Benchmark-Models-PEtab-SciML/Benchmark-Models/Ko_NeurIPS2023/model_Ko_NeurIPS2023.xml at main · dilpath/Benchmark-Models-PEtab-SciML · GitHub

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<?xml version="1.0" encoding="UTF-8"?>
<sbml xmlns="http://www.sbml.org/sbml/level3/version2/core"
      level="3"
      version="2">
  <model id="Ko_NeurIPS2023"
         name="Ko_NeurIPS2023"
         timeUnits="second">

    <notes>
      <body xmlns="http://www.w3.org/1999/xhtml">
        <p>
          Second-order neural ODE model of double-pendulum dynamics, based on
          Ko et al., NeurIPS 2023. The angular accelerations are supplied by
          the neural-network outputs through the PEtab-SciML hybridization table.
        </p>
      </body>
    </notes>

    <annotation>
      <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
               xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
        <rdf:Description rdf:about="#Ko_NeurIPS2023">
          <bqmodel:isDescribedBy>
            <rdf:Bag>
              <rdf:li rdf:resource="https://openreview.net/forum?id=rUFckPrzXR"/>
            </rdf:Bag>
          </bqmodel:isDescribedBy>
        </rdf:Description>
      </rdf:RDF>
    </annotation>

    <listOfUnitDefinitions>
      <unitDefinition id="per_second2" name="per second squared">
        <listOfUnits>
          <unit kind="second" exponent="-2" scale="0" multiplier="1"/>
        </listOfUnits>
      </unitDefinition>
    </listOfUnitDefinitions>

    <listOfParameters>
      <parameter id="theta1"
                 name="theta1"
                 value="-1.1336150169372559"
                 units="dimensionless"
                 constant="false"/>

      <parameter id="theta2"
                 name="theta2"
                 value="-1.3008047342300415"
                 units="dimensionless"
                 constant="false"/>

      <parameter id="omega1"
                 name="omega1"
                 value="-0.5385388135910034"
                 units="dimensionless"
                 constant="false"/>

      <parameter id="omega2"
                 name="omega2"
                 value="-6.1550583839416495"
                 units="dimensionless"
                 constant="false"/>

      <parameter id="acceleration1"
                 name="neural_network_angular_acceleration_1"
                 units="per_second2"
                 constant="true"/>

      <parameter id="acceleration2"
                 name="neural_network_angular_acceleration_2"
                 units="per_second2"
                 constant="true"/>
    </listOfParameters>

    <listOfRules>
      <rateRule variable="theta1">
        <math xmlns="http://www.w3.org/1998/Math/MathML">
          <ci> omega1 </ci>
        </math>
      </rateRule>

      <rateRule variable="theta2">
        <math xmlns="http://www.w3.org/1998/Math/MathML">
          <ci> omega2 </ci>
        </math>
      </rateRule>

      <rateRule variable="omega1">
        <math xmlns="http://www.w3.org/1998/Math/MathML">
          <ci> acceleration1 </ci>
        </math>
      </rateRule>

      <rateRule variable="omega2">
        <math xmlns="http://www.w3.org/1998/Math/MathML">
          <ci> acceleration2 </ci>
        </math>
      </rateRule>
    </listOfRules>
  </model>
</sbml>