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  • 1
    Online Resource
    Online Resource
    Oxford University Press (OUP) ; 2017
    In:  Bioinformatics Vol. 33, No. 11 ( 2017-06-01), p. 1639-1646
    In: Bioinformatics, Oxford University Press (OUP), Vol. 33, No. 11 ( 2017-06-01), p. 1639-1646
    Abstract: The computational investigation of DNA binding motifs from binding sites is one of the classic tasks in bioinformatics and a prerequisite for understanding gene regulation as a whole. Due to the development of sequencing technologies and the increasing number of available genomes, approaches based on phylogenetic footprinting become increasingly attractive. Phylogenetic footprinting requires phylogenetic trees with attached substitution probabilities for quantifying the evolution of binding sites, but these trees and substitution probabilities are typically not known and cannot be estimated easily. Results Here, we investigate the influence of phylogenetic trees with different substitution probabilities on the classification performance of phylogenetic footprinting using synthetic and real data. For synthetic data we find that the classification performance is highest when the substitution probability used for phylogenetic footprinting is similar to that used for data generation. For real data, however, we typically find that the classification performance of phylogenetic footprinting surprisingly increases with increasing substitution probabilities and is often highest for unrealistically high substitution probabilities close to one. This finding suggests that choosing realistic model assumptions might not always yield optimal predictions in general and that choosing unrealistically high substitution probabilities close to one might actually improve the classification performance of phylogenetic footprinting. Availability and Implementation The proposed PF is implemented in JAVA and can be downloaded from https://github.com/mgledi/PhyFoo Supplementary information Supplementary data are available at Bioinformatics online.
    Type of Medium: Online Resource
    ISSN: 1367-4803 , 1367-4811
    Language: English
    Publisher: Oxford University Press (OUP)
    Publication Date: 2017
    detail.hit.zdb_id: 1468345-3
    SSG: 12
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  • 2
    Online Resource
    Online Resource
    Association for Computing Machinery (ACM) ; 2017
    In:  ACM Transactions on Intelligent Systems and Technology Vol. 8, No. 4 ( 2017-07-31), p. 1-24
    In: ACM Transactions on Intelligent Systems and Technology, Association for Computing Machinery (ACM), Vol. 8, No. 4 ( 2017-07-31), p. 1-24
    Abstract: Coalition formation typically involves the coming together of multiple, heterogeneous, agents to achieve both their individual and collective goals. In this article, we focus on a special case of coalition formation known as Graph-Constrained Coalition Formation (GCCF) whereby a network connecting the agents constrains the formation of coalitions. We focus on this type of problem given that in many real-world applications, agents may be connected by a communication network or only trust certain peers in their social network. We propose a novel representation of this problem based on the concept of edge contraction, which allows us to model the search space induced by the GCCF problem as a rooted tree. Then, we propose an anytime solution algorithm (Coalition Formation for Sparse Synergies (CFSS)), which is particularly efficient when applied to a general class of characteristic functions called m + a functions. Moreover, we show how CFSS can be efficiently parallelised to solve GCCF using a nonredundant partition of the search space. We benchmark CFSS on both synthetic and realistic scenarios, using a real-world dataset consisting of the energy consumption of a large number of households in the UK. Our results show that, in the best case, the serial version of CFSS is four orders of magnitude faster than the state of the art, while the parallel version is 9.44 times faster than the serial version on a 12-core machine. Moreover, CFSS is the first approach to provide anytime approximate solutions with quality guarantees for very large systems of agents (i.e., with more than 2,700 agents).
