Choon Hwai Yap

Md. Kamrul Hasan, Md. Asif Ahamad, Choon Hwai Yap et al.

The Computer-aided Diagnosis or Detection (CAD) approach for skin lesion analysis is an emerging field of research that has the potential to alleviate the burden and cost of skin cancer screening. Researchers have recently indicated increasing interest in developing such CAD systems, with the intention of providing a user-friendly tool to dermatologists to reduce the challenges encountered or associated with manual inspection. This article aims to provide a comprehensive literature survey and review of a total of 594 publications (356 for skin lesion segmentation and 238 for skin lesion classification) published between 2011 and 2022. These articles are analyzed and summarized in a number of different ways to contribute vital information regarding the methods for the development of CAD systems. These ways include relevant and essential definitions and theories, input data (dataset utilization, preprocessing, augmentations, and fixing imbalance problems), method configuration (techniques, architectures, module frameworks, and losses), training tactics (hyperparameter settings), and evaluation criteria. We intend to investigate a variety of performance-enhancing approaches, including ensemble and post-processing. We also discuss these dimensions to reveal their current trends based on utilization frequencies. In addition, we highlight the primary difficulties associated with evaluating skin lesion segmentation and classification systems using minimal datasets, as well as the potential solutions to these difficulties. Findings, recommendations, and trends are disclosed to inform future research on developing an automated and robust CAD system for skin lesion analysis.

Hong Shen Wong, Wei Xuan Chan, Bing Huan Li et al.

Fluid dynamics computations for tube-like geometries are important for biomedical evaluation of vascular and airway fluid dynamics. Physics-Informed Neural Networks (PINNs) have recently emerged as a good alternative to traditional computational fluid dynamics (CFD) methods. The vanilla PINN, however, requires much longer training time than the traditional CFD methods for each specific flow scenario and thus does not justify its mainstream use. Here, we explore the use of the multi-case PINN approach for calculating biomedical tube flows, where varied geometry cases are parameterized and pre-trained on the PINN, such that results for unseen geometries can be obtained in real time. Our objective is to identify network architecture, tube-specific, and regularization strategies that can optimize this, via experiments on a series of idealized 2D stenotic tube flows.

Yiying Sheng, Wenhao Ding, Dylan Roi et al.

Extensive studies suggested that fluid mechanical markers of intracranial aneurysms (IAs) derived from Computational Fluid Dynamics (CFD) can indicate disease progression risks, but to date this has not been translated clinically. This is because CFD requires specialized expertise and is time-consuming and low throughput, making it difficult to support clinical trials. A deep learning model that maps IA morphology to biomechanical markers can address this, enabling physicians to obtain these markers in real time without performing CFD. Here, we show that a Graph Transformer model that incorporates temporal information, which is supervised by large CFD data, can accurately predict Wall Shear Stress (WSS) across the cardiac cycle from IA surface meshes. The model effectively captures the temporal variations of the WSS pattern, achieving a Structural Similarity Index (SSIM) of up to 0.981 and a maximum-based relative L2 error of 2.8%. Ablation studies and SOTA comparison confirmed its optimality. Further, as pulsatile CFD data is computationally expensive to generate and sample sizes are limited, we engaged a strategy of injecting a large amount of steady-state CFD data, which are extremely low-cost to generate, as augmentation. This approach enhances network performance substantially when pulsatile CFD data sample size is small. Our study provides a proof of concept that temporal sequences cardiovascular fluid mechanical parameters can be computed in real time using a deep learning model from the geometric mesh, and this is achievable even with small pulsatile CFD sample size. Our approach is likely applicable to other cardiovascular scenarios.

Siyu Mu, Wei Xuan Chan, Choon Hwai Yap

Image-based patient-specific simulation of left ventricular (LV) mechanics is valuable for understanding cardiac function and supporting clinical intervention planning, but conventional finite-element analysis (FEA) is computationally intensive. Current graph-based surrogates do not have full-cycle prediction capabilities, and physics-informed neural networks often struggle to converge on complex cardiac geometries. We present CardioGraphFENet (CGFENet), a unified graph-based surrogate for rapid full-cycle estimation of LV myocardial biomechanics, supervised by a large FEA simulation dataset. The proposed model integrates (i) a global--local graph encoder to capture mesh features with weak-form-inspired global coupling, (ii) a gated recurrent unit-based temporal encoder conditioned on the target volume-time signal to model cycle-coherent dynamics, and (iii) a cycle-consistent bidirectional formulation for both loading and inverse unloading within a single framework. These strategies enable high fidelity with respect to traditional FEA ground truths and produce physiologically plausible pressure-volume loops that match FEA results when coupled with a lumped-parameter model. In particular, the cycle-consistency strategy enables a significant reduction in FEA supervision with only minimal loss in accuracy.

