A linear programming approach for estimating the structure of a sparse linear genetic network from transcript profiling data

Background: A genetic network can be represented as a directed graph in which a node corresponds to a gene and a directed edge specifies the direction of influence of one gene on another. The reconstruction of such networks from transcript profiling data remains an important yet challenging endeavor. A transcript profile specifies the abundances of many genes in a biological sample of interest. Prevailing strategies for learning the structure of a genetic network from high-dimensional transcript profiling data assume sparsity and linearity. Many methods consider relatively small directed graphs, inferring graphs with up to a few hundred nodes. This work examines large undirected graphs representations of genetic networks, graphs with many thousands of nodes where an undirected edge between two nodes does not indicate the direction of influence, and the problem of estimating the structure of such a sparse linear genetic network (SLGN) from transcript profiling data. Results: The structure learning task is cast as a sparse linear regression problem which is then posed as a LASSO (l1-constrained fitting) problem and solved finally by formulating a Linear Program (LP). A bound on the Generalization Error of this approach is given in terms of the Leave-One-Out Error. The accuracy and utility of LP-SLGNs is assessed quantitatively and qualitatively using simulated and real data. The Dialogue for Reverse Engineering Assessments and Methods (DREAM) initiative provides gold standard data sets and evaluation metrics that enable and facilitate the comparison of algorithms for deducing the structure of networks. The structures of LP-SLGNs estimated from the INSILICO1, INSILICO2 and INSILICO3 simulated DREAM2 data sets are comparable to those proposed by the first and/or second ranked teams in the DREAM2 competition. The structures of LP-SLGNs estimated from two published Saccharomyces cerevisae cell cycle transcript profiling data sets capture known regulatory associations. In each S. cerevisiae LP-SLGN, the number of nodes with a particular degree follows an approximate power law suggesting that its degree distributions is similar to that observed in real-world networks. Inspection of these LP-SLGNs suggests biological hypotheses amenable to experimental verification. Conclusion: A statistically robust and computationally efficient LP-based method for estimating the topology of a large sparse undirected graph from high-dimensional data yields representations of genetic networks that are biologically plausible and useful abstractions of the structures of real genetic networks. Analysis of the statistical and topological properties of learned LP-SLGNs may have practical value; for example, genes with high random walk betweenness, a measure of the centrality of a node in a graph, are good candidates for intervention studies and hence integrated computational – experimental investigations designed to infer more realistic and sophisticated probabilistic directed graphical model representations of genetic networks. The LP-based solutions of the sparse linear regression problem described here may provide a method for learning the structure of transcription factor networks from transcript profiling and transcription factor binding motif data.

The process of technological innovations in small enterprises: the Indian way

This paper probes how two small foundries in Belgaum, Karnataka State, India, have achieved technological innovations successfully based on their technological capability and customer needs, enabling them to sail through the competitive environment. This study brought out that technically qualified entrepreneurs of both the foundries have carried out technological innovations, mainly due to their self-motivation and self-efforts. Changing product designs, as desired or directed by the customers, cost reduction, quality improvement and import substitution through reverse engineering are the characteristics of these technological innovations. These incremental innovations have enabled the entrepreneurs of the two foundries to enhance competitiveness, grow in the domestic market and penetrate the international market and grow in size over time.

The process of technological innovations in small enterprises: the Indian way

This paper probes how two small foundries in Belgaum, Karnataka State, India, have achieved technological innovations successfully based on their technological capability and customer needs, enabling them to sail through the competitive environment. This study brought out that technically qualified entrepreneurs of both the foundries have carried out technological innovations, mainly due to their self-motivation and self-efforts. Changing product designs, as desired or directed by the customers, cost reduction, quality improvement and import substitution through reverse engineering are the characteristics of these technological innovations. These incremental innovations have enabled the entrepreneurs of the two foundries to enhance competitiveness, grow in the domestic market and penetrate the international market and grow in size over time.

