Location via proxy:   [ UP ]  
[Report a bug]   [Manage cookies]                
skip to main content
research-article

Data-driven reduced order surrogate modeling for coronary in-stent restenosis

Published: 01 December 2024 Publication History

Abstract

Background:

The intricate process of coronary in-stent restenosis (ISR) involves the interplay between different mediators, including platelet-derived growth factor, transforming growth factor-β, extracellular matrix, smooth muscle cells, endothelial cells, and drug elution from the stent. Modeling such complex multiphysics phenomena demands extensive computational resources and time.

Methods:

This paper proposes a novel non-intrusive data-driven reduced order modeling approach for the underlying multiphysics time-dependent parametrized problem. In the offline phase, a 3D convolutional autoencoder, comprising an encoder and decoder, is trained to achieve dimensionality reduction. The encoder condenses the full-order solution into a lower-dimensional latent space, while the decoder facilitates the reconstruction of the full solution from the latent space. To deal with the 5D input datasets (3D geometry + time series + multiple output channels), two ingredients are explored. The first approach incorporates time as an additional parameter and applies 3D convolution on individual time steps, encoding a distinct latent variable for each parameter instance within each time step. The second approach reshapes the 3D geometry into a 2D plane along a less interactive axis and stacks all time steps in the third direction for each parameter instance. This rearrangement generates a larger and complete dataset for one parameter instance, resulting in a singular latent variable across the entire discrete time-series. In both approaches, the multiple outputs are considered automatically in the convolutions. Moreover, Gaussian process regression is applied to establish correlations between the latent variable and the input parameter.

Results:

The constitutive model reveals a significant acceleration in neointimal growth between 30 − 60 days post percutaneous coronary intervention (PCI). The surrogate models applying both approaches exhibit high accuracy in pointwise error, with the first approach showcasing smaller errors across the entire evaluation period for all outputs. The parameter study on drug dosage against ISR rates provides noteworthy insights of neointimal growth, where the nonlinear dependence of ISR rates on the peak drug flux exhibits intriguing periodic patterns. Applying the trained model, the rate of ISR is effectively evaluated, and the optimal parameter range for drug dosage is identified.

Conclusion:

The demonstrated non-intrusive reduced order surrogate model proves to be a powerful tool for predicting ISR outcomes. Moreover, the proposed method lays the foundation for real-time simulations and optimization of PCI parameters.

Highlights

Consideration of key influential factors of ISR: the continuum mechanics based constitutive framework incorporates critical factors such as platelet-derived growth factor, transforming growth factor- β, extracellular matrix, density of smooth muscle cells, endothelial cells and drug concentration. These factors are tracked using coupled advection–reaction–diffusion equations.
Integration of patient-specific parameters: our model facilitates the integration of patient-specific parameters, enhancing prediction accuracy and enabling the optimization of stent implantation strategies. This personalized approach holds significant potential for improving clinical outcomes.
Data-driven reduced order surrogate modeling: the dimensionality reduction of the surrogate model is based on 3D convolutional autoencoder. In the offline phase, the full-order solution is effectively condensed into a lower-dimensional latent space, and the full solution is recovered using the transposed convolution.
Clinical impact: The demonstrated non-intrusive reduced order surrogate model proves to be a powerful tool for predicting ISR outcomes, offering potential for real-time simulations and optimization of PCI parameters.

