440 research outputs found

    Cross-docking: A systematic literature review

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    This paper identifies the major research concepts, techniques, and models covered in the cross-docking literature. A systematic literature review is conducted using the BibExcel bibliometric analysis and Gephi network analysis tools. A research focus parallelship network (RFPN) analysis and keyword co-occurrence network (KCON) analysis are used to identify the primary research themes. The RFPN results suggest that vehicle routing, inventory control, scheduling, warehousing, and distribution are most studied. Of the optimization and simulation techniques applied in cross-docking, linear and integer programming has received much attention. The paper informs researchers interested in investigating cross-docking through an integrated perspective of the research gaps in this domain. This paper systematically reviews the literature on cross-docking, identifies the major research areas, and provides a survey of the techniques and models adopted by researchers in the areas related to cross-docking

    Multi-objective optimization with a Gaussian PSO algorithm

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    Particle Swarm Optimization es una heurística popular usada para resolver adecuada y efectivamente problemas mono-objetivo. En este artículo, presentamos una primera adaptación de esta heurística para tratar problemas multi-objetivo sin restricciones. La propuesta (llamada G-MOPSO) incorpora una actualización Gaussiana, dominancia Pareto, una política elitista, un archivo externo y un shake-mecanismo para mantener la diversidad. Para validar nuestro algoritmo, usamos cuatro funciones de prueba bien conocidas, con diferentes características. Los resultados preliminares son comparados con los valores obtenidos por un algoritmo evolutivo multi-objetivo representativo del estado del arte en el área: NSGA-II. También comparamos los resultados con los obtenidos por OMOPSO, un algoritmo multi-objetivo basado en la heurística PSO. La performance de nuestra propuesta es comparable con la de NSGA-II y supera a la de OMOPSOParticle Swarm Optimization is a popular heuristic used to solve suitably and effectively mono-objective problems. In this paper, we present an adaptation of this heuristic to treat unconstrained multi-objective problems. The proposed approach (called G-MOPSO) incorporates a Gaussian update of individuals, Pareto dominance, an elitist policy, and a shake-mechanism to maintain diversity. In order to validate our algorithm, we use four well-known test functions with different characteristics. Preliminary results are compared with respect to those obtained by a multi-objective evolutionary algorithm representative of the state-of-the-art: NSGA-II. We also compare the results with those obtained by OMOPSO, a multi-objective PSO based algorithm. The performance of our approach is comparable with the NSGA-II and outperforms the OMOPSO.Workshop de Agentes y Sistemas Inteligentes (WASI)Red de Universidades con Carreras en Informática (RedUNCI

    SwarmDock and the Use of Normal Modes in Protein-Protein Docking

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    Here is presented an investigation of the use of normal modes in protein-protein docking, both in theory and in practice. Upper limits of the ability of normal modes to capture the unbound to bound conformational change are calculated on a large test set, with particular focus on the binding interface, the subset of residues from which the binding energy is calculated. Further, the SwarmDock algorithm is presented, to demonstrate that the modelling of conformational change as a linear combination of normal modes is an effective method of modelling flexibility in protein-protein docking

    Volumetric Techniques for Product Routing and Loading Optimisation in Industry 4.0: A Review

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    Industry 4.0 has become a crucial part in the majority of processes, components, and related modelling, as well as predictive tools that allow a more efficient, automated and sustainable approach to industry. The availability of large quantities of data, and the advances in IoT, AI, and data-driven frameworks, have led to an enhanced data gathering, assessment, and extraction of actionable information, resulting in a better decision-making process. Product picking and its subsequent packing is an important area, and has drawn increasing attention for the research community. However, depending of the context, some of the related approaches tend to be either highly mathematical, or applied to a specific context. This article aims to provide a survey on the main methods, techniques, and frameworks relevant to product packing and to highlight the main properties and features that should be further investigated to ensure a more efficient and optimised approach

