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We present a novel computational model for the dynamics of alveolar recruitment/derecruitment (RD), which reproduces the underlying characteristics typically observed in injured lungs. The basic idea is a pressure- and time-dependent variation of the stress-free reference volume in reduced dimensional viscoelastic elements representing the acinar tissue. We choose a variable reference volume triggered by critical opening and closing pressures in a time-dependent manner from a straightforward mechanical point of view. In the case of (partially and progressively) collapsing alveolar structures, the volume available for expansion during breathing reduces and vice versa, eventually enabling consideration of alveolar collapse and reopening in our model. We further introduce a method for patient-specific determination of the underlying critical parameters of the new alveolar RD dynamics when integrated into the tissue elements, referred to as terminal units, of a spatially resolved physics-based lung model that simulates the human respiratory system in an anatomically correct manner. Relevant patient-specific parameters of the terminal units are herein determined based on medical image data and the macromechanical behavior of the lung during artificial ventilation. We test the whole modeling approach for a real-life scenario by applying it to the clinical data of a mechanically ventilated patient. The generated lung model is capable of reproducing clinical measurements such as tidal volume and pleural pressure during various ventilation maneuvers. We conclude that this new model is an important step toward personalized treatment of ARDS patients by considering potentially harmful mechanisms - such as cyclic RD and overdistension - and might help in the development of relevant protective ventilation strategies to reduce ventilator-induced lung injury (VILI).

Magnetic resonance imaging has evolved as a key component for prostate cancer (PCa) detection, substantially increasing the radiologist workload. Artificial intelligence (AI) systems can support radiological assessment by segmenting and classifying lesions in clinically significant (csPCa) and non-clinically significant (ncsPCa). Commonly, AI systems for PCa detection involve an automatic prostate segmentation followed by the lesion detection using the extracted prostate. However, evaluation reports are typically presented in terms of detection under the assumption of the availability of a highly accurate segmentation and an idealistic scenario, omitting the propagation of errors between modules. For that purpose, we evaluate the effect of two different segmentation networks (s1 and s2) with heterogeneous performances in the detection stage and compare it with an idealistic setting (s1:89.90+-2.23 vs 88.97+-3.06 ncsPCa, P<.001, 89.30+-4.07 and 88.12+-2.71 csPCa, P<.001). Our results depict the relevance of a holistic evaluation, accounting for all the sub-modules involved in the system.

Conventional neural network elastoplasticity models are often perceived as lacking interpretability. This paper introduces a two-step machine-learning approach that returns mathematical models interpretable by human experts. In particular, we introduce a surrogate model where yield surfaces are expressed in terms of a set of single-variable feature mappings obtained from supervised learning. A postprocessing step is then used to re-interpret the set of single-variable neural network mapping functions into mathematical form through symbolic regression. This divide-and-conquer approach provides several important advantages. First, it enables us to overcome the scaling issue of symbolic regression algorithms. From a practical perspective, it enhances the portability of learned models for partial differential equation solvers written in different programming languages. Finally, it enables us to have a concrete understanding of the attributes of the materials, such as convexity and symmetries of models, through automated derivations and reasoning. Numerical examples have been provided, along with an open-source code to enable third-party validation.

Current physics-informed (standard or operator) neural networks still rely on accurately learning the initial conditions of the system they are solving. In contrast, standard numerical methods evolve such initial conditions without needing to learn these. In this study, we propose to improve current physics-informed deep learning strategies such that initial conditions do not need to be learned and are represented exactly in the predicted solution. Moreover, this method guarantees that when a DeepONet is applied multiple times to time step a solution, the resulting function is continuous.

Although the applications of Non-Homogeneous Poisson Processes to model and study the threshold overshoots of interest in different time series of measurements have proven to provide good results, they needed to be complemented with an efficient and automatic diagnostic technique to establish the location of the change-points, which, when taken into account, make the estimated model fit poorly in regards of the information contained in the real model. For this reason, we propose a new method to solve the segmentation uncertainty of the time series of measurements, where the emission distribution of exceedances of a specific threshold is the focus of investigation. One of the great contributions of the present algorithm is that all the days that overflowed are candidates to be a change-point, so all the possible configurations of overflow days are the possible chromosomes, which will unite to have offspring. Under the heuristics of a genetic algorithm, the solution to the problem of finding such change points will be guaranteed to be non-local and the best possible one, reducing wasted machine time evaluating the least likely chromosomes to be a solution to the problem. The analytical evaluation technique will be by means of the Minimum Description Length (\textit{MDL}) as the objective function, which is the joint posterior distribution function of the parameters of each regime and the change points that determines them and which account as well for the influence of the presence of said times.

