Boosting Cardiac Color Doppler Frame Rates with Deep Learning.

Color Doppler echocardiography enables visualization of blood flow within the heart. However, the limited frame rate impedes the quantitative assessment of blood velocity throughout the cardiac cycle, thereby compromising a comprehensive analysis of ventricular filling. Concurrently, deep learning is demonstrating promising outcomes in post-processing of echocardiographic data for various applications. This work explores the use of deep learning models for intracardiac Doppler velocity estimation from a reduced number of filtered I/Q signals. We used a supervised learning approach by simulating patient-based cardiac color Doppler acquisitions and proposed data augmentation strategies to enlarge the training dataset. We implemented architectures based on convolutional neural networks. In particular, we focused on comparing the U-Net model and the recent ConvNeXt models, alongside assessing real-valued versus complex-valued representations. We found that both models outperformed the state-of-the-art autocorrelator method, effectively mitigating aliasing and noise. We did not observe significant differences between the use of real and complex data. Finally, we validated the models on in vitro and in vivo experiments. All models produced quantitatively comparable results to the baseline and were more robust to noise. ConvNeXt emerged as the sole model to achieve high-quality results on in vivo aliased samples. These results demonstrate the interest of supervised deep learning methods for Doppler velocity estimation from a reduced number of acquisitions.

Physics-Guided Neural Networks for Intraventricular Vector Flow Mapping.

Intraventricular vector flow mapping (iVFM) seeks to enhance and quantify color Doppler in cardiac imaging. In this study, we propose novel alternatives to the traditional iVFM optimization scheme by utilizing physics-informed neural networks (PINNs) and a physics-guided nnU-Net-based supervised approach. When evaluated on simulated color Doppler images derived from a patient-specific computational fluid dynamics model and in vivo Doppler acquisitions, both approaches demonstrate comparable reconstruction performance to the original iVFM algorithm. The efficiency of PINNs is boosted through dual-stage optimization and pre-optimized weights. On the other hand, the nnU-Net method excels in generalizability and real-time capabilities. Notably, nnU-Net shows superior robustness on sparse and truncated Doppler data while maintaining independence from explicit boundary conditions. Overall, our results highlight the effectiveness of these methods in reconstructing intraventricular vector blood flow. The study also suggests potential applications of PINNs in ultrafast color Doppler imaging and the incorporation of fluid dynamics equations to derive biomarkers for cardiovascular diseases based on blood flow.

Latent network-based representations for large-scale gene expression data analysis.

BACKGROUND: With the recent advancements in high-throughput experimental procedures, biologists are gathering huge quantities of data. A main priority in bioinformatics and computational biology is to provide system level analytical tools capable of meeting an ever-growing production of high-throughput biological data while taking into account its biological context. In gene expression data analysis, genes have widely been considered as independent components. However, a systemic view shows that they act synergistically in living cells, forming functional complexes and more generally a biological system. RESULTS: In this paper, we propose LATNET, a signal transformation framework that, starting from an initial large-scale gene expression data, allows to generate new representations based on latent network-based relationships between the genes. LATNET aims to leverage system level relations between the genes as an underlying hidden structure to derive the new transformed latent signals. We present a concrete implementation of our framework, based on a gene regulatory network structure and two signal transformation approaches, to quantify latent network-based activity of regulators, as well as gene perturbation signals. The new gene/regulator signals are at the level of each sample of the input data and, thus, could directly be used instead of the initial expression signals for major bioinformatics analysis, including diagnosis and personalized medicine. CONCLUSION: Multiple patterns could be hidden or weakly observed in expression data. LATNET helps in uncovering latent signals that could emphasize hidden patterns based on the relations between the genes and, thus, enhancing the performance of gene expression-based analysis algorithms. We use LATNET for the analysis of real-world gene expression data of bladder cancer and we show the efficiency of our transformation framework as compared to using the initial expression data.