali Sarrami-Foroushani, Toni Lassila, and Alejandro F. Frangi
The Royal Society
Vascular flow modelling can improve our understanding of vascular pathologies and aid in developing safe and effective medical devices. Vascular flow models typically involve solving the nonlinear Navier–Stokes equations in complex anatomies and using physiological boundary conditions, often presenting a multi-physics and multi-scale computational problem to be solved. This leads to highly complex and expensive models that require excessive computational time. This review explores accelerated simulation methodologies, specifically focusing on computational vascular flow modelling. We review reduced order modelling (ROM) techniques like zero-/one-dimensional and modal decomposition-based ROMs and machine learning (ML) methods including ML-augmented ROMs, ML-based ROMs and physics-informed ML models. We discuss the applicability of each method to vascular flow acceleration and the effectiveness of the method in addressing domain-specific challenges. When available, we provide statistics on accuracy and speed-up factors for various applications related to vascular flow simulation acceleration. Our findings indicate that each type of model has strengths and limitations depending on the context. To accelerate real-world vascular flow problems, we propose future research on developing multi-scale acceleration methods capable of handling the significant geometric variability inherent to such problems.
Haoran Dou, Seppo Virtanen, Nishant Ravikumar, and Alejandro F. Frangi
Institute of Electrical and Electronics Engineers (IEEE)
Generating virtual organ populations that capture sufficient variability while remaining plausible is essential to conduct in silico trials (ISTs) of medical devices. However, not all anatomical shapes of interest are always available for each individual in a population. The imaging examinations and modalities used can vary between subjects depending on their individualized clinical pathways. Different imaging modalities may have various fields of view and are sensitive to signals from other tissues/organs, or both. Hence, missing/partially overlapping anatomical information is often available across individuals. We introduce a generative shape model for multipart anatomical structures, learnable from sets of unpaired datasets, i.e., where each substructure in the shape assembly comes from datasets with missing or partially overlapping substructures from disjoint subjects of the same population. The proposed generative model can synthesize complete multipart shape assemblies coined virtual chimeras (VCs). We applied this framework to build VCs from databases of whole-heart shape assemblies that each contribute samples for heart substructures. Specifically, we propose a graph neural network-based generative shape compositional framework, which comprises two components, a part-aware generative shape model that captures the variability in shape observed for each structure of interest in the training population and a spatial composition network that assembles/composes the structures synthesized by the former into multipart shape assemblies (i.e., VCs). We also propose a novel self-supervised learning scheme that enables the spatial composition network to be trained with partially overlapping data and weak labels. We trained and validated our approach using shapes of cardiac structures derived from cardiac magnetic resonance (MR) images in the UK Biobank (UKBB). When trained with complete and partially overlapping data, our approach significantly outperforms a principal component analysis (PCA)-based shape model (trained with complete data) in terms of generalizability and specificity. This demonstrates the superiority of the proposed method, as the synthesized cardiac virtual populations are more plausible and capture a greater degree of shape variability than those generated by the PCA-based shape model.
Yash Deo, Haoran Dou, Nishant Ravikumar, Alejandro F. Frangi, and Toni Lassila
Springer Nature Switzerland
Zain Girach, Arni Sarian, Cynthia Maldonado-García, Nishant Ravikumar, Panagiotis I. Sergouniotis, Peter M. Rothwell, Alejandro F. Frangi, and Thomas H. Julian
Springer Science and Business Media LLC
Abstract Background Stroke is a leading cause of morbidity and mortality. Retinal imaging allows non-invasive assessment of the microvasculature. Consequently, retinal imaging is a technology which is garnering increasing attention as a means of assessing cardiovascular health and stroke risk. Methods A biomedical literature search was performed to identify prospective studies that assess the role of retinal imaging derived biomarkers as indicators of stroke risk. Results Twenty-four studies were included in this systematic review. The available evidence suggests that wider retinal venules, lower fractal dimension, increased arteriolar tortuosity, presence of retinopathy, and presence of retinal emboli are associated with increased likelihood of stroke. There is weaker evidence to suggest that narrower arterioles and the presence of individual retinopathy traits such as microaneurysms and arteriovenous nicking indicate increased stroke risk. Our review identified three models utilizing artificial intelligence algorithms for the analysis of retinal images to predict stroke. Two of these focused on fundus photographs, whilst one also utilized optical coherence tomography (OCT) technology images. The constructed models performed similarly to conventional risk scores but did not significantly exceed their performance. Only two studies identified in this review used OCT imaging, despite the higher dimensionality of this data. Conclusion Whilst there is strong evidence that retinal imaging features can be used to indicate stroke risk, there is currently no predictive model which significantly outperforms conventional risk scores. To develop clinically useful tools, future research should focus on utilization of deep learning algorithms, validation in external cohorts, and analysis of OCT images.
