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Journal articles on the topic 'Combinatorial nature'

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Published: 10 December 2022

Last updated: 29 January 2023

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1

Armstrong, D. M. "The Nature of Possibility." Canadian Journal of Philosophy 16, no. 4 (December 1986): 575–94. http://dx.doi.org/10.1080/00455091.1986.10717137.

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I want to defend a Combinatorialtheory of possibility. Such a view traces the very idea of possibility to the idea of the combinations – all the combinations which respect a certain simple form – of given, actual, elements. Combination is to be understood widely enough to cover the notions of expansion and contraction. (My central metaphysical hypothesis is that all there is is the world of space and time. It is this world which is to supply the actual elements for the totality of combinations. So what is proposed is a Naturalistic form of a combinatorial theory.)The combinatorial idea is not new, of course. Wittgenstein gave a classical exposition of it in the Tractatus. Perhaps its charter is 3.4: ‘A proposition determines a place in logical space. The existence of this logical place is guaranteed by the mere existence of the constituents’ (my italics). There is a small additional combinatorial literature. I myself was converted to a combinatorial view by Brian Skyrms’ brief but fascinating article ‘Tractarian Nominalism.’

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2

Reynolds, K. A. "Combinatorial biosynthesis: Lesson learned from nature." Proceedings of the National Academy of Sciences 95, no. 22 (October 27, 1998): 12744–46. http://dx.doi.org/10.1073/pnas.95.22.12744.

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3

Timofieva, N. K. "The Fractal Nature of Combinatorial Sets and Finding Formulas for Combinatorial Numbers." Cybernetics and Systems Analysis 56, no. 1 (January 2020): 110–17. http://dx.doi.org/10.1007/s10559-020-00226-9.

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4

Kültz, Dietmar. "The Combinatorial Nature of Osmosensing in Fishes." Physiology 27, no. 4 (August 2012): 259–75. http://dx.doi.org/10.1152/physiol.00014.2012.

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Organisms exposed to altered salinity must be able to perceive osmolality change because metabolism has evolved to function optimally at specific intracellular ionic strength and composition. Such osmosensing comprises a complex physiological process involving many elements at organismal and cellular levels of organization. Input from numerous osmosensors is integrated to encode magnitude, direction, and ionic basis of osmolality change. This combinatorial nature of osmosensing is discussed with emphasis on fishes.

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ALTREUTER, D., and D. CLARK. "Combinatorial biocatalysis: taking the lead from Nature." Current Opinion in Biotechnology 10, no. 2 (April 1, 1999): 130–36. http://dx.doi.org/10.1016/s0958-1669(99)80022-6.

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6

Tymofijeva, Nadiya К. "Sign Combinatorial Spaces, Finite Sequences and Logarithmic Spirals." Control Systems and Computers, no. 1 (297) (2022): 32–43. http://dx.doi.org/10.15407/csc.2022.01.032.

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Introduction. Sign combinatorial spaces that exist in two states: convolute (tranquility) and deployed (dynamics), are considered. Spaces, in particular biological, physical, informational and some others, for which the axioms of sign combinatorial spaces, are valid, have a combinatorial nature. When they are deployed, combinatorial numbers (Fibonacci numbers) are formed, through which logarithmic spirals appear in living nature. These spirals are formed due to the finite sequences that take place during the deployment of the agreed spaces and which are presented geometrically using polar coordinates. Formulation of the problem. The logarithmic spiral is geometrically represented through a “golden rectangle” in which one side is 1,618 times longer (“golden” number or golden section). The presence of the golden ratio in nature is manifested through Fibonacci numbers, which are formed from an arithmetic triangle from elements of finite sequences formed by the deployment of sign combinatorial spaces. But this spiral is transmitted through the “golden rectangle” indirectly. The problem is to trace its formation in nature through constructed sequences, the elements of which are represented by polar coordinates. The approach proposed. Using the finite sequences that are formed during the unfolding of sign combinatorial spaces and the representation of their elements in polar coordinates, we can trace the dynamics of the formation of logarithmic spirals in nature. Conclusion. Representation of biological space as a sign combinatorial space can explain various phenomena in nature. When unfolding these spaces from the convolute spaces finite sequences are formed, the sums of the members of which determine the number of combinatorial configurations in a subset of isomorphic combinatorial configurations and form an arithmetic triangle (Pascal’s triangle). Fibonacci numbers and, accordingly, a golden number are formed from an arithmetic triangle. The logarithmic spiral fits into a golden rectangle. The dynamics of the formation of the logarithmic spiral is traced due to the finite sequences formed as a result of the deployment of the sign combinatorial spaces, the elements of which are presented in polar coordinates.

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Colorni, A., M. Dorigo, F. Maffioli, V. Maniezzo, G. Righini, and M. Trubian. "Heuristics from Nature for Hard Combinatorial Optimization Problems." International Transactions in Operational Research 3, no. 1 (January 1996): 1–21. http://dx.doi.org/10.1111/j.1475-3995.1996.tb00032.x.

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8

Rahman, Md Ashikur, Rajalingam Sokkalingam, Mahmod Othman, Kallol Biswas, Lazim Abdullah, and Evizal Abdul Kadir. "Nature-Inspired Metaheuristic Techniques for Combinatorial Optimization Problems: Overview and Recent Advances." Mathematics 9, no. 20 (October 19, 2021): 2633. http://dx.doi.org/10.3390/math9202633.