References

[1]
Manjunatha K., Behr M., Vogt F., Reese S., A multiphysics modeling approach for in-stent restenosis: Theoretical aspects and finite element implementation, Comput. Biol. Med. 150 (2022),. URL https://www.sciencedirect.com/science/article/pii/S0010482522008745.
[2]
Manjunatha K., Schaaps N., Behr M., Vogt F., Reese S., Computational modeling of in-stent restenosis: Pharmacokinetic and pharmacodynamic evaluation, Comput. Biol. Med. 167 (2023),.
[3]
Shi J., Manjunatha K., Behr M., Vogt F., Reese S., A physics-informed deep learning framework for modeling of coronary in-stent restenosis, Biomech. Model. Mechanobiol. (2014),. URL https://doi.org/10.1007/s10237-023-01796-1.
[4]
Hesthaven J., Ubbiali S., Non-intrusive reduced order modeling of nonlinear problems using neural networks, J. Comput. Phys. 363 (2018) 55–78,. URL https://www.sciencedirect.com/science/article/pii/S0021999118301190.
[5]
Benner P., Gugercin S., Willcox K., A survey of projection-based model reduction methods for parametric dynamical systems, SIAM Rev. 57 (4) (2015) 483–531,. arXiv:https://doi.org/10.1137/130932715.
[6]
Duan J., Hesthaven J.S., Non-intrusive data-driven reduced-order modeling for time-dependent parametrized problems, J. Comput. Phys. 497 (2024),. URL https://www.sciencedirect.com/science/article/pii/S0021999123007167.
[7]
Ritzert S., Macek D., Simon J.-W., Reese S., An adaptive model order reduction technique for parameter-dependent modular structures, Comput. Mech. (2023),.
[8]
Halder R., Fidkowski K.J., Maki K.J., Non-intrusive reduced-order modeling using convolutional autoencoders, Internat. J. Numer. Methods Engrg. 123 (21) (2022) 5369–5390,. arXiv:https://onlinelibrary.wiley.com/doi/pdf/10.1002/nme.7072 URL https://onlinelibrary.wiley.com/doi/abs/10.1002/nme.7072.
[9]
Lee K., Carlberg K.T., Model reduction of dynamical systems on nonlinear manifolds using deep convolutional autoencoders, J. Comput. Phys. 404 (2020),. URL https://www.sciencedirect.com/science/article/pii/S0021999119306783.
[10]
Barrault M., Maday Y., Nguyen N.C., Patera A.T., An ‘empirical interpolation’ method: application to efficient reduced-basis discretization of partial differential equations, C. R. Math. 339 (9) (2004) 667–672,. URL https://www.sciencedirect.com/science/article/pii/S1631073X04004248.
[11]
Chaturantabut S., Sorensen D.C., Nonlinear model reduction via discrete empirical interpolation, SIAM J. Sci. Comput. 32 (5) (2010) 2737–2764,.
[12]
Negri F., Manzoni A., Amsallem D., Efficient model reduction of parametrized systems by matrix discrete empirical interpolation, J. Comput. Phys. 303 (2015) 431–454,. URL https://www.sciencedirect.com/science/article/pii/S0021999115006543.
[13]
Amsallem D., Farhat C., Interpolation method for adapting reduced-order models and application to aeroelasticity, AIAA J. 46 (7) (2008) 1803–1813,. arXiv:https://doi.org/10.2514/1.35374.
[14]
Amsallem D., Zahr M.J., Farhat C., Nonlinear model order reduction based on local reduced-order bases, Internat. J. Numer. Methods Engrg. 92 (10) (2012) 891–916,. arXiv:https://onlinelibrary.wiley.com/doi/pdf/10.1002/nme.4371 URL https://onlinelibrary.wiley.com/doi/abs/10.1002/nme.4371.
[15]
Astrid P., Weiland S., Willcox K., Backx T., Missing point estimation in models described by proper orthogonal decomposition, IEEE Trans. Autom. Control 53 (10) (2008) 2237–2251,.
[16]
