24,362 research outputs found
Flexible protein folding by ant colony optimization
Protein structure prediction is one of the most challenging topics in bioinformatics.
As the protein structure is found to be closely related to its functions,
predicting the folding structure of a protein to judge its functions is meaningful to
the humanity. This chapter proposes a flexible ant colony (FAC) algorithm for solving
protein folding problems (PFPs) based on the hydrophobic-polar (HP) square lattice
model. Different from the previous ant algorithms for PFPs, the pheromones in the
proposed algorithm are placed on the arcs connecting adjacent squares in the lattice.
Such pheromone placement model is similar to the one used in the traveling salesmen
problems (TSPs), where pheromones are released on the arcs connecting the cities.
Moreover, the collaboration of effective heuristic and pheromone strategies greatly
enhances the performance of the algorithm so that the algorithm can achieve good
results without local search methods. By testing some benchmark two-dimensional
hydrophobic-polar (2D-HP) protein sequences, the performance shows that the proposed
algorithm is quite competitive compared with some other well-known methods
for solving the same protein folding problems
Protein folding in hydrophobic-polar lattice model: a flexible ant colony optimization approach
This paper proposes a flexible ant colony (FAC) algorithm for solving protein folding problems based on the hydrophobic-polar square lattice model. Collaborations of novel pheromone and heuristic strategies in the proposed algorithm make it more effective in predicting structures of proteins compared with other state-of-the-art algorithms
Quantum Structure in Competing Lizard Communities
Almost two decades of research on applications of the mathematical formalism
of quantum theory as a modeling tool in domains different from the micro-world
has given rise to many successful applications in situations related to human
behavior and thought, more specifically in cognitive processes of
decision-making and the ways concepts are combined into sentences. In this
article, we extend this approach to animal behavior, showing that an analysis
of an interactive situation involving a mating competition between certain
lizard morphs allows to identify a quantum theoretic structure. More in
particular, we show that when this lizard competition is analyzed structurally
in the light of a compound entity consisting of subentities, the contextuality
provided by the presence of an underlying rock-paper-scissors cyclic dynamics
leads to a violation of Bell's inequality, which means it is of a non-classical
type. We work out an explicit quantum-mechanical representation in Hilbert
space for the lizard situation and show that it faithfully models a set of
experimental data collected on three throat-colored morphs of a specific lizard
species. Furthermore, we investigate the Hilbert space modeling, and show that
the states describing the lizard competitions contain entanglement for each one
of the considered confrontations of lizards with different competing
strategies, which renders it no longer possible to interpret these states of
the competing lizards as compositions of states of the individual lizards.Comment: 28 page
Toward Entity-Aware Search
As the Web has evolved into a data-rich repository, with the standard "page view," current search engines are becoming increasingly inadequate for a wide range of query tasks. While we often search for various data "entities" (e.g., phone number, paper PDF, date), today's engines only take us indirectly to pages. In my Ph.D. study, we focus on a novel type of Web search that is aware of data entities inside pages, a significant departure from traditional document retrieval. We study the various essential aspects of supporting entity-aware Web search. To begin with, we tackle the core challenge of ranking entities, by distilling its underlying conceptual model Impression Model and developing a probabilistic ranking framework, EntityRank, that is able to seamlessly integrate both local and global information in ranking. We also report a prototype system built to show the initial promise of the proposal. Then, we aim at distilling and abstracting the essential computation requirements of entity search. From the dual views of reasoning--entity as input and entity as output, we propose a dual-inversion framework, with two indexing and partition schemes, towards efficient and scalable query processing. Further, to recognize more entity instances, we study the problem of entity synonym discovery through mining query log data. The results we obtained so far have shown clear promise of entity-aware search, in its usefulness, effectiveness, efficiency and scalability
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