Eutils-search - manual do usuário.

O software Eutils-search tem por objetivo trazer do banco de dados PubMed informações sobre artigos relacionados a genes de um organismo específico, de acordo com as regras referentes à taxa de acesso impostas pelo site. As informações trazidas são, então, armazenadas localmente em um banco de dados para acesso rápido. Além disso, o software também gera documentos XML correspondentes às informações do organismo requisitado. O eutils-search é uma ferramenta de apoio ao desenvolvimento de aplicações de mineração de textos voltadas para os domínios de biotecnologia e biologia molecular, baseada em informações textuais obtidas do banco de dados PubMed. Este documento apresenta os pré-requisitos e a descrição dos parâmetros necessários para utilização do software, bem como uma descrição de alguns aspectos internos do software, para melhor entendimento do processo que ele automatiza, além de alguns exemplos e uso.

A dichotomic search algorithm for mining and learning in domain-specific logics

Ferr?, S. and King, R. D. (2004) A dichotomic search algorithm for mining and learning in domain-specific logics. Fundamenta Informaticae. IOS Press. To appear

A Framework for the Scoring of Operators on the Search Space of Equivalence Classes of Bayesian Network Structures

R. Daly and Q. Shen. A Framework for the Scoring of Operators on the Search Space of Equivalence Classes of Bayesian Network Structures. Proceedings of the 2005 UK Workshop on Computational Intelligence, pages 67-74.

A tale untold: The Search for a Story in Byron's Lara

Shears, J. (2006). A tale untold: The Search for a Story in Byron's Lara. The Byron Journal. 34(1), pp.1-8. RAE2008

Dedicated global optimization search for ground state silica nanoclusters: (SiO2)(N) (N=6-12)

Flikkema, E., & Bromley, S. T. (2004). Dedicated global optimization search for ground state silica nanoclusters: (SiO2)(N) (N=6-12). Journal of Physical Chemistry B, 108 (28), 9638-9645. RAE2008

Search/ing for missing people: families living with ambiguous absence

Families of missing people are often understood as inhabiting a particular space of ambiguity, captured in the phrase ‘living in limbo’ (Holmes, 2008). To explore this uncertain ground, we interviewed 25 family members to consider how human absence is acted upon and not just felt within this space ‘in between’ grief and loss (Wayland, 2007). In the paper, we represent families as active agents in spatial stories of ‘living in limbo’, and we provide insights into the diverse strategies of search/ing (technical, physical and emotional) in which they engage to locate either their missing member or news of them. Responses to absence are shown to be intimately bound up with unstable spatial knowledges of the missing person and emotional actions that are subject to change over time. We suggest that practices of search are not just locative actions, but act as transformative processes providing insights into how families inhabit emotional dynamism and transition in response to the on-going ‘missing situation’ and ambiguous loss (Boss, 1999, 2013).

Beyond Myth: in Search of Archaic Greek Theology

The author examines several passages from Homer, Hesiod and the Hymns for content appropriate for religious instruction, a function both traditionally attributed to those works (by Herodotus) and denied them (at the earliest, by Xenophanes). The issues cover theodicy, the nature of deities and their honours, the efficacy of prayer and the meaning of sacrifices and food offering.

Search by Shape Examples: Modeling Nonrigid Deformation

We describe our work on shape-based image database search using the technique of modal matching. Modal matching employs a deformable shape decomposition that allows users to select example objects and have the computer efficiently sort the set of objects based on the similarity of their shape. Shapes are compared in terms of the types of nonrigid deformations (differences) that relate them. The modal decomposition provides deformation "control knobs" for flexible matching and thus allows for selecting weighted subsets of shape parameters that are deemed significant for a particular category or context. We demonstrate the utility of this approach for shape comparison in 2-D image databases; however, the general formulation is applicable to signals of any dimensionality.

On the Effectiveness of Genetic Search in Combinatorial Optimization

In this paper, we study the efficacy of genetic algorithms in the context of combinatorial optimization. In particular, we isolate the effects of cross-over, treated as the central component of genetic search. We show that for problems of nontrivial size and difficulty, the contribution of cross-over search is marginal, both synergistically when run in conjunction with mutation and selection, or when run with selection alone, the reference point being the search procedure consisting of just mutation and selection. The latter can be viewed as another manifestation of the Metropolis process. Considering the high computational cost of maintaining a population to facilitate cross-over search, its marginal benefit renders genetic search inferior to its singleton-population counterpart, the Metropolis process, and by extension, simulated annealing. This is further compounded by the fact that many problems arising in practice may inherently require a large number of state transitions for a near-optimal solution to be found, making genetic search infeasible given the high cost of computing a single iteration in the enlarged state-space.

World Wide Web Image Search Engines

We propose the development of a world wide web image search engine that crawls the web collecting information about the images it finds, computes the appropriate image decompositions and indices, and stores this extracted information for searches based on image content. Indexing and searching images need not require solving the image understanding problem. Instead, the general approach should be to provide an arsenal of image decompositions and discriminants that can be precomputed for images. At search time, users can select a weighted subset of these decompositions to be used for computing image similarity measurements. While this approach avoids the search-time-dependent problem of labeling what is important in images, it still holds several important problems that require further research in the area of query by image content. We briefly explore some of these problems as they pertain to shape.

