Motivation SBML is the most widespread language for the definition of biochemical models. Although dozens of SBML simulators are available, there is a general lack of support to the integration of SBML models within open-standard general-purpose simulation ecosystems. This hinders co-simulation and integration of SBML models within larger model networks, in order to, e.g. enable in silico clinical trials of drugs, pharmacological protocols, or engineering artefacts such as biomedical devices against Virtual Physiological Human models. Modelica is one of the most popular existing open-standard general-purpose simulation languages, supported by many simulators. Modelica models are especially suited for the definition of complex networks of heterogeneous models from virtually all application domains. Models written in Modelica (and in 100+ other languages) can be readily exported into black-box Functional Mock-Up Units (FMUs), and seamlessly co-simulated and integrated into larger model networks within open-standard language-independent simulation ecosystems. Results In order to enable SBML model integration within heterogeneous model networks, we present SBML2Modelica, a software system translating SBML models into well-structured, user-intelligible, easily modifiable Modelica models. SBML2Modelica is SBML Level 3 Version 2—compliant and succeeds on 96.47% of the SBML Test Suite Core (with a few rare, intricate and easily avoidable combinations of constructs unsupported and cleanly signalled to the user). Our experimental campaign on 613 models from the BioModels database (with up to 5438 variables) shows that the major open-source (general-purpose) Modelica and FMU simulators achieve performance comparable to state-of-the-art specialized SBML simulators. Availability and implementation SBML2Modelica is written in Java and is freely available for non-commercial use at https://bitbucket.org/mclab/sbml2modelica.

source order 1 order 2 order 3 order 4 order 5Figure 1: Surface approximation using orthogonalized polynomials of increasing order, where order 1 corresponds to the plain Laplacian eigenbasis. All of these approximations are obtained starting from just 5 eigenfunctions. Reconstruction error is encoded by color, growing from white to dark red.

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Spectral geometric methods have brought revolutionary changes to the field of geometry processing. Of particular interest is the study of the Laplacian spectrum as a compact, isometry and permutation-invariant representation of a shape. Some recent works show how the intrinsic geometry of a full shape can be recovered from its spectrum, but there are approaches that consider the more challenging problem of recovering the geometry from the spectral information of partial shapes. In this paper, we propose a possible way to fill this gap. We introduce a learning-based method to estimate the Laplacian spectrum of the union of partial non-rigid 3D shapes, without actually computing the 3D geometry of the union or any correspondence between those partial shapes. We do so by operating purely in the spectral domain and by defining the union operation between short sequences of eigenvalues. We show that the approximated union spectrum can be used as-is to reconstruct the complete geometry [MRC*19], perform region localization on a template [RTO*19] and retrieve shapes from a database, generalizing ShapeDNA [RWP06] to work with partialities. Working with eigenvalues allows us to deal with unknown correspondence, different sampling, and different discretizations (point clouds and meshes alike), making this operation especially robust and general. Our approach is data-driven and can generalize to isometric and non-isometric deformations of the surface, as long as these stay within the same semantic class (e.g., human bodies or horses), as well as to partiality artifacts not seen at training time.