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Combinatorial optimization problems are often considered NP-hard problems in the field of decision science and the industrial revolution. As a successful transformation to tackle complex dimensional problems, metaheuristic algorithms have been implemented in a wide area of combinatorial optimization problems. Metaheuristic algorithms have been evolved and modified with respect to the problem nature since it was recommended for the first time. As there is a growing interest in incorporating necessary methods to develop metaheuristics, there is a need to rediscover the recent advancement of metaheuristics in combinatorial optimization. From the authors’ point of view, there is still a lack of comprehensive surveys on current research directions. Therefore, a substantial part of this paper is devoted to analyzing and discussing the modern age metaheuristic algorithms that gained popular use in mostly cited combinatorial optimization problems such as vehicle routing problems, traveling salesman problems, and supply chain network design problems. A survey of seven different metaheuristic algorithms (which are proposed after 2000) for combinatorial optimization problems is carried out in this study, apart from conventional metaheuristics like simulated annealing, particle swarm optimization, and tabu search. These metaheuristics have been filtered through some key factors like easy parameter handling, the scope of hybridization as well as performance efficiency. In this study, a concise description of the framework of the selected algorithm is included. Finally, a technical analysis of the recent trends of implementation is discussed, along with the impacts of algorithm modification on performance, constraint handling strategy, the handling of multi-objective situations using hybridization, and future research opportunities.

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Semenkina, Olga Ev, Eugene A. Popov, and Olga Er Semenkina. "Self-configuring Nature Inspired Algorithms for Combinatorial Optimization Problems." Journal of Siberian Federal University. Mathematics & Physics 10, no. 4 (December 2017): 463–73. http://dx.doi.org/10.17516/1997-1397-2017-10-4-463-473.

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10

Coja-Oghlan, Amin, Tobias Kapetanopoulos, and Noela Müller. "The replica symmetric phase of random constraint satisfaction problems." Combinatorics, Probability and Computing 29, no. 3 (December 3, 2019): 346–422. http://dx.doi.org/10.1017/s0963548319000440.

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AbstarctRandom constraint satisfaction problems play an important role in computer science and combinatorics. For example, they provide challenging benchmark examples for algorithms, and they have been harnessed in probabilistic constructions of combinatorial structures with peculiar features. In an important contribution (Krzakala et al. 2007, Proc. Nat. Acad. Sci.), physicists made several predictions on the precise location and nature of phase transitions in random constraint satisfaction problems. Specifically, they predicted that their satisfiability thresholds are quite generally preceded by several other thresholds that have a substantial impact both combinatorially and computationally. These include the condensation phase transition, where long-range correlations between variables emerge, and the reconstruction threshold. In this paper we prove these physics predictions for a broad class of random constraint satisfaction problems. Additionally, we obtain contiguity results that have implications for Bayesian inference tasks, a subject that has received a great deal of interest recently (e.g. Banks et al. 2016, Proc. 29th COLT).

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Balaga, Ohad, Yitzhak Friedman, and Michal Linial. "Toward a combinatorial nature of microRNA regulation in human cells." Nucleic Acids Research 40, no. 19 (August 13, 2012): 9404–16. http://dx.doi.org/10.1093/nar/gks759.

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Batalha, Iris L., Houjiang Zhou, Kathryn Lilley, Christopher R. Lowe, and Ana C. A. Roque. "Mimicking nature: Phosphopeptide enrichment using combinatorial libraries of affinity ligands." Journal of Chromatography A 1457 (July 2016): 76–87. http://dx.doi.org/10.1016/j.chroma.2016.06.032.

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13

Scott-Phillips, Thomas C., and Richard A. Blythe. "Why is combinatorial communication rare in the natural world, and why is language an exception to this trend?" Journal of The Royal Society Interface 10, no. 88 (November 6, 2013): 20130520. http://dx.doi.org/10.1098/rsif.2013.0520.

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In a combinatorial communication system, some signals consist of the combinations of other signals. Such systems are more efficient than equivalent, non-combinatorial systems, yet despite this they are rare in nature. Why? Previous explanations have focused on the adaptive limits of combinatorial communication, or on its purported cognitive difficulties, but neither of these explains the full distribution of combinatorial communication in the natural world. Here, we present a nonlinear dynamical model of the emergence of combinatorial communication that, unlike previous models, considers how initially non-communicative behaviour evolves to take on a communicative function. We derive three basic principles about the emergence of combinatorial communication. We hence show that the interdependence of signals and responses places significant constraints on the historical pathways by which combinatorial signals might emerge, to the extent that anything other than the most simple form of combinatorial communication is extremely unlikely. We also argue that these constraints can be bypassed if individuals have the socio-cognitive capacity to engage in ostensive communication. Humans, but probably no other species, have this ability. This may explain why language, which is massively combinatorial, is such an extreme exception to nature's general trend for non-combinatorial communication.

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INCITTI, ROBERTO. "THE BURNSIDE PROBLEM FOR GROUPS OF LOW QUADRATIC GROWTH." International Journal of Algebra and Computation 06, no. 03 (June 1996): 369–77. http://dx.doi.org/10.1142/s0218196796000209.

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We show with a combinatorial argument that a finitely generated infinite group whose growth function relative to some finite generating system is less or equal to [Formula: see text], r<2, contains an element of infinite order. This result is aimed at investigating the combinatorial nature of M. Gromov’s theorem on groups of polynomial growth.