    Type of Medium: Online Resource
    ISSN: 2157-6904 , 2157-6912
    Language: English
    Publisher: Association for Computing Machinery (ACM)
    Publication Date: 2017
    detail.hit.zdb_id: 2584437-4
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  • 3
    In: BMC Neurology, Springer Science and Business Media LLC, Vol. 21, No. 1 ( 2021-01-12)
    Abstract: Residual motor deficits of the upper limb in patients with chronic stroke are common and have a negative impact on autonomy, participation and quality of life. Music-Supported Therapy (MST) is an effective intervention to enhance motor and cognitive function, emotional well-being and quality of life in chronic stroke patients. We have adapted the original MST training protocol to a home-based intervention, which incorporates increased training intensity and variability, group sessions, and optimisation of learning to promote autonomy and motivation. Methods A randomised controlled trial will be conducted to test the effectiveness of this enriched MST (eMST) protocol in improving motor functions, cognition, emotional well-being and quality of life of chronic stroke patients when compared to a program of home-based exercises utilizing the Graded Repetitive Arm Supplementary Program (GRASP). Sixty stroke patients will be recruited and randomly allocated to an eMST group ( n  = 30) or a control GRASP intervention group ( n  = 30). Patients will be evaluated before and after a 10-week intervention, as well as at 3-month follow-up. The primary outcome of the study is the functionality of the paretic upper limb measured with the Action Research Arm Test. Secondary outcomes include other motor and cognitive functions, emotional well-being and quality of life measures as well as self-regulation and self-efficacy outcomes. Discussion We hypothesize that patients treated with eMST will show larger improvements in their motor and cognitive functions, emotional well-being and quality of life than patients treated with a home-based GRASP intervention. Trial registration The trial has been registered at ClinicalTrials.gov and identified as NCT04507542 on 8 August 2020.
    Type of Medium: Online Resource
    ISSN: 1471-2377
    Language: English
    Publisher: Springer Science and Business Media LLC
    Publication Date: 2021
    detail.hit.zdb_id: 2041347-6
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  • 4
    Online Resource
    Online Resource
    Oxford University Press (OUP) ; 2021
    In:  Logic Journal of the IGPL Vol. 29, No. 1 ( 2021-01-25), p. 72-95
    In: Logic Journal of the IGPL, Oxford University Press (OUP), Vol. 29, No. 1 ( 2021-01-25), p. 72-95
    Abstract: In the context of solving large distributed constraint optimization problems, belief-propagation and incomplete inference algorithms are candidates of choice. However, in general, when the problem structure is very cyclic, these solution methods suffer from bad performance, due to non-convergence and many exchanged messages. As to improve performances of the MaxSum inference algorithm when solving cyclic constraint optimization problems, we propose here to take inspiration from the belief-propagation-guided decimation used to solve sparse random graphs ($k$-satisfiability). We propose the novel DeciMaxSum method, which is parameterized in terms of policies to decide when to trigger decimation, which variables to decimate and which values to assign to decimated variables. Based on an empirical evaluation on a classical constraint optimization benchmarks (graph coloring, random graph and Ising model), some of these combinations of policies, using periodic decimation, cycle detection-based decimation, parallel and non parallel decimation, random or deterministic variable selection and deterministic or random sampling for value selection, outperform state-of-the-art competitors in many settings.