Image Digestion and Relevance Feedback in the ImageRover WWW Search Engine

ImageRover is a search by image content navigation tool for the world wide web. The staggering size of the WWW dictates certain strategies and algorithms for image collection, digestion, indexing, and user interface. This paper describes two key components of the ImageRover strategy: image digestion and relevance feedback. Image digestion occurs during image collection; robots digest the images they find, computing image decompositions and indices, and storing this extracted information in vector form for searches based on image content. Relevance feedback occurs during index search; users can iteratively guide the search through the selection of relevant examples. ImageRover employs a novel relevance feedback algorithm to determine the weighted combination of image similarity metrics appropriate for a particular query. ImageRover is available and running on the web site.

Indexing Distances in Large Graphs and Applications in Search Tasks

This thesis elaborates on the problem of preprocessing a large graph so that single-pair shortest-path queries can be answered quickly at runtime. Computing shortest paths is a well studied problem, but exact algorithms do not scale well to real-world huge graphs in applications that require very short response time. The focus is on approximate methods for distance estimation, in particular in landmarks-based distance indexing. This approach involves choosing some nodes as landmarks and computing (offline), for each node in the graph its embedding, i.e., the vector of its distances from all the landmarks. At runtime, when the distance between a pair of nodes is queried, it can be quickly estimated by combining the embeddings of the two nodes. Choosing optimal landmarks is shown to be hard and thus heuristic solutions are employed. Given a budget of memory for the index, which translates directly into a budget of landmarks, different landmark selection strategies can yield dramatically different results in terms of accuracy. A number of simple methods that scale well to large graphs are therefore developed and experimentally compared. The simplest methods choose central nodes of the graph, while the more elaborate ones select central nodes that are also far away from one another. The efficiency of the techniques presented in this thesis is tested experimentally using five different real world graphs with millions of edges; for a given accuracy, they require as much as 250 times less space than the current approach which considers selecting landmarks at random. Finally, they are applied in two important problems arising naturally in large-scale graphs, namely social search and community detection.

Search Space Reduction in QoS Routing

To provide real-time service or engineer constrained-based paths, networks require the underlying routing algorithm to be able to find low-cost paths that satisfy given Quality-of-Service (QoS) constraints. However, the problem of constrained shortest (least-cost) path routing is known to be NP-hard, and some heuristics have been proposed to find a near-optimal solution. However, these heuristics either impose relationships among the link metrics to reduce the complexity of the problem which may limit the general applicability of the heuristic, or are too costly in terms of execution time to be applicable to large networks. In this paper, we focus on solving the delay-constrained minimum-cost path problem, and present a fast algorithm to find a near-optimal solution. This algorithm, called DCCR (for Delay-Cost-Constrained Routing), is a variant of the k-shortest path algorithm. DCCR uses a new adaptive path weight function together with an additional constraint imposed on the path cost, to restrict the search space. Thus, DCCR can return a near-optimal solution in a very short time. Furthermore, we use the method proposed by Blokh and Gutin to further reduce the search space by using a tighter bound on path cost. This makes our algorithm more accurate and even faster. We call this improved algorithm SSR+DCCR (for Search Space Reduction+DCCR). Through extensive simulations, we confirm that SSR+DCCR performs very well compared to the optimal but very expensive solution.

View-Invariant Object Category Learning, Recognition, and Search: How Spatial and Object Attention Are Coordinated Using Surface-Based Attentional Shrouds

Air Force Office of Scientific Research (F49620-01-1-0397); National Science Foundation (SBE-0354378); Office of Naval Research (N00014-01-1-0624)

Cortical Dynamics of Contextually-Cued Attentive Visual Learning and Search: Spatial and Object Evidence Accumulation

How do humans use predictive contextual information to facilitate visual search? How are consistently paired scenic objects and positions learned and used to more efficiently guide search in familiar scenes? For example, a certain combination of objects can define a context for a kitchen and trigger a more efficient search for a typical object, such as a sink, in that context. A neural model, ARTSCENE Search, is developed to illustrate the neural mechanisms of such memory-based contextual learning and guidance, and to explain challenging behavioral data on positive/negative, spatial/object, and local/distant global cueing effects during visual search. The model proposes how global scene layout at a first glance rapidly forms a hypothesis about the target location. This hypothesis is then incrementally refined by enhancing target-like objects in space as a scene is scanned with saccadic eye movements. The model clarifies the functional roles of neuroanatomical, neurophysiological, and neuroimaging data in visual search for a desired goal object. In particular, the model simulates the interactive dynamics of spatial and object contextual cueing in the cortical What and Where streams starting from early visual areas through medial temporal lobe to prefrontal cortex. After learning, model dorsolateral prefrontal cortical cells (area 46) prime possible target locations in posterior parietal cortex based on goalmodulated percepts of spatial scene gist represented in parahippocampal cortex, whereas model ventral prefrontal cortical cells (area 47/12) prime possible target object representations in inferior temporal cortex based on the history of viewed objects represented in perirhinal cortex. The model hereby predicts how the cortical What and Where streams cooperate during scene perception, learning, and memory to accumulate evidence over time to drive efficient visual search of familiar scenes.