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				<title level="a" type="main">Graph-Informed Neural Networks</title>
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							<persName><forename type="first">Søren</forename><surname>Taverniers</surname></persName>
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								<orgName type="department">Palo Alto Research Center (PARC)</orgName>
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									<addrLine>3333 Coyote Hill Road</addrLine>
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								<orgName type="department">Department of Mathematics and Statistics</orgName>
								<orgName type="institution">University of Massachusetts Amherst</orgName>
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									<postCode>01003</postCode>
									<settlement>Amherst</settlement>
									<region>MA</region>
									<country key="US">USA</country>
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							<persName><forename type="first">Eric</forename><forename type="middle">J</forename><surname>Hall</surname></persName>
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								<orgName type="department">Division of Mathematics</orgName>
								<orgName type="institution">University of Dundee</orgName>
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									<postCode>DD1 4HN</postCode>
									<settlement>Dundee</settlement>
									<country key="GB">UK</country>
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							<persName><forename type="first">Markos</forename><forename type="middle">A</forename><surname>Katsoulakis</surname></persName>
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							<persName><forename type="first">Daniel</forename><forename type="middle">M</forename><surname>Tartakovsky</surname></persName>
							<email>tartakovsky@stanford.edu</email>
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								<orgName type="department">Department of Energy Resources Engineering</orgName>
								<orgName type="institution">Stanford University</orgName>
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									<postCode>94305</postCode>
									<settlement>Stanford</settlement>
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						<title level="a" type="main">Graph-Informed Neural Networks</title>
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<div xmlns="http://www.tei-c.org/ns/1.0"><p>Graph-Informed Neural Networks (GINNs) present a strategy for incorporating domain knowledge into scientific machine learning for complex physical systems. The construction utilizes probabilistic graphical models (PGMs) to incorporate expert knowledge, available data, constraints, etc. with physics-based models such as systems of ordinary and partial differential equations (ODEs and PDEs). Computationally intensive nodes in this hybrid model are replaced by the hidden nodes of a neural network (i.e., learned features). Once trained, the resulting GINN surrogate can cheaply generate physically-relevant predictions at scale thereby enabling robust sensitivity analysis and uncertainty quantification (UQ). As proof of concept, we build a GINN for a multiscale model of electrical double-layer capacitor dynamics embedded into a Bayesian network (BN) PDE hybrid model.</p></div>
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<div xmlns="http://www.tei-c.org/ns/1.0"><p>In recent years, several approaches have been proposed to inform deep neural networks (DNNs) of physical laws and constraints to ensure they produce physically sound predictions. Two main classes of DNNs for building surrogate representations of physics-based models described by PDEs have emerged: physics-informed NNs (PINNs) <ref type="bibr" target="#b1">(Raissi, Perdikaris, and Karniadakis 2019)</ref> and "data-free" physics-constrained NNs <ref type="bibr" target="#b3">(Zhu et al. 2019)</ref>. Our approach uses the well-known concept of PGMs to embed domain knowledge, including correlations between control variables (CVs), into standard DNNs by only modifying their input layer structure and enabling the use of a standard penalty in the loss function, e.g., 1 (lasso regression) or 2 (ridge regression) regularization. This non-intrusive approach permits the use of off-the-shelf software like TensorFlow or PyTorch with minimal effort from the user, while remaining compatible with PINNs and other customized NN architectures which can be used to replace individual computational bottlenecks in the physics-based representation.</p><p>GINNs are particularly suited to enhance the computational workflow for complex systems featuring intrinsic computational bottlenecks and intricate physical relations among input CVs. Hence, to showcase the potential of this approach, we apply a GINN to simulation-based decisionmaking in electrical double-layer (EDL) supercapacitors, where it is deployed to build highly accurate kernel density estimators (KDEs) for the probability density functions (PDFs) of relevant output quantities of interest (QoIs).  </p></div>
<div xmlns="http://www.tei-c.org/ns/1.0"><head>Constructing and training a GINN</head><p>Simulation-based decision-making for design tasks involving complex multiscale/multiphysics systems requires predicting the impact of tunable CVs on the system's QoIs. Typically, this is modeled by recasting the problem in a probabilistic framework where CVs and QoIs are represented as random quantities that can be sampled from their corresponding probability distributions. For most real-world applications, these are continuous, non-Gaussian variables that need to be characterized by their full PDF rather than through a finite set of moments.</p><p>Figure <ref type="figure" target="#fig_1">1</ref>   </p></div>
