Cooperative combinatorial optimization: evolutionary computation case study

This paper presents a formalization of the notion of cooperation and competition of multiple systems that work toward a common optimization goal of the population using evolutionary computation techniques. It is proved that evolutionary algorithms are more expressive than conventional recursive algorithms, such as Turing machines. Three classes of evolutionary computations are introduced and studied: bounded finite, unbounded finite, and infinite computations. Universal evolutionary algorithms are constructed. Such properties of evolutionary algorithms as completeness, optimality, and search decidability are examined. A natural extension of evolutionary Turing machine (ETM) model is proposed to properly reflect phenomena of cooperation and competition in the whole population.     

Fast and accurate three-dimensional reconstruction from projections with random orientations via radon transforms

A new algorithm for three-dimensional reconstruction from randomly oriented projections has been developed. The algorithm recovers the 3D Radon transform from the 2D Radon transforms (sinograms) of the projections. The structure in direct space is obtained by an inversion of the 3D Radon transform. The mathematical properties of the Radon transform are exploited to design a special filter that can be used to correct inconsistencies in a data set and to fill the gaps in the Radon transform that originate from missing projections. Several versions of the algorithm have been implemented, with and without a filter and with different interpolation methods for merging the sinograms into the 3D Radon transform. The algorithms have been tested on analytical phantoms and experimental data and have been compared with a weighted back projection algorithm (WBP). A quantitative analysis of phantoms reconstructed from noise-free and noise-corrupted projections shows that the new algorithms are more accurate than WBP when the number of projections is small. Experimental structures obtained by the new methods are strictly comparable to those obtained by WBP. Moreover, the algorithm is more than 10 times faster than WPB when applied to a data set of 1000-5000 projections. Copyright 1999 Academic Press.     

Markov dynamics as a zooming lens for multiscale community detection: non clique-like communities and the field-of-view limit

In recent years, there has been a surge of interest in community detection algorithms for complex networks. A variety of computational heuristics, some with a long history, have been proposed for the identification of communities or, alternatively, of good graph partitions. In most cases, the algorithms maximize a particular objective function, thereby finding the 'right' split into communities. Although a thorough comparison of algorithms is still lacking, there has been an effort to design benchmarks, i.e., random graph models with known community structure against which algorithms can be evaluated. However, popular community detection methods and benchmarks normally assume an implicit notion of community based on clique-like subgraphs, a form of community structure that is not always characteristic of real networks. Specifically, networks that emerge from geometric constraints can have natural non clique-like substructures with large effective diameters, which can be interpreted as long-range communities. In this work, we show that long-range communities escape detection by popular methods, which are blinded by a restricted 'field-of-view' limit, an intrinsic upper scale on the communities they can detect. The field-of-view limit means that long-range communities tend to be overpartitioned. We show how by adopting a dynamical perspective towards community detection [1], [2], in which the evolution of a Markov process on the graph is used as a zooming lens over the structure of the network at all scales, one can detect both clique- or non clique-like communities without imposing an upper scale to the detection. Consequently, the performance of algorithms on inherently low-diameter, clique-like benchmarks may not always be indicative of equally good results in real networks with local, sparser connectivity. We illustrate our ideas with constructive examples and through the analysis of real-world networks from imaging, protein structures and the power grid, where a multiscale structure of non clique-like communities is revealed.     

Strategies for identifying statistically significant dense regions in microarray data

We propose and study the notion of dense regions for the analysis of categorized gene expression data and present some searching algorithms for discovering them. The algorithms can be applied to any categorical data matrices derived from gene expression level matrices. We demonstrate that dense regions are simple but useful and statistically significant patterns that can be used to 1) identify genes and/or samples of interest and 2) eliminate genes and/or samples corresponding to outliers, noise, or abnormalities. Some theoretical studies on the properties of the dense regions are presented which allow us to characterize dense regions into several classes and to derive tailor-made algorithms for different classes of regions. Moreover, an empirical simulation study on the distribution of the size of dense regions is carried out which is then used to assess the significance of dense regions and to derive effective pruning methods to speed up the searching algorithms. Real microarray data sets are employed to test our methods. Comparisons with six other well-known clustering algorithms using synthetic and real data are also conducted which confirm the superiority of our methods in discovering dense regions. The DRIFT code and a tutorial are available as supplemental material, which can be found on the Computer Society Digital Library at http://computer.org/tcbb/archives.htm.     

