15 papers · ranked by Valyu relevance
Chen-Hsiang Yeang
Many methods have been developed to detect coevolution from aligned sequences. However, all the existing methods require a one-to-one mapping of candidate coevolving partners (nucleotides, amino acids) a priori. When two families of sequences have distinct duplication and loss histories, finding the one-to-one mapping…
Xingsi Xue, Jie Chen, Junfeng Chen, Dongxu Chen
Over the recent years, ontologies are widely used in various domains such as medical records annotation, medical knowledge representation and sharing, clinical guideline management, and medical decision-making. To implement the cooperation between intelligent applications based on biomedical ontologies, it is crucial…
Alistair Benford, Per Kristian Lehre
Due to their complex dynamics, combinatorial games are a key test case and application for algorithms that train game playing agents. Among those algorithms that train using self-play are coevolutionary algorithms (CoEAs). However, the successful application of CoEAs for game playing is difficult due to pathological…
Je-Gun Joung, Soo-Jin Kim, Soo-Yong Shin, Byoung-Tak Zhang
Background Biclustering has been utilized to find functionally important patterns in biological problem. Here a bicluster is a submatrix that consists of a subset of rows and a subset of columns in a matrix, and contains homogeneous patterns. The problem of finding biclusters is still challengeable due to computational…
Jiao Shi, Maoguo Gong, Wenping Ma, Licheng Jiao
How to maintain the population diversity is an important issue in designing a multiobjective evolutionary algorithm. This paper presents an enhanced nondominated neighbor-based immune algorithm in which a multipopulation coevolutionary strategy is introduced for improving the population diversity. In the proposed…
Sizhe Yuen, Thomas H. G. Ezard, Adam J. Sobey
Evolutionary computation is a group of biologically inspired algorithms used to solve complex optimization problems. It can be split into evolutionary algorithms, which take inspiration from genetic inheritance, and swarm intelligence algorithms, that take inspiration from cultural inheritance. However, much of the…
Daniel Y. Little, Lu Chen, Shin-Han Shiu
The structure and function of a protein is dependent on coordinated interactions between its residues. The selective pressures associated with a mutation at one site should therefore depend on the amino acid identity of interacting sites. Mutual information has previously been applied to multiple sequence alignments as…
José Fiorote, João Alves, Letícia Stock, Werner Treptow
Conditions of Coevolutionary Signals that Enable Algorithmic Predictions of Protein Partners Authors: ['José Fiorote' 'João Alves' 'Letícia Stock' 'Werner Treptow'] This study examines the statistical conditions of coevolutionary signals that allow algorithmic predictions of protein partners based on amino acid…
Scott L. Nuismer, Bob Week, Daniel B. Stouffer
Exaggerated traits involved in species interactions have long captivated the imagination of evolutionary biologists and inspired the durable metaphor of the coevolutionary arms race. Despite decades of research, however, we have only a handful of examples where reciprocal coevolutionary change has been rigorously…
Benjamin Drinkwater, Michael A Charleston
Background Cophylogeny mapping is used to uncover deep coevolutionary associations between two or more phylogenetic histories at a macro coevolutionary scale. As cophylogeny mapping is NP-Hard, this technique relies heavily on heuristics to solve all but the most trivial cases. One notable approach utilises a…
John J. Dennehy
The outcomes of host-parasite interactions depend on the coevolutionary forces acting upon them, but because every host-parasite relation is enmeshed in a web of biotic and abiotic interactions across a heterogeneous landscape, host-parasite coevolution has proven difficult to study. Simple laboratory phage-bacteria…
Shan Li, Liying Kang, Xing-Ming Zhao
With the rapid advance in genomics, proteomics, metabolomics, and other types of omics technologies during the past decades, a tremendous amount of data related to molecular biology has been produced. It is becoming a big challenge for the bioinformatists to analyze and interpret these data with conventional…
Licheng Jiao, Jiaxuan Zhao, Chao Wang, Xu Liu + 6 more
'Lingling Li' 'Ronghua Shang' 'Yangyang Li' 'Wenping Ma' 'Shuyuan Yang'] Nature, with its numerous surprising rules, serves as a rich source of creativity for the development of artificial intelligence, inspiring researchers to create several nature-inspired intelligent computing paradigms based on natural mechanisms.…
Antoine Frénoy, François Taddei, Dusan Misevic, Claus O. Wilke
When cooperation has a direct cost and an indirect benefit, a selfish behavior is more likely to be selected for than an altruistic one. Kin and group selection do provide evolutionary explanations for the stability of cooperation in nature, but we still lack the full understanding of the genomic mechanisms that can…
Nazmul Siddique, Hojjat Adeli
This paper presents an overview of significant advances made in the emerging field of nature-inspired computing (NIC) with a focus on the physics- and biology-based approaches and algorithms. A parallel development in the past two decades has been the emergence of the field of computational intelligence (CI) consisting…