Forming Networks of Strategic Agents with Desired Topologies

Many networks such as social networks and organizational networks in global companies consist of self-interested agents. The topology of these networks often plays a crucial role in important tasks such as information diffusion and information extraction. Consequently, growing a stable network having a certain topology is of interest. Motivated by this, we study the following important problem: given a certain desired network topology, under what conditions would best response (link addition/deletion) strategies played by self-interested agents lead to formation of a stable network having that topology. We study this interesting reverse engineering problem by proposing a natural model of recursive network formation and a utility model that captures many key features. Based on this model, we analyze relevant network topologies and derive a set of sufficient conditions under which these topologies emerge as pairwise stable networks, wherein no node wants to delete any of its links and no two nodes would want to create a link between them.

Sufficient conditions for formation of a network topology by self-interested agents

Networks such as organizational network of a global company play an important role in a variety of knowledge management and information diffusion tasks. The nodes in these networks correspond to individuals who are self-interested. The topology of these networks often plays a crucial role in deciding the ease and speed with which certain tasks can be accomplished using these networks. Consequently, growing a stable network having a certain topology is of interest. Motivated by this, we study the following important problem: given a certain desired network topology, under what conditions would best response (link addition/deletion) strategies played by self-interested agents lead to formation of a pairwise stable network with only that topology. We study this interesting reverse engineering problem by proposing a natural model of recursive network formation. In this model, nodes enter the network sequentially and the utility of a node captures principal determinants of network formation, namely (1) benefits from immediate neighbors, (2) costs of maintaining links with immediate neighbors, (3) benefits from indirect neighbors, (4) bridging benefits, and (5) network entry fee. Based on this model, we analyze relevant network topologies such as star graph, complete graph, bipartite Turan graph, and multiple stars with interconnected centers, and derive a set of sufficient conditions under which these topologies emerge as pairwise stable networks. We also study the social welfare properties of the above topologies.

Using Relationships for Matching Textual Domain Models with Existing Code

We address the task of mapping a given textual domain model (e.g., an industry-standard reference model) for a given domain (e.g., ERP), with the source code of an independently developed application in the same domain. This has applications in improving the understandability of an existing application, migrating it to a more flexible architecture, or integrating it with other related applications. We use the vector-space model to abstractly represent domain model elements as well as source-code artifacts. The key novelty in our approach is to leverage the relationships between source-code artifacts in a principled way to improve the mapping process. We describe experiments wherein we apply our approach to the task of matching two real, open-source applications to corresponding industry-standard domain models. We demonstrate the overall usefulness of our approach, as well as the role of our propagation techniques in improving the precision and recall of the mapping task.

Algoritmos multi-objetivos para la optimización de una secuencia de matrices generadoras en computación cuántica topológica

Quantum Computing is a relatively modern field which simulates quantum computation conditions. Moreover, it can be used to estimate which quasiparticles would endure better in a quantum environment. Topological Quantum Computing (TQC) is an approximation for reducing the quantum decoherence problem1, which is responsible for error appearance in the representation of information. This project tackles specific instances of TQC problems using MOEAs (Multi-objective Optimization Evolutionary Algorithms). A MOEA is a type of algorithm which will optimize two or more objectives of a problem simultaneously, using a population based approach. We have implemented MOEAs that use probabilistic procedures found in EDAs (Estimation of Distribution Algorithms), since in general, EDAs have found better solutions than ordinary EAs (Evolutionary Algorithms), even though they are more costly. Both, EDAs and MOEAs are population-based algorithms. The objective of this project was to use a multi-objective approach in order to find good solutions for several instances of a TQC problem. In particular, the objectives considered in the project were the error approximation and the length of a solution. The tool we used to solve the instances of the problem was the multi-objective framework PISA. Because PISA has not too much documentation available, we had to go through a process of reverse-engineering of the framework to understand its modules and the way they communicate with each other. Once its functioning was understood, we began working on a module dedicated to the braid problem. Finally, we submitted this module to an exhaustive experimentation phase and collected results.

