arXiv subjects

Abhirup Banerjee

Publications and source records attributed to Abhirup Banerjee.

At least 19 recordsLinked to original sources

arXiv2026

Decoupling Wavelet Sub-bands for Single Source Domain Generalization in Fundus Image Segmentation

Domain generalization in fundus imaging is challenging due to variations in acquisition conditions across devices and clinical settings. The inability to adapt to these variations causes performance degradation on unseen domains for deep learning models. Besides, obtaining annotated data across domains is often expensive and privacy constraints restricts their availability. Although single-source domain generalization (SDG) offers a realistic solution to this problem, the existing approaches frequently fail to capture anatomical topology or decouple appearance from anatomical features. This research introduces WaveSDG, a new wavelet-guided segmentation network for SDG. It decouples anatomical structure from domain-specific appearance through a wavelet sub-band decomposition. A novel Wavelet-based Invariant Structure Extraction and Refinement (WISER) module is proposed to process encoder features by leveraging distinct semantic roles of each wavelet sub-band. The module refines low-frequency components to anchor global anatomy, while selectively enhancing directional edges and suppressing noise within the high-frequency sub-bands. Extensive ablation studies validate the effectiveness of the WISER module and its decoupling strategy. Our evaluations on optic cup and optic disc segmentation across one source and five unseen target datasets show that WaveSDG consistently outperforms seven state-of-the-art methods. Notably, it achieves the best balanced Dice score and lowest 95th percentile Hausdorff distance with reduced variance, indicating improved accuracy, robustness, and cross-domain stability.

cs.CV↗

arXiv2026

Weakly Supervised Patch Annotation for Improved Screening of Diabetic Retinopathy

Diabetic Retinopathy (DR) requires timely screening to prevent irreversible vision loss. However, its early detection remains a significant challenge since often the subtle pathological manifestations (lesions) get overlooked due to insufficient annotation. Existing literature primarily focuses on image-level supervision, weakly-supervised localization, and clustering-based representation learning, which fail to systematically annotate unlabeled lesion region(s) for refining the dataset. Expert-driven lesion annotation is labor-intensive and often incomplete, limiting the performance of deep learning models. We introduce Similarity-based Annotation via Feature-space Ensemble (SAFE), a two-stage framework that unifies weak supervision, contrastive learning, and patch-wise embedding inference, to systematically expand sparse annotations in the pathology. SAFE preserves fine-grained details of the lesion(s) under partial clinical supervision. In the first stage, a dual-arm Patch Embedding Network learns semantically structured, class-discriminative embeddings from expert annotated patches. Next, an ensemble of independent embedding spaces extrapolates labels to the unannotated regions based on spatial and semantic proximity. An abstention mechanism ensures trade-off between highly reliable annotation and noisy coverage. Experimental results demonstrate reliable separation of healthy and diseased patches, achieving upto 0.9886 accuracy. The annotation generated from SAFE substantially improves downstream tasks such as DR classification, demonstrating a substantial increase in F1-score of the diseased class and a performance gain as high as 0.545 in Area Under the Precision-Recall Curve (AUPRC). Qualitative analysis, with explainability, confirms that SAFE focuses on clinically relevant lesion patterns; and is further validated by ophthalmologists.

cs.CV↗

arXiv2025

Female anatomies disguise ECG abnormalities following myocardial infarction: an AI-enabled modelling and simulation study

The electrocardiogram (ECG) is modulated by torso-heart anatomy, and this challenges patients' diagnosis and risk stratification. This study aims to quantify how torso-heart anatomical factors affect sex-differences in ECG biomarkers in acute and chronic myocardial infarction (MI). We exploit the perfect control of AI-augmented multiscale modelling and simulation, based on clinical magnetic resonance imaging (MRI) data and ECGs for model construction and validation. A cohort of 1720 torso-ventricular anatomies (50% female) was constructed from MRIs of healthy and post-MI participants in the UK Biobank study. 8600 ECG simulations were performed considering anatomical variability and 3 electrophysiological stages (healthy, acutely ischemic, and infarcted). The effect of cardiac size, position, and orientation on each ECG biomarker was quantified. Female anatomies had larger distances between the infarct and ECG electrodes (relative to cardiac size), and larger angles between the infarct normal and ECG lead axes, both primarily caused by their more superior cardiac position. This reduced ST-elevation and caused low-amplitude late depolarisation and repolarisation tails to be missed, shortening QRS duration (QRSd) and T-peak-to-end interval (TpTe). The position and orientation of the heart impacted TpTe more severely than QRSd. AI-enabled mechanistic modelling and simulation identify smaller ventricles, superior cardiac position, and different ventricular orientation as key anatomical contributors of shorter QRS and T waves, and lower ST-elevation, in female versus male anatomies. This provides a blueprint for quantifying the impact of anatomical sex differences on functional markers and enables future work in tailoring clinical guidelines considering unique patient anatomy to reduce biased outcomes.