This study examines the efficacy of various neural network (NN) models in interpreting mental constructs via electroencephalogram (EEG) signals. Through the assessment of 16 prevalent NN models and their variants across four brain-computer interface (BCI) paradigms, we gauged their information representation capability. Rooted in comprehensive literature review findings, we proposed EEGNeX, a novel, purely ConvNet-based architecture. We pitted it against both existing cutting-edge strategies and the Mother of All BCI Benchmarks (MOABB) involving 11 distinct EEG motor imagination (MI) classification tasks and revealed that EEGNeX surpasses other state-of-the-art methods. Notably, it shows up to 2.1%-8.5% improvement in the classification accuracy in different scenarios with statistical significance (p < 0.05) compared to its competitors. This study not only provides deeper insights into designing efficient NN models for EEG data but also lays groundwork for future explorations into the relationship between bioelectric brain signals and NN architectures. For the benefit of broader scientific collaboration, we have made all benchmark models, including EEGNeX, publicly available at (//github.com/chenxiachan/EEGNeX).

Untargeted metabolomic profiling through liquid chromatography-mass spectrometry (LC-MS) measures a vast array of metabolites within biospecimens, advancing drug development, disease diagnosis, and risk prediction. However, the low throughput of LC-MS poses a major challenge for biomarker discovery, annotation, and experimental comparison, necessitating the merging of multiple datasets. Current data pooling methods encounter practical limitations due to their vulnerability to data variations and hyperparameter dependence. Here we introduce GromovMatcher, a flexible and user-friendly algorithm that automatically combines LC-MS datasets using optimal transport. By capitalizing on feature intensity correlation structures, GromovMatcher delivers superior alignment accuracy and robustness compared to existing approaches. This algorithm scales to thousands of features requiring minimal hyperparameter tuning. Applying our method to experimental patient studies of liver and pancreatic cancer, we discover shared metabolic features related to patient alcohol intake, demonstrating how GromovMatcher facilitates the search for biomarkers associated with lifestyle risk factors linked to several cancer types.

We introduce a novel approach called the Bayesian Jackknife empirical likelihood method for analyzing survey data obtained from various unequal probability sampling designs. This method is particularly applicable to parameters described by U-statistics. Theoretical proofs establish that under a non-informative prior, the Bayesian Jackknife pseudo-empirical likelihood ratio statistic converges asymptotically to a normal distribution. This statistic can be effectively employed to construct confidence intervals for complex survey samples. In this paper, we investigate various scenarios, including the presence or absence of auxiliary information and the use of design weights or calibration weights. We conduct numerical studies to assess the performance of the Bayesian Jackknife pseudo-empirical likelihood ratio confidence intervals, focusing on coverage probability and tail error rates. Our findings demonstrate that the proposed methods outperform those based solely on the jackknife pseudo-empirical likelihood, addressing its limitations.

This study focuses on the use of model and data fusion for improving the Spalart-Allmaras (SA) closure model for Reynolds-averaged Navier-Stokes solutions of separated flows. In particular, our goal is to develop of models that not-only assimilate sparse experimental data to improve performance in computational models, but also generalize to unseen cases by recovering classical SA behavior. We achieve our goals using data assimilation, namely the Ensemble Kalman Filtering approach (EnKF), to calibrate the coefficients of the SA model for separated flows. A holistic calibration strategy is implemented via a parameterization of the production, diffusion, and destruction terms. This calibration relies on the assimilation of experimental data collected velocity profiles, skin friction, and pressure coefficients for separated flows. Despite using of observational data from a single flow condition around a backward-facing step (BFS), the recalibrated SA model demonstrates generalization to other separated flows, including cases such as the 2D-bump and modified BFS. Significant improvement is observed in the quantities of interest, i.e., skin friction coefficient ($C_f$) and pressure coefficient ($C_p$) for each flow tested. Finally, it is also demonstrated that the newly proposed model recovers SA proficiency for external, unseparated flows, such as flow around a NACA-0012 airfoil without any danger of extrapolation, and that the individually calibrated terms in the SA model are targeted towards specific flow-physics wherein the calibrated production term improves the re-circulation zone while destruction improves the recovery zone.

A method for sound field decomposition based on neural networks is proposed. The method comprises two stages: a sound field separation stage and a single-source localization stage. In the first stage, the sound pressure at microphones synthesized by multiple sources is separated into one excited by each sound source. In the second stage, the source location is obtained as a regression from the sound pressure at microphones consisting of a single sound source. The estimated location is not affected by discretization because the second stage is designed as a regression rather than a classification. Datasets are generated by simulation using Green's function, and the neural network is trained for each frequency. Numerical experiments reveal that, compared with conventional methods, the proposed method can achieve higher source-localization accuracy and higher sound-field-reconstruction accuracy.