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15

Ruijne, Fleur, and Oscar P. Kuipers. "Combinatorial biosynthesis for the generation of new-to-nature peptide antimicrobials." Biochemical Society Transactions 49, no. 1 (January 13, 2021): 203–15. http://dx.doi.org/10.1042/bst20200425.

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Natural peptide products are a valuable source of important therapeutic agents, including antibiotics, antivirals and crop protection agents. Aided by an increased understanding of structure–activity relationships of these complex molecules and the biosynthetic machineries that produce them, it has become possible to re-engineer complete machineries and biosynthetic pathways to create novel products with improved pharmacological properties or modified structures to combat antimicrobial resistance. In this review, we will address the progress that has been made using non-ribosomally produced peptides and ribosomally synthesized and post-translationally modified peptides as scaffolds for designed biosynthetic pathways or combinatorial synthesis for the creation of novel peptide antimicrobials.

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16

Kuznietsova, Yana, and Halyna Osychenko. "COMBINATORIAL TECHNIQUE AND MEANS OF INTEGRATING NATURE INTO AN ARCHITECTURAL FORM." space&FORM 2020, no. 41 (February 15, 2020): 43–54. http://dx.doi.org/10.21005/pif.2020.41.b-03.

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17

van der Velde, Frank, and Marc de Kamps. "From neural dynamics to true combinatorial structures." Behavioral and Brain Sciences 29, no. 1 (February 2006): 88–104. http://dx.doi.org/10.1017/s0140525x06399025.

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Various issues concerning the neural blackboard architectures for combinatorial structures are discussed and clarified. They range from issues related to neural dynamics, the structure of the architectures for language and vision, and alternative architectures, to linguistic issues concerning the language architecture. Particular attention is given to the nature of true combinatorial structures and the way in which information can be retrieved from them in a productive and systematic manner.

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18

Yin, Peng-Yeng, and Ray-I. Chang. "Special Features and Applications on Applied Metaheuristic Computing." Applied Sciences 12, no. 18 (September 18, 2022): 9342. http://dx.doi.org/10.3390/app12189342.

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19

Muazu, Aminu Aminu, Ahmad Sobri Hashim, and Aliza Sarlan. "Review of Nature Inspired Metaheuristic Algorithm Selection for Combinatorial t-Way Testing." IEEE Access 10 (2022): 27404–31. http://dx.doi.org/10.1109/access.2022.3157400.

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20

Gonchikov, G. G. "On the nature and origin of cellular complexity: The combinatorial–eukaryogenetic scenario." Paleontological Journal 51, no. 13 (December 2017): 1422–39. http://dx.doi.org/10.1134/s0031030117130020.

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21

Escher, Sina, Yvan Niclass, Matthijs van de Waal, and Christian Starkenmann. "Combinatorial Synthesis by Nature: Volatile Organic Sulfur-Containing Constituents ofRuta chalepensis L." Chemistry & Biodiversity 3, no. 9 (September 2006): 943–57. http://dx.doi.org/10.1002/cbdv.200690103.

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22

Fujii, Kaito, and Shinsaku Sakaue. "Algorithmic Bayesian Persuasion with Combinatorial Actions." Proceedings of the AAAI Conference on Artificial Intelligence 36, no. 5 (June 28, 2022): 5016–24. http://dx.doi.org/10.1609/aaai.v36i5.20433.

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Bayesian persuasion is a model for understanding strategic information revelation: an agent with an informational advantage, called a sender, strategically discloses information by sending signals to another agent, called a receiver. In algorithmic Bayesian persuasion, we are interested in efficiently designing the sender's signaling schemes that lead the receiver to take action in favor of the sender. This paper studies algorithmic Bayesian-persuasion settings where the receiver's feasible actions are specified by combinatorial constraints, e.g., matroids or paths in graphs. We first show that constant-factor approximation is NP-hard even in some special cases of matroids or paths. We then propose a polynomial-time algorithm for general matroids by assuming the number of states of nature to be a constant. We finally consider a relaxed notion of persuasiveness, called CCE-persuasiveness, and present a sufficient condition for polynomial-time approximability.

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Acer, Seher, Ariful Azad, Erik G. Boman, Aydın Buluç, Karen D. Devine, SM Ferdous, Nitin Gawande, et al. "EXAGRAPH: Graph and combinatorial methods for enabling exascale applications." International Journal of High Performance Computing Applications 35, no. 6 (September 30, 2021): 553–71. http://dx.doi.org/10.1177/10943420211029299.

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Combinatorial algorithms in general and graph algorithms in particular play a critical enabling role in numerous scientific applications. However, the irregular memory access nature of these algorithms makes them one of the hardest algorithmic kernels to implement on parallel systems. With tens of billions of hardware threads and deep memory hierarchies, the exascale computing systems in particular pose extreme challenges in scaling graph algorithms. The codesign center on combinatorial algorithms, ExaGraph, was established to design and develop methods and techniques for efficient implementation of key combinatorial (graph) algorithms chosen from a diverse set of exascale applications. Algebraic and combinatorial methods have a complementary role in the advancement of computational science and engineering, including playing an enabling role on each other. In this paper, we survey the algorithmic and software development activities performed under the auspices of ExaGraph from both a combinatorial and an algebraic perspective. In particular, we detail our recent efforts in porting the algorithms to manycore accelerator (GPU) architectures. We also provide a brief survey of the applications that have benefited from the scalable implementations of different combinatorial algorithms to enable scientific discovery at scale. We believe that several applications will benefit from the algorithmic and software tools developed by the ExaGraph team.