physics.med-ph↗

arXiv2025

HeartFormer: Semantic-Aware Dual-Structure Transformers for 3D Four-Chamber Cardiac Point Cloud Reconstruction

We present the first geometric deep learning framework based on point cloud representation for 3D four-chamber cardiac reconstruction from cine MRI data. This work addresses a long-standing limitation in conventional cine MRI, which typically provides only 2D slice images of the heart, thereby restricting a comprehensive understanding of cardiac morphology and physiological mechanisms in both healthy and pathological conditions. To overcome this, we propose \textbf{HeartFormer}, a novel point cloud completion network that extends traditional single-class point cloud completion to the multi-class. HeartFormer consists of two key components: a Semantic-Aware Dual-Structure Transformer Network (SA-DSTNet) and a Semantic-Aware Geometry Feature Refinement Transformer Network (SA-GFRTNet). SA-DSTNet generates an initial coarse point cloud with both global geometry features and substructure geometry features. Guided by these semantic-geometry representations, SA-GFRTNet progressively refines the coarse output, effectively leveraging both global and substructure geometric priors to produce high-fidelity and geometrically consistent reconstructions. We further construct \textbf{HeartCompv1}, the first publicly available large-scale dataset with 17,000 high-resolution 3D multi-class cardiac meshes and point-clouds, to establish a general benchmark for this emerging research direction. Extensive cross-domain experiments on HeartCompv1 and UK Biobank demonstrate that HeartFormer achieves robust, accurate, and generalizable performance, consistently surpassing state-of-the-art (SOTA) methods. Code and dataset will be released upon acceptance at: https://github.com/10Darren/HeartFormer.

cs.CV↗

arXiv2025

AngioDG: Interpretable Channel-informed Feature-modulated Single-source Domain Generalization for Coronary Vessel Segmentation in X-ray Angiography

Cardiovascular diseases are the leading cause of death globally, with X-ray Coronary Angiography (XCA) as the gold standard during real-time cardiac interventions. Segmentation of coronary vessels from XCA can facilitate downstream quantitative assessments, such as measurement of the stenosis severity and enhancing clinical decision-making. However, developing generalizable vessel segmentation models for XCA is challenging due to variations in imaging protocols and patient demographics that cause domain shifts. These limitations are exacerbated by the lack of annotated datasets, making Single-source Domain Generalization (SDG) a necessary solution for achieving generalization. Existing SDG methods are largely augmentation-based, which may not guarantee the mitigation of overfitting to augmented or synthetic domains. We propose a novel approach, ``AngioDG", to bridge this gap by channel regularization strategy to promote generalization. Our method identifies the contributions of early feature channels to task-specific metrics for DG, facilitating interpretability, and then reweights channels to calibrate and amplify domain-invariant features while attenuating domain-specific ones. We evaluate AngioDG on 6 x-ray angiography datasets for coronary vessels segmentation, achieving the best out-of-distribution performance among the compared methods, while maintaining consistent in-domain test performance.

cs.CV↗

arXiv2025

From 2D to 3D, Deep Learning-based Shape Reconstruction in Magnetic Resonance Imaging: A Review

Deep learning-based 3-dimensional (3D) shape reconstruction from 2-dimensional (2D) magnetic resonance imaging (MRI) has become increasingly important in medical disease diagnosis, treatment planning, and computational modeling. This review surveys the methodological landscape of 3D MRI reconstruction, focusing on 4 primary approaches: point cloud, mesh-based, shape-aware, and volumetric models. For each category, we analyze the current state-of-the-art techniques, their methodological foundation, limitations, and applications across anatomical structures. We provide an extensive overview ranging from cardiac to neurological to lung imaging. We also focus on the clinical applicability of models to diseased anatomy, and the influence of their training and testing data. We examine publicly available datasets, computational demands, and evaluation metrics. Finally, we highlight the emerging research directions including multimodal integration and cross-modality frameworks. This review aims to provide researchers with a structured overview of current 3D reconstruction methodologies to identify opportunities for advancing deep learning towards more robust, generalizable, and clinically impactful solutions.

