10,692 research outputs found
Biochemical parameter estimation vs. benchmark functions: A comparative study of optimization performance and representation design
© 2019 Elsevier B.V. Computational Intelligence methods, which include Evolutionary Computation and Swarm Intelligence, can efficiently and effectively identify optimal solutions to complex optimization problems by exploiting the cooperative and competitive interplay among their individuals. The exploration and exploitation capabilities of these meta-heuristics are typically assessed by considering well-known suites of benchmark functions, specifically designed for numerical global optimization purposes. However, their performances could drastically change in the case of real-world optimization problems. In this paper, we investigate this issue by considering the Parameter Estimation (PE) of biochemical systems, a common computational problem in the field of Systems Biology. In order to evaluate the effectiveness of various meta-heuristics in solving the PE problem, we compare their performance by considering a set of benchmark functions and a set of synthetic biochemical models characterized by a search space with an increasing number of dimensions. Our results show that some state-of-the-art optimization methods – able to largely outperform the other meta-heuristics on benchmark functions – are characterized by considerably poor performances when applied to the PE problem. We also show that a limiting factor of these optimization methods concerns the representation of the solutions: indeed, by means of a simple semantic transformation, it is possible to turn these algorithms into competitive alternatives. We corroborate this finding by performing the PE of a model of metabolic pathways in red blood cells. Overall, in this work we state that classic benchmark functions cannot be fully representative of all the features that make real-world optimization problems hard to solve. This is the case, in particular, of the PE of biochemical systems. We also show that optimization problems must be carefully analyzed to select an appropriate representation, in order to actually obtain the performance promised by benchmark results
Designing labeled graph classifiers by exploiting the R\'enyi entropy of the dissimilarity representation
Representing patterns as labeled graphs is becoming increasingly common in
the broad field of computational intelligence. Accordingly, a wide repertoire
of pattern recognition tools, such as classifiers and knowledge discovery
procedures, are nowadays available and tested for various datasets of labeled
graphs. However, the design of effective learning procedures operating in the
space of labeled graphs is still a challenging problem, especially from the
computational complexity viewpoint. In this paper, we present a major
improvement of a general-purpose classifier for graphs, which is conceived on
an interplay between dissimilarity representation, clustering,
information-theoretic techniques, and evolutionary optimization algorithms. The
improvement focuses on a specific key subroutine devised to compress the input
data. We prove different theorems which are fundamental to the setting of the
parameters controlling such a compression operation. We demonstrate the
effectiveness of the resulting classifier by benchmarking the developed
variants on well-known datasets of labeled graphs, considering as distinct
performance indicators the classification accuracy, computing time, and
parsimony in terms of structural complexity of the synthesized classification
models. The results show state-of-the-art standards in terms of test set
accuracy and a considerable speed-up for what concerns the computing time.Comment: Revised versio
Instantaneous modelling and reverse engineering of data-consistent prime models in seconds!
A theoretical framework that supports automated construction of dynamic prime models purely from experimental time series data has been invented and developed, which can automatically generate (construct) data-driven models of any time series data in seconds. This has resulted in the formulation and formalisation of new reverse engineering and dynamic methods for automated systems modelling of complex systems, including complex biological, financial, control, and artificial neural network systems. The systems/model theory behind the invention has been formalised as a new, effective and robust system identification strategy complementary to process-based modelling. The proposed dynamic modelling and network inference solutions often involve tackling extremely difficult parameter estimation challenges, inferring unknown underlying network structures, and unsupervised formulation and construction of smart and intelligent ODE models of complex systems. In underdetermined conditions, i.e., cases of dealing with how best to instantaneously and rapidly construct data-consistent prime models of unknown (or well-studied) complex system from small-sized time series data, inference of unknown underlying network of interaction is more challenging. This article reports a robust step-by-step mathematical and computational analysis of the entire prime model construction process that determines a model from data in less than a minute
An integrative top-down and bottom-up qualitative model construction framework for exploration of biochemical systems
The authors would like to thank the support on this research by the CRISP project (Combinatorial Responses In Stress Pathways) funded by the BBSRC (BB/F00513X/1) under the Systems Approaches to Biological Research (SABR) Initiative.Peer reviewedPublisher PD
Joint estimation of multiple related biological networks
Graphical models are widely used to make inferences concerning interplay in
multivariate systems. In many applications, data are collected from multiple
related but nonidentical units whose underlying networks may differ but are
likely to share features. Here we present a hierarchical Bayesian formulation
for joint estimation of multiple networks in this nonidentically distributed
setting. The approach is general: given a suitable class of graphical models,
it uses an exchangeability assumption on networks to provide a corresponding
joint formulation. Motivated by emerging experimental designs in molecular
biology, we focus on time-course data with interventions, using dynamic
Bayesian networks as the graphical models. We introduce a computationally
efficient, deterministic algorithm for exact joint inference in this setting.
We provide an upper bound on the gains that joint estimation offers relative to
separate estimation for each network and empirical results that support and
extend the theory, including an extensive simulation study and an application
to proteomic data from human cancer cell lines. Finally, we describe
approximations that are still more computationally efficient than the exact
algorithm and that also demonstrate good empirical performance.Comment: Published in at http://dx.doi.org/10.1214/14-AOAS761 the Annals of
Applied Statistics (http://www.imstat.org/aoas/) by the Institute of
Mathematical Statistics (http://www.imstat.org
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