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Youn, Hyejin, Deborah Strumsky, Luis M. A. Bettencourt, and José Lobo. "Invention as a combinatorial process: evidence from US patents." Journal of The Royal Society Interface 12, no. 106 (May 2015): 20150272. http://dx.doi.org/10.1098/rsif.2015.0272.

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Invention has been commonly conceptualized as a search over a space of combinatorial possibilities. Despite the existence of a rich literature, spanning a variety of disciplines, elaborating on the recombinant nature of invention, we lack a formal and quantitative characterization of the combinatorial process underpinning inventive activity. Here, we use US patent records dating from 1790 to 2010 to formally characterize invention as a combinatorial process. To do this, we treat patented inventions as carriers of technologies and avail ourselves of the elaborate system of technology codes used by the United States Patent and Trademark Office to classify the technologies responsible for an invention's novelty. We find that the combinatorial inventive process exhibits an invariant rate of ‘exploitation’ (refinements of existing combinations of technologies) and ‘exploration’ (the development of new technological combinations). This combinatorial dynamic contrasts sharply with the creation of new technological capabilities—the building blocks to be combined—that has significantly slowed down. We also find that, notwithstanding the very reduced rate at which new technologies are introduced, the generation of novel technological combinations engenders a practically infinite space of technological configurations.

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Verma, Jyotsna, and Nishtha Kesswani. "A Review on Bio-Inspired Migration Optimization Techniques." International Journal of Business Data Communications and Networking 11, no. 1 (January 2015): 24–35. http://dx.doi.org/10.4018/ijbdcn.2015010103.

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Nature inspired computing techniques has become a very popular topic in recent years. Number of applications in computer networks, robotics, biology, combinatorial optimization, etc. can be seen in literatures which are based on the bio-inspired techniques. Nature inspired techniques are proven to solve complex optimization problems irrespective of their problem size. This review summarizes various nature inspired migration algorithms and comparison between them, based on the automated tools, evolutionary techniques and applications.

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Pan, Guohui, Zhengren Xu, Zhikai Guo, Hindra, Ming Ma, Dong Yang, Hao Zhou, et al. "Discovery of the leinamycin family of natural products by mining actinobacterial genomes." Proceedings of the National Academy of Sciences 114, no. 52 (December 11, 2017): E11131—E11140. http://dx.doi.org/10.1073/pnas.1716245115.

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Nature’s ability to generate diverse natural products from simple building blocks has inspired combinatorial biosynthesis. The knowledge-based approach to combinatorial biosynthesis has allowed the production of designer analogs by rational metabolic pathway engineering. While successful, structural alterations are limited, with designer analogs often produced in compromised titers. The discovery-based approach to combinatorial biosynthesis complements the knowledge-based approach by exploring the vast combinatorial biosynthesis repertoire found in Nature. Here we showcase the discovery-based approach to combinatorial biosynthesis by targeting the domain of unknown function and cysteine lyase domain (DUF–SH) didomain, specific for sulfur incorporation from the leinamycin (LNM) biosynthetic machinery, to discover the LNM family of natural products. By mining bacterial genomes from public databases and the actinomycetes strain collection at The Scripps Research Institute, we discovered 49 potential producers that could be grouped into 18 distinct clades based on phylogenetic analysis of the DUF–SH didomains. Further analysis of the representative genomes from each of the clades identified 28 lnm-type gene clusters. Structural diversities encoded by the LNM-type biosynthetic machineries were predicted based on bioinformatics and confirmed by in vitro characterization of selected adenylation proteins and isolation and structural elucidation of the guangnanmycins and weishanmycins. These findings demonstrate the power of the discovery-based approach to combinatorial biosynthesis for natural product discovery and structural diversity and highlight Nature’s rich biosynthetic repertoire. Comparative analysis of the LNM-type biosynthetic machineries provides outstanding opportunities to dissect Nature’s biosynthetic strategies and apply these findings to combinatorial biosynthesis for natural product discovery and structural diversity.

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Jinhui Wu, Sarah, Steven A. Melnyk, and Morgan Swink. "An empirical investigation of the combinatorial nature of operational practices and operational capabilities." International Journal of Operations & Production Management 32, no. 2 (February 3, 2012): 121–55. http://dx.doi.org/10.1108/01443571211208605.

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Razumov, A. V., and Yu G. Stroganov. "Combinatorial Nature of the Ground-State Vector of the O(1) Loop Model." Theoretical and Mathematical Physics 138, no. 3 (March 2004): 333–37. http://dx.doi.org/10.1023/b:tamp.0000018450.36514.d7.

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29

Ruiz, Eduardo Lalla, Jesica De Armas, Christopher Expósito Izquierdo, Belén Melián Batista, and J. Marcos Moreno Vega. "Multi-leader migrating birds optimisation: a novel nature-inspired metaheuristic for combinatorial problems." International Journal of Bio-Inspired Computation 10, no. 2 (2017): 89. http://dx.doi.org/10.1504/ijbic.2017.085890.

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Exposito Izquierdo, Christopher, Jesica De Armas, and Eduardo Lalla Ruiz. "Multi-Leader Migrating Birds Optimization: A novel nature-inspired metaheuristic for combinatorial problems." International Journal of Bio-Inspired Computation 10, no. 4 (2017): 1. http://dx.doi.org/10.1504/ijbic.2017.10004319.