Bloqueo de publicidad en la Web: enfoque técnico en la búsqueda de un compromiso entre anunciantes y lectores

[ES]Este proyecto trata el problema del bloqueo de anuncios que existe actualmente en la web. Teniendo en cuenta la opinión de diversos autores sobre el tema, se analiza la problemática del uso de bloqueadores de anuncios. Además, se estudia cómo funcionan estos bloqueadores. En concreto, se analiza cómo está construido y cómo funciona, mediante ingeniería inversa, la extensión más popular en este campo, es decir, AdBlock Plus. Aparte de esto, se proponen una serie de soluciones para atacar al problema. Por último, se desarrolla e implementa una de las propuestas. Como resultado, se mejora el funcionamiento de AdBlock Plus, en el sentido de que da más libertad al usuario para elegir lo que bloquea dando la oportunidad a anunciantes y proveedores de contenido de mantener su modelo de negocio basado en la publicidad.

土石混合体细观结构力学及其边坡稳定性研究

Soil-rock mixture (S-RM) refers to one extremely uneven loose rock and soil materials system with certain stone content. Its formation has started since Quaternary and it is composed of block stone, fine grained soil and pore with certain project scale and high strength. S-RM has extensive distribution in nature, especially in southwest China where the geotectonic background is complicated, the fracture activity is developed and the geomorphological characteristics of high mountain and steep gorge area are protuberant. This kind of complicated geologic body has developed wider in these areas. S-RM has obvious difference with the general soil or rock (rock mass) in physical and mechanical properties because its two components-“soil” and “rock-block” has extreme differences in physical and mechanical properties. The proposition of S-RM and its deep research are needed in the modern engineering construction. It is also the necessity in the modern development of rock and soil mechanics. The dissertation starts from the meso-structural characteristics of soil-rock and takes a systematic research on its meso-structural mechanics, deformation and failure mechanism and the stability of S-RM slope. In summary, it achieves the following innovative results and conclusions. There are various views on the conception of S-RM and its classification system. Based on the large number of field tests, the dissertation makes the conception and classification of S-RM more systematic. It systematically proposed the conception of meso-structural mechanics of S-RM. Thus the dissertation has laid a foundation for its deep study. With the fast development of the computer technology and digital image processing theory, digital image processing technology has been successfully applied in many fields and provided reliable technology support for the quantitative description of the structural characteristics of S-RM. Based on the digital image processing technology, the dissertation systematically proposes and developed the quantitative analysis method and quantitative index for the meso-structure of S-RM. The results indicate that the meso-structure such as its internal soil-rock granularity composition, the soil-rock shape and the orientability has obvious self-organization in the macro statistical level. The dissertation makes a systematic research on the physical mechanical properties, deformation and failure mechanism of S-RM based on large field test. It proposes the field test for the underwater S-RM and deduces the 3D data analysis method of in-situ horizontal push-shear test. The result indicates that S-RM has significant phenomenon of shear dilatancy in the shearing process, and its dilatancy will be more obvious with the increased proportion of rock or the decreased confining pressure. The proportion of rock has great effect on the strength of S-RM and rock-block, especially the spatial position of particles with comparatively big size has great effect on the shape and spatial position of the sample shear zone. The dissertation makes some improvements in the single ring infiltration test equipment and its application on the permeability of S-RM. The results indicate that the increasing of rock-block would make it more difficult for the soil to fill in the vacuity between the rock-block and the proportion would increase which would result in the increased permeability coefficient. The dissertation builds the real meso-structural model of S-RM based on the digital image processing technology. By using geometric reconstruction technology, it transfers the structural mode represented by Binary image into CAD format, which makes it possible to introduce the present finite element analysis software to take research on numerical experimental investigation. It systematically realizes leaping research from the image，geometric mode, to meso-structural mechanics numerical experiment. By using this method, the dissertation takes large scale numerical direct-shear test on the section of S-RM. From the mesoscopic perspective, it reveals three extended modes about the shear failure plane of S-RM. Based on the real meso-structural model and by using the numerical simulation test, the character and mechanics of seepage failure of S-RM are studied. At the same time, it builds the real structural mode of the slope based on the analysis about the slope crosssection of S-RM. By using the strength reduction method, it takes the research on the stability of S-RM and gets great achievements. The three dimensional geometric reconstruction technology of rock block is proposed, which provides technical support for the reconstruction of the 3D meso-structural model of S-RM. For the first time, the dissertation builds the stochastic structure model of two-dimensional and three-dimensional polygons or polyhedron based on the stochastic simulation technique of monte carlo method. It breaks the traditional research which restricted to the random generation method of regular polygon and develops the relevant software system (R-SRM2D/3D) which has great effect on meso-structural mechanics of S-RM. Based on the R-SRM software system which randomly generates the meso-structural mode of S-RM according to the different meso-structural characteristics, the dissertation takes a series of research on numerical test of dual axis and real three-axis, systematically analyses the meso destroy system, the effects of meso-structural characteristics such as on the stone content, size composition and block directionality on the macro mechanical behavior and macro-permeability. Then it proposes the expression of the upper and lower limit for the macro-permeability coefficient of the inhomogeneous geomaterials, such as S-RM. By using the strength reduction FEM, the dissertation takes the research on the stability of the slope structural mode of the randomly formed S-RM. The results indicate that generally, the stability coefficient of S-RM slope increases with the increasing of stone content; on the condition of the same stone content, the stability coefficient of slope will be different with different size composition and the space position of large block at the internal slop has great effect on the stability. It suggests that meso-structural characteristics, especially the space position of large block should be considered when analyzing the stability of this kind of slope and strengthening design. Taking Xiazanri S-RM slope as an example, the dissertation proposes the fine modeling of complicated geologic body based on reverse engineering and the generation method of FLAC3D mode. It resolves the bottleneck problem about building the fine structural mode of three-dimensional geological body. By using FLAC3D, the dissertation takes research on the seepage field and the displacement field of Xiazanri S-RM slope in the process of reservoir water level rising and decreasing. By using strength reduction method, it analyses the three-dimension stability in the process of reservoir water level rising and decreasing. The results indicate that the slope stability firstly show downward trend in the process of reservoir water level rising and then rebound to increase; the sudden drawdown of reservoir water level has great effect on the slope stability and this effect will increase with the sudden drawdown amplitude rising. Based on the result of the rock block size analysis of S-RM, and using R-SRM2D the stochastic structure model of Xiazanri S-RM slope is built. By using strength reduction method, the stability of the stochastic structure model is analysis, the results shows that the stability factor increases significantly after considering the block.