Removing noise and ambiguities from comparative maps in rearrangement analysis

Comparison of genomic maps is hampered by errors and ambiguities introduced by mapping technology, incorrectly resolved paralogy, small samples of markers, and extensive genome rearrangement. We design an analysis to remove or resolve most of these problems and to extract corrected data where markers occur in consecutive strips in both genomes. To do this, we introduce the notion of prestrip, an efficient way of generating these and a compatibility analysis culminating in a maximum weighted clique (MWC) search. The output can be directly analyzed with genome rearrangement algorithms, allowing the restoration of some of the data not incorporated into the clique solution. We investigate the trade-off between criteria for discarding excessive prestrips to make MWC feasible in terms of retaining as many markers as possible in the solution and producing an economical rearrangement analysis. We explore these questions through simulation and through comparison of the rice and sorghum genomes.     

A kinetic model of RNA folding

The RNA folding process is represented as a Markov process with states corresponding to RNA secondary structures and transition probabilities corresponding to transformations of a secondary structure caused by formation or disintegration of a helix. Transition probabilities (kinetic constants) are determined. A notion of a group of structures is introduced, and it allows to reduce the state space. Energetic and kinetic parameters of pseudoknots are estimated. Algorithms for computation of a kinetic ensemble for structures and groups of structures are presented, as well as their modifications that take into account pseudoknots. The described algorithms are implemented as a procedure for prediction of RNA secondary structure that is included in the package DNA-SUN.     

On the nature of 2D crystal unbending

Crystal unbending, the process that aims to recover a perfect crystal from experimental data, is one of the more important steps in electron crystallography image processing. The unbending process involves three steps: estimation of the unit cell displacements from their ideal positions, extension of the deformation field to the whole image and transformation of the image in order to recover an ideal crystal. In this work, we present a systematic analysis of the second step oriented to address two issues. First, whether the unit cells remain undistorted and only the distance between them should be changed (rigid case) or should be modified with the same deformation suffered by the whole crystal (elastic case). Second, the performance of different extension algorithms (interpolation versus approximation) is explored. Our experiments show that there is no difference between elastic and rigid cases or among the extension algorithms. This implies that the deformation fields are constant over large areas. Furthermore, our results indicate that the main source of error is the transformation of the crystal image.     

31P NMR first spectral moment study of the partial magnetic orientation of phospholipid membranes.

Structural data can be obtained on proteins inserted in magnetically oriented phospholipid membranes such as bicelles, which are most often made of a mixture of long and short chain phosphatidylcholine. Possible shapes for these magnetically oriented membranes have been postulated in the literature, such as discoidal structures with a thickness of one bilayer and with the short acyl chain phosphatidylcholine on the edges. In the present paper, a geometrical study of these oriented structures is done to determine the validity of this model. The method used is based on the determination of the first spectral moment of solid-state (31)P nuclear magnetic resonance spectra. From this first moment, an order parameter is defined that allows a quantitative analysis of partially oriented spectra. The validity of this method is demonstrated in the present study for oriented samples made of DMPC, DMPC:DHPC, DMPC:DHPC:gramicidin A and adriamycin:cardiolipin.     