Nurbanu Aksoy, Serge Sharoff, Selcuk Baser, Nishant Ravikumar, and Alejandro F. Frangi
Frontiers Media SA
Image-to-text radiology report generation aims to automatically produce radiology reports that describe the findings in medical images. Most existing methods focus solely on the image data, disregarding the other patient information accessible to radiologists. In this paper, we present a novel multi-modal deep neural network framework for generating chest x-rays reports by integrating structured patient data, such as vital signs and symptoms, alongside unstructured clinical notes. We introduce a conditioned cross-multi-head attention module to fuse these heterogeneous data modalities, bridging the semantic gap between visual and textual data. Experiments demonstrate substantial improvements from using additional modalities compared to relying on images alone. Notably, our model achieves the highest reported performance on the ROUGE-L metric compared to relevant state-of-the-art models in the literature. Furthermore, we employed both human evaluation and clinical semantic similarity measurement alongside word-overlap metrics to improve the depth of quantitative analysis. A human evaluation, conducted by a board-certified radiologist, confirms the model’s accuracy in identifying high-level findings, however, it also highlights that more improvement is needed to capture nuanced details and clinical context.
Asma Alzaid, Beth Lineham, Sanja Dogramadzi, Hemant Pandit, Alejandro F. Frangi, and Sheng Quan Xie
Institute of Electrical and Electronics Engineers (IEEE)
The assessment of implant status and complications of Total Hip Replacement (THR) relies mainly on the clinical evaluation of the X-ray images to analyse the implant and the surrounding rigid structures. Current clinical practise depends on the manual identification of important landmarks to define the implant boundary and to analyse many features in arthroplasty X-ray images, which is time-consuming and could be prone to human error. Semantic segmentation based on the convolutional neural network (CNN) has demonstrated successful results in many medical segmentation tasks. However, these networks cannot define explicit properties that lead to inaccurate segmentation, especially with the limited size of image datasets. Our work integrates clinical knowledge with CNN to segment the implant and detect important features simultaneously. This is instrumental in the diagnosis of complications of arthroplasty, particularly for loose implant and implant-closed bone fractures, where the location of the fracture in relation to the implant must be accurately determined. In this work, we define the points of interest using Gruen zones that represent the interface of the implant with the surrounding bone to build a Statistical Shape Model (SSM). We propose a multitask CNN that combines regression of pose and shape parameters constructed from the SSM and semantic segmentation of the implant. This integrated approach has improved the estimation of implant shape, from 74% to 80% dice score, making segmentation realistic and allowing automatic detection of Gruen zones. To train and evaluate our method, we generated a dataset of annotated hip arthroplasty X-ray images that will be made available.
Shahabedin Nabavi, Hossein Simchi, Mohsen Ebrahimi Moghaddam, Ahmad Ali Abin, and Alejandro F. Frangi
Elsevier BV
Mohsen Farzi, Sam Coveney, Maryam Afzali, Marie‐Christine Zdora, Craig A. Lygate, Christoph Rau, Alejandro F. Frangi, Erica Dall'Armellina, Irvin Teh, and Jürgen E. Schneider
Wiley
PurposeThis paper presents a hierarchical modeling approach for estimating cardiomyocyte major and minor diameters and intracellular volume fraction (ICV) using diffusion‐weighted MRI (DWI) data in ex vivo mouse hearts.MethodsDWI data were acquired on two healthy controls and two hearts 3 weeks post transverse aortic constriction (TAC) using a bespoke diffusion scheme with multiple diffusion times (), q‐shells and diffusion encoding directions. Firstly, a bi‐exponential tensor model was fitted separately at each diffusion time to disentangle the dependence on diffusion times from diffusion weightings, that is, b‐values. The slow‐diffusing component was attributed to the restricted diffusion inside cardiomyocytes. ICV was then extrapolated at using linear regression. Secondly, given the secondary and the tertiary diffusion eigenvalue measurements for the slow‐diffusing component obtained at different diffusion times, major and minor diameters were estimated assuming a cylinder model with an elliptical cross‐section (ECS). High‐resolution three‐dimensional synchrotron X‐ray imaging (SRI) data from the same specimen was utilized to evaluate the biophysical parameters.ResultsEstimated parameters using DWI data were (control 1/control 2 vs. TAC 1/TAC 2): major diameter—17.4 m/18.0 m versus 19.2 m/19.0 m; minor diameter—10.2 m/9.4 m versus 12.8 m/13.4 m; and ICV—62%/62% versus 68%/47%. These findings were consistent with SRI measurements.ConclusionThe proposed method allowed for accurate estimation of biophysical parameters suggesting cardiomyocyte diameters as sensitive biomarkers of hypertrophy in the heart.