Automated Program Recognition by Graph Parsing

Recognizing standard computational structures (cliches) in a program can help an experienced programmer understand the program. We develop a graph parsing approach to automating program recognition in which programs and cliches are represented in an attributed graph grammar formalism and recognition is achieved by graph parsing. In studying this approach, we evaluate our representation's ability to suppress many common forms of variation which hinder recognition. We investigate the expressiveness of our graph grammar formalism for capturing programming cliches. We empirically and analytically study the computational cost of our recognition approach with respect to two medium-sized, real-world simulator programs.

Recognition of Planar Segments in Point Cloud Based on Wavelet Transform

© 2005-2012 IEEE.Within industrial automation systems, three-dimensional (3-D) vision provides very useful feedback information in autonomous operation of various manufacturing equipment (e.g., industrial robots, material handling devices, assembly systems, and machine tools). The hardware performance in contemporary 3-D scanning devices is suitable for online utilization. However, the bottleneck is the lack of real-time algorithms for recognition of geometric primitives (e.g., planes and natural quadrics) from a scanned point cloud. One of the most important and the most frequent geometric primitive in various engineering tasks is plane. In this paper, we propose a new fast one-pass algorithm for recognition (segmentation and fitting) of planar segments from a point cloud. To effectively segment planar regions, we exploit the orthonormality of certain wavelets to polynomial function, as well as their sensitivity to abrupt changes. After segmentation of planar regions, we estimate the parameters of corresponding planes using standard fitting procedures. For point cloud structuring, a z-buffer algorithm with mesh triangles representation in barycentric coordinates is employed. The proposed recognition method is tested and experimentally validated in several real-world case studies.