    Type of Medium: Online Resource
    ISSN: 1367-0751 , 1368-9894
    Language: English
    Publisher: Oxford University Press (OUP)
    Publication Date: 2021
    detail.hit.zdb_id: 2000006-6
    detail.hit.zdb_id: 2042330-5
    SSG: 17,1
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  • 5
    Online Resource
    Online Resource
    Springer Science and Business Media LLC ; 2007
    In:  Electronic Commerce Research Vol. 7, No. 3-4 ( 2007-11-14), p. 189-220
    In: Electronic Commerce Research, Springer Science and Business Media LLC, Vol. 7, No. 3-4 ( 2007-11-14), p. 189-220
    Type of Medium: Online Resource
    ISSN: 1389-5753 , 1572-9362
    Language: English
    Publisher: Springer Science and Business Media LLC
    Publication Date: 2007
    detail.hit.zdb_id: 2106016-2
    detail.hit.zdb_id: 2038488-9
    SSG: 3,2
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  • 6
    Online Resource
    Online Resource
    Springer Science and Business Media LLC ; 2016
    In:  Machine Learning Vol. 104, No. 2-3 ( 2016-9), p. 151-194
    In: Machine Learning, Springer Science and Business Media LLC, Vol. 104, No. 2-3 ( 2016-9), p. 151-194
    Type of Medium: Online Resource
    ISSN: 0885-6125 , 1573-0565
    Language: English
    Publisher: Springer Science and Business Media LLC
    Publication Date: 2016
    detail.hit.zdb_id: 1475529-4
    detail.hit.zdb_id: 54638-0
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  • 7
    Online Resource
    Online Resource
    MDPI AG ; 2021
    In:  Mathematics Vol. 9, No. 23 ( 2021-12-02), p. 3112-
    In: Mathematics, MDPI AG, Vol. 9, No. 23 ( 2021-12-02), p. 3112-
    Abstract: Probabilistic graphical models allow us to encode a large probability distribution as a composition of smaller ones. It is oftentimes the case that we are interested in incorporating in the model the idea that some of these smaller distributions are likely to be similar to one another. In this paper we provide an information geometric approach on how to incorporate this information and see that it allows us to reinterpret some already existing models. Our proposal relies on providing a formal definition of what it means to be close. We provide an example on how this definition can be actioned for multinomial distributions. We use the results on multinomial distributions to reinterpret two already existing hierarchical models in terms of closeness distributions.
    Type of Medium: Online Resource
    ISSN: 2227-7390
    Language: English
    Publisher: MDPI AG
    Publication Date: 2021
    detail.hit.zdb_id: 2704244-3
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  • 8
    Online Resource
    Online Resource
    Elsevier BV ; 2016
    In:  International Journal of Approximate Reasoning Vol. 78 ( 2016-11), p. 33-61
    In: International Journal of Approximate Reasoning, Elsevier BV, Vol. 78 ( 2016-11), p. 33-61
    Type of Medium: Online Resource
    ISSN: 0888-613X
    Language: English
    Publisher: Elsevier BV
    Publication Date: 2016
    detail.hit.zdb_id: 2002042-9
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  • 9
    Online Resource
    Online Resource
    Elsevier BV ; 2022
    In:  Reproductive BioMedicine Online Vol. 45, No. 5 ( 2022-11), p. 1039-1045
    In: Reproductive BioMedicine Online, Elsevier BV, Vol. 45, No. 5 ( 2022-11), p. 1039-1045
    Type of Medium: Online Resource
    ISSN: 1472-6483
    Language: English
    Publisher: Elsevier BV
    Publication Date: 2022
    detail.hit.zdb_id: 2057455-1
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  • 10
    Online Resource
    Online Resource
    Association for the Advancement of Artificial Intelligence (AAAI) ; 2021
    In:  Proceedings of the AAAI Conference on Artificial Intelligence Vol. 26, No. 1 ( 2021-09-20), p. 1436-1442
    In: Proceedings of the AAAI Conference on Artificial Intelligence, Association for the Advancement of Artificial Intelligence (AAAI), Vol. 26, No. 1 ( 2021-09-20), p. 1436-1442
    Abstract: Supply Chain Formation (SCF) is the process of determining the participants in a supply chain, who will exchange what with whom, and the terms of the exchanges. Decentralized SCF appears as a highly intricate task because agents only possess local information and have limited knowledge about the capabilities of other agents. The decentralized SCF problem has been recently cast as an optimization problem that can be efficiently approximated using max-sum loopy belief propagation. Along this direction, in this paper we propose a novel encoding of the problem into a binary factor graph (containing only binary variables) as well as an alternative algorithm. We empirically show that our approach allows to significantly increase scalability, hence allowing to form supply chains in market scenarios with a large number of participants and high competition.
    Type of Medium: Online Resource
    ISSN: 2374-3468 , 2159-5399
    Language: Unknown
    Publisher: Association for the Advancement of Artificial Intelligence (AAAI)
    Publication Date: 2021
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