Using machine learning to characterize heart failure across the scales

Mathias Peirlinck1, Francisco Sahli Costabal2, K Sack3, Jenny S. Choy4, Ghassan S. Kassab4, Julius M. Guccione5, Matthieu De Beule1, Patrick Segers1, Ellen Kuhl6
1Biofluid, Tissue and Solid Mechanics for Medical Applications (IBiTech, bioMMeda), Ghent University, Ghent, Belgium
2Department of Mechanical Engineering, Stanford University, Stanford, CA, USA
3Department of Human Biology, University of Cape Town, Cape Town, South Africa
4California Medical Innovations Institute, Inc., San Diego, CA, USA
5Department of Surgery, University of California at San Francisco, San Francisco, CA, USA
6Departments of Mechanical Engineering and Bioengineering, Stanford University, Stanford, CA, USA

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Ambrosi D, Ateshian GA, Arruda EM, Cowin SC, Dumais J, Goriely A, Holzapfel GA, Humphrey JD, Kemkemer R, Kuhl E, Olberding JE, Taber LA, Garikipati K (2011) Perspectives on biological growth and remodeling. J Mech Phys Solids 59:863–883

Arts T, Delhaas T, Bovendeerd P, Verbeek X, Prinzen FW (2005) Adaptation to mechanical load determines shape and properties of heart and circulation: the CircAdapt model. Am J Phys Heart Circ Phys 288:H1943–H1954

Baillargeon B, Rebelo N, Fox DD, Taylor RL, Kuhl E (2014) The Living Heart Project: a robust and integrative simulator for human heart function. Eur J Mech A/Solids 48:38–47

Bray MA, Sheehy SP, Parker KK (2008) Sarcomere alignment is regulated by myocyte shape. Cell Motil Cytoskel 65:641–651

Campos JO, Sundnes J, dos Santos RW, Rocha BM (2019) Effects of left ventricle wall thickness uncertainties on cardiac mechanics. Biomech Model Mechanobiol. https://doi.org/10.1007/s10237-019-01153-1

Chabiniok R, Wang V, Hadjicharalambous M, Asner L, Lee J, Sermesant M, Kuhl E, Young A, Moireau P, Nash M, Chapelle D, Nordsletten DA (2016) Multiphysics and multiscale modeling, data-model fusion and integration of organ physiology in the clinic: ventricular cardiac mechanics. Interface Focus 6:20150083

Choy JS, Leng S, Awakeem Y, Sack K.L, Dabiri Y, Zhong L, Guccione JM, Kassab GS Mechanical stretch as stimulus for growth and remodeling in mitral regurgitation. submitted for publication

Dassault Systèmes SIMULIA (2018) Abaqus 2018. Documentation, Dassault Systèmes, Rhode Island

Dokos S, Smaill BH, Young AA, LeGrice IJ (2002) Shear properties of passive ventricular myocardium. Am J Physiol Heart Circ Physiol 283:H2650–H2659

Eriksson TSE, Prassl AJ, Plank G, Holzapfel GA (2013) Influence of myocardial fiber/sheet orientations on left ventricular mechanical contraction. Math Mech Solids 18:592–606

Gelman A (2006) Prior distributions for variance parameters in hierarchical models. Bayesian Anal 1:515–534

Gelman A, Hill J (2006) Data analysis using regression and multilevel/hierarchical models. Cambridge University Press, Cambridge

Genet M, Lee LC, Baillargeon B, Guccione JM, Kuhl E (2016) Modeling pathologies of systolic and diastolic heart failure. Ann Biomed Eng 44:112–127

Gerdes AM, Kellerman SE, Moore JA, Muffly KE, Clark LC, Reaves PY, Malec KB, Mc Keown PP, Schocken DD (1992) Structural remodeling of cardiac myocytes in patients with ischemic cardiomyopathy. Circulation 86:426–430

Gerdes AM, Capasso JM (1995) Structural remodeling and mechanical dysfunction of cardiac myocytes in heart failure. J Mol Cell Cardiol 27:849–856

Göktepe S, Abilez OJ, Kuhl E (2010) A generic approach towards finite growth with examples of athlete’s heart, cardiac dilation, and cardiac wall thickening. J Mech Phys Solids 58:1661–1680

Göktepe S, Abilez OJ, Parker KK, Kuhl E (2010) A multiscale model for eccentric and concentric cardiac growth through sarcomerogenesis. J Theor Biol 265:433–442