Huaifei Hu, Ning Pan, and Alejandro F. Frangi
Elsevier BV
Qiongyao Liu, Ali Sarrami-Foroushani, Yongxing Wang, Michael MacRaild, Christopher Kelly, Fengming Lin, Yan Xia, Shuang Song, Nishant Ravikumar, Tufail Patankar,et al.
AIP Publishing
How prevalent is spontaneous thrombosis in a population containing all sizes of intracranial aneurysms? How can we calibrate computational models of thrombosis based on published data? How does spontaneous thrombosis differ in normo- and hypertensive subjects? We address the first question through a thorough analysis of published datasets that provide spontaneous thrombosis rates across different aneurysm characteristics. This analysis provides data for a subgroup of the general population of aneurysms, namely, those of large and giant size (>10 mm). Based on these observed spontaneous thrombosis rates, our computational modeling platform enables the first in silico observational study of spontaneous thrombosis prevalence across a broader set of aneurysm phenotypes. We generate 109 virtual patients and use a novel approach to calibrate two trigger thresholds: residence time and shear rate, thus addressing the second question. We then address the third question by utilizing this calibrated model to provide new insight into the effects of hypertension on spontaneous thrombosis. We demonstrate how a mechanistic thrombosis model calibrated on an intracranial aneurysm cohort can help estimate spontaneous thrombosis prevalence in a broader aneurysm population. This study is enabled through a fully automatic multi-scale modeling pipeline. We use the clinical spontaneous thrombosis data as an indirect population-level validation of a complex computational modeling framework. Furthermore, our framework allows exploration of the influence of hypertension in spontaneous thrombosis. This lays the foundation for in silico clinical trials of cerebrovascular devices in high-risk populations, e.g., assessing the performance of flow diverters in aneurysms for hypertensive patients.
Yan Xia, Nishant Ravikumar, Toni Lassila, and Alejandro F. Frangi
Elsevier BV
Mingyuan Luo, Xin Yang, Hongzhang Wang, Haoran Dou, Xindi Hu, Yuhao Huang, Nishant Ravikumar, Songcheng Xu, Yuanji Zhang, Yi Xiong,et al.
Elsevier BV
Selin Aviyente, Alejandro F. Frangi, Erik Meijering, Arrate Muñoz-Barrutia, Michael Liebling, Dimitri Van De Ville, Jean-Christophe Olivo-Marin, Jelena Kovačević, and Michael Unser
Institute of Electrical and Electronics Engineers (IEEE)
The Bio Image and Signal Processing (BISP) Technical Committee (TC) of the IEEE Signal Processing Society (SPS) promotes activities within the broad technical field of biomedical image and signal processing. Areas of interest include medical and biological imaging, digital pathology, molecular imaging, microscopy, and associated computational imaging, image analysis, and image-guided treatment, alongside physiological signal processing, computational biology, and bioinformatics. BISP has 40 members and covers a wide range of EDICS, including CIS-MI: Medical Imaging, BIO-MIA: Medical Image Analysis, BIO-BI: Biological Imaging, BIO: Biomedical Signal Processing, BIO-BCI: Brain/Human-Computer Interfaces, and BIO-INFR: Bioinformatics. BISP plays a central role in the organization of the IEEE International Symposium on Biomedical Imaging (ISBI) and contributes to the technical sessions at the IEEE International Conference on Acoustics, Speech and Signal Processing (ICASSP), and the IEEE International Conference on Image Processing (ICIP). In this paper, we provide a brief history of the TC, review the technological and methodological contributions its community delivered, and highlight promising new directions we anticipate.