cs.LG↗

arXiv2025

3D Cardiac Anatomy Generation Using Mesh Latent Diffusion Models

Diffusion models have recently gained immense interest for their generative capabilities, specifically the high quality and diversity of the synthesized data. However, examples of their applications in 3D medical imaging are still scarce, especially in cardiology. Generating diverse realistic cardiac anatomies is crucial for applications such as in silico trials, electromechanical computer simulations, or data augmentations for machine learning models. In this work, we investigate the application of Latent Diffusion Models (LDMs) for generating 3D meshes of human cardiac anatomies. To this end, we propose a novel LDM architecture -- MeshLDM. We apply the proposed model on a dataset of 3D meshes of left ventricular cardiac anatomies from patients with acute myocardial infarction and evaluate its performance in terms of both qualitative and quantitative clinical and 3D mesh reconstruction metrics. The proposed MeshLDM successfully captures characteristics of the cardiac shapes at end-diastolic (relaxation) and end-systolic (contraction) cardiac phases, generating meshes with a 2.4% difference in population mean compared to the gold standard.

eess.IV↗

arXiv2025

An Automated Computational Pipeline for Generating Large-Scale Cohorts of Patient-Specific Ventricular Models in Electromechanical In Silico Trials

In recent years, human in silico trials have gained significant traction as a powerful approach to evaluate the effects of drugs, clinical interventions, and medical devices. In silico trials not only minimise patient risks but also reduce reliance on animal testing. However, the implementation of in silico trials presents several time-consuming challenges. It requires the creation of large cohorts of virtual patients. Each virtual patient is described by their anatomy with a volumetric mesh and electrophysiological and mechanical dynamics through mathematical equations and parameters. Furthermore, simulated conditions need definition including stimulation protocols and therapy evaluation. For large virtual cohorts, this requires automatic and efficient pipelines for generation of corresponding files. In this work, we present a computational pipeline to automatically create large virtual patient cohort files to conduct large-scale in silico trials through cardiac electromechanical simulations. The pipeline generates the files describing meshes, labels, and data required for the simulations directly from unprocessed surface meshes. We applied the pipeline to generate over 100 virtual patients from various datasets and performed simulations to demonstrate capacity to conduct in silico trials for virtual patients using verified and validated electrophysiology and electromechanics models for the context of use. The proposed pipeline is adaptable to accommodate different types of ventricular geometries and mesh processing tools, ensuring its versatility in handling diverse clinical datasets. By establishing an automated framework for large scale simulation studies as required for in silico trials and providing open-source code, our work aims to support scalable, personalised cardiac simulations in research and clinical applications.

cs.CE↗

arXiv2025

Personalized Topology-Informed Localization of Standard 12-Lead ECG Electrode Placement from Incomplete Cardiac MRIs for Efficient Cardiac Digital Twins

Cardiac digital twins (CDTs) offer personalized in-silico cardiac representations for the inference of multi-scale properties tied to cardiac mechanisms. The creation of CDTs requires precise information about the electrode position on the torso, especially for the personalized electrocardiogram (ECG) calibration. However, current studies commonly rely on additional acquisition of torso imaging and manual/semi-automatic methods for ECG electrode localization. In this study, we propose a novel and efficient topology-informed model to fully automatically extract personalized ECG standard electrode locations from 2D clinically standard cardiac MRIs. Specifically, we obtain the sparse torso contours from the cardiac MRIs and then localize the standard electrodes of 12-lead ECG from the contours. Cardiac MRIs aim at imaging of the heart instead of the torso, leading to incomplete torso geometry within the imaging. To tackle the missing topology, we incorporate the electrodes as a subset of the keypoints, which can be explicitly aligned with the 3D torso topology. The experimental results demonstrate that the proposed model outperforms the time-consuming conventional model projection-based method in terms of accuracy (Euclidean distance: $1.24 \pm 0.293$ cm vs. $1.48 \pm 0.362$ cm) and efficiency ($2$~s vs. $30$-$35$~min). We further demonstrate the effectiveness of using the detected electrodes for in-silico ECG simulation, highlighting their potential for creating accurate and efficient CDT models. The code is available at https://github.com/lileitech/12lead_ECG_electrode_localizer.

eess.IV↗

arXiv2025

Network science disentangles internal climate variability in global spatial dependence structures