Rational Disagreements in Phylogenetics

This paper addresses the general problem of how to rationally choose an algorithm for phylogenetic inference. Specifically, the controversy between maximum likelihood (ML) and maximum parsimony (MP) perspectives is reframed within the philosophical issue of theory choice. A Kuhnian approach in which rationality is bounded and value-laden is offered and construed through the notion of a Style of Modeling. A Style is divided into four stages: collecting remnant models, constructing models of taxonomical identity, implementing modeling algorithms, and finally inferring and confirming evolutionary trees or cladograms. The identification and investigation of styles is useful for exploring sociological and epistemological issues such as individuating scientific communities and assessing the rationality of algorithm choice. Regarding the last point, this paper suggests that the values motivating ML and MP perspectives are justified but only contextually; these algorithms also have normative force because they can be therapeutic by allowing us to rationally choose among several competing trees, nonetheless this force is limited and cannot be used in order to decide the controversy tout court.     

The Research and Design of SOA-Based Systems

According to the traditional IT system to integrated the parts and brings much repetition and high cost is insufficient,service oriented architecture is put forward solutions.Further introduces the service oriented architecture theory knowledge,transverse relative to the traditional development advantages,fully demonstrates the main trend of the service oriented architecture that drive.Discusses in detail the service oriented architecture(SOA),the core concept and design principles,and security measures to IBM led the company put forward using the service oriented architecture modeling,and to service the abstract concept to carry on the analysis.The core of service oriented is the component architecture and service data object,combining components and data on the part of the object oriented service principle.And Web services and SOA are compared to further understanding the connotation of SOA,and can support is given based on SOA application system of the specific technology,finally,the paper discusses the SOA further research direction.     

An additional example of the ichnogenus Zoophycos in Cambrian strata (Gallatin Formation; Wyoming,USA)

The ichnogenus Zoophycos is relatively rare in Cambrian-age sedimentary rocks, being far more commonly encountered in post-Devonian, and particularly post-Paleozoic, strata. A new occurrence of Zoophycos from the Upper Cambrian Gallatin Formation of the Bighorn Mountains, north-central Wyoming, USA, is reported herein. Material consists of a single specimen preserved within quartz silt representing the upper surface of a graded quartz arenite bed. The burrow is a relatively wide, curved, horizontally oriented lobe with a poorly visible marginal tube but well-developed internal lamellae. Discovery of this specimen contributes to the paleobiogeographic distribution of lower Paleozoic Zoophycos, adds to the literature suggesting that most Cambrian Zoophycos were horizontal and shallow-tier structures, and provides further support to the notion that relatively complex deposit-feeding behavior evolved earlier in the Phanerozoic than had long been recognized.     

WASHING THE CITIZEN: WASHING, CLEANLINESS AND CITIZENSHIP IN MENTAL HEALTH CARE

Participation in the community and citizenship for patients are common ideals that inspire improvements in mental health care. But what is meant by citizenship? Here an analysis is made of washing practices in psychiatric nursing in long-term mental health institutions. Four repertoires of washing are described, each oriented towards a specific notion of citizenship. In the first repertoire, washing is part of individual privacy; the patient is “enacted” as an individual whose authenticity should be respected in order to equip him or her for participation in the community. In the second repertoire, washing is a basic skill; the patient must learn to take care of her body in order to become an independent citizen. In the third repertoire washing is a precondition to citizenship; patients are to be helped to develop their potentials so that they can find their way in the community. In the fourth repertoire, washing is one opportunity among others to develop social relations; the extent and quality of these relations define a citizen. This analysis opens up not the question if, but which type of citizenship should be promoted.     