Carlberg K., Farhat C., Cortial J., Amsallem D., The GNAT method for nonlinear model reduction: Effective implementation and application to computational fluid dynamics and turbulent flows, J. Comput. Phys. 242 (2013) 623–647,. URL https://www.sciencedirect.com/science/article/pii/S0021999113001472.
[17]
Farhat C., Chapman T., Avery P., Structure-preserving, stability, and accuracy properties of the energy-conserving sampling and weighting method for the hyper reduction of nonlinear finite element dynamic models, Internat. J. Numer. Methods Engrg. 102 (5) (2015) 1077–1110,. arXiv:https://onlinelibrary.wiley.com/doi/pdf/10.1002/nme.4820 URL https://onlinelibrary.wiley.com/doi/abs/10.1002/nme.4820.
[18]
Maierhofer J., Rixen D.J., Model order reduction using hyperreduction methods (DEIM, ECSW) for magnetodynamic FEM problems, Finite Elem. Anal. Des. 209 (2022),. URL https://www.sciencedirect.com/science/article/pii/S0168874X22000671.
[19]
Xiao D., Yang P., Fang F., Xiang J., Pain C., Navon I., Non-intrusive reduced order modelling of fluid–structure interactions, Comput. Methods Appl. Mech. Engrg. 303 (2016) 35–54,. URL https://www.sciencedirect.com/science/article/pii/S0045782516300068.
[20]
Chakir R., Hammond J., A non-intrusive reduced basis method for elastoplasticity problems in geotechnics, J. Comput. Appl. Math. 337 (2018) 1–17,. URL https://www.sciencedirect.com/science/article/pii/S0377042718300128.
[21]
Wang Z., Xiao D., Fang F., Govindan R., Pain C.C., Guo Y., Model identification of reduced order fluid dynamics systems using deep learning, Internat. J. Numer. Methods Fluids 86 (4) (2018) 255–268,. arXiv:https://onlinelibrary.wiley.com/doi/pdf/10.1002/fld.4416 URL https://onlinelibrary.wiley.com/doi/abs/10.1002/fld.4416.
[22]
San O., Maulik R., Neural network closures for nonlinear model order reduction, Adv. Comput. Math. 44 (6) (2018) 1717–1750,.
[23]
Pawar S., Rahman S.M., Vaddireddy H., San O., Rasheed A., Vedula P., A deep learning enabler for nonintrusive reduced order modeling of fluid flows, Phys. Fluids 31 (8) (2019),. arXiv:https://pubs.aip.org/aip/pof/article-pdf/doi/10.1063/1.5113494/14800114/085101_1_online.pdf.
[24]
Murata T., Fukami K., Fukagata K., Nonlinear mode decomposition with convolutional neural networks for fluid dynamics, J. Fluid Mech. 882 (2020) A13,.
[25]
Wu P., Sun J., Chang X., Zhang W., Arcucci R., Guo Y., Pain C.C., Data-driven reduced order model with temporal convolutional neural network, Comput. Methods Appl. Mech. Engrg. 360 (2020),. URL https://www.sciencedirect.com/science/article/pii/S0045782519306589.
[26]
Fresca S., Dede’ L., Manzoni A., A comprehensive deep learning-based approach to reduced order modeling of nonlinear time-dependent parametrized PDEs, J. Sci. Comput. 87 (2) (2021),.
[27]
Mücke N.T., Bohté S.M., Oosterlee C.W., Reduced order modeling for parameterized time-dependent PDEs using spatially and memory aware deep learning, J. Comput. Sci. 53 (2021),. URL https://www.sciencedirect.com/science/article/pii/S1877750321000934.
[28]
Pant P., Doshi R., Bahl P., Barati Farimani A., Deep learning for reduced order modelling and efficient temporal evolution of fluid simulations, Phys. Fluids 33 (10) (2021),. arXiv:https://pubs.aip.org/aip/pof/article-pdf/doi/10.1063/5.0062546/16118714/107101_1_online.pdf.
[29]
Nikolopoulos S., Kalogeris I., Papadopoulos V., Non-intrusive surrogate modeling for parametrized time-dependent partial differential equations using convolutional autoencoders, Eng. Appl. Artif. Intell. 109 (2022),. URL https://www.sciencedirect.com/science/article/pii/S0952197621004541.