    Evolutionary Computation and QSAR Research

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    [Abstract] The successful high throughput screening of molecule libraries for a specific biological property is one of the main improvements in drug discovery. The virtual molecular filtering and screening relies greatly on quantitative structure-activity relationship (QSAR) analysis, a mathematical model that correlates the activity of a molecule with molecular descriptors. QSAR models have the potential to reduce the costly failure of drug candidates in advanced (clinical) stages by filtering combinatorial libraries, eliminating candidates with a predicted toxic effect and poor pharmacokinetic profiles, and reducing the number of experiments. To obtain a predictive and reliable QSAR model, scientists use methods from various fields such as molecular modeling, pattern recognition, machine learning or artificial intelligence. QSAR modeling relies on three main steps: molecular structure codification into molecular descriptors, selection of relevant variables in the context of the analyzed activity, and search of the optimal mathematical model that correlates the molecular descriptors with a specific activity. Since a variety of techniques from statistics and artificial intelligence can aid variable selection and model building steps, this review focuses on the evolutionary computation methods supporting these tasks. Thus, this review explains the basic of the genetic algorithms and genetic programming as evolutionary computation approaches, the selection methods for high-dimensional data in QSAR, the methods to build QSAR models, the current evolutionary feature selection methods and applications in QSAR and the future trend on the joint or multi-task feature selection methods.Instituto de Salud Carlos III, PIO52048Instituto de Salud Carlos III, RD07/0067/0005Ministerio de Industria, Comercio y Turismo; TSI-020110-2009-53)Galicia. Consellería de Economía e Industria; 10SIN105004P

    On the role of metaheuristic optimization in bioinformatics

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    Metaheuristic algorithms are employed to solve complex and large-scale optimization problems in many different fields, from transportation and smart cities to finance. This paper discusses how metaheuristic algorithms are being applied to solve different optimization problems in the area of bioinformatics. While the text provides references to many optimization problems in the area, it focuses on those that have attracted more interest from the optimization community. Among the problems analyzed, the paper discusses in more detail the molecular docking problem, the protein structure prediction, phylogenetic inference, and different string problems. In addition, references to other relevant optimization problems are also given, including those related to medical imaging or gene selection for classification. From the previous analysis, the paper generates insights on research opportunities for the Operations Research and Computer Science communities in the field of bioinformatics

    Internet of Things in urban waste collection

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    Nowadays, the waste collection management has an important role in urban areas. This paper faces this issue and proposes the application of a metaheuristic for the optimization of a weekly schedule and routing of the waste collection activities in an urban area. Differently to several contributions in literature, fixed periodic routes are not imposed. The results significantly improve the performance of the company involved, both in terms of resources used and costs saving

    Advances in De Novo Drug Design : From Conventional to Machine Learning Methods

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    De novo drug design is a computational approach that generates novel molecular structures from atomic building blocks with no a priori relationships. Conventional methods include structure-based and ligand-based design, which depend on the properties of the active site of a biological target or its known active binders, respectively. Artificial intelligence, including ma-chine learning, is an emerging field that has positively impacted the drug discovery process. Deep reinforcement learning is a subdivision of machine learning that combines artificial neural networks with reinforcement-learning architectures. This method has successfully been em-ployed to develop novel de novo drug design approaches using a variety of artificial networks including recurrent neural networks, convolutional neural networks, generative adversarial networks, and autoencoders. This review article summarizes advances in de novo drug design, from conventional growth algorithms to advanced machine-learning methodologies and high-lights hot topics for further development.Peer reviewe

    Novel multi-objective affinity approach allows to identify pH-specific μ-opioid receptor agonists

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    Opioids are essential pharmaceuticals due to their analgesic properties, however, lethal side effects, addiction, and opioid tolerance are extremely challenging. The development of novel molecules targeting the -opioid receptor (MOR) in inflamed, but not in healthy tissue, could significantly reduce these unwanted effects. Finding such novel molecules can be achieved by maximizing the binding affinity to the MOR at acidic pH while minimizing it at neutral pH, thus combining two conflicting objectives. Here, this multi-objective optimal affinity approach is presented, together with a virtual drug discovery pipeline for its practical implementation. When applied to finding pH-specific drug candidates, it combines protonation state-dependent structure and ligand preparation with high-throughput virtual screening. We employ this pipeline to characterize a set of MOR agonists identifying a morphine-like opioid derivative with higher predicted binding affinities to the MOR at low pH compared to neutral pH. Our results also confirm existing experimental evidence that NFEPP, a previously described fentanyl derivative with reduced side effects, and recently reported -fluorofentanyls and -morphines show an increased specificity for the MOR at acidic pH when compared to fentanyl and morphine. We further applied our approach to screen a >50K ligand library identifying novel molecules with pH-specific predicted binding affinities to the MOR. The presented differential docking pipeline can be applied to perform multi-objective affinity optimization to identify safer and more specific drug candidates at large scale
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