1782369
Designing and executing scientific workflows with a programmable integrator
MOTIVATION
As in many other fields of science, computational methods in molecular biology need to intersperse information access and algorithm execution in a computational workflow. Users often find difficulties when transferring data between data sources and applications. In most cases there is no standard solution for workflow design and execution and tailored scripting mechanisms are implemented in a case by case basis.


RESULTS
In this paper, we present a general purpose 'programmable integrator' that can access information from a variety of sources in a coordinated manner. Its usefulness in complex bioinformatics applications is claimed and supported by some application examples.


AVAILABILITY
Tools are freely available to non-profit educations and research institutions. Usage by commercial organizations requires a license agreement. Software requirements: Java v1.3 (http://java.sun.com), Xerces XML Parser (http://xml.apache.org/xerces-j) and Kweelt implementation of XQuery (http://kweelt.sourceforge.net/).
14666453
An Interpolated Volume Data Model
Publisher Summary This chapter explores the basic functionality of the volume data model. It considers examples from biology and volumes of measurement from quantum physics. The data model is similar in the two cases, but the operations that are commonly used are quite different. In the second case, for instance, one is often interested in conditions on the behavior of local differential operators, such as zero-flow surfaces, while in the biological case one has a mix of value conditions and geometric condition. With these two application fields, this chapter highlights the generality and flexibility of the model. The system is based on a commercial database, augmented with specialized functions to manipulate the volume data model. The chapter demonstrates various operations specifying queries both using a graphical user interface and entering them directly in structured query language (SQL) augmented with the volume algebra operations.
2635468
A System for Managing Alternate Models in Model-Based Mediation
In [1,3], we have described the problem of model-based mediation (MBM) as an extension of the global-as-view paradigm of information integration. The need for this extension arises in many application domains where the information sources to be integrated not only differ in their export formats, data models, and query capabilities, but have widely different schema with very little overlap in attributes. In scientific applications, the information sources come from different subdisciplines, and despite their poorly overlapping schema, can be integrated because they capture different aspects of the same scientific objects or phenomena, and can be conceptually integrated due to scientific reasons. In the MBM paradigm, a “mediation engineer” consults with domain experts to explicitly model the “glue knowledge” using a set of facts and rules at the mediator. Integrated views are defined in MBM on top of the exported schemas from the information sources together with the glue knowledge source that ties them together. We have successfully applied the MBM technique to develop the KIND mediator or Neuroscience information sources [1]-[4]. To accomplish this, sources in the MBM framework export their conceptual models (CMs), consisting of the logical schema, domain constraints, and object contexts, i.e., formulas that relate their conceptual schema with the global domain knowledge maintained at the mediator. Thus model-based mediation has a hybrid approach to information integration - on the one hand at the mediator integrated views are defined over source CMs and the Knowledge Map using a global-as-view approach; on the other hand, object-contexts of the source are defined as local-as-view.
28954888
Modeling shape and topology of 3D images of biological specimens
This paper presents an efficient way of representing the geometry and topology of 3D images of biological specimens derived from electron microscopy. A vector quantization algorithm is used in order to select a reduced set of interior points that best approximates the probability density function of the original volumetric data. Object's geometry and topology are obtained from the point set by the use of the alpha shapes theory.
9743987
Complex Visual Activity Recognition Using a Temporally Ordered Database
We propose using a temporally ordered database for complex visual activity recognition. We use a temporal precedence relation together with the assumption of fixed bounded temporal uncertainty of occurrence time of an atomic activity and comparatively large temporal extent of the complex activity. Under these conditions we identify the temporal structure of complex activities as a semiorder and design a database that has semiorder as its data model. A query algebra is then defined for this data model.
8323337
Modeling Functional Data Sources as Relations
In this paper we present a model of functional access to data that, we argue, is suitable for modeling a class of data repositories characterized by functional access, such as web sites. We discuss the problem of modeling such data sources as a set of relations, of determining whether a given query expressed on these relations can be translated into a combination of functions defined by the data sources, and of finding an optimal plan to do so.