[30]
Abdedou A., Soulaimani A., Reduced-order modeling for stochastic large-scale and time-dependent flow problems using deep spatial and temporal convolutional autoencoders, Adv. Model. Simul. Eng. Sci. 10 (1) (2023) 7,.
[31]
Lee S., Lee S., Jang K., Cho H., Shin S., Data-driven nonlinear parametric model order reduction framework using deep hierarchical variational autoencoder, Eng. Comput. (2024),.
[32]
Pichi F., Moya B., Hesthaven J.S., A graph convolutional autoencoder approach to model order reduction for parametrized PDEs, J. Comput. Phys. 501 (2024),. URL https://www.sciencedirect.com/science/article/pii/S0021999124000111.
[33]
Maulik R., Lusch B., Balaprakash P., Reduced-order modeling of advection-dominated systems with recurrent neural networks and convolutional autoencoders, Phys. Fluids 33 (3) (2021),. arXiv:https://pubs.aip.org/aip/pof/article-pdf/doi/10.1063/5.0039986/15666155/037106_1_online.pdf.
[34]
Dutta S., Farthing M.W., Perracchione E., Savant G., Putti M., A greedy non-intrusive reduced order model for shallow water equations, J. Comput. Phys. 439 (2021),. URL https://www.sciencedirect.com/science/article/pii/S0021999121002734.
[35]
Lee S., Jang K., Lee S., Cho H., Shin S., Parametric model order reduction by machine learning for fluid–structure interaction analysis, Eng. Comput. (2023),.
[36]
Dupont C., De Vuyst F., Salsac A.-V., Data-driven kinematics-consistent model-order reduction of fluid–structure interaction problems: application to deformable microcapsules in a Stokes flow, J. Fluid Mech. 955 (2023) A2,.
[37]
Kneifl J., Grunert D., Fehr J., A nonintrusive nonlinear model reduction method for structural dynamical problems based on machine learning, Internat. J. Numer. Methods Engrg. 122 (17) (2021) 4774–4786,. arXiv:https://onlinelibrary.wiley.com/doi/pdf/10.1002/nme.6712 URL https://onlinelibrary.wiley.com/doi/abs/10.1002/nme.6712.
[38]
Fresca S., Gobat G., Fedeli P., Frangi A., Manzoni A., Deep learning-based reduced order models for the real-time simulation of the nonlinear dynamics of microstructures, Internat. J. Numer. Methods Engrg. 123 (20) (2022) 4749–4777,. arXiv:https://onlinelibrary.wiley.com/doi/pdf/10.1002/nme.7054 URL https://onlinelibrary.wiley.com/doi/abs/10.1002/nme.7054.
[39]
Kadeethum T., Ballarin F., Choi Y., O’Malley D., Yoon H., Bouklas N., Non-intrusive reduced order modeling of natural convection in porous media using convolutional autoencoders: Comparison with linear subspace techniques, Adv. Water Resour. 160 (2022),. URL https://www.sciencedirect.com/science/article/pii/S0309170821002499.
[40]
Kneifl J., Rosin D., Avci O., Röhrle O., Fehr J., Low-dimensional data-based surrogate model of a continuum-mechanical musculoskeletal system based on non-intrusive model order reduction, Arch. Appl. Mech. 93 (9) (2023) 3637–3663,.
[41]
Fresca S., Manzoni A., Dedè L., Quarteroni A., Deep learning-based reduced order models in cardiac electrophysiology, PLOS ONE 15 (10) (2020) 1–32,.
[42]
Fresca S., Manzoni A., Dedè L., Quarteroni A., POD-enhanced deep learning-based reduced order models for the real-time simulation of cardiac electrophysiology in the left atrium, Front. Phys. 12 (2021),. URL https://www.frontiersin.org/articles/10.3389/fphys.2021.679076.
[43]
Eivazi H., Veisi H., Naderi M.H., Esfahanian V., Deep neural networks for nonlinear model order reduction of unsteady flows, Phys. Fluids 32 (10) (2020),.
