Automatic Cardiac Pathology Recognition in Echocardiography Images Using Higher Order Dynamic Mode Decomposition and a Vision Transformer for Small Datasets

Heart diseases are the main international cause of human defunction. According to the WHO, nearly 18 million people decease each year because of heart diseases. Also considering the increase of medical data, much pressure is put on the health industry to develop systems for early and accurate heart disease recognition. In this work, an automatic cardiac pathology recognition system based on a novel deep learning framework is proposed, which analyses in real-time echocardiography video sequences. The system works in two stages. The first one transforms the data included in a database of echocardiography sequences into a machine-learning-compatible collection of annotated images which can be used in the training stage of any kind of machine learning-based framework, and more specifically with deep learning. This includes the use of the Higher Order Dynamic Mode Decomposition (HODMD) algorithm, for the first time to the authors' knowledge, for both data augmentation and feature extraction in the medical field. The second stage is focused on building and training a Vision Transformer (ViT), barely explored in the related literature. The ViT is adapted for an effective training from scratch, even with small datasets. The designed neural network analyses images from an echocardiography sequence to predict the heart state. The results obtained show the superiority of the proposed system and the efficacy of the HODMD algorithm, even outperforming pretrained Convolutional Neural Networks (CNNs), which are so far the method of choice in the literature.

Exploring the efficacy of a hybrid approach with modal decomposition over fully deep learning models for flow dynamics forecasting

Fluid dynamics problems are characterized by being multidimensional and nonlinear, causing the experiments and numerical simulations being complex, time-consuming and monetarily expensive. In this sense, there is a need to find new ways to obtain data in a more economical manner. Thus, in this work we study the application of time series forecasting to fluid dynamics problems, where the aim is to predict the flow dynamics using only past information. We focus our study on models based on deep learning that do not require a high amount of data for training, as this is the problem we are trying to address. Specifically in this work we have tested three autoregressive models where two of them are fully based on deep learning and the other one is a hybrid model that combines modal decomposition with deep learning. We ask these models to generate $200$ time-ahead predictions of two datasets coming from a numerical simulation and experimental measurements, where the latter is characterized by being turbulent. We show how the hybrid model generates more reliable predictions in the experimental case, as it is physics-informed in the sense that the modal decomposition extracts the physics in a way that allows us to predict it.

A predictive physics-aware hybrid reduced order model for reacting flows

In this work, a new hybrid predictive Reduced Order Model (ROM) is proposed to solve reacting flow problems. This algorithm is based on a dimensionality reduction using Proper Orthogonal Decomposition (POD) combined with deep learning architectures. The number of degrees of freedom is reduced from thousands of temporal points to a few POD modes with their corresponding temporal coefficients. Two different deep learning architectures have been tested to predict the temporal coefficients, based on recursive (RNN) and convolutional (CNN) neural networks. From each architecture, different models have been created to understand the behavior of each parameter of the neural network. Results show that these architectures are able to predict the temporal coefficients of the POD modes, as well as the whole snapshots. The RNN shows lower prediction error for all the variables analyzed. The model was also found capable of predicting more complex simulations showing transfer learning capabilities.

Forecasting through deep learning and modal decomposition in multi-phase concentric jets

This work presents a set of neural network (NN) models specifically designed for accurate and efficient fluid dynamics forecasting. In this work, we show how neural networks training can be improved by reducing data complexity through a modal decomposition technique called higher order dynamic mode decomposition (HODMD), which identifies the main structures inside flow dynamics and reconstructs the original flow using only these main structures. This reconstruction has the same number of samples and spatial dimension as the original flow, but with a less complex dynamics and preserving its main features. We also show the low computational cost required by the proposed NN models, both in their training and inference phases. The core idea of this work is to test the limits of applicability of deep learning models to data forecasting in complex fluid dynamics problems. Generalization capabilities of the models are demonstrated by using the same neural network architectures to forecast the future dynamics of four different multi-phase flows. Data sets used to train and test these deep learning models come from Direct Numerical Simulations (DNS) of these flows.

A Novel Data-Driven Method for the Analysis and Reconstruction of Cardiac Cine MRI

Cardiac cine magnetic resonance imaging (MRI) can be considered the optimal criterion for measuring cardiac function. This imaging technique can provide us with detailed information about cardiac structure, tissue composition and even blood flow. This work considers the application of the higher order dynamic mode decomposition (HODMD) method to a set of MR images of a heart, with the ultimate goal of identifying the main patterns and frequencies driving the heart dynamics. A novel algorithm based on singular value decomposition combined with HODMD is introduced, providing a three-dimensional reconstruction of the heart. This algorithm is applied (i) to reconstruct corrupted or missing images, and (ii) to build a reduced order model of the heart dynamics.

Higher Order Dynamic Mode Decomposition: from Fluid Dynamics to Heart Disease Analysis

In this work, we study in detail the performance of Higher Order Dynamic Mode Decomposition (HODMD) technique when applied to echocardiography images. HODMD is a data-driven method generally used in fluid dynamics and in the analysis of complex non-linear dynamical systems modeling several complex industrial applications. In this paper we apply HODMD, for the first time to the authors knowledge, for patterns recognition in echocardiography, specifically, echocardiography data taken from several mice, either in healthy conditions or afflicted by different cardiac diseases. We exploit the HODMD advantageous properties in dynamics identification and noise cleaning to identify the relevant frequencies and coherent patterns for each one of the diseases. The echocardiography datasets consist of video loops taken with respect to a long axis view (LAX) and a short axis view (SAX), where each video loop covers at least three cardiac cycles, formed by (at most) 300 frames each (called snapshots). The proposed algorithm, using only a maximum quantity of 200 snapshots, was able to capture two branches of frequencies, representing the heart rate and respiratory rate. Additionally, the algorithm provided a number of modes, which represent the dominant features and patterns in the different echocardiography images, also related to the heart and the lung. Six datasets were analyzed: one echocardiography taken from a healthy subject and five different sets of echocardiography taken from subjects with either Diabetic Cardiomyopathy, Obesity, SFSR4 Hypertrophy, TAC Hypertrophy or Myocardial Infarction. The results show that HODMD is robust and a suitable tool to identify characteristic patterns able to classify the different pathologies studied.

Towards extraction of orthogonal and parsimonious non-linear modes from turbulent flows

We propose a deep probabilistic-neural-network architecture for learning a minimal and near-orthogonal set of non-linear modes from high-fidelity turbulent-flow-field data useful for flow analysis, reduced-order modeling, and flow control. Our approach is based on $\beta$-variational autoencoders ($\beta$-VAEs) and convolutional neural networks (CNNs), which allow us to extract non-linear modes from multi-scale turbulent flows while encouraging the learning of independent latent variables and penalizing the size of the latent vector. Moreover, we introduce an algorithm for ordering VAE-based modes with respect to their contribution to the reconstruction. We apply this method for non-linear mode decomposition of the turbulent flow through a simplified urban environment, where the flow-field data is obtained based on well-resolved large-eddy simulations (LESs). We demonstrate that by constraining the shape of the latent space, it is possible to motivate the orthogonality and extract a set of parsimonious modes sufficient for high-quality reconstruction. Our results show the excellent performance of the method in the reconstruction against linear-theory-based decompositions. Moreover, we compare our method with available AE-based models. We show the ability of our approach in the extraction of near-orthogonal modes that may lead to interpretability.