Göktepe S, Acharya SNS, Wong J, Kuhl E (2011) Computational modeling of passive myocardium. Int J Num Meth Biomed Eng 27:1–12

Grossman W, Jones D, McLaurin LP (1975) Wall stress and patterns of hypertrophy in the human left ventricle. J Clin Invest 56:56–64

Grossman W (1980) Cardiac hypertrophy: useful adaptation or pathologic process? Am J Med 69:576–584

Holmes JW (2004) Candidate mechanical stimuli for hypertrophy during volume overload. J Appl Physiol 97:1453–1460

Holzapfel GA, Ogden RW (2009) Constitutive modelling of passive myocardium: a structurally based framework for material characterization. Philos Trans A Math Phys Eng Sci 367:3445–3475

Inman HF, Bradley EL Jr (1989) The overlapping coefficient as a measure of agreement between probability distributions and point estimation of the overlap of two normal densities. Commun Stat Methods 18:3851–3874

Jones E, Oliphant T, Peterson P (2014) SciPy: open source scientific tools for Python. http://www.scipy.org/

Kerckhoffs RCP, Omens JH, McCulloch AD (2012) A single strain-based growth law predicts concentric and eccentric cardiac growth during pressure and volume overload. Mech Res Commun 42:40–50

Kerkhof PLM (2015) Characterizing heart failure in the ventricular volume domain. Clin Med Ins Cardiol 9:11–31

Kleiber M (1947) Body size and metabolic rate. Physiol Rev 27:511–541

Klotz S, Hay I, Dickstein ML, Yi G-H, Wang J, Maurer MS, Kass DA, Burkhoff D (2006) Single-beat estimation of end-diastolic pressure-volume relationship: a novel method with potential for noninvasive application. Am J Physiol Circ Physiol 291:H403–H412

Kroon W, Delhaas T, Arts T, Bovendeerd P (2009) Computational modeling of volumetric soft tissue growth: application to the cardiac left ventricle. Biomech Model Mechanobiol 8:301–309

Kuhl E (2014) Growing matter—a review of growth in living systems. J Mech Behavior Biomed Mat 29:529–543

Kumar V, Abbas AK, Aster JC (2015) Robbins and Cotran pathologic basis of disease, 9th edn. Elsevier, Amsterdam

Lee JD, Sasayama S, Kihara Y, Ohyagi A, Fujisawa A, Yui Y, Kawai C (1985) Adaptations of the left ventricle to chronic volume overload induced by mitral regurgitation in conscious dogs. Heart Vessels 1:9–15

Lee LC, Kassab GS, Guccione JM (2016) Mathematical modeling of cardiac growth and remodeling WIREs Syst. Biol Med 8:211–226

Legrice IJ, Hunter PJ, Smaill BH (1997) Laminar structure of the heart: a mathematical model. Am J Physiol 272:H2466–H2476

Lewandowski D, Kurowicka D, Joe H (2009) Generating random correlation matrices based on vines and extended onion method. J Multivar Anal 100:1989–2001

Limpert E, Stahel WA, Abbt M (2001) Log-normal distribution across the sciences: Keys and clues. Bioscience 51:341–352

Menzel A (2005) Modelling of anisotropic growth in biological tissues. Biomech Model Mechanobio 3:147–171

Menzel A, Kuhl E (2012) Frontiers in growth and remodeling. Mech Res Commun 42:1–14

Omens JH (1998) Stress and strain as regulators of myocardial growth. Prog Biophys Mol Biol 69:559–572

Opie LH, Commerford PJ, Gersh BJ, Pfeffer MA (2006) Controversies in ventricular remodelling. Lancet 367:356–367

Peirlinck M, Sack KL, De Backer P, Morais P, Segers P, Franz T, De Beule M (2019) Kinematic boundary conditions substantially impact in silico ventricular function. Int J Num Meth Biomed Eng 35:e3151

Perdikaris P (2017) Gaussian processess. A hands-on tutorial. https://github.com/paraklas/GPTutorial

Raissi M, Perdikaris P, Karniadakis G (2017) Machine learning of linear differential equations using Gaussian processes. J Comp Phys 348:683–693

Raissi M, Perdikaris P, Karniadakis G (2018) Numerical Gaussian processes for time-dependent and nonlinear partial differential equations. SIAM J Sci Comp 40:A172–A198

Rausch MK, Dam A, Göktepe S, Abilez OJ, Kuhl E (2011) Computational modeling of growth: systemic and pulmonary hypertension in the heart. Biomech Model Mechanobio 10:799–811

