361 research outputs found

    Enhanced parallel Differential Evolution algorithm for problems in computational systems biology

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    [Abstract] Many key problems in computational systems biology and bioinformatics can be formulated and solved using a global optimization framework. The complexity of the underlying mathematical models require the use of efficient solvers in order to obtain satisfactory results in reasonable computation times. Metaheuristics are gaining recognition in this context, with Differential Evolution (DE) as one of the most popular methods. However, for most realistic applications, like those considering parameter estimation in dynamic models, DE still requires excessive computation times. Here we consider this latter class of problems and present several enhancements to DE based on the introduction of additional algorithmic steps and the exploitation of parallelism. In particular, we propose an asynchronous parallel implementation of DE which has been extended with improved heuristics to exploit the specific structure of parameter estimation problems in computational systems biology. The proposed method is evaluated with different types of benchmarks problems: (i) black-box global optimization problems and (ii) calibration of non-linear dynamic models of biological systems, obtaining excellent results both in terms of quality of the solution and regarding speedup and scalability.Ministerio de Economía y Competitividad; DPI2011-28112-C04-03Consejo Superior de Investigaciones Científicas; PIE-201170E018Ministerio de Ciencia e Innovación; TIN2013-42148-PGalicia. Consellería de Cultura, Educación e Ordenación Universitaria; GRC2013/05

    Artificial Bee Colony algorithm in estimating kinetic parameters for yeast fermentation pathway

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    Analyzing metabolic pathways in systems biology requires accurate kinetic parameters that represent the simulated in vivo processes. Simulation of the fermentation pathway in the Saccharomyces cerevisiae kinetic model help saves much time in the optimization process. Fitting the simulated model into the experimental data is categorized under the parameter estimation problem. Parameter estimation is conducted to obtain the optimal values for parameters related to the fermentation process. This step is essential because insufficient identification of model parameters can cause erroneous conclusions. The kinetic parameters cannot be measured directly. Therefore, they must be estimated from the experimental data either in vitro or in vivo. Parameter estimation is a challenging task in the biological process due to the complexity and nonlinearity of the model. Therefore, we propose the Artificial Bee Colony algorithm (ABC) to estimate the parameters in the fermentation pathway of S. cerevisiae to obtain more accurate values. A metabolite with a total of six parameters is involved in this article. The experimental results show that ABC outperforms other estimation algorithms and gives more accurate kinetic parameter values for the simulated model. Most of the estimated kinetic parameter values obtained from the proposed algorithm are the closest to the experimental data

    Comprehensive review of models and methods for inferences in bio-chemical reaction networks

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    The key processes in biological and chemical systems are described by networks of chemical reactions. From molecular biology to biotechnology applications, computational models of reaction networks are used extensively to elucidate their non-linear dynamics. The model dynamics are crucially dependent on the parameter values which are often estimated from observations. Over the past decade, the interest in parameter and state estimation in models of (bio-) chemical reaction networks (BRNs) grew considerably. The related inference problems are also encountered in many other tasks including model calibration, discrimination, identifiability, and checking, and optimum experiment design, sensitivity analysis, and bifurcation analysis. The aim of this review paper is to examine the developments in literature to understand what BRN models are commonly used, and for what inference tasks and inference methods. The initial collection of about 700 documents concerning estimation problems in BRNs excluding books and textbooks in computational biology and chemistry were screened to select over 270 research papers and 20 graduate research theses. The paper selection was facilitated by text mining scripts to automate the search for relevant keywords and terms. The outcomes are presented in tables revealing the levels of interest in different inference tasks and methods for given models in the literature as well as the research trends are uncovered. Our findings indicate that many combinations of models, tasks and methods are still relatively unexplored, and there are many new research opportunities to explore combinations that have not been considered—perhaps for good reasons. The most common models of BRNs in literature involve differential equations, Markov processes, mass action kinetics, and state space representations whereas the most common tasks are the parameter inference and model identification. The most common methods in literature are Bayesian analysis, Monte Carlo sampling strategies, and model fitting to data using evolutionary algorithms. The new research problems which cannot be directly deduced from the text mining data are also discussed

    Efficiency and Reliability in Bringing AI into Transport and Smart Cities Solutions

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    capacity and the low cost of the Cloud have facilitated the development of new, powerful algorithms. The efficiency of these algorithms in Big Data processing, Deep Learning and Convolutional Networks is transforming the way we work and is opening new horizons. Thanks to them, we can now analyse data and obtain unimaginable solutions to today’s problems. Nevertheless, our success is not entirely based on algorithms, it also comes from our ability to follow our “gut” when choosing the best combination of algorithms for an intelligent artefact. Their development involves the use of both connectionist and symbolic systems, that is to say data and knowledge. Moreover, it is necessary to work with both historical and real-time data. It is also important to consider development time, costs and the ability to create systems that will interact with their environment, will connect with the objects that surround them and will manage the data they obtain in a reliable manner. In this keynote, the evolution of intelligent computer systems will be examined, especially that of convolutional networks. The need for human capital will be discussed, as well as the need to follow one’s “gut instinct” in problem-solving. Furthermore, the importance of IoT and Blockchain in the development of intelligent systems will be analysed and it will be shown how tools like "Deep Intelligence" make it possible to create computer systems efficiently and effectively. "Smart" infrastructures need to incorporate all added-value resources so they can offer useful services to the society, while reducing costs, ensuring reliability and improving the quality of life of the citizens. The combination of AI with IoT and with blockchain offers a world of possibilities and opportunities. The development of transport, smart cities, urbanizations and leisure areas can be improved through the use of distributed intelligent computer systems. In this regard, edge platforms or fog computing help increase efficiency, reduce network latency, improve security and bring intelligence to the edge of the network, the sensors, users and the environment. Several use cases of intelligent systems will be presented, and it will be analysed how the processes of implementation and use have been optimized by means of different tools

    Rapid Deployment of Deep AI Models in Engineering Solutions

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    The blockchain system, appeared in 2009 together with the virtual currency bitcoin, is a record of digital transactions based on a huge database in which all financial operations carried out with electronic currency are registered. The Blockchain (or chain of blocks) is a shared database that works as a book for the record of purchase-sale operations or any other transaction. It is the technological base of the operation of bitcoin, for example. It consists of a set of notes that are in a shared online database in which operations, quantities, dates and participants are registered by means of codes. By using cryptographic keys and being distributed by many computers (people), it presents security advantages against manipulation and fraud. A modification in one of the copies would be useless, but the change must be made in all the copies because the database is open and public
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