Prediction of the Secondary Structure of Myelin Basic Protein

An investigation into the probable secondary structure of the myelin basic protein was carried out by the application of three procedures currently in use to predict the secondary structures of proteins from knowledge of their amino acid sequences. In order to increase the accuracy of the predictions, the amino acid substitutions that occur in the basic protein from different species were incorporated into the predictive algorithms. It was possible to locate regions of probable alpha-helix, beta-structure, beta-turn, and unordered conformation (coil) in the protein. One of the predictive methods introduces a bias into the algorithm to maximize or minimize the amounts of alpha-helix and/or beta-structure present; this made it possible to assess how conditions such as pH and protein concentration or the presence of anionic amphiphilic molecules could influence the protein's secondary structure. The predictions made by the three methods were in reasonably good agreement with one another. They were consistent with experimental data, provided that the stabilizing or destabilizing effects of the environment were taken into account. According to the predictions, the extent of possible alpha-helix and beta-structure formation in the protein s severely restricted by the low frequency and extensive scattering of hydrophobic residues, along with a high frequency and extensive scattering of residues that favor the formation of beta-turns and coils. Neither prolyl residues nor cationic residues per se are responsible for the low content of alpha-helix predicted in the protein. The principal ordered conformation predicted is the beta-turn. Many of the predicted beta-turns overlap extensively, involving in some cases up to 10 residues. In some of these structures it is possible for the peptide backbone to oscillate in a sinusoidal manner, generating a flat, pleated sheetlike structure. Cationic residues located in these structures would appear to be ideally oriented for interaction with lipid phosphate groups located at the cytoplasmic surface of the myelin membrane. An analysis of possible and probable conformations that the triproline sequence could assume questions the popular notion that this sequence produces a hairpin turn in the basic protein.     

Locality and gaps in RNA comparison.

Locality is an important and well-studied notion in comparative analysis of biological sequences. Similarly, taking into account affine gap penalties when calculating biological sequence alignments is a well-accepted technique for obtaining better alignments. When dealing with RNA, one has to take into consideration not only sequential features, but also structural features of the inspected molecule. This makes the computation more challenging, and usually prohibits the comparison only to small RNAs. In this paper we introduce two local metrics for comparing RNAs that extend the Smith-Waterman metric and its normalized version used for string comparison. We also present a global RNA alignment algorithm which handles affine gap penalties. Our global algorithm runs in O(m(2)n(1 + lg n/m)) time, while our local algorithms run in O(m(2)n(1 + lg n/m)) and O(n(2)m) time, respectively, where m 相似文献   

The Temporality of “Chronic” Mental Illness

Although multiple concepts of time can be found in psychiatric discourses and practices, the notion of time as an absolute category seems to predominate. In particular, the notion of “chronicity” implies the persistence of symptoms over the temporal course of a disease, thereby following a logic that conceptualizes time as an objective and universal measure. I argue that such a notion of time impedes the development of patients and the metrics by which to map change. This article, therefore, aims to present a different concept of time that should enable dealing with "chronic" mental illness in more flexible and creative ways. A case study of an everyday psychiatric routine is presented, followed by an in-depth analysis of its temporal implications. I conceptualize the notion of time as an extended field, being relationally and intersubjectively structured and linked to performed activities. Such a notion of time needs to be seen as a flexible and fluid matrix that possesses the character of an event-oriented and productive space. This conception favors an individualized temporality of change, suggesting concrete therapeutic procedures that can be implemented in clinical practice.     

Fluorescence polarization studies of squid giant axons stained with N-methylanilinonaphthalenesulfonates

The polarized components of the extrinsic fluorescence of squid giant axons stained with 2,6-MANS or 1,8-MANS were studied. The polarization properties of the fluorescence changes associated with voltage-clamp pulses were found to be very different from those of the static fluorescence, supporting the notion that the optical changes involve highly oriented membrane adsorbed fluorophores. The theoretical expectations according to this hypothesis are discussed in detail. The experimental results are in good agreement with the theory assuming that possible probes reorientations are solely due to the action of the applied electric field upon the probes electric dipole. The quantitative analysis of the data for 2,6 MANS provides a fairly accurate determination of the orientation of the membrane bound 2,6-MANS molecules responsible for the fluorescence changes. Such orientation appears to be independent of the membrane face exposed to staining. The data for 1,8-MANS indicate a very different orientation of this isomer. The results suggest a profitable use of extrinsic fluorophores for studies of the structural organization of nerve membranes.