A reliable measure of similarity based on dependency for short time series: an application to gene expression networks

Background: Microarray techniques have become an important tool to the investigation of genetic relationships and the assignment of different phenotypes. Since microarrays are still very expensive, most of the experiments are performed with small samples. This paper introduces a method to quantify dependency between data series composed of few sample points. The method is used to construct gene co-expression subnetworks of highly significant edges. Results: The results shown here are for an adapted subset of a Saccharomyces cerevisiae gene expression data set with low temporal resolution and poor statistics. The method reveals common transcription factors with a high confidence level and allows the construction of subnetworks with high biological relevance that reveals characteristic features of the processes driving the organism adaptations to specific environmental conditions. Conclusion: Our method allows a reliable and sophisticated analysis of microarray data even under severe constraints. The utilization of systems biology improves the biologists ability to elucidate the mechanisms underlying celular processes and to formulate new hypotheses.

Multistability and Self-Similarity in the Parameter-Space of a Vibro-Impact System

The dynamics of a dissipative vibro-impact system called impact-pair is investigated. This system is similar to Fermi-Ulam accelerator model and consists of an oscillating one-dimensional box containing a point mass moving freely between successive inelastic collisions with the rigid walls of the box. In our numerical simulations, we observed multistable regimes, for which the corresponding basins of attraction present a quite complicated structure with smooth boundary. In addition, we characterize the system in a two-dimensional parameter space by using the largest Lyapunov exponents, identifying self-similar periodic sets. Copyright (C) 2009 Silvio L.T. de Souza et al.

SELF-SIMILARITY AND LAMPERTI CONVERGENCE FOR FAMILIES OF STOCHASTIC PROCESSES

We define a new type of self-similarity for one-parameter families of stochastic processes, which applies to certain important families of processes that are not self-similar in the conventional sense. This includes Hougaard Levy processes such as the Poisson processes, Brownian motions with drift and the inverse Gaussian processes, and some new fractional Hougaard motions defined as moving averages of Hougaard Levy process. Such families have many properties in common with ordinary self-similar processes, including the form of their covariance functions, and the fact that they appear as limits in a Lamperti-type limit theorem for families of stochastic processes.

Nestmate recognition in a stingless bee: does the similarity of chemical cues determine guard acceptance?

The ability to discriminate nestmates from non-nestmates is critical to the maintenance of the integrity of social insect colonies. Guard workers compare the chemical cues of an incoming individual with their internal template to determine whether the entrant belongs to their colony. In contrast to honeybees, Apis mellifera, stingless bees have singly mated queens and, therefore, are expected to have a higher chemical homogeneity in their colonies. We tested whether aggressive behaviour of Frieseomelitta varia guards towards nestmate and non-nestmate foragers reflects chemical similarities and dissimilarities, respectively, of cuticular hydrocarbon profiles. We also introduced individuals of Lestrimelitta limao, an obligatory robber species, to test the ability of guards to react effectively to intruders from other taxa. We verified that foraging nestmates were almost invariably accepted, while heterospecific and conspecific non-nestmates were rejected at relatively high rates. However, non-nestmate individuals with higher chemical profile similarity were likely to be accepted by guards. We conclude that guards compare the chemical cuticular blend of incoming individuals and make acceptance decisions according to the similarity of the compounds between the colonies. (c) 2007 The Association for the Study of Animal Behaviour. Published by Elsevier Ltd. All rights reserved.

Self-Similarity of Air-Water Flows in Skimming Flows on Stepped Spillways

Skimming flows on stepped spillways are characterised by a significant rate of turbulent dissipation on the chute. Herein an advanced signal processing of traditional conductivity probe signals is developed to provide further details on the turbulent time and length scales. The technique is applied to a 22° stepped chute operating with flow Reynolds numbers between 3.8 and 7.1 E+5. The new correlation analyses yielded a characterisation of large eddies advecting the bubbles. The turbulent length scales were related to the characteristic depth Y90. Some self-similar relationships were observed systematically at both macroscopic and microscopic levels. These included the distributions of void fraction, bubble count rate, interfacial velocity and turbulence level, and turbulence time and length scales. The self-similarity results were significant because they provided a picture general enough to be used to characterise the air-water flow field in prototype spillways.

Dynamic Similarity and Scale Effects Affecting Air Bubble Entrainment in Hydraulic Jumps

In an open channel, the transition from super- to sub-critical flow is a flow singularity (the hydraulic jump) characterised by a sharp rise in free-surface elevation, strong turbulence and air entrainment in the roller. A key feature of the hydraulic jump flow is the strong free-surface aeration and air-water flow turbulence. In the present study, similar experiments were conducted with identical inflow Froude numbers Fr1 using a geometric scaling ratio of 2:1. The results of the Froude-similar experiments showed some drastic scale effects in the smaller hydraulic jumps in terms of void fraction, bubble count rate and bubble chord time distributions. Void fraction distributions implied comparatively greater detrainment at low Reynolds numbers yielding some lesser aeration of the jump roller. The dimensionless bubble count rates were significantly lower in the smaller channel, especially in the mixing layer. The bubble chord time distributions were quantitatively close in both channels, and they were not scaled according to a Froude similitude. Simply the hydraulic jump remains a fascinating two-phase flow motion that is still poorly understood.