11198288
Why the Information Explosion Can Be Bad for Data Mining, and How Data Fusion Provides a Way Out
One may claim that the exponential growth in the amount of data provides great opportunities for data mining. Reality can be different though. In many real world applications, the number of sources over which this information is fragmented grows at an even faster rate, resulting in barriers to widespread application of data mining and missed business opportunities. Let us illustrate this paradox with a motivating example from database marketing. In marketing, direct forms of communication are becoming increasingly popular. Instead of broadcasting a single message to all customers through traditional mass media such as television and print, the most promising potential customers receive personalized offers through the most appropriate channels. So it becomes more important to gather information about media consumption, attitudes, product propensity etc. at an individual level. Basic, company specific customer information resides in customer databases, but market survey data depicting a richer view of the customer are only available for a small sample or a disjoint set of reference customers. Collecting all this information for the whole customer database in a single source survey would certainly be valuable but is usually a very expensive proposition. The common alternative within business to
8665183
Dynamic detection and removal of inactive clauses in SAT with application in image computation
In this paper, we present a new technique for the efficient dynamic detection and removal of inactive clauses, i.e. clauses that do not affect the solutions of interest of a Boolean satisfiability (SAT) problem. The algorithm is based on the extraction of gate connectivity information during generation of the Boolean formula from the circuit, and its use in the inner loop of a branch-and-bound SAT algorithm. The motivation for this optimization is to exploit the circuit structure information, which can be used to find unobservable gates at circuit outputs under dynamic conditions. It has the potential to speed up all applications of SAT in which the SAT formula is derived from a logic circuit. In particular, we find that it has considerable impact on an image computation algorithm based on SAT. We present practical results for benchmark circuits which show that the use of this optimization consistently improves the performance for reachability analysis, in some cases enabling the prototype tool to reach more states than otherwise possible.
2125509
Improved results for directed multicut
We give a simple algorithm for the Minimum Directed Multicut problem, and show that it gives an <i>O</i>(√<i>n</i>)-approximation. This improves on the previous approximation guarantee of <i>O</i>(√<i>n</i> log <i>k</i>) of Cheriyan, Karloff and Rabani [1], which was obtained by a more sophisticated algorithm.
100323
Tree based MPLS routing
MPLS (MultiProtocol Label Switching) is a new technology proposed by the IETF [4,10] for network routing, and is being increasingly deployed by the largest Internet service providers. The MPLS technology differs from conventional network protocols in a crucial way: instead of reading the entire packet header at all switching points, the analysis of the packet header is done just once, when the packet header is assigned a stack of labels, and thenceforth, each switching point or router just gets to look at the label at the top of the stack (and the ingress edge), and based only on this information, it has to make a decision about the next-hop node [17,16]. In another departure from conventional routing and in particular from IP source routing, where the entire packet route is explicitly put in the header and popped off along the route, the router can not only pop the top label, it can push other labels on top of the stack.The two parameters of interest in designing MPLS routing protocols are the number of labels used, and the depth of the stack used for routing. Clearly, both cannot be simultaneously minimized, and there is often an interesting trade-off between label size and stack depth: it is obvious that if k labels are used, one must have a stack depth of logk n.In fact, it was not known whether this bound could be achieved even for trees; the best stack depth previously achieved with a constant number of labels was O(log2 n). In this paper, we show that one can indeed get asymptotically optimal upper bounds and route on trees using k labels and a maximum stack depth of O(logk n), and that this trade-off can be achieved using a simpler and more intuitive protocol than the one given in [9]. These tree-routing ideas are then shown to give better routing protocols for planar graphs as well. In particular, we show how to route along near-shortest paths (of length at most (1 + ε) times the shortest-path) with O(log2 n/ε) labels and logarithmic stack depth. We also apply them to graphs with smaller separators, including most large ISP networks.
18557537
Localization and Register Sharing for Predicate Abstraction
In the domain of software verification, predicate abstraction has emerged to be a powerful and popular technique for extracting finite-state models from often complex source code. In this paper, we report on the application of three techniques for improving the performance of the predicate abstraction refinement loop. The first technique allows faster computation of the abstraction. Instead of maintaining a global set of predicates, we find predicates relevant to various basic blocks of the program by weakest pre-condition propagation along spurious program traces. The second technique enables faster model checking of the abstraction by reducing the number of state variables in the abstraction. This is done by re-using Boolean variables to represent different predicates in the ion. However, some predicates are useful at many program locations and discovering them lazily in various parts of the program leads to a large number of abstraction refinement iterations. The third technique attempts to identify such predicates early in the abstraction refinement loop and handles them separately by introducing dedicated state variables for such predicates. We have incorporated these techniques into NEC's software verification tool F-SOFT, and present promising experimental results for various case studies using these techniques.