Dynamical Language Research Articles

CGRWDL: alignment-free phylogeny reconstruction method for viruses based on chaos game representation weighted by dynamical language model.

Traditional alignment-based methods meet serious challenges in genome sequence comparison and phylogeny reconstruction due to their high computational complexity. Here, we propose a new alignment-free method to analyze the phylogenetic relationships (classification) among species. In our method, the dynamical language (DL) model and the chaos game representation (CGR) method are used to characterize the frequency information and the context information of k-mers in a sequence, respectively. Then for each DNA sequence or protein sequence in a dataset, our method converts the sequence into a feature vector that represents the sequence information based on CGR weighted by the DL model to infer phylogenetic relationships. We name our method CGRWDL. Its performance was tested on both DNA and protein sequences of 8 datasets of viruses to construct the phylogenetic trees. We compared the Robinson-Foulds (RF) distance between the phylogenetic tree constructed by CGRWDL and the reference tree by other advanced methods for each dataset. The results show that the phylogenetic trees constructed by CGRWDL can accurately classify the viruses, and the RF scores between the trees and the reference trees are smaller than that with other methods.

On Educational Assessment Theory: A High-Level Discussion of Adolphe Quetelet, Platonism, and Ergodicity

Educational assessments, specifically standardized and normalized exams, owe most of their foundations to psychological test theory in psychometrics. While the theoretical assumptions of these practices are widespread and relatively uncontroversial in the testing community, there are at least two that are philosophically and mathematically suspect and have troubling implications in education. Assumption 1 is that repeated assessment measures that are calculated into an arithmetic mean are thought to represent some real stable, quantitative psychological trait or ability plus some error. Assumption 2 is that aggregated, group-level educational data collected from assessments can then be interpreted to make inferences about a given individual person over time without explicit justification. It is argued that the former assumption cannot be taken for granted; it is also argued that, while it is typically attributed to 20th century thought, the assumption in a rigorous form can be traced back at least to the 1830s via an unattractive Platonistic statistical thesis offered by one of the founders of the social sciences—Belgian mathematician Adolphe Quetelet (1796–1874). While contemporary research has moved away from using his work directly, it is demonstrated that cognitive psychology is still facing the preservation of assumption 1, which is becoming increasingly challenged by current paradigms that pitch human cognition as a dynamical, complex system. However, how to deal with assumption 1 and whether it is broadly justified is left as an open question. It is then argued that assumption 2 is only justified by assessments having ergodic properties, which is a criterion rarely met in education; specifically, some forms of normalized standardized exams are intrinsically non-ergodic and should be thought of as invalid assessments for saying much about individual students and their capability. The article closes with a call for the introduction of dynamical mathematics into educational assessment at a conceptual level (e.g., through Bayesian networks), the critical analysis of several key psychological testing assumptions, and the introduction of dynamical language into philosophical discourse. Each of these prima facie distinct areas ought to inform each other more closely in educational studies.

Contact tracking algorithms in case of the omni-directional wheel rolling on the horizontal surface

An omni-wheel is defined as a wheel having rollers along its rim. Vehicles with omni-wheels are able to maneuver in any direction. For modeling the dynamics of omni-wheels we use general formalisms, previously developed by the authors for the multibody dynamics description in the framework of the object-oriented dynamical modeling language Modelica. Such an omni-wheel model, which is a class component, can be built into a vehicle model of any type. The axes of the rollers are usually set along the rim of the wheel either (a) parallel to the mid-plane of the wheel or (b) at some angle to this plane. Case (a) is the simplest one and the floor–roller contact tracking algorithm provides the fastest dynamical model. The more flexible case (b) consumes longer computation time. At the same time the suggested implementation of the case (b) turns out to be more efficient as compared with the approach based on the general formulas of contact problems. As an example, here these algorithms are combined with the simplest and fastest point-contact model, which runs regularly in the process of motion simulation. The proposed algorithms demonstrate the reliability and a nonimpact method of transferring contact point from one roller to another in the process of rolling the wheel. The implementation of these algorithms is described and computational experiments for numerical verification of the model are presented.

DLTree: efficient and accurate phylogeny reconstruction using the dynamical language method.

A number of alignment-free methods have been proposed for phylogeny reconstruction over the past two decades. But there are some long-standing challenges in these methods, including requirement of huge computer memory and CPU time, and existence of duplicate computations. In this article, we address these challenges with the idea of compressed vector, fingerprint and scalable memory management. With these ideas we developed the DLTree algorithm for efficient implementation of the dynamical language model and whole genome-based phylogenetic analysis. The DLTree algorithm was compared with other alignment-free tools, demonstrating that it is more efficient and accurate for phylogeny reconstruction. The DLTree algorithm is freely available at http://dltree.xtu.edu.cn. yuzuguo@aliyun.com or yangjy@nankai.edu.cn. Supplementary data are available at Bioinformatics online.

