PQ, a new program for phylogeny reconstruction
Background. Many algorithms and programs are available for phylogenetic reconstruction of families of proteins. Methods used widely at present use either a number of distance-based principles or character-based principles of maximum parsimony or maximum likelihood.
Results. We developed a novel program, named PQ, for reconstructing protein and nucleic acid phylogenies following a new character-based principle. Being tested on natural sequences PQ improves upon the results of maximum parsimony and maximum likelihood. Working with alignments of 10 and 15 sequences, it also outperforms the FastME program, which is based on one of the distance-based principles. Among all tested programs PQ is proved to be the least susceptible to long branch attraction. FastME outperforms PQ when processing alignments of 45 sequences, however. We confirm a recent result that on natural sequences FastME outperforms maximum parsimony and maximum likelihood. At the same time, both PQ and FastME are inferior to maximum parsimony and maximum likelihood on simulated sequences. PQ is open source and available to the public via an online interface.
Conclusions. The software we developed offers an open-source alternative for phylogenetic reconstruction for relatively small sets of proteins and nucleic acids, with up to a few tens of sequences.
The problem of axiomatic and algorithmic constructions of the threshold decision making is studied in the case when individual opinions are given as m-graded strict preferences (with m ≥ 3). It is shown that the only rule satisfying the introduced axioms is the threshold rule. Two explicit algorithms are presented: the ordering algorithm, under which the vector-grades of alternatives are successively written out, and an enumerating social decision function corresponding to the natural order of the weak order equivalence classes.
At the particular article we provide a methodological approach to selection of companies for horizontal cooperation in procurement logistics. In context of modern logistics (globalization, high customer expectations, high transportation costs), and changes regarding Russia’s plans to join WTO, this topic is highly relevant from a practical point of view. The purpose of this article is to provide single methodological approach to selection of companies for horizontal cooperation.
1. Description of the problem. Instrumental analysis makes it possible to find the arguments of adjudication on the bounders and structure of corpus delicti, its correlation to criminal and filling-up legislation. 2. Initial theses. Corpus delicti is regarded as that expressed in criminal law doctrine result of reorganization of orders of criminal law into other practically necessary form. That happens in the process of theory and practical experience accumulation. The construction of corpus delicti is transformed for practical needs, textually expressed system of features, regulated by criminal law and characterizing deeds as a crime of a definite type. Correlation of construction of corpus delicti with law and doctrine. Corpus delicti, its algorithm. Transition from law regulations to corpus delicti can be done: 1) prog-nostically; 2) within constant analysis of law; 3) in the process of law application. 3. Stages of instrumental building of corpus delicti: prognostic, doctrinal, law applicatory. Instrumental approach to corpus delicti includes within each stage: 1) based on criminal law decision of classification of corpus delicti and its borders; 2) objective description of a factual model; 3) acception of meaning correlated with legal notions and constructions; 4) choice of the construction of the corpus delicti and disposal of characteristics; 5) verification of legitimacy, necessity and adequacy of foundation. 4. Instrumental analysis of disputable questions of understanding and application of constructions of corpus delicti. A. Functions and purposes of application of construction of corpus delicti. Functions of corpus delicti: a) modeling; b) communicative; c) identificatory; d) technological. B. Contents of corpus delicti. Contents of corpus delicti as it is traditionally regarded does not correspond to indications of crime, does not characterize features of social danger; sign of danger of penalty also does go into corpus delicti. Two variants are proposed for the discussion: widening of the borders of corpus delicti by means of introduction of signs of social danger and signs, defining individualization of penalty and to limitate corpus delicti by characteristic of criminally punished act, separating it from contents of guilt and contents of social danger. C. Structure of corpus delicti. There are two problems: division of elements of crime seems to be extremely harsh and inadequate - it is expedient to include signs of special and time limits of act, causal links, crossing signs of objective and subjective sides, first of all consequences and an object of crime, into the structure of corpus delicti. Forms of committing a criminally punished act is a crime commitment in complicity, ideal system, not finished crime.
We present an approach based on a two-stage ltration of the set of feasible solutions for the multiprocessor job-shop scheduling problem. On the rst stage we use extensive dominance relations, whereas on the second stage we use lower bounds. We show that several lower bounds can eciently be obtained and implemented.
A model for organizing cargo transportation between two node stations connected by a railway line which contains a certain number of intermediate stations is considered. The movement of cargo is in one direction. Such a situation may occur, for example, if one of the node stations is located in a region which produce raw material for manufacturing industry located in another region, and there is another node station. The organization of freight traﬃc is performed by means of a number of technologies. These technologies determine the rules for taking on cargo at the initial node station, the rules of interaction between neighboring stations, as well as the rule of distribution of cargo to the ﬁnal node stations. The process of cargo transportation is followed by the set rule of control. For such a model, one must determine possible modes of cargo transportation and describe their properties. This model is described by a ﬁnite-dimensional system of diﬀerential equations with nonlocal linear restrictions. The class of the solution satisfying nonlocal linear restrictions is extremely narrow. It results in the need for the “correct” extension of solutions of a system of diﬀerential equations to a class of quasi-solutions having the distinctive feature of gaps in a countable number of points. It was possible numerically using the Runge–Kutta method of the fourth order to build these quasi-solutions and determine their rate of growth. Let us note that in the technical plan the main complexity consisted in obtaining quasi-solutions satisfying the nonlocal linear restrictions. Furthermore, we investigated the dependence of quasi-solutions and, in particular, sizes of gaps (jumps) of solutions on a number of parameters of the model characterizing a rule of control, technologies for transportation of cargo and intensity of giving of cargo on a node station.
Event logs collected by modern information and technical systems usually contain enough data for automated process models discovery. A variety of algorithms was developed for process models discovery, conformance checking, log to model alignment, comparison of process models, etc., nevertheless a quick analysis of ad-hoc selected parts of a journal still have not get a full-fledged implementation. This paper describes an ROLAP-based method of multidimensional event logs storage for process mining. The result of the analysis of the journal is visualized as directed graph representing the union of all possible event sequences, ranked by their occurrence probability. Our implementation allows the analyst to discover process models for sublogs defined by ad-hoc selection of criteria and value of occurrence probability
It is well-known that the class of sets that can be computed by polynomial size circuits is equal to the class of sets that are polynomial time reducible to a sparse set. It is widely believed, but unfortunately up to now unproven, that there are sets in EXPNP, or even in EXP that are not computable by polynomial size circuits and hence are not reducible to a sparse set. In this paper we study this question in a more restricted setting: what is the computational complexity of sparse sets that are selfreducible? It follows from earlier work of Lozano and Torán (in: Mathematical systems theory, 1991) that EXPNP does not have sparse selfreducible hard sets. We define a natural version of selfreduction, tree-selfreducibility, and show that NEXP does not have sparse tree-selfreducible hard sets. We also construct an oracle relative to which all of EXP is reducible to a sparse tree-selfreducible set. These lower bounds are corollaries of more general results about the computational complexity of sparse sets that are selfreducible, and can be interpreted as super-polynomial circuit lower bounds for NEXP.
The Handbook of CO₂ in Power Systems' objective is to include the state-of-the-art developments that occurred in power systems taking CO₂ emission into account. The book includes power systems operation modeling with CO₂ emissions considerations, CO₂ market mechanism modeling, CO₂ regulation policy modeling, carbon price forecasting, and carbon capture modeling. For each of the subjects, at least one article authored by a world specialist on the specific domain is included.