Related papers: ODEbase: A Repository of ODE Systems for Systems B…
Declarative modeling uses symbolic expressions to represent models. With such expressions one can formalize high-level mathematical computations on models that would be difficult or impossible to perform directly on a lower-level simulation…
Advances in bioengineering and biomedicine demand a deep understanding of the dynamic behavior of biological systems, ranging from protein pathways to complex cellular processes. Biological networks like gene regulatory networks and protein…
Computer Algebra Systems (e.g. Maple) are used in research, education, and industrial settings. One of their key functionalities is symbolic integration, where there are many sub-algorithms to choose from that can affect the form of the…
Agent-based modeling and simulation is a useful method to study biological phenomena in a wide range of fields, from molecular biology to ecology. Since there is currently no agreed-upon standard way to specify such models it is not always…
Symbolic Computation algorithms and their implementation in computer algebra systems often contain choices which do not affect the correctness of the output but can significantly impact the resources required: such choices can benefit from…
Integrating dynamical systems models with time series data is a central part of contemporary mathematical biology. With the rich variety of available models and data, numerous methods and computational tools have been developed for these…
As dynamic and control systems become more complex, relying purely on numerical computations for systems analysis and design might become extremely expensive or totally infeasible. Computer algebra can act as an enabler for analysis and…
Understanding the behaviour of biological systems requires a complex setting of in vitro and in vivo experiments, which attracts high costs in terms of time and resources. The use of mathematical models allows researchers to perform…
The modelling and analysis of biological systems has deep roots in Mathematics, specifically in the field of ordinary differential equations (ODEs). Alternative approaches based on formal calculi, often derived from process algebras or term…
Many interesting and useful symbolic computation algorithms manipulate mathematical expressions in mathematically meaningful ways. Although these algorithms are commonplace in computer algebra systems, they can be surprisingly difficult to…
We introduce ODEFormer, the first transformer able to infer multidimensional ordinary differential equation (ODE) systems in symbolic form from the observation of a single solution trajectory. We perform extensive evaluations on two…
Background: Qualitative frameworks, especially those based on the logical discrete formalism, are increasingly used to model regulatory and signalling networks. A major advantage of these frameworks is that they do not require precise…
This volume contains papers presented at the Ninth International Symposium on Symbolic Computation in Software Science, SCSS 2021. Symbolic Computation is the science of computing with symbolic objects (terms, formulae, programs,…
Motivation: Computational models in biology can increase our understanding of biological systems, be used to answer research questions, and make predictions. Accessibility and reusability of computational models is limited and often…
Understanding the mechanisms of interactions within cells, tissues, and organisms is crucial to driving developments across biology and medicine. Mathematical modeling is an essential tool for simulating biological systems and revealing…
We advocate here the use of computational logic for systems biology, as a \emph{unified and safe} framework well suited for both modeling the dynamic behaviour of biological systems, expressing properties of them, and verifying these…
Quantum simulation is a leading candidate for demonstrating practical quantum advantage over classical computation, as it is believed to provide exponentially more compute power than any classical system. It offers new means of studying the…
Mathematical methods provide useful framework for the analysis and design of complex systems. In newer contexts such as biology, however, there is a need to both adapt existing methods as well as to develop new ones. Using a combination of…
Ordinary differential equations (ODEs) are the primary means to modelling dynamical systems in many natural and engineering sciences. The number of equations required to describe a system with high heterogeneity limits our capability of…
Document preparation systems like LaTeX offer the ability to render mathematical expressions as one would write these on paper. Using LaTeX, LaTeXML, and tools generated for use in the National Institute of Standards (NIST) Digital Library…