Designing Organizations for Dynamic Fit: System Stability, Maneuverability, and Opportunity Loss

Fit represents a central concept for organizational design, but extant research maintains a static focus on fit, a focus that is incommensurate with the fundamentally dynamic nature of organizations and their environments. Most key organizational environments are inherently dynamic; hence, the corresponding organizational designs required for fit are necessarily dynamic too. The problem is, the dynamics of fit are not addressed well by extant theory in organization and management sciences. Alternatively, organizations can be viewed as systems of purposeful design, and designing organizations to maintain fit and respond to dynamic environments over time may be informed well by theory and practice in engineering fields where such design is well established. In this paper, we abstract to the level of airplane design, and we utilize the dynamical language and integrated system of concepts, definitions, and interrelationships from the engineering field Aerodynamics to extend organization and management sciences and address the problem of organizational design in a dynamic context. We begin with a focused summary of the literature regarding the nature of organizational fitness. We then outline a conceptual model adapted to organizational design from Aerodynamics, and we summarize the key aerodynamics concepts stability and maneuverability to inform our conceptualization in terms of both airplane and organization design. This paper enables us to articulate a set of propositions and measures that form a basis for empirical testing. This paper also reveals important, dynamic organizational design tradeoffs and implications, and it shows how such conceptualization can elucidate new insights via comparison with and extension to extant theory.

Whole-proteome phylogeny of large dsDNA viruses and parvoviruses through a composition vector method related to dynamical language model.

BackgroundThe vast sequence divergence among different virus groups has presented a great challenge to alignment-based analysis of virus phylogeny. Due to the problems caused by the uncertainty in alignment, existing tools for phylogenetic analysis based on multiple alignment could not be directly applied to the whole-genome comparison and phylogenomic studies of viruses. There has been a growing interest in alignment-free methods for phylogenetic analysis using complete genome data. Among the alignment-free methods, a dynamical language (DL) method proposed by our group has successfully been applied to the phylogenetic analysis of bacteria and chloroplast genomes.ResultsIn this paper, the DL method is used to analyze the whole-proteome phylogeny of 124 large dsDNA viruses and 30 parvoviruses, two data sets with large difference in genome size. The trees from our analyses are in good agreement to the latest classification of large dsDNA viruses and parvoviruses by the International Committee on Taxonomy of Viruses (ICTV).ConclusionsThe present method provides a new way for recovering the phylogeny of large dsDNA viruses and parvoviruses, and also some insights on the affiliation of a number of unclassified viruses. In comparison, some alignment-free methods such as the CV Tree method can be used for recovering the phylogeny of large dsDNA viruses, but they are not suitable for resolving the phylogeny of parvoviruses with a much smaller genome size.

Proper distance metrics for phylogenetic analysis using complete genomes without sequence alignment.

A shortcoming of most correlation distance methods based on the composition vectors without alignment developed for phylogenetic analysis using complete genomes is that the “distances” are not proper distance metrics in the strict mathematical sense. In this paper we propose two new correlation-related distance metrics to replace the old one in our dynamical language approach. Four genome datasets are employed to evaluate the effects of this replacement from a biological point of view. We find that the two proper distance metrics yield trees with the same or similar topologies as/to those using the old “distance” and agree with the tree of life based on 16S rRNA in a majority of the basic branches. Hence the two proper correlation-related distance metrics proposed here improve our dynamical language approach for phylogenetic analysis.

Stockbot: a monitoring and acting software agent for stock markets

Stockbot is a software agent designed for the task of monitoring an electronic stock market in order to execute investor purchase or sale orders. Stockbot represents a tool for managing the dynamical complexity of electronic stock markets by establishing a virtual portfolio manager. Its main goal is to exhibit a behaviour which is a timely, continuous, dynamical response to changes in the market situations in accordance to the user profile and goals. The software agent maintains and dynamically updates a user model which records histories of previous user orders, patterns of user observed behaviour, and user preferences and goals. The software architecture integrates conventional and knowledge-based software technologies such as conditional and iterative planning, continuous conditions monitoring, robust failure management, inter-agent communication primitives and events networks. A Dynamical Query Language is used to describe stockbot behaviour. Copyright © 1999 John Wiley & Sons, Ltd.

Units of Weight, Mass, and Force

YOUR reviewer, of the well-known initials “P. G. T.,” has taken exception to some of the terminology employed by Mr. Anderson in his book “On the Conversion of Heat into Work,” particularly to the expressions of “pounds on the square inch” and “tons on the square inch,” which he says would define a superficial density if used in their proper sense; and it is this opinion I wish, with your permission, to dispute, as I think “P. G. T.” and mathematicians generally, are at present in this endeavour to avoid one ambiguity in dynamical language only creating greater confusion.