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LISKAMP, R. M. J. "ChemInform Abstract: Combinatorial Chemistry: A Basic Necessity Inspired by Nature′s Own Approaches." ChemInform 29, no. 44 (June 19, 2010): no. http://dx.doi.org/10.1002/chin.199844330.

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Barrett, Thomas, William Clements, Jakob Foerster, and Alex Lvovsky. "Exploratory Combinatorial Optimization with Reinforcement Learning." Proceedings of the AAAI Conference on Artificial Intelligence 34, no. 04 (April 3, 2020): 3243–50. http://dx.doi.org/10.1609/aaai.v34i04.5723.

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Many real-world problems can be reduced to combinatorial optimization on a graph, where the subset or ordering of vertices that maximize some objective function must be found. With such tasks often NP-hard and analytically intractable, reinforcement learning (RL) has shown promise as a framework with which efficient heuristic methods to tackle these problems can be learned. Previous works construct the solution subset incrementally, adding one element at a time, however, the irreversible nature of this approach prevents the agent from revising its earlier decisions, which may be necessary given the complexity of the optimization task. We instead propose that the agent should seek to continuously improve the solution by learning to explore at test time. Our approach of exploratory combinatorial optimization (ECO-DQN) is, in principle, applicable to any combinatorial problem that can be defined on a graph. Experimentally, we show our method to produce state-of-the-art RL performance on the Maximum Cut problem. Moreover, because ECO-DQN can start from any arbitrary configuration, it can be combined with other search methods to further improve performance, which we demonstrate using a simple random search.

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Buluç, Aydın, and John R. Gilbert. "The Combinatorial BLAS: design, implementation, and applications." International Journal of High Performance Computing Applications 25, no. 4 (May 19, 2011): 496–509. http://dx.doi.org/10.1177/1094342011403516.

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This paper presents a scalable high-performance software library to be used for graph analysis and data mining. Large combinatorial graphs appear in many applications of high-performance computing, including computational biology, informatics, analytics, web search, dynamical systems, and sparse matrix methods. Graph computations are difficult to parallelize using traditional approaches due to their irregular nature and low operational intensity. Many graph computations, however, contain sufficient coarse-grained parallelism for thousands of processors, which can be uncovered by using the right primitives. We describe the parallel Combinatorial BLAS, which consists of a small but powerful set of linear algebra primitives specifically targeting graph and data mining applications. We provide an extensible library interface and some guiding principles for future development. The library is evaluated using two important graph algorithms, in terms of both performance and ease-of-use. The scalability and raw performance of the example applications, using the Combinatorial BLAS, are unprecedented on distributed memory clusters.

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Terekhova, Natalya. "Nonlinear Interaction of High-Intensity Disturbances into the Supersonic Boundary Layer." Siberian Journal of Physics 7, no. 1 (March 1, 2012): 38–52. http://dx.doi.org/10.54362/1818-7919-2012-7-1-38-52.

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A nonlinear model of interaction of disturbances in the regime of coupled combinatorial relations is used to explain the dynamics of unstable waves. The model includes effects of self-action and combinatorial interaction of unstable waves. Considered effects in the boundary layer with M = 2 controlled disturbance large enough intensity. In the second case when M = 5,35 examines the interrelationship of two-dimensional perturbations of various nature – vortex and acoustic. Shows the direction of impact of the different components of the nonlinear process. Found that this model of the second order nonlinearity can accurately describe the features of longitudinal dynamics of plane waves

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Ahmed, Bilal, Hazlina Hamdan, Abdullah Muhammed, and Nor Azura Husin. "Review on the parameter settings in harmony search algorithm applied to combinatorial optimization problems." Indonesian Journal of Electrical Engineering and Computer Science 27, no. 1 (July 1, 2022): 431. http://dx.doi.org/10.11591/ijeecs.v27.i1.pp431-441.

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Harmony search algorithm (HSA) is relatively considered as one of the most recent metaheuristic algorithms. HSA is a modern - nature algorithm that simulates the musicians’ natural process of musical improvisation to enhance their instrument’s note to find a state of pleasant (harmony) according to aesthetic standards. Lots of variants of HSA have been suggested to tackle combinatorial optimization problems. They range from hybridizing some components of other metaheuristic approaches (to improve the HSA) to taking some concepts of HSA and utilizing them to improve other metaheuristic methods. This stud y reviews research pertaining to parameter settings of HSA and its applications to efficiently solve hard combinatorial optimization problems.

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Maclean, D., J. J. Baldwin, V. T. Ivanov, Y. Kato, A. Shaw, P. Schneider, and E. M. Gordon. "Glossary of Terms Used in Combinatorial Chemistry." Pure and Applied Chemistry 71, no. 12 (January 1, 1999): 2349–65. http://dx.doi.org/10.1351/pac199971122349.