Computational Journalism: from Answering Question to Questioning Answers and Raising Good Questions

Our media is saturated with claims of ``facts'' made from data. Database research has in the past focused on how to answer queries, but has not devoted much attention to discerning more subtle qualities of the resulting claims, e.g., is a claim ``cherry-picking''? This paper proposes a Query Response Surface (QRS) based framework that models claims based on structured data as parameterized queries. A key insight is that we can learn a lot about a claim by perturbing its parameters and seeing how its conclusion changes. This framework lets us formulate and tackle practical fact-checking tasks --- reverse-engineering vague claims, and countering questionable claims --- as computational problems. Within the QRS based framework, we take one step further, and propose a problem along with efficient algorithms for finding high-quality claims of a given form from data, i.e. raising good questions, in the first place. This is achieved to using a limited number of high-valued claims to represent high-valued regions of the QRS. Besides the general purpose high-quality claim finding problem, lead-finding can be tailored towards specific claim quality measures, also defined within the QRS framework. An example of uniqueness-based lead-finding is presented for ``one-of-the-few'' claims, landing in interpretable high-quality claims, and an adjustable mechanism for ranking objects, e.g. NBA players, based on what claims can be made for them. Finally, we study the use of visualization as a powerful way of conveying results of a large number of claims. An efficient two stage sampling algorithm is proposed for generating input of 2d scatter plot with heatmap, evalutaing a limited amount of data, while preserving the two essential visual features, namely outliers and clusters. For all the problems, we present real-world examples and experiments that demonstrate the power of our model, efficiency of our algorithms, and usefulness of their results.

Management in distributed systems: A semi-formal approach

The reverse engineering of a skeleton based programming environment and redesign to distribute management activities of the system and thereby remove a potential single point of failure is considered. The Ore notation is used to facilitate abstraction of the design and analysis of its properties. It is argued that Ore is particularly suited to this role as this type of management is essentially an orchestration activity. The Ore specification of the original version of the system is modified via a series of semi-formally justified derivation steps to obtain a specification of the decentralized management version which is then used as a basis for its implementation. Analysis of the two specifications allows qualitative prediction of the expected performance of the derived version with respect to the original, and this prediction is borne out in practice.

Análise de um veículo todo o terreno do tipo KARTCROSS

O presente trabalho descreve a análise feita a um veículo de todo o terreno. O kartcross/buggy em estudo é usado em provas do tipo Baja, sendo estas provas longas e com traçados sinuosos. O veículo, já construído, foi testado através de softwares, a nível estrutural e ciclístico, pretendendo-se assim efetuar engenharia inversa sobre o mesmo. No decorrer da sua utilização normal o kartcross/buggy sofre vários tipos de solicitações, como sejam aceleração, travagem e força centrípta em curva. Portanto, o veículo deve ser capaz de suportar estes esforços e ter uma boa habilidade. Além dos testes em uso corrente foi analisada também a rigidez torsional do quadro do veículo e do veículo completo, podendo-se assim melhorar estes valores. A nível ciclístico foram analisados os parâmetros das suspensões como o camber, convergência/divergência, caster, entre outros. Da análise destes parâmetros e possível fazerem-se melhorias de forma a que o veículo tenha um melhor desempenho. Para validar os testes computacionais efetuados foi reproduzido experimentalmente o teste da rigidez torsional. No final, compararam-se os valores numéricos com os experimentais e aferir se o modelo se encontra bem representado.

Rétro-ingénierie des diagrammes de séquence par visualisation interactive

Nous proposons une approche semi-automatique pour la rétro-ingénierie des diagrammes de séquence d’UML. Notre approche commence par un ensemble de traces d'exécution qui sont automatiquement alignées pour déterminer le comportement commun du système. Les diagrammes de séquence sont ensuite extraits avec l’aide d’une visualisation interactive, qui permet la navigation dans les traces d'exécution et la production des opérations d'extraction. Nous fournissons une illustration concrète de notre approche avec une étude de cas, et nous montrons en particulier que nos diagrammes de séquence générés sont plus significatifs et plus compacts que ceux qui sont obtenus par les méthodes automatisées.