A comprehensive characterization of internal climate variability and irreducible uncertainty through initial-condition large ensembles of Earth system models across different spatiotemporal scales remains a significant challenge in climate science. In this study, we find significant differences in the spatial connectivity structures of temperature networks across ensemble members, with variations in long-range connections providing a distinguishing feature across the outcomes of initial conditions. Based on this, we introduce a novel quantifier, the 'Connectivity Ratio' (R), to encapsulate the spatial connectivity structure of each ensemble member by investigating the influence of internal climate variability on the global connectivity patterns in air temperatures. R allows us to characterize the variability of spatial dependence structure across the initial condition ensemble members as well as multiple models. Furthermore, we examine changes in spatial connectivity between near-term and long-term projections using R, which shows a potential shift in climate predictability under anthropogenic influence on a spatial scale.

physics.ao-ph↗

arXiv2024

DeepCA: Deep Learning-based 3D Coronary Artery Tree Reconstruction from Two 2D Non-simultaneous X-ray Angiography Projections

Cardiovascular diseases (CVDs) are the most common cause of death worldwide. Invasive x-ray coronary angiography (ICA) is one of the most important imaging modalities for the diagnosis of CVDs. ICA typically acquires only two 2D projections, which makes the 3D geometry of coronary vessels difficult to interpret, thus requiring 3D coronary artery tree reconstruction from two projections. State-of-the-art approaches require significant manual interactions and cannot correct the non-rigid cardiac and respiratory motions between non-simultaneous projections. In this study, we propose a novel deep learning pipeline named \emph{DeepCA}. We leverage the Wasserstein conditional generative adversarial network with gradient penalty, latent convolutional transformer layers, and a dynamic snake convolutional critic to implicitly compensate for the non-rigid motion and provide 3D coronary artery tree reconstruction. Through simulating projections from coronary computed tomography angiography (CCTA), we achieve the generalisation of 3D coronary tree reconstruction on real non-simultaneous ICA projections. We incorporate an application-specific evaluation metric to validate our proposed model on both a CCTA dataset and a real ICA dataset, together with Chamfer $\ell_2$ distance. The results demonstrate promising performance of our DeepCA model in vessel topology preservation, recovery of missing features, and generalisation ability to real ICA data. To the best of our knowledge, this is the first study that leverages deep learning to achieve 3D coronary tree reconstruction from two real non-simultaneous x-ray angiographic projections.

eess.IV↗

arXiv2024

NeCA: 3D Coronary Artery Tree Reconstruction from Two 2D Projections via Neural Implicit Representation

Cardiovascular diseases (CVDs) are the most common health threats worldwide. 2D X-ray invasive coronary angiography (ICA) remains the most widely adopted imaging modality for CVD assessment during real-time cardiac interventions. However, it is often difficult for cardiologists to interpret the 3D geometry of coronary vessels based on 2D planes. Moreover, due to the radiation limit, often only two angiographic projections are acquired, providing limited information of the vessel geometry and necessitating 3D coronary tree reconstruction based only on two ICA projections. In this paper, we propose a self-supervised deep learning method called NeCA, which is based on neural implicit representation using the multiresolution hash encoder and differentiable cone-beam forward projector layer, in order to achieve 3D coronary artery tree reconstruction from two 2D projections. We validate our method using six different metrics on a dataset generated from coronary computed tomography angiography of right coronary artery and left anterior descending artery. The evaluation results demonstrate that our NeCA method, without requiring 3D ground truth for supervision or large datasets for training, achieves promising performance in both vessel topology and branch-connectivity preservation compared to the supervised deep learning model.

eess.IV↗

arXiv2024

Local and Remote Forcing Factors of Heatwave in India -A Reanalysis and Adjoint model based study

Continental heatwaves can dramatically impact ecosystems and societies, e.g., by leading to excess mortality, wildfires, and harvest failures. With a warming climate, their impacts potentially intensify globally, but the Indian subcontinent appears to be particularly vulnerable to such extreme events. In this study, we use reanalysis and the adjoint of the atmospheric model, PlaSim, to identify drivers of heatwaves occurring April and May over north-central India. Reanalysis results suggest that the existence of high temperatures in the study region is highly sensitive to the low local soil moisture which is observed weeks before a heatwave commences. Soil moisture variability in northern India is influenced by moisture transport from the west during winter--spring. Preceding dry soil moisture conditions can be associated with a `persistent jet' conditions linked to atmospheric dynamical changes in the North Atlantic region. An associated northward shift in the upper tropospheric zonal wind occurs approximately a month prior to the heatwaves, influencing the area and intensity of western disturbances embedded in the jet stream. This weakens the moisture flow from the north of the Arabian Sea, further reducing soil moisture levels and creating conditions conducive to heatwaves. An adjoint sensitivity analysis and forward model perturbation experiments confirm the causal relationships for the proposed heatwave development mechanism over north-central India, identifying the remote influence of North Atlantic sea surface temperature variability on extreme temperatures in India. Our findings highlight the complex interplay of local and remote factors in heatwave development over India.