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Introduction: The development of combinatorial chemistry has generated a wide variety of new concepts and much associated terminology. In addition, the nature of research in this area has brought together scientists from diverse backgrounds: statisticians may discuss their work with biologists and heterocyclic chemists; medicinal chemists are talking to engineers, analytical chemists, and polymer scientists. In recognition of the potential for confusion and lack of communication in this field, the International Union of Pure and Applied Chemistry (IUPAC) convened a working party (within the Division of Human Health, Medicinal Chemistry Section) to attempt to capture and define the terminology at the interface of these endeavours. The following Glossary is the result of their efforts. It is hoped that it will provide a resource for those new to the area encountering terms for the first time, and, perhaps, to increase the clarity of communication between more experienced workers in the field. The Glossary is not intended as a comprehensive review or encyclopaedia of combinatorial chemistry, although occasional attempts have been made to broaden the scope beyond a strict dictionary-type definition of terms by providing illustrative examples of some terms, and directing readers to literature sources where appropriate. These references have not necessarily been chosen to attribute credit for the discovery or invention of a term; rather they should provide the most pertinent information for the topic. Ideally this will be an article or review with the Glossary term as its central theme, in which proper accreditation for the seminal contributions to that area may be found. Because of the intrinsic interdisciplinary nature of this area of research, it has not been possible to provide a comprehensive coverage of each of the sub-fields, neither has this been the intent. Rather it has been attempted to identify those elements which are particularly pertinent to combinatorial chemistry. Thus, in the analytical sciences "magic angle spinning" gains an entry whereas "mass spectrometry" does not. The interested reader will readily be able to find more detailed treatments of these specialized areas. Trademarks have been included where, in the judgement of the authors, their use has become sufficiently widespread that they often do not receive appropriate citation; the implicit assumption being that the reader will understand what is meant. This criterion has been adopted over one of inclusiveness, which would rapidly become extreme in many areas. In a field which is developing as rapidly as combinatorial chemistry a document such as this Glossary may soon require revision. The authors welcome suggestions for new terms, clarifications, references, and other comments which will aid in the development of this resource.

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Kopecky, Eva-Maria, Sabine Greinstetter, Ingrid Pabinger, Andrea Buchacher, Jürgen Römisch, and Alois Jungbauer. "Combinatorial peptides directed to inhibitory antibodies against human blood clotting factor VIII." Thrombosis and Haemostasis 94, no. 11 (2005): 933–41. http://dx.doi.org/10.1160/th05-04-0254.

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SummaryThe development of antibodies against blood clotting factorVIII is a major complication affecting 20–30% of hemophilia A patients receiving replacement with FVIII concentrates. This study investigated generating peptides acting as broadly neutralizing agents to block factor VIII antibodies. These peptides were selected from dual positional scanning decapeptide libraries on cellulose membranes. From this library comprising 6.8×1012 peptides we selected 468 peptides for further screening rounds. Finally we identified two decapeptides with the ability to block 8 out of 10 inhibitory antibodies from sera of patients with FVIII inhibitors demonstrated by competition assays. Sequence alignment of the peptides showed similarity with several domains in the FVIII molecule demonstrating the mimotope nature of the selected peptides. Our results show the efficiency of the combinatorial library approach and show the potential of combinatorial peptides to compete out polyclonal inhibitor IgG from a broad range of patients’ sera. Combinatorial peptides could be novel and highly effective drug candidates for alternative treatment in patients with factor VIII inhibitors.

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SHEIKH, SAAD I., TANYA Y. BERGER-WOLF, ASHFAQ A. KHOKHAR, ISABEL C. CABALLERO, MARY V. ASHLEY, WANPRACHA CHAOVALITWONGSE, CHUN-AN CHOU, and BHASKAR DASGUPTA. "COMBINATORIAL RECONSTRUCTION OF HALF-SIBLING GROUPS FROM MICROSATELLITE DATA." Journal of Bioinformatics and Computational Biology 08, no. 02 (April 2010): 337–56. http://dx.doi.org/10.1142/s0219720010004793.

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While full-sibling group reconstruction from microsatellite data is a well-studied problem, reconstruction of half-sibling groups is much less studied, theoretically challenging, and computationally demanding. In this paper, we present a formulation of the half-sibling reconstruction problem and prove its APX-hardness. We also present exact solutions for this formulation and develop heuristics. Using biological and synthetic datasets we present experimental results and compare them with the leading alternative software COLONY. We show that our results are competitive and allow half-sibling group reconstruction in the presence of polygamy, which is prevalent in nature.

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Karas, Christina, and Michael Hecht. "A Strategy for Combinatorial Cavity Design in De Novo Proteins." Life 10, no. 2 (January 23, 2020): 9. http://dx.doi.org/10.3390/life10020009.

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Protein sequence space is vast; nature uses only an infinitesimal fraction of possible sequences to sustain life. Are there solutions to biological problems other than those provided by nature? Can we create artificial proteins that sustain life? To investigate these questions, we have created combinatorial collections, or libraries, of novel sequences with no homology to those found in living organisms. Previously designed libraries contained numerous functional proteins. However, they often formed dynamic, rather than well-ordered structures, which complicated structural and mechanistic characterization. To address this challenge, we describe the development of new libraries based on the de novo protein S-824, a 4-helix bundle with a very stable 3-dimensional structure. Distinct from previous libraries, we targeted variability to a specific region of the protein, seeking to create potential functional sites. By characterizing variant proteins from this library, we demonstrate that the S-824 scaffold tolerates diverse amino acid substitutions in a putative cavity, including buried polar residues suitable for catalysis. We designed and created a DNA library encoding 1.7 × 106 unique protein sequences. This new library of stable de novo α-helical proteins is well suited for screens and selections for a range of functional activities in vitro and in vivo.

