923 research outputs found
Revealing networks from dynamics: an introduction
What can we learn from the collective dynamics of a complex network about its
interaction topology? Taking the perspective from nonlinear dynamics, we
briefly review recent progress on how to infer structural connectivity (direct
interactions) from accessing the dynamics of the units. Potential applications
range from interaction networks in physics, to chemical and metabolic
reactions, protein and gene regulatory networks as well as neural circuits in
biology and electric power grids or wireless sensor networks in engineering.
Moreover, we briefly mention some standard ways of inferring effective or
functional connectivity.Comment: Topical review, 48 pages, 7 figure
Computational Logic for Biomedicine and Neurosciences
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 properties. The potential candidate logics should have a traditional
proof theoretic pedigree (including either induction, or a sequent calculus
presentation enjoying cut-elimination and focusing), and should come with
certified proof tools. Beyond providing a reliable framework, this allows the
correct encodings of our biological systems. % For systems biology in general
and biomedicine in particular, we have so far, for the modeling part, three
candidate logics: all based on linear logic. The studied properties and their
proofs are formalized in a very expressive (non linear) inductive logic: the
Calculus of Inductive Constructions (CIC). The examples we have considered so
far are relatively simple ones; however, all coming with formal semi-automatic
proofs in the Coq system, which implements CIC. In neuroscience, we are
directly using CIC and Coq, to model neurons and some simple neuronal circuits
and prove some of their dynamic properties. % In biomedicine, the study of
multi omic pathway interactions, together with clinical and electronic health
record data should help in drug discovery and disease diagnosis. Future work
includes using more automatic provers. This should enable us to specify and
study more realistic examples, and in the long term to provide a system for
disease diagnosis and therapy prognosis
Complex event types for agent-based simulation
This thesis presents a novel formal modelling language, complex event types (CETs), to describe behaviours
in agent-based simulations. CETs are able to describe behaviours at any computationally
represented level of abstraction. Behaviours can be specified both in terms of the state transition rules of
the agent-based model that generate them and in terms of the state transition structures themselves.
Based on CETs, novel computational statistical methods are introduced which allow statistical dependencies
between behaviours at different levels to be established. Different dependencies formalise
different probabilistic causal relations and Complex Systems constructs such as ‘emergence’ and ‘autopoiesis’.
Explicit links are also made between the different types of CET inter-dependency and the
theoretical assumptions they represent.
With the novel computational statistical methods, three categories of model can be validated and
discovered: (i) inter-level models, which define probabilistic dependencies between behaviours at different
levels; (ii) multi-level models, which define the set of simulations for which an inter-level model
holds; (iii) inferred predictive models, which define latent relationships between behaviours at different
levels.
The CET modelling language and computational statistical methods are then applied to a novel
agent-based model of Colonic Cancer to demonstrate their applicability to Complex Systems sciences
such as Systems Biology. This proof of principle model provides a framework for further development
of a detailed integrative model of the system, which can progressively incorporate biological data from
different levels and scales as these become available
emgr - The Empirical Gramian Framework
System Gramian matrices are a well-known encoding for properties of
input-output systems such as controllability, observability or minimality.
These so-called system Gramians were developed in linear system theory for
applications such as model order reduction of control systems. Empirical
Gramian are an extension to the system Gramians for parametric and nonlinear
systems as well as a data-driven method of computation. The empirical Gramian
framework - emgr - implements the empirical Gramians in a uniform and
configurable manner, with applications such as Gramian-based (nonlinear) model
reduction, decentralized control, sensitivity analysis, parameter
identification and combined state and parameter reduction
(Mathematical) Logic for Systems Biology (Invited Paper)
International audienceWe advocates here the use of (mathematical) logic for systems biology, as a unified framework well suited for both modeling the dynamic behaviour of biological systems, expressing properties of them, and verifying these properties. The potential candidate logics should have a traditional proof theoretic pedigree (including a sequent calculus presentation enjoying cut-elimination and focusing), and should come with (certified) proof tools. Beyond providing a reliable framework, this allows the adequate encodings of our biological systems. We present two candidate logics (two modal extensions of linear logic, called HyLL and SELL), along with biological examples. The examples we have considered so far are very simple ones-coming with completely formal (interactive) proofs in Coq. Future works includes using automatic provers, which would extend existing automatic provers for linear logic. This should enable us to specify and study more realistic examples in systems biology, biomedicine (diagnosis and prognosis), and eventually neuroscience
Graph Modelling and Transformation: Theory meets Practice
In this paper, we focus on the role of graphs and graph transformation for four practical application areas from software system development. We present the typical problems in these areas and investigate how the respective systems are
modelled by graphs and graph transformation. In particular, we are interested in the usefulness of theoretical graph transformation results and graph transformation tools in order to solve these problems. Finally, we characterize concepts and tool features
which are still missing in practice to solve the presented and related problems even better.
Keywords: graph modelling, graph transformation, graph transformation tool
Non-associative, Non-commutative Multi-modal Linear Logic
Adding multi-modalities (called subexponentials) to linear logic enhances its power as a logical framework, which has been extensively used in the specification of e.g. proof systems, programming languages and bigraphs. Initially, subexponentials allowed for classical, linear, affine or relevant behaviors. Recently, this framework was enhanced so to allow for commutativity as well. In this work, we close the cycle by considering associativity. We show that the resulting system (acLLΣ ) admits the (multi)cut rule, and we prove two undecidability results for fragments/variations of acLLΣ
The free energy principle induces neuromorphic development
We show how any finite physical system with morphological, i.e. three-dimensional embedding or shape, degrees of freedom and locally limited free energy will, under the constraints of the free energy principle, evolve over time towards a neuromorphic morphology that supports hierarchical computations in which each ‘level’ of the hierarchy enacts a coarse-graining of its inputs, and dually, a fine-graining of its outputs. Such hierarchies occur throughout biology, from the architectures of intracellular signal transduction pathways to the large-scale organization of perception and action cycles in the mammalian brain. The close formal connections between cone-cocone diagrams (CCCD) as models of quantum reference frames on the one hand, and between CCCDs and topological quantum field theories on the other, allow the representation of such computations in the fully-general quantum-computational framework of topological quantum neural networks
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