Wenhao Ding, Choon Hwai Yap, Kangjun Ji et al.

A generative model for the mesh geometry of intracranial aneurysms (IA) is crucial for training networks to predict blood flow forces in real time, which is a key factor affecting disease progression. This need is necessitated by the absence of a large IA image datasets. Existing shape generation methods struggle to capture realistic IA features and ignore the relationship between IA pouches and parent vessels, limiting physiological realism and their generation cannot be controlled to have specific morphological measurements. We propose AneuG, a two-stage Variational Autoencoder (VAE)-based IA mesh generator. In the first stage, AneuG generates low-dimensional Graph Harmonic Deformation (GHD) tokens to encode and reconstruct aneurysm pouch shapes, constrained to morphing energy statistics truths. GHD enables more accurate shape encoding than alternatives. In the second stage, AneuG generates parent vessels conditioned on GHD tokens, by generating vascular centreline and propagating the cross-section. AneuG's IA shape generation can further be conditioned to have specific clinically relevant morphological measurements. This is useful for studies to understand shape variations represented by clinical measurements, and for flow simulation studies to understand effects of specific clinical shape parameters on fluid dynamics. Source code and implementation details are available at https://github.com/anonymousaneug/AneuG.

Siyu Mu, Wei Xuan Chan, Choon Hwai Yap

Elucidating the biomechanical behavior of the myocardium is crucial for understanding cardiac physiology, but cannot be directly inferred from clinical imaging and typically requires finite element (FE) simulations. However, conventional FE methods are computationally expensive and often fail to reproduce observed cardiac motions. We propose IMC-PINN-FE, a physics-informed neural network (PINN) framework that integrates imaged motion consistency (IMC) with FE modeling for patient-specific left ventricular (LV) biomechanics. Cardiac motion is first estimated from MRI or echocardiography using either a pre-trained attention-based network or an unsupervised cyclic-regularized network, followed by extraction of motion modes. IMC-PINN-FE then rapidly estimates myocardial stiffness and active tension by fitting clinical pressure measurements, accelerating computation from hours to seconds compared to traditional inverse FE. Based on these parameters, it performs FE modeling across the cardiac cycle at 75x speedup. Through motion constraints, it matches imaged displacements more accurately, improving average Dice from 0.849 to 0.927, while preserving realistic pressure-volume behavior. IMC-PINN-FE advances previous PINN-FE models by introducing back-computation of material properties and better motion fidelity. Using motion from a single subject to reconstruct shape modes also avoids the need for large datasets and improves patient specificity. IMC-PINN-FE offers a robust and efficient approach for rapid, personalized, and image-consistent cardiac biomechanical modeling.

Md. Kamrul Hasan, Guang Yang, Choon Hwai Yap

Cardiac anatomy segmentation is useful for clinical assessment of cardiac morphology to inform diagnosis and intervention. Deep learning (DL), especially with motion information, has improved segmentation accuracy. However, existing techniques for motion enhancement are not yet optimal, and they have high computational costs due to increased dimensionality or reduced robustness due to suboptimal approaches that use non-DL motion registration, non-attention models, or single-headed attention. They further have limited adaptability and are inconvenient for incorporation into existing networks where motion awareness is desired. Here, we propose a novel, computationally efficient Temporal Attention Module (TAM) that offers robust motion enhancement, modeled as a small, multi-headed, cross-temporal attention module. TAM's uniqueness is that it is a lightweight, plug-and-play module that can be inserted into a broad range of segmentation networks (CNN-based, Transformer-based, or hybrid) for motion enhancement without requiring substantial changes in the network's backbone. This feature enables high adaptability and ease of integration for enhancing both existing and future networks. Extensive experiments on multiple 2D and 3D cardiac ultrasound and MRI datasets confirm that TAM consistently improves segmentation across a range of networks while maintaining computational efficiency and improving on currently reported performance. The evidence demonstrates that it is a robust, generalizable solution for motion-awareness enhancement that is scalable (such as from 2D to 3D).