Behnaz Elhaminia, Alexandra Gilbert, John Lilley, Moloud Abdar, Alejandro F. Frangi, Andrew Scarsbrook, Ane Appelt, and Ali Gooya
Institute of Electrical and Electronics Engineers (IEEE)
Modern radiotherapy delivers treatment plans optimised on an individual patient level, using CT-based 3D models of patient anatomy. This optimisation is fundamentally based on simple assumptions about the relationship between radiation dose delivered to the cancer (increased dose will increase cancer control) and normal tissue (increased dose will increase rate of side effects). The details of these relationships are still not well understood, especially for radiation-induced toxicity. We propose a convolutional neural network based on multiple instance learning to analyse toxicity relationships for patients receiving pelvic radiotherapy. A dataset comprising of 315 patients were included in this study; with 3D dose distributions, pre-treatment CT scans with annotated abdominal structures, and patient-reported toxicity scores provided for each participant. In addition, we propose a novel mechanism for segregating the attentions over space and dose/imaging features independently for a better understanding of the anatomical distribution of toxicity. Quantitative and qualitative experiments were performed to evaluate the network performance. The proposed network could predict toxicity with 80% accuracy. Attention analysis over space demonstrated that there was a significant association between radiation dose to the anterior and right iliac of the abdomen and patient-reported toxicity. Experimental results showed that the proposed network had outstanding performance for toxicity prediction, localisation and explanation with the ability of generalisation for an unseen dataset.
Fengming Lin, Yan Xia, Shuang Song, Nishant Ravikumar, and Alejandro F. Frangi
Elsevier BV
Amin Kassab-Bachi, Nishant Ravikumar, Ruth K. Wilcox, Alejandro F. Frangi, and Zeike A. Taylor
Springer Science and Business Media LLC
Huazhu Fu, Yitian Zhao, Pew-Thian Yap, Carola-Bibiane Schönlieb, and Alejandro F. Frangi
Institute of Electrical and Electronics Engineers (IEEE)
Xuegang Song, Feng Zhou, Alejandro F. Frangi, Jiuwen Cao, Xiaohua Xiao, Yi Lei, Tianfu Wang, and Baiying Lei
Institute of Electrical and Electronics Engineers (IEEE)
For significant memory concern (SMC) and mild cognitive impairment (MCI), their classification performance is limited by confounding features, diverse imaging protocols, and limited sample size. To address the above limitations, we introduce a dual-modality fused brain connectivity network combining resting-state functional magnetic resonance imaging (fMRI) and diffusion tensor imaging (DTI), and propose three mechanisms in the current graph convolutional network (GCN) to improve classifier performance. First, we introduce a DTI-strength penalty term for constructing functional connectivity networks. Stronger structural connectivity and bigger structural strength diversity between groups provide a higher opportunity for retaining connectivity information. Second, a multi-center attention graph with each node representing a subject is proposed to consider the influence of data source, gender, acquisition equipment, and disease status of those training samples in GCN. The attention mechanism captures their different impacts on edge weights. Third, we propose a multi-channel mechanism to improve filter performance, assigning different filters to features based on feature statistics. Applying those nodes with low-quality features to perform convolution would also deteriorate filter performance. Therefore, we further propose a pooling mechanism, which introduces the disease status information of those training samples to evaluate the quality of nodes. Finally, we obtain the final classification results by inputting the multi-center attention graph into the multi-channel pooling GCN. The proposed method is tested on three datasets (i.e., an ADNI 2 dataset, an ADNI 3 dataset, and an in-house dataset). Experimental results indicate that the proposed method is effective and superior to other related algorithms, with a mean classification accuracy of 93.05% in our binary classification tasks. Our code is available at: https://github.com/Xuegang-S.
Jianyang Xie, Quanyong Yi, Yufei Wu, Yalin Zheng, Yonghuai Liu, Antonella Macerollo, Huazhu Fu, Yanwu Xu, Jiong Zhang, Ardhendu Behera,et al.