<div xmlns="http://www.tei-c.org/ns/1.0"><head>GINN-based decision-making</head><p>A GINN's ability to cheaply generate io sample pairs can be leveraged to construct KDEs for the marginal and joint PDFs of QoIs with appropriate confidence intervals. Such nonparametric estimators form the building blocks for UQ tasks such as sensitivity analysis.</p><p>In Fig. <ref type="figure">3</ref>, we plot KDEs for QoIs based on 8 × 10 3 samples simulated using the BN PDE (the minimum amount of io data needed to train the GINN) and on 10 7 samples predicted with the GINN. We find that the GINN-predicted KDEs do not include spurious features observed with the smaller, expensive-to-compute data set generated with the physics-based model, and achieve much tighter confidence intervals for an equivalent computational cost (since learning the GINN's parameters and predicting new data with the GINN carries a negligible computational expense). Figure <ref type="figure">3</ref>: Estimated marginal densities for the QoIs in the supercapacitor testbed based on 8 × 10 3 samples computed with the hybrid BN PDE (solid/blue) or 10 7 samples computed with the GINN (dashed/red) <ref type="bibr" target="#b0">(Hall et al. 2021)</ref>.</p></div>
<div xmlns="http://www.tei-c.org/ns/1.0"><head>Conclusions</head><p>Our full analysis, in <ref type="bibr" target="#b0">(Hall et al. 2021;</ref><ref type="bibr" target="#b2">Taverniers et al. 2020</ref>), suggests that GINNs, which take structured PGMs as inputs, produce physically relevant QoIs that can be used to generate KDEs for robust and reliable sensitivity analysis and further UQ. Trained on a small set of high-fidelity input-output data from a domain-aware hybrid model, GINNs can quickly generate large amounts of output predictions, yielding an approach that is orders of magnitude faster than counterparts that rely on physics-based models alone.</p></div><figure xmlns="http://www.tei-c.org/ns/1.0" xml:id="fig_1"><head>Figure 1 :</head><label>1</label><figDesc>Figure1: A domain-aware PGM encoding structured priors on CVs serves as input to both the BN PDE (lower route) and trained GINN (upper route) for a homogenized model of ion diffusion in supercapacitors<ref type="bibr" target="#b2">(Taverniers et al. 2020</ref>).</figDesc></figure>
<figure xmlns="http://www.tei-c.org/ns/1.0" xml:id="fig_2"><head>Figure 2 :</head><label>2</label><figDesc>Figure 2: Overview of the global algorithm for GINN-based training, testing, and predicting (Hall et al. 2021).</figDesc></figure>
<figure xmlns="http://www.tei-c.org/ns/1.0" type="table" xml:id="tab_0"><head></head><label></label><figDesc>visualizes the construction of a GINN surrogate for a multiscale model of EDL supercapacitor dynamics. A BN, a type of directed acyclic PGM, systematically incorporates domain knowledge into the physics-based model through structured priors on CVs, resulting in a hybrid BN PDE model for macroscopic diffusion QoIs. The GINN retains the structured priors as inputs but replaces the hybrid model's computationally intensive nodes, related to upscaling via homogenization, with learned features to speed up the generation of QoIs while maintaining physical relevance.The GINN workflow, summarized in Fig.2, consists of: 1. Data generation: Generate N sam input-output (io) samples, divided into N train training and N test test samples. 2. Training: Train the GINN with N train training samples. 3. Testing: Test the trained GINN's ability to handle unseen data using the N test test samples. 4. Repeat steps 1 through 3 (modifying N train ) until both the training and test error tolerance are satisfied. 5. Prediction: Draw N pred sam inputs from the structured priors on the CVs and predict corresponding QoIs with the trained GINN surrogate.</figDesc><table><row><cell></cell><cell>(PB) or surrogate? Physics-based</cell><cell>PB</cell><cell>PB computations in, e.g., COMSOL,</cell></row><row><cell></cell><cell></cell><cell></cell><cell>MATLAB, FENICS</cell></row><row><cell>Learning</cell><cell></cell><cell></cell><cell></cell></row><row><cell>completed?</cell><cell></cell><cell></cell><cell></cell></row><row><cell></cell><cell cols="2">PB outputs</cell><cell></cell></row><row><cell></cell><cell cols="2">computed?</cell><cell></cell></row><row><cell></cell><cell></cell><cell>forward propagation</cell><cell></cell></row><row><cell></cell><cell></cell><cell>using initial guesses</cell><cell>PB outputs</cell><cell>NO</cell></row><row><cell></cell><cell></cell><cell>for weights/biases</cell><cell>computed?</cell></row><row><cell>hidden layers</cell><cell></cell><cell></cell><cell>YES</cell></row><row><cell>from trained GINN</cell><cell></cell><cell></cell><cell></cell></row><row><cell></cell><cell></cell><cell></cell><cell>forward</cell></row><row><cell></cell><cell></cell><cell></cell><cell cols="2">propagation</cell></row><row><cell></cell><cell cols="2">learned weights/biases</cell><cell cols="2">using learned weights/biases</cell></row><row><cell></cell><cell></cell><cell></cell><cell></cell><cell>modify</cell></row><row><cell></cell><cell>modify</cell><cell></cell><cell></cell><cell>NO</cell></row><row><cell>DATA-DRIVEN UQ</cell><cell>NN hyperparameters</cell><cell>NO</cell><cell>YES</cell></row></table></figure>
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			<div type="acknowledgement">
<div xmlns="http://www.tei-c.org/ns/1.0"><head>Acknowledgments</head><p>This work was performed while S. T. was employed by Stanford University.</p></div>
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			<div type="references">

