4,688 research outputs found
Gene Expression with General Purpose Graph Rewriting Systems
We show that a general purpose graph rewriting system (GRS) nowadays is capable of simulating gene expression, the intra-cellular synthesis of proteins. The model organism we use is one of the best-studied prokaryotic life-forms in genetics, the E. coli bacteria. Our graph representation of the E. coli DNA consists of 23 Million graph elements. In our case study we correctly synthesize the proteins of 30 consecutive genes. In this paper we describe our approach as well as our observations. Further on, we discuss some potential extensions to GRSs that would support more sophisticated simulations
A Graph Grammar for Modelling RNA Folding
We propose a new approach for modelling the process of RNA folding as a graph
transformation guided by the global value of free energy. Since the folding
process evolves towards a configuration in which the free energy is minimal,
the global behaviour resembles the one of a self-adaptive system. Each RNA
configuration is a graph and the evolution of configurations is constrained by
precise rules that can be described by a graph grammar.Comment: In Proceedings GaM 2016, arXiv:1612.0105
Answering SPARQL queries modulo RDF Schema with paths
SPARQL is the standard query language for RDF graphs. In its strict
instantiation, it only offers querying according to the RDF semantics and would
thus ignore the semantics of data expressed with respect to (RDF) schemas or
(OWL) ontologies. Several extensions to SPARQL have been proposed to query RDF
data modulo RDFS, i.e., interpreting the query with RDFS semantics and/or
considering external ontologies. We introduce a general framework which allows
for expressing query answering modulo a particular semantics in an homogeneous
way. In this paper, we discuss extensions of SPARQL that use regular
expressions to navigate RDF graphs and may be used to answer queries
considering RDFS semantics. We also consider their embedding as extensions of
SPARQL. These SPARQL extensions are interpreted within the proposed framework
and their drawbacks are presented. In particular, we show that the PSPARQL
query language, a strict extension of SPARQL offering transitive closure,
allows for answering SPARQL queries modulo RDFS graphs with the same complexity
as SPARQL through a simple transformation of the queries. We also consider
languages which, in addition to paths, provide constraints. In particular, we
present and compare nSPARQL and our proposal CPSPARQL. We show that CPSPARQL is
expressive enough to answer full SPARQL queries modulo RDFS. Finally, we
compare the expressiveness and complexity of both nSPARQL and the corresponding
fragment of CPSPARQL, that we call cpSPARQL. We show that both languages have
the same complexity through cpSPARQL, being a proper extension of SPARQL graph
patterns, is more expressive than nSPARQL.Comment: RR-8394; alkhateeb2003
Reduction of dynamical biochemical reaction networks in computational biology
Biochemical networks are used in computational biology, to model the static
and dynamical details of systems involved in cell signaling, metabolism, and
regulation of gene expression. Parametric and structural uncertainty, as well
as combinatorial explosion are strong obstacles against analyzing the dynamics
of large models of this type. Multi-scaleness is another property of these
networks, that can be used to get past some of these obstacles. Networks with
many well separated time scales, can be reduced to simpler networks, in a way
that depends only on the orders of magnitude and not on the exact values of the
kinetic parameters. The main idea used for such robust simplifications of
networks is the concept of dominance among model elements, allowing
hierarchical organization of these elements according to their effects on the
network dynamics. This concept finds a natural formulation in tropical
geometry. We revisit, in the light of these new ideas, the main approaches to
model reduction of reaction networks, such as quasi-steady state and
quasi-equilibrium approximations, and provide practical recipes for model
reduction of linear and nonlinear networks. We also discuss the application of
model reduction to backward pruning machine learning techniques
Search Based Software Engineering in Membrane Computing
This paper presents a testing approach for kernel P Systems (kP systems),
based on test data generation for a given scenario. This method uses Genetic Algorithms
to generate the input sets needed to trigger the given computation steps
Graph Kernels
We present a unified framework to study graph kernels, special cases of which include the random
walk (Gärtner et al., 2003; Borgwardt et al., 2005) and marginalized (Kashima et al., 2003, 2004;
Mahé et al., 2004) graph kernels. Through reduction to a Sylvester equation we improve the time
complexity of kernel computation between unlabeled graphs with n vertices from O(n^6) to O(n^3).
We find a spectral decomposition approach even more efficient when computing entire kernel matrices.
For labeled graphs we develop conjugate gradient and fixed-point methods that take O(dn^3)
time per iteration, where d is the size of the label set. By extending the necessary linear algebra to
Reproducing Kernel Hilbert Spaces (RKHS) we obtain the same result for d-dimensional edge kernels,
and O(n^4) in the infinite-dimensional case; on sparse graphs these algorithms only take O(n^2)
time per iteration in all cases. Experiments on graphs from bioinformatics and other application
domains show that these techniques can speed up computation of the kernel by an order of magnitude
or more. We also show that certain rational kernels (Cortes et al., 2002, 2003, 2004) when
specialized to graphs reduce to our random walk graph kernel. Finally, we relate our framework to
R-convolution kernels (Haussler, 1999) and provide a kernel that is close to the optimal assignment
kernel of Fröhlich et al. (2006) yet provably positive semi-definite
Epigenetic Chromatin Silencing: Bistability and Front Propagation
The role of post-translational modification of histones in eukaryotic gene
regulation is well recognized. Epigenetic silencing of genes via heritable
chromatin modifications plays a major role in cell fate specification in higher
organisms. We formulate a coarse-grained model of chromatin silencing in yeast
and study the conditions under which the system becomes bistable, allowing for
different epigenetic states. We also study the dynamics of the boundary between
the two locally stable states of chromatin: silenced and unsilenced. The model
could be of use in guiding the discussion on chromatin silencing in general. In
the context of silencing in budding yeast, it helps us understand the phenotype
of various mutants, some of which may be non-trivial to see without the help of
a mathematical model. One such example is a mutation that reduces the rate of
background acetylation of particular histone side-chains that competes with the
deacetylation by Sir2p. The resulting negative feedback due to a Sir protein
depletion effect gives rise to interesting counter-intuitive consequences. Our
mathematical analysis brings forth the different dynamical behaviors possible
within the same molecular model and guides the formulation of more refined
hypotheses that could be addressed experimentally.Comment: 19 pages, 5 figure
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