BMJ
BackgroundOptical coherence tomography angiography (OCTA) enables fast and non-invasive high-resolution imaging of retinal microvasculature and is suggested as a potential tool in the early detection of retinal microvascular changes in Alzheimer’s Disease (AD). We developed a standardised OCTA analysis framework and compared their extracted parameters among controls and AD/mild cognitive impairment (MCI) in a cross-section study.MethodsWe defined and extracted geometrical parameters of retinal microvasculature at different retinal layers and in the foveal avascular zone (FAZ) from segmented OCTA images obtained using well-validated state-of-the-art deep learning models. We studied these parameters in 158 subjects (62 healthy control, 55 AD and 41 MCI) using logistic regression to determine their potential in predicting the status of our subjects.ResultsIn the AD group, there was a significant decrease in vessel area and length densities in the inner vascular complexes (IVC) compared with controls. The number of vascular bifurcations in AD is also significantly lower than that of healthy people. The MCI group demonstrated a decrease in vascular area, length densities, vascular fractal dimension and the number of bifurcations in both the superficial vascular complexes (SVC) and the IVC compared with controls. A larger vascular tortuosity in the IVC, and a larger roundness of FAZ in the SVC, can also be observed in MCI compared with controls.ConclusionOur study demonstrates the applicability of OCTA for the diagnosis of AD and MCI, and provides a standard tool for future clinical service and research. Biomarkers from retinal OCTA images can provide useful information for clinical decision-making and diagnosis of AD and MCI.
Zhenhong Liu, Xingce Wang, Zhongke Wu, Yi-Cheng Zhu, and Alejandro F. Frangi
IEEE
Magnetic resonance imaging (MRI) scans often suffer from noise and low-resolution (LR), which affect the diagnosis and treatment results obtained for patients. LR images and noise come together with MRI, and the existing methods solve image super-resolution (SR) reconstruction and denoising tasks in a step-by-step manner, which influences the overall real distribution of the MRI data. In this paper, we present a simultaneous SR and denoising algorithm based on a stochastic normalizing flow (SNF), named the MR image SR and denoising model based on an SNF (SRDSNF). SRDSNF adds the encoded information of the input image as the conditional information to each reverse step of the stochastic normalizing flow, which realizes a consistent description of the spatial distribution between the reconstruction result and the input image. We introduce rangenull space decomposition and subsequence sampling strategies to enhance the consistency of the input and output data and increase the generation speed of the model. Simultaneous SR and denoising tasks experiment is carried out using the BrainWeb and NFBS datasets. The experimental results show that good SR and denoising results are obtained with fewer sampling steps, these results are consistent with the ground truths, and the structural similarity and peak signal-to-noise ratio of the results are also higher than those of the comparison methods. The proposed method demonstrates potential clinical promise.
Shahabedin Nabavi, Mohsen Ebrahimi Moghaddam, Ahmad Ali Abin, and Alejandro F. Frangi
IEEE
Cardiovascular magnetic resonance (CMR) imaging is a radiation-free modality widely used for functional and structural evaluation of the cardiovascular system. Achieving an accurate diagnosis requires having good-quality images. Subjective CMR image quality assessment is a tedious, time-consuming and costly process. This paper presents an automated scoring framework for CMR image quality assessment that uses deep learning models to evaluate left ventricular coverage and CMR imaging artefacts. The quality scoring in the proposed framework is an attempt to automate some of the subjective quality control criteria of the EuroCMR registry for the short-axis cine steady-state free precession (SSFP) CMR images. The scores given by a radiologist and a cardiologist with experience in CMR imaging for the images of 50 subjects from the UK Biobank were used to validate the proposed framework. The Pearson correlation coefficient (PCC) and the Spearman rank-order correlation coefficient (SRCC) calculated for the experts’ quality scores versus ones obtained from the proposed framework are 0.908 and 0.806 on average. The results show that the quality scoring by the proposed framework is highly correlated with the experts’ opinions. The proposed framework can be used for post-imaging quality assessment of short-axis cine SSFP CMR images and quality control of large population studies such as the UK Biobank.
Arezoo Zakeri, Yan Xia, Nishant Ravikumar, and Alejandro F. Frangi
Elsevier
Alejandro F. Frangi, Jerry L. Prince, and Milan Sonka
Elsevier