Perceived self-other differences in persuasibility: the effects of interpersonal and group-based similarity

Two experiments examined the effects of interpersonal and group-based similarity on perceived self-other differences in persuasibility (i.e. on third-person effects, Davison, 1983). Results of Experiment 1 (N=121), based on experimentally-created groups, indicated that third-person perceptions with respect to the impact of televised product ads were accentuated when the comparison was made with interpersonally different others. Contrary to predictions, third-person perceptions were not affected by group-based similarity (i.e. ingroup or outgroup other). Results of Experiment 2 (N = 102), based an an enduring social identity, indicated that both interpersonal and group-based similarity moderated perceptions of the impact on self and other of least-liked product ads. Overall, third-person effects were more pronounced with respect to interpersonally dissimilar others. However, when social identity was salient, information about interpersonal similarity of the target did not affect perceived self-other differences with respect to ingroup targets. Results also highlighted significant differences in third-person perceptions according to the perceiver's affective evaluation of the persuasive message. (C) 1998 John Wiley & Sons, Ltd.

Target similarity effects: Support for the parallel distributed processing assumptions

Recent research has begun to provide support for the assumptions that memories are stored as a composite and are accessed in parallel (Tehan & Humphreys, 1998). New predictions derived from these assumptions and from the Chappell and Humphreys (1994) implementation of these assumptions were tested. In three experiments, subjects studied relatively short lists of words. Some of the Lists contained two similar targets (thief and theft) or two dissimilar targets (thief and steal) associated with the same cue (ROBBERY). AS predicted, target similarity affected performance in cued recall but not free association. Contrary to predictions, two spaced presentations of a target did not improve performance in free association. Two additional experiments confirmed and extended this finding. Several alternative explanations for the target similarity effect, which incorporate assumptions about separate representations and sequential search, are rejected. The importance of the finding that, in at least one implicit memory paradigm, repetition does not improve performance is also discussed.

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A comparative study of similarity measures for manufacturing cell formation

We introduced a spectral clustering algorithm based on the bipartite graph model for the Manufacturing Cell Formation problem in [Oliveira S, Ribeiro JFF, Seok SC. A spectral clustering algorithm for manufacturing cell formation. Computers and Industrial Engineering. 2007 [submitted for publication]]. It constructs two similarity matrices; one for parts and one for machines. The algorithm executes a spectral clustering algorithm on each separately to find families of parts and cells of machines. The similarity measure in the approach utilized limited information between parts and between machines. This paper reviews several well-known similarity measures which have been used for Group Technology. Computational clustering results are compared by various performance measures. (C) 2008 The Society of Manufacturing Engineers. Published by Elsevier Ltd. All rights reserved.

A New Family of Distance Functions for Perceptual Similarity Retrieval of Medical Images

A long-standing challenge of content-based image retrieval (CBIR) systems is the definition of a suitable distance function to measure the similarity between images in an application context which complies with the human perception of similarity. In this paper, we present a new family of distance functions, called attribute concurrence influence distances (AID), which serve to retrieve images by similarity. These distances address an important aspect of the psychophysical notion of similarity in comparisons of images: the effect of concurrent variations in the values of different image attributes. The AID functions allow for comparisons of feature vectors by choosing one of two parameterized expressions: one targeting weak attribute concurrence influence and the other for strong concurrence influence. This paper presents the mathematical definition and implementation of the AID family for a two-dimensional feature space and its extension to any dimension. The composition of the AID family with L (p) distance family is considered to propose a procedure to determine the best distance for a specific application. Experimental results involving several sets of medical images demonstrate that, taking as reference the perception of the specialist in the field (radiologist), the AID functions perform better than the general distance functions commonly used in CBIR.

Public choice of species for the ark: Phylogenetic similarity and preferred wildlife species for survival

Humans play a role in deciding the fate of species in the current extinction wave. Because of the previous Similarity Principle, physical attractiveness and likeability, it has been argued that public choice favours the survival of species that satisfy these criteria at the expense of other species. This paper empirically tests this argument by considering a hypothetical ‘Ark’ situation. Surveys of 204 members of the Australian public inquired whether they are in favour of the survival of each of 24 native mammal, bird and reptile species (prior to and after information provision about each species). The species were ranked by percentage of ‘yes’ votes received. Species composition by taxon in various fractions of the ranking was determined. If the previous Similarity Principle holds, mammals should rank highly and dominate the top fractions of animals saved in the hierarchical list. We find that although mammals would be over-represented in the ‘Ark’, birds and reptiles are unlikely to be excluded when social choice is based on numbers ‘voting’ for the survival of each species. Support for the previous Similarity Principle is apparent particularly after information provision. Public policy implications of this are noted and recommendations are given.

A similarity measure for music signals

One of the goals in the field of Music Information Retrieval is to obtain a measure of similarity between two musical recordings. Such a measure is at the core of automatic classification, query, and retrieval systems, which have become a necessity due to the ever increasing availability and size of musical databases. This paper proposes a method for calculating a similarity distance between two music signals. The method extracts a set of features from the audio recordings, models the features, and determines the distance between models. While further work is needed, preliminary results show that the proposed method has the potential to be used as a similarity measure for musical signals.

Self-similarity principle: the reduced description of randomness

A new general fitting method based on the Self-Similar (SS) organization of random sequences is presented. The proposed analytical function helps to fit the response of many complex systems when their recorded data form a self-similar curve. The verified SS principle opens new possibilities for the fitting of economical, meteorological and other complex data when the mathematical model is absent but the reduced description in terms of some universal set of the fitting parameters is necessary. This fitting function is verified on economical (price of a commodity versus time) and weather (the Earth’s mean temperature surface data versus time) and for these nontrivial cases it becomes possible to receive a very good fit of initial data set. The general conditions of application of this fitting method describing the response of many complex systems and the forecast possibilities are discussed.