Siyu Mu, Wei Xuan Chan, Choon Hwai Yap

The unloaded cardiac geometry (i.e., the state of the heart devoid of luminal pressure) serves as a valuable zero-stress and zero-strain reference and is critical for personalized biomechanical modeling of cardiac function, to understand both healthy and diseased physiology and to predict the effects of cardiac interventions. However, estimating the unloaded geometry from clinical images remains a challenging task. Traditional approaches rely on inverse finite element (FE) solvers that require iterative optimization and are computationally expensive. In this work, we introduce HeartUnloadNet, a deep learning framework that predicts the unloaded left ventricular (LV) shape directly from the end diastolic (ED) mesh while explicitly incorporating biophysical priors. The network accepts a mesh of arbitrary size along with physiological parameters such as ED pressure, myocardial stiffness scale, and fiber helix orientation, and outputs the corresponding unloaded mesh. It adopts a graph attention architecture and employs a cycle-consistency strategy to enable bidirectional (loading and unloading) prediction, allowing for partial self-supervision that improves accuracy and reduces the need for large training datasets. Trained and tested on 20,700 FE simulations across diverse LV geometries and physiological conditions, HeartUnloadNet achieves sub-millimeter accuracy, with an average DSC of 0.986 and HD of 0.083 cm, while reducing inference time to just 0.02 seconds per case, over 10^5 times faster and significantly more accurate than traditional inverse FE solvers. Ablation studies confirm the effectiveness of the architecture. Notably, the cycle-consistent design enables the model to maintain a DSC of 97% even with as few as 200 training samples. This work thus presents a scalable and accurate surrogate for inverse FE solvers, supporting real-time clinical applications in the future.

Chenyu Zhang, Yihao Luo, Yinzhe Wu et al.

Accurate cardiac mesh reconstruction from volumetric data is essential for personalized cardiac modeling and clinical analysis. However, existing deformation-based approaches are prone to topological inconsistencies, particularly membrane penetration, which undermines the anatomical plausibility of the reconstructed mesh. To address this issue, we introduce Topology-Preserving Mesh Loss (TPM Loss), a novel loss function that explicitly enforces topological constraints during mesh deformation. By identifying topology-violating points, TPM Loss ensures spatially consistent reconstructions. Extensive experiments on CT and MRI datasets show that TPM Loss reduces topology violations by up to 93.1% while maintaining high segmentation accuracy (DSC: 89.1%-92.9%) and improving mesh fidelity (Chamfer Distance reduction up to 0.26 mm). These results demonstrate that TPM Loss effectively prevents membrane penetration and significantly improves cardiac mesh quality, enabling more accurate and anatomically consistent cardiac reconstructions.

Md. Kamrul Hasan, Haobo Zhu, Guang Yang et al.

Temporal echocardiography image registration is a basis for clinical quantifications such as cardiac motion estimation, myocardial strain assessments, and stroke volume quantifications. In past studies, deep learning image registration (DLIR) has shown promising results and is consistently accurate and precise, requiring less computational time. We propose that a greater focus on the warped moving image's anatomic plausibility and image quality can support robust DLIR performance. Further, past implementations have focused on adult echocardiography, and there is an absence of DLIR implementations for fetal echocardiography. We propose a framework that combines three strategies for DLIR in both fetal and adult echo: (1) an anatomic shape-encoded loss to preserve physiological myocardial and left ventricular anatomical topologies in warped images; (2) a data-driven loss that is trained adversarially to preserve good image texture features in warped images; and (3) a multi-scale training scheme of a data-driven and anatomically constrained algorithm to improve accuracy. Our tests show that good anatomical topology and image textures are strongly linked to shape-encoded and data-driven adversarial losses. They improve different aspects of registration performance in a non-overlapping way, justifying their combination. Despite fundamental distinctions between adult and fetal echo images, we show that these strategies can provide excellent registration results in both adult and fetal echocardiography using the publicly available CAMUS adult echo dataset and our private multi-demographic fetal echo dataset. Our approach outperforms traditional non-DL gold standard registration approaches, including Optical Flow and Elastix. Registration improvements could be translated to more accurate and precise clinical quantification of cardiac ejection fraction, demonstrating a potential for translation.