[44]
Kim M.S., Dean L.S., In-stent restenosis, Cardiovasc. Therap. 29 (3) (2011) 190–198,.
[45]
Reese S., Manjunatha K., Shi J., Sesa M., Multiphysical modeling of soft tissue-stent interaction, in: Conference: 10th Edition of the International Conference on Computational Methods for Coupled Problems in Science and Engineering, 2023,.
[46]
Shi J., Manjunatha K., Reese S., Deep learning-based surrogate modeling of coronary in-stent restenosis, Proc. Appl. Math. Mech. (2023),.
[47]
Barilli A., Visigalli R., Sala R., Gazzola G.C., Parolari A., Tremoli E., Bonomini S., Simon A., Closs E.I., Dall’Asta V., Bussolati O., In human endothelial cells rapamycin causes mTORC2 inhibition and impairs cell viability and function, Cardiovasc. Res. 78 (3) (2008) 563–571,.
[48]
Korelc J., Automation of primal and sensitivity analysis of transient coupled problems, Comput. Mech. 44 (5) (2009) 631–649,.
[49]
Schenk O., Gärtner K., Fichtner W., Stricker A., PARDISO: a high-performance serial and parallel sparse linear solver in semiconductor device simulation, Future Gener. Comput. Syst. 18 (1) (2001) 69–78,. URL https://www.sciencedirect.com/science/article/pii/S0167739X00000765 I. High Performance Numerical Methods and Applications. II. Performance Data Mining: Automated Diagnosis, Adaption, and Optimization.
[50]
Zeiler M.D., Fergus R., Visualizing and understanding convolutional networks, 2013, arXiv:1311.2901.
[51]
Zeiler M.D., Krishnan D., Taylor G.W., Fergus R., Deconvolutional networks, in: 2010 IEEE Computer Society Conference on Computer Vision and Pattern Recognition, 2010, pp. 2528–2535,.
[52]
Noh H., Hong S., Han B., Learning deconvolution network for semantic segmentation, in: 2015 IEEE International Conference on Computer Vision, ICCV, IEEE Computer Society, Los Alamitos, CA, USA, 2015, pp. 1520–1528,. URL https://doi.ieeecomputersociety.org/10.1109/ICCV.2015.178.
[53]
Dumoulin V., Visin F., A guide to convolution arithmetic for deep learning, 2018, arXiv:1603.07285.
[54]
Gruber A., Gunzburger M., Ju L., Wang Z., A comparison of neural network architectures for data-driven reduced-order modeling, Comput. Methods Appl. Mech. Engrg. 393 (2022),. URL https://www.sciencedirect.com/science/article/pii/S004578252200113X.
[55]
Barwey S., Shankar V., Viswanathan V., Maulik R., Multiscale graph neural network autoencoders for interpretable scientific machine learning, J. Comput. Phys. 495 (2023),. URL https://www.sciencedirect.com/science/article/pii/S0021999123006320.

Recommendations

Comments

Information & Contributors

Information

Published In

cover image Computer Methods and Programs in Biomedicine
Computer Methods and Programs in Biomedicine  Volume 257, Issue C
Dec 2024
836 pages

Publisher

Elsevier North-Holland, Inc.

United States

Publication History

Published: 01 December 2024

Author Tags

  1. In-stent restenosis (ISR)
  2. Drug-eluting stents (DES)
  3. Surrogate model
  4. 3D convolutional neural networks
  5. Autoencoder
  6. Non-intrusive model order reduction

Qualifiers

  • Research-article

Contributors

Other Metrics

Bibliometrics & Citations

Bibliometrics

Article Metrics

  • 0
    Total Citations
  • 0
    Total Downloads
  • Downloads (Last 12 months)0
  • Downloads (Last 6 weeks)0
Reflects downloads up to 25 Jan 2025

Other Metrics

Citations

View Options

View options

Figures

Tables

Media

Share

Share

Share this Publication link

Share on social media