Rausch MK, Zöllner AM, Genet M, Baillargeon B, Bothe W, Kuhl E (2017) A virtual sizing tool for mitral valve annuloplasty. Int J Num Meth Biomed Eng 33:e02788

Rodrigues JCL, Amadu AM, Dastidar AG, Szantho GV, Lyen SM, Godsave C, Ratcliffe LEK, Burchell AE, Hart EC, Hamilton MCK, Nightingale AK, Paton JFR, Manghat NE, Bucciarelli-Ducci C (2016) Comprehensive characterisation of hypertensive heart disease left ventricular phenotypes. Heart 102:1671–1679

Rodriguez E, Hoger A, McCulloch AD (1994) Stress-dependent finite growth in soft elastic tissues. J Biomech 27:455–467

Rodríguez-Cantano R, Sundnes J, Rognes ME (2019) Uncertainty in cardiac myofiber orientation and stiffnesses dominate the variability of left ventricle deformation response Int. J Num Meth Biomed Eng 35:e3178

Sack KL, Aliotta E, Ennis DB, Choy JS, Kassab GS, Guccione JM, Franz T (2018) Construction and validation of subject-specific biventricular finite-element models of healthy and failing swine hearts from high-resolution DT-MRI. Front Physiol 9:539

Saez P, Pena E, Martinez MA, Kuhl E (2014) Computational modeling of hypertensive growth in the human carotid artery. Comp Mech 53:1183–1196

Sahli Costabal F, Concha FA, Hurtado DE, Kuhl E (2017) The importance of mechano-electrical feedback and inertia in cardiac electromechanics. Comp Meth Appl Mech Eng 320:352–368

Sahli Costabal F, Choy JS, Sack KL, Guccione JM, Kassab G, Kuhl E (2019) Multiscale characterization of heart failure. Acta Biomat 86:66–76

Sahli Costabal F, Matsuno K, Yao J, Perdikaris P, Kuhl E (2019) Machine learning in drug development: characterizing the effect of 30 drugs on the QT interval using Gaussian process regression, sensitivity analysis, and uncertainty quantification. Comp Meth Appl Mech Eng 348:313–333

Salvatier J, Wiecki TV, Fonnesbeck C (2016) Probabilistic programming in Python using PyMC3. Peer J Comput Sci 2:e55

Sandler H, Dodge HT (1963) Left ventricular tension and stress in man. Circ Res 8:437–445

Sasayama S, Ross JJ, Franklin D, Bloor CM, Bishop S, Dilley RB (1976) Adaptations of the left ventricle to chronic pressure overload. Circ Res 38:172–178

Savinova OV, Gerdes AM (2012) Myocyte changes in heart failure. Heart Fail Clin 8:1–6

Sommer G, Schriefl AJ, Andre M, Sacherer M, Viertler C, Wolinski H, Holzapfel GA (2015) Biomechanical properties and microstructure of human ventricular myocardium. Acta Biomat 24:172–192

Tsamis A, Cheng A, Nguyen TC, Langer F, Miller DC, Kuhl E (2012) Kinematics of cardiac growth: in vivo charactierzaion of growth tensors and strains. J Mech Beh Biomed Mat 8:165–177

Townsend N, Wilson L, Bhatnagar P, Wickramasinghe K, Rayner M, Nichols M (2016) Cardiovascular disease in Europe: epidemiological update 2016. Eur Heart J 37:3232–3245

Wong J, Kuhl E (2014) Generating fiber orientation maps in human heart models using Poisson interpolation. Comp Meth Biomech Biomed Eng 17:1217–1226

Yoshida M, Sho E, Nanjo H, Takahashi M, Koboyashi M, Kawamura K, Honma M, Komatsu M, Sugita A, Yamauchi M, Hosoi T, Ito Y, Matsuda H (2010) Weaving hypothesis of cardiomyocyte sarcomeres. Am J Path 176:660–678

Wisdom KM, Delp SL, Kuhl E (2015) Use it or lose it: multiscale skeletal muscle adaptation to mechanical stimuli. Biomech Model Mechanobiol 14:195–215

Witzenburg CM, Holmes JW (2017) A comparison of phenomenologic growth laws for myocardial hypertrophy. J Elast 129:257–281

Zöllner AM, Abilez OJ, Böl M, Kuhl E (2012) Stretching skeletal muscle. Chronic muscle lengthening through sarcomerogenesis. PLoS ONE 7:e45661