Physiological Modeling and Simulation-Validation, Credibility, and Application

Guidelines for mechanistic modeling and analysis in cardiovascular research

Computational, or in silico, models are an effective, noninvasive tool for investigating cardiovascular function. These models can be used in the analysis of experimental and clinical data to identify possible mechanisms of (ab)normal cardiovascular physiology. Recent advances in computing power and data management have led to innovative and complex modeling frameworks that simulate cardiovascular function across multiple scales. While commonly used in multiple disciplines, there is a lack of concise guidelines for the implementation of computer models in cardiovascular research. In line with recent calls for more reproducible research, it is imperative that scientists adhere to credible practices when developing and applying computational models to their research. The goal of this manuscript is to provide a consensus document that identifies best practices for in silico computational modeling in cardiovascular research. These guidelines provide the necessary methods for mechanistic model development, model analysis, and formal model calibration using fundamentals from statistics. We outline rigorous practices for computational, mechanistic modeling in cardiovascular research and discuss its synergistic value to experimental and clinical data.

Parametric Modeling and Deep Learning for Enhancing Pain Assessment in Postanesthesia

OBJECTIVE

The problem of reliable and widely accepted measures of pain is still open. It follows the objective of this work as pain estimation through post-surgical trauma modeling and classification, to increase the needed reliability compared to measurements only.

METHODS

This article proposes (i) a recursive identification method to obtain the frequency response and parameterization using fractional-order impedance models (FOIM), and (ii) deep learning with convolutional neural networks (CNN) classification algorithms using time-frequency data and spectrograms. The skin impedance measurements were conducted on 12 patients throughout the postanesthesia care in a proof-of-concept clinical trial. Recursive least-squares system identification was performed using a genetic algorithm for initializing the parametric model. The online parameter estimates were compared to the self-reported level by the Numeric Rating Scale (NRS) for analysis and validation of the results. Alternatively, the inputs to CNNs were the spectrograms extracted from the time-frequency dataset, being pre-labeled in four intensities classes of pain during offline and online training with the NRS.

RESULTS

The tendency of nociception could be predicted by monitoring the changes in the FOIM parameters' values or by retraining online the network. Moreover, the tissue heterogeneity, assumed during nociception, could follow the NRS trends. The online predictions of retrained CNN have more specific trends to NRS than pain predicted by the offline population-trained CNN.

CONCLUSION

We propose tailored online identification and deep learning for artefact corrupted environment. The results indicate estimations with the potential to avoid over-dosing due to the objectivity of the information.

SIGNIFICANCE

Models and artificial intelligence (AI) allow objective and personalized nociception-antinociception prediction in the patient safety era for the design and evaluation of closed-loop analgesia controllers.

Elucidating yeast glycolytic dynamics at steady state growth and glucose pulses through kinetic metabolic modeling

Microbial cell factories face changing environments during industrial fermentations. Kinetic metabolic models enable the simulation of the dynamic metabolic response to these perturbations, but their development is challenging due to model complexity and experimental data requirements. An example of this is the well-established microbial cell factory Saccharomyces cerevisiae, for which no consensus kinetic model of central metabolism has been developed and implemented in industry. Here, we aim to bring the academic and industrial communities closer to this consensus model. We developed a physiology informed kinetic model of yeast glycolysis connected to central carbon metabolism by including the effect of anabolic reactions precursors, mitochondria and the trehalose cycle. To parametrize such a large model, a parameter estimation pipeline was developed, consisting of a divide and conquer approach, supplemented with regularization and global optimization. Additionally, we show how this first mechanistic description of a growing yeast cell captures experimental dynamics at different growth rates and under a strong glucose perturbation, is robust to parametric uncertainty and explains the contribution of the different pathways in the network. Such a comprehensive model could not have been developed without using steady state and glucose perturbation data sets. The resulting metabolic reconstruction and parameter estimation pipeline can be applied in the future to study other industrially-relevant scenarios. We show this by generating a hybrid CFD-metabolic model to explore intracellular glycolytic dynamics for the first time. The model suggests that all intracellular metabolites oscillate within a physiological range, except carbon storage metabolism, which is sensitive to the extracellular environment.

A Multitask Learning Approach to Personalised Blood Glucose Prediction

Blood glucose prediction algorithms are key tools in the development of decision support systems and closed-loop insulin delivery systems for blood glucose control in diabetes. Deep learning models have provided leading results among machine learning algorithms to date in glucose prediction. However these models typically require large amounts of data to obtain best personalised glucose prediction results. Multitask learning facilitates an approach for leveraging data from multiple subjects while still learning accurate personalised models. In this work we present results comparing the effectiveness of multitask learning over sequential transfer learning, and learning only on subject-specific data with neural networks and support vector regression. The multitask learning approach shows consistent leading performance in predictive metrics at both short-term and long-term prediction horizons. We obtain a predictive accuracy (RMSE) of 18.8 2.3, 25.3 2.9, 31.8 3.9, 41.2 4.5, 47.2 4.6 mg/dL at 30, 45, 60, 90, and 120 min prediction horizons respectively, with at least 93\% clinically acceptable predictions using the Clarke Error Grid (EGA) at each prediction horizon. We also identify relevant prior information such as glycaemic variability that can be incorporated to improve predictive performance at long-term prediction horizons. Furthermore, we demonstrate consistent performance - 5% change in both RMSE and EGA (Zone A) - in rare cases of adverse glycaemic events with 1-6 weeks of training data. In conclusion, a multitask approach can allow for deploying personalised models even with significantly less subject-specific data without compromising performance.