				<listBibl>

<biblStruct xml:id="b0">
	<analytic>
		<title level="a" type="main">GINNs: Graph-Informed Neural Networks for Multiscale Physics</title>
		<author>
			<persName><forename type="first">E</forename><forename type="middle">J</forename><surname>Hall</surname></persName>
		</author>
		<author>
			<persName><forename type="first">S</forename><surname>Taverniers</surname></persName>
		</author>
		<author>
			<persName><forename type="first">M</forename><forename type="middle">A</forename><surname>Katsoulakis</surname></persName>
		</author>
		<author>
			<persName><forename type="first">D</forename><forename type="middle">M</forename><surname>Tartakovsky</surname></persName>
		</author>
		<idno type="DOI">10.1016/j.jcp.2021.110192</idno>
		<ptr target=".elsevier.com/a/1ccIO508Hokchvaliduntil2021-04-10" />
	</analytic>
	<monogr>
		<title level="j">J. Comput. Phys</title>
		<imprint>
			<biblScope unit="volume">433</biblScope>
			<biblScope unit="page">110192</biblScope>
			<date type="published" when="2021">2021</date>
		</imprint>
	</monogr>
	<note>Share link authors</note>
</biblStruct>

<biblStruct xml:id="b1">
	<analytic>
		<title level="a" type="main">neural networks: A deep learning framework for solving forward and inverse problems involving nonlinear partial differential equations</title>
		<author>
			<persName><forename type="first">M</forename><surname>Raissi</surname></persName>
		</author>
		<author>
			<persName><forename type="first">P</forename><surname>Perdikaris</surname></persName>
		</author>
		<author>
			<persName><forename type="first">G</forename><surname>Karniadakis</surname></persName>
		</author>
	</analytic>
	<monogr>
		<title level="j">J. Comput. Phys</title>
		<imprint>
			<biblScope unit="volume">378</biblScope>
			<biblScope unit="page" from="686" to="707" />
			<date type="published" when="2019">2019</date>
		</imprint>
	</monogr>
</biblStruct>

<biblStruct xml:id="b2">
	<monogr>
		<title level="m" type="main">Mutual Information for Explainable Deep Learning of Multiscale Systems</title>
		<author>
			<persName><forename type="first">S</forename><surname>Taverniers</surname></persName>
		</author>
		<author>
			<persName><forename type="first">E</forename><forename type="middle">J</forename><surname>Hall</surname></persName>
		</author>
		<author>
			<persName><forename type="first">M</forename><forename type="middle">A</forename><surname>Katsoulakis</surname></persName>
		</author>
		<author>
			<persName><forename type="first">D</forename><forename type="middle">M</forename><surname>Tartakovsky</surname></persName>
		</author>
		<idno>ArXiv:2009.04570</idno>
		<imprint>
			<date type="published" when="2020">2020</date>
		</imprint>
	</monogr>
</biblStruct>

<biblStruct xml:id="b3">
	<analytic>
		<title level="a" type="main">Physics-constrained deep learning for highdimensional surrogate modeling and uncertainty quantification without labeled data</title>
		<author>
			<persName><forename type="first">Y</forename><surname>Zhu</surname></persName>
		</author>
		<author>
			<persName><forename type="first">N</forename><surname>Zabaras</surname></persName>
		</author>
		<author>
			<persName><forename type="first">P.-S</forename><surname>Koutsourelakis</surname></persName>
		</author>
		<author>
			<persName><forename type="first">P</forename><surname>Perdikaris</surname></persName>
		</author>
	</analytic>
	<monogr>
		<title level="j">J. Comput. Phys</title>
		<imprint>
			<biblScope unit="volume">394</biblScope>
			<biblScope unit="page" from="56" to="81" />
			<date type="published" when="2019">2019</date>
		</imprint>
	</monogr>
</biblStruct>

				</listBibl>
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