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Appell, Kenneth C., Thomas D. Y. Chung, Michael J. H. Ohlmeyer, Nolan H. Sigal, John J. Baldwin, and Daniel Chelsky. "Biological Screening of a Large Combinatorial Library." Journal of Biomolecular Screening 1, no. 1 (February 1996): 27–31. http://dx.doi.org/10.1177/108705719600100111.

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Encoding technology has allowed for the creation of libraries of 50,000 or more low-molecular-weight compounds for biological testing. The current challenge is to properly and efficiently screen among these compounds for useful biological activities. In this example, actives against two related G-protein coupled receptors were sought from a combinatorial library of 56,000 members. The library was synthesized on solid phase using the split synthesis method and photochemically released for testing. At a screening concentration of 0.5-1 /LM, 86 unique structures were identified as active against one receptor and 24 were active against the other. Due to the random nature of compound sampling, five library equivalents or 280,000 beads were screened to ensure greater than 99% representation of library members. As a result, many actives appeared multiple times in the screen, verifying the encoding process. Further confirmation was obtained by resynthesis and testing of predicted active structures. A clear bias for specific "R" groups at each point of variation in the combinatorial library with little overlap between the two receptors has produced a clear structure-activity relationship on which to base further work.

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Sagban, Rafid, Ku Ruhana Ku-Mahamud, and Muhamad Shahbani Abu Bakar. "ACOustic: A Nature-Inspired Exploration Indicator for Ant Colony Optimization." Scientific World Journal 2015 (2015): 1–11. http://dx.doi.org/10.1155/2015/392345.

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A statistical machine learning indicator,ACOustic, is proposed to evaluate the exploration behavior in the iterations of ant colony optimization algorithms. This idea is inspired by the behavior of some parasites in their mimicry to the queens’ acoustics of their ant hosts. The parasites’ reaction results from their ability to indicate the state of penetration. The proposed indicator solves the problem of robustness that results from the difference of magnitudes in the distance’s matrix, especially when combinatorial optimization problems with rugged fitness landscape are applied. The performance of the proposed indicator is evaluated against the existing indicators in six variants of ant colony optimization algorithms. Instances for travelling salesman problem and quadratic assignment problem are used in the experimental evaluation. The analytical results showed that the proposed indicator is more informative and more robust.

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WYSOCZAŃSKI, JANUSZ. "BM-CENTRAL LIMIT THEOREMS FOR POSITIVE DEFINITE REAL SYMMETRIC MATRICES." Infinite Dimensional Analysis, Quantum Probability and Related Topics 11, no. 01 (March 2008): 33–51. http://dx.doi.org/10.1142/s0219025708002963.

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The bm-central limit theorem for positive-definite real symmetric matrices and for homogeneous rooted trees are studied. The combinatorial nature of it is described. In addition, the construction of bm-product of graphs is given, which generalizes comb and boolean products. General properties of bm-extension operators are shown.

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Umeno, Daisuke, and Frances H. Arnold. "A C35 Carotenoid Biosynthetic Pathway." Applied and Environmental Microbiology 69, no. 6 (June 2003): 3573–79. http://dx.doi.org/10.1128/aem.69.6.3573-3579.2003.

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ABSTRACT Upon coexpression with Erwinia geranylgeranyldiphosphate (GGDP) synthase in Escherichia coli, C30 carotenoid synthase CrtM from Staphylococcus aureus produces novel carotenoids with the asymmetrical C35 backbone. The products of condensation of farnesyldiphosphate and GDP, C35 structures comprise 40 to 60% of total carotenoid accumulated. Carotene desaturases and carotene cyclases from C40 or C30 pathways accepted and converted the C35 substrate, thus creating a C35 carotenoid biosynthetic pathway in E. coli. Directed evolution to modulate desaturase step number, together with combinatorial expression of the desaturase variants with lycopene cyclases, allowed us to produce at least 10 compounds not previously described. This result highlights the plastic and expansible nature of carotenoid pathways and illustrates how combinatorial biosynthesis coupled with directed evolution can rapidly access diverse chemical structures.

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Vasilyeva, L. N. "The hierarchy and combinatorial space of characters in evolutionary systematics." Species and speciation. Analysis of new views and trends 313, Supplement 1 (July 25, 2009): 235–49. http://dx.doi.org/10.31610/trudyzin/2009.supl.1.235.

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In this paper, the Linnaean hierarchy is discussed as the taxonomic model for the evolutionary differentiation of the earth’s biota. This model allows us to understand why a number of ideas and arguments in the evolutionary theory are unfortunate. Among these is the idea of a linear ladder of nature («scala natura»). The arguments about species constancy versus species variability, natural species versus «artificial» higher taxa, a single type of animals versus multiple types, as well as about the connection versus disconnection of microevolution and macroevolution are meaningless. Two kinds of phylogeny are considered. The first reflects the appearance of new characters in the course of evolution, and their sequence provides the nesting hierarchy of groups. The second reflects the appearance of new character states and provides a basis for the diversity of taxa at each hierarchical level. The taxonomic hierarchy is an embodiment of the first kind of phylogeny and does not require the tracing of ancestors and descendants along the lines of character development. Character ranking and the improvement of a tentative taxonomic hierarchy with the help of a posteriori weighting of differences are discussed. The method of character weighting leads to the construction of prognostic combinatorial arrangements that can predict the existence of organisms with certain character state combinations at each hierarchical level. The drawbacks of cladistic methodology, especially the «synapomorphy principle», the «dichotomy principle», and the monophyly «definition» through the internal composition of groups, are noted. It is pointed out that these principles only lead to the creation of heterogeneous groups and wrong character ranking.