physics.ao-ph↗

arXiv2024

Feasibility and benefits of joint learning from MRI databases with different brain diseases and modalities for segmentation

Models for segmentation of brain lesions in multi-modal MRI are commonly trained for a specific pathology using a single database with a predefined set of MRI modalities, determined by a protocol for the specific disease. This work explores the following open questions: Is it feasible to train a model using multiple databases that contain varying sets of MRI modalities and annotations for different brain pathologies? Will this joint learning benefit performance on the sets of modalities and pathologies available during training? Will it enable analysis of new databases with different sets of modalities and pathologies? We develop and compare different methods and show that promising results can be achieved with appropriate, simple and practical alterations to the model and training framework. We experiment with 7 databases containing 5 types of brain pathologies and different sets of MRI modalities. Results demonstrate, for the first time, that joint training on multi-modal MRI databases with different brain pathologies and sets of modalities is feasible and offers practical benefits. It enables a single model to segment pathologies encountered during training in diverse sets of modalities, while facilitating segmentation of new types of pathologies such as via follow-up fine-tuning. The insights this study provides into the potential and limitations of this paradigm should prove useful for guiding future advances in the direction. Code and pretrained models: https://github.com/WenTXuL/MultiUnet

cs.CV↗

arXiv2024

Hunting imaging biomarkers in pulmonary fibrosis: Benchmarks of the AIIB23 challenge

Airway-related quantitative imaging biomarkers are crucial for examination, diagnosis, and prognosis in pulmonary diseases. However, the manual delineation of airway trees remains prohibitively time-consuming. While significant efforts have been made towards enhancing airway modelling, current public-available datasets concentrate on lung diseases with moderate morphological variations. The intricate honeycombing patterns present in the lung tissues of fibrotic lung disease patients exacerbate the challenges, often leading to various prediction errors. To address this issue, the 'Airway-Informed Quantitative CT Imaging Biomarker for Fibrotic Lung Disease 2023' (AIIB23) competition was organized in conjunction with the official 2023 International Conference on Medical Image Computing and Computer Assisted Intervention (MICCAI). The airway structures were meticulously annotated by three experienced radiologists. Competitors were encouraged to develop automatic airway segmentation models with high robustness and generalization abilities, followed by exploring the most correlated QIB of mortality prediction. A training set of 120 high-resolution computerised tomography (HRCT) scans were publicly released with expert annotations and mortality status. The online validation set incorporated 52 HRCT scans from patients with fibrotic lung disease and the offline test set included 140 cases from fibrosis and COVID-19 patients. The results have shown that the capacity of extracting airway trees from patients with fibrotic lung disease could be enhanced by introducing voxel-wise weighted general union loss and continuity loss. In addition to the competitive image biomarkers for prognosis, a strong airway-derived biomarker (Hazard ratio>1.5, p<0.0001) was revealed for survival prognostication compared with existing clinical measurements, clinician assessment and AI-based biomarkers.

eess.IV↗

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

Long-window tandem variational data assimilation methods for chaotic climate models tested with the Lorenz 63 system

4D-variational data assimilation is applied to the Lorenz '63 model to introduce a new method for parameter estimation in chaotic climate models. The approach aims to optimise an Earth system model (ESM), for which no adjoint exists, by utilising the adjoint of a different, potentially simpler ESM. This relies on the synchronisation of the model to observed data. Dynamical state and parameter estimation (DSPE) is used to stabilise the tangent linear system by reducing all positive Lyapunov exponents to negative values, thereby improving parameter estimation by enabling long assimilation windows. The method introduces a second layer of synchronisation between the two models, with and without an adjoint, to facilitate linearisation around the trajectory of the model for which no adjoint exists. This is achieved by synchronising two Lorenz '63 systems, one with and the other without an adjoint model. Results are presented for an idealised case of identical, perfect models and for a more realistic case in which they differ from one another. If employed on a high-resolution ESM for which a coarse resolution adjoint exists, the method will save computational resources as only one forward run with the full high-resolution ESM per iteration is needed. It is demonstrated that there is negligible error and uncertainty change compared to the traditional optimisation of a full ESM with an adjoint. Stemming from this approach, it is shown that the synchronisation between two identical models can be used to filter noisy data in a dynamical way which reduces the parametric uncertainty of the optimised model by approximately one third. Such a precision gain could prove valuable for seasonal, annual, and decadal predictions.

physics.ao-ph↗

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↗