14,196 research outputs found
An Abstraction Theory for Qualitative Models of Biological Systems
Multi-valued network models are an important qualitative modelling approach
used widely by the biological community. In this paper we consider developing
an abstraction theory for multi-valued network models that allows the state
space of a model to be reduced while preserving key properties of the model.
This is important as it aids the analysis and comparison of multi-valued
networks and in particular, helps address the well-known problem of state space
explosion associated with such analysis. We also consider developing techniques
for efficiently identifying abstractions and so provide a basis for the
automation of this task. We illustrate the theory and techniques developed by
investigating the identification of abstractions for two published MVN models
of the lysis-lysogeny switch in the bacteriophage lambda.Comment: In Proceedings MeCBIC 2010, arXiv:1011.005
Basins of Attraction, Commitment Sets and Phenotypes of Boolean Networks
The attractors of Boolean networks and their basins have been shown to be
highly relevant for model validation and predictive modelling, e.g., in systems
biology. Yet there are currently very few tools available that are able to
compute and visualise not only attractors but also their basins. In the realm
of asynchronous, non-deterministic modeling not only is the repertoire of
software even more limited, but also the formal notions for basins of
attraction are often lacking. In this setting, the difficulty both for theory
and computation arises from the fact that states may be ele- ments of several
distinct basins. In this paper we address this topic by partitioning the state
space into sets that are committed to the same attractors. These commitment
sets can easily be generalised to sets that are equivalent w.r.t. the long-term
behaviours of pre-selected nodes which leads us to the notions of markers and
phenotypes which we illustrate in a case study on bladder tumorigenesis. For
every concept we propose equivalent CTL model checking queries and an extension
of the state of the art model checking software NuSMV is made available that is
capa- ble of computing the respective sets. All notions are fully integrated as
three new modules in our Python package PyBoolNet, including functions for
visualising the basins, commitment sets and phenotypes as quotient graphs and
pie charts
Abstracting Asynchronous Multi-Valued Networks: An Initial Investigation
Multi-valued networks provide a simple yet expressive qualitative state based
modelling approach for biological systems. In this paper we develop an
abstraction theory for asynchronous multi-valued network models that allows the
state space of a model to be reduced while preserving key properties of the
model. The abstraction theory therefore provides a mechanism for coping with
the state space explosion problem and supports the analysis and comparison of
multi-valued networks. We take as our starting point the abstraction theory for
synchronous multi-valued networks which is based on the finite set of traces
that represent the behaviour of such a model. The problem with extending this
approach to the asynchronous case is that we can now have an infinite set of
traces associated with a model making a simple trace inclusion test infeasible.
To address this we develop a decision procedure for checking asynchronous
abstractions based on using the finite state graph of an asynchronous
multi-valued network to reason about its trace semantics. We illustrate the
abstraction techniques developed by considering a detailed case study based on
a multi-valued network model of the regulation of tryptophan biosynthesis in
Escherichia coli.Comment: Presented at MeCBIC 201
Controllability Metrics on Networks with Linear Decision Process-type Interactions and Multiplicative Noise
This paper aims at the study of controllability properties and induced
controllability metrics on complex networks governed by a class of (discrete
time) linear decision processes with mul-tiplicative noise. The dynamics are
given by a couple consisting of a Markov trend and a linear decision process
for which both the "deterministic" and the noise components rely on
trend-dependent matrices. We discuss approximate, approximate null and exact
null-controllability. Several examples are given to illustrate the links
between these concepts and to compare our results with their continuous-time
counterpart (given in [16]). We introduce a class of backward stochastic
Riccati difference schemes (BSRDS) and study their solvability for particular
frameworks. These BSRDS allow one to introduce Gramian-like controllability
metrics. As application of these metrics, we propose a minimal
intervention-targeted reduction in the study of gene networks
CHR(PRISM)-based Probabilistic Logic Learning
PRISM is an extension of Prolog with probabilistic predicates and built-in
support for expectation-maximization learning. Constraint Handling Rules (CHR)
is a high-level programming language based on multi-headed multiset rewrite
rules.
In this paper, we introduce a new probabilistic logic formalism, called
CHRiSM, based on a combination of CHR and PRISM. It can be used for high-level
rapid prototyping of complex statistical models by means of "chance rules". The
underlying PRISM system can then be used for several probabilistic inference
tasks, including probability computation and parameter learning. We define the
CHRiSM language in terms of syntax and operational semantics, and illustrate it
with examples. We define the notion of ambiguous programs and define a
distribution semantics for unambiguous programs. Next, we describe an
implementation of CHRiSM, based on CHR(PRISM). We discuss the relation between
CHRiSM and other probabilistic logic programming languages, in particular PCHR.
Finally we identify potential application domains
Neural Nearest Neighbors Networks
Non-local methods exploiting the self-similarity of natural signals have been
well studied, for example in image analysis and restoration. Existing
approaches, however, rely on k-nearest neighbors (KNN) matching in a fixed
feature space. The main hurdle in optimizing this feature space w.r.t.
application performance is the non-differentiability of the KNN selection rule.
To overcome this, we propose a continuous deterministic relaxation of KNN
selection that maintains differentiability w.r.t. pairwise distances, but
retains the original KNN as the limit of a temperature parameter approaching
zero. To exploit our relaxation, we propose the neural nearest neighbors block
(N3 block), a novel non-local processing layer that leverages the principle of
self-similarity and can be used as building block in modern neural network
architectures. We show its effectiveness for the set reasoning task of
correspondence classification as well as for image restoration, including image
denoising and single image super-resolution, where we outperform strong
convolutional neural network (CNN) baselines and recent non-local models that
rely on KNN selection in hand-chosen features spaces.Comment: to appear at NIPS*2018, code available at
https://github.com/visinf/n3net
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