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Saraiva, Luis R., Kunio Kondoh, Xiaolan Ye, Kyoung-hye Yoon, Marcus Hernandez, and Linda B. Buck. "Combinatorial effects of odorants on mouse behavior." Proceedings of the National Academy of Sciences 113, no. 23 (May 20, 2016): E3300—E3306. http://dx.doi.org/10.1073/pnas.1605973113.

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The mechanisms by which odors induce instinctive behaviors are largely unknown. Odor detection in the mouse nose is mediated by >1, 000 different odorant receptors (ORs) and trace amine-associated receptors (TAARs). Odor perceptions are encoded combinatorially by ORs and can be altered by slight changes in the combination of activated receptors. However, the stereotyped nature of instinctive odor responses suggests the involvement of specific receptors and genetically programmed neural circuits relatively immune to extraneous odor stimuli and receptor inputs. Here, we report that, contrary to expectation, innate odor-induced behaviors can be context-dependent. First, different ligands for a given TAAR can vary in behavioral effect. Second, when combined, some attractive and aversive odorants neutralize one another’s behavioral effects. Both a TAAR ligand and a common odorant block aversion to a predator odor, indicating that this ability is not unique to TAARs and can extend to an aversive response of potential importance to survival. In vitro testing of single receptors with binary odorant mixtures indicates that behavioral blocking can occur without receptor antagonism in the nose. Moreover, genetic ablation of a single receptor prevents its cognate ligand from blocking predator odor aversion, indicating that the blocking requires sensory input from the receptor. Together, these findings indicate that innate odor-induced behaviors can depend on context, that signals from a single receptor can block innate odor aversion, and that instinctive behavioral responses to odors can be modulated by interactions in the brain among signals derived from different receptors.

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BEJINARIU, S. I., H. COSTIN, and D. COSTIN. "Combinatorial versus Priority Based Optimization in Resource Constrained Project Scheduling Problems by Nature Inspired Metaheuristics." Advances in Electrical and Computer Engineering 19, no. 1 (2019): 17–26. http://dx.doi.org/10.4316/aece.2019.01003.

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Hallis, Tina M., and Hung-Wen Liu. "ChemInform Abstract: Learning Nature′s Strategies for Making Deoxy Sugars: Pathways, Mechanisms, and Combinatorial Applications." ChemInform 30, no. 40 (June 13, 2010): no. http://dx.doi.org/10.1002/chin.199940265.

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Sidman, Jessica, and Seth Sullivant. "Prolongations and Computational Algebra." Canadian Journal of Mathematics 61, no. 4 (August 1, 2009): 930–49. http://dx.doi.org/10.4153/cjm-2009-047-5.

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Abstract.We explore the geometric notion of prolongations in the setting of computational algebra, extending results of Landsberg and Manivel which relate prolongations to equations for secant varieties. We also develop methods for computing prolongations that are combinatorial in nature. As an application, we use prolongations to derive a new family of secant equations for the binary symmetric model in phylogenetics.

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Blumstein, Sheila E. "The mapping from acoustic structure to the phonetic categories of speech: The invariance problem." Behavioral and Brain Sciences 21, no. 2 (April 1998): 260. http://dx.doi.org/10.1017/s0140525x98221170.

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This commentary focuses on the nature of combinatorial properties for speech and the locus equation. The presence of some overlap in locus equation space suggests that this higher order property may not be strictly invariant and may require other cues or properties for the perception of place of articulation. Moreover, combinatorial analysis in two-dimensional space and the resultant linearity appear to have a “special” status in the development of this theoretical framework. However, place of articulation is only one of many phonetic dimensions in language. It is suggested that a multidimensional space including patterns derived in the frequency, amplitude, and time domains will be needed to characterize the phonetic categories of speech, and that although the derived properties ultimately may not meet the conditions of linearity, they will reflect a higher order acoustic invariance.

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Abdelaali, Bekhouche, Haouassi Hichem, Rafik Mahdaoui, Rahab Hichem, and Ledmi Makhlouf. "ADCSA-WSD: Adapted Discrete Crow Search Algorithm for Word Sense Disambiguation." Revue d'Intelligence Artificielle 36, no. 1 (February 28, 2022): 131–38. http://dx.doi.org/10.18280/ria.360115.

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In the field of natural language processing, the semantic disambiguation of words is beneficial to several applications, which helps us to identify the correct meaning of a word or a sequence of words according to the given context. It can be formulated as a combinatorial optimization problem where the goal is to find the set of meanings that contribute to improving the semantic relationship between target words. The Crow Search Algorithm (CSA) is a nature-inspired algorithm. It mimics the food foraging behavior of crow birds and their social interaction. CSA can deal with both continuous and discrete optimization problems. In this paper, the Word Sense Disambiguation (WSD) is modelled as a combinatorial optimization problem that is by nature a discrete problem. For this propose the discrete version of CSA has been adapted for solving the WSD problem and a DCSA-based WSD approach is proposed and called ADCSA-WSD. The proposed approach has been evaluated and compared with state-of-the-art approaches using three well-known benchmark datasets (SemCor 3.0, SensEval-02, SensEval-03). Experimental results show that ADCSA-WSD approach is performing better than other approaches.

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