10145188
Towards a formalization of disease-specific ontologies for neuroinformatics
We present issues arising when trying to formalize disease maps, i.e. ontologies to represent the terminological relationships among concepts necessary to construct a knowledge-base of neurological disorders. These disease maps are being created in the context of a large-scale data mediation system being created for the Biomedical Informatics Research Network (BIRN). The BIRN is a multi-university consortium collaborating to establish a large-scale data and computational grid around neuroimaging data, collected across multiple scales. Test bed projects within BIRN involve both animal and human studies of Alzheimer's disease, Parkinson's disease and schizophrenia. Incorporating both the static 'terminological' relationships and dynamic processes, disease maps are being created to encapsulate a comprehensive theory of a disease. Terms within the disease map can also be connected to the relevant terms within other ontologies (e.g. the Unified Medical Language System), in order to allow the disease map management system to derive relationships between a larger set of terms than what is contained within the disease map itself. In this paper, we use the basic structure of a disease map we are developing for Parkinson's disease to illustrate our initial formalization for disease maps.
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.
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.
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.
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.
8374849
Quorum placement in networks to minimize access delays
A quorum system is a family of sets (themselves called quorums), each pair of which intersect. In many distributed algorithms, the basic unit accessed by a client is a quorum of nodes. Such algorithms are used for applications such as mutual exclusion, data replication, and dissemination of information. However, accessing spread-out quorums causes access delays that we would like to minimize. Furthermore, every member of the quorum incurs processing load to handle quorum accesses by clients.In this paper we study the problem of placing quorums in a physical network so as to minimize the delay that clients incur by accessing quorums, and while respecting each physical node's capacity (in terms of the load of client requests it can handle). We provide approximation algorithms for this problem for two natural measures of delay (the max-delay and total-delay). All our algorithms ensure that each node's load is within a constant factor of its capacity, and minimize delay to within a constant factor of the optimal delay for all capacity-respecting solutions. We also provide better approximations for several well-known quorum systems.
3246043
Parallel organization and performance of an information system
This paper investigates a directory structure, based on an M-B-T directory, that provides for parallel retrieval of information with low communication overhead. An information system of documents is assumed. It is compatible with current automatic retrieval and query processing techniques. It is also compatible with any organization of the documents. Weights that are assigned to keywords can be included in the directory with the keywords at no additional cost. In addition, it provides for indexing a secondary keyword within a primary keyword with no additional cost. Given a p-processor massively parallel computer, our organization allows a maximum of p retrievals to be performed concurrently and thus achieves an approximate speed up of p in the best case. The new, revised organization improves on previous work. An eecient parallel searching algorithm and its performance is also discussed.
193663
SAT-Based Image Computation with Application in Reachability Analysis
Image computation nds wide application in VLSI CAD, such as state reachability analysis in formal veri cation and synthesis, combinational veri cation, combinational and sequential test. Existing BDD-based symbolic algorithms for image computation are limited by memory resources in practice, while SAT-based algorithms that can obtain the image by enumerating satisfying assignments to a CNF representation of the Boolean relation are potentially limited by time resources. We propose new algorithms that combine BDDs and SAT in order to exploit their complementary bene ts, and to o er a mechanism for trading o space vs. time. In particular, (1) our integrated algorithm uses BDDs to represent the input and image sets, and a CNF formula to represent the Boolean relation, (2) a fundamental enhancement called BDD Bounding is used whereby the SAT solver uses the BDDs for the input set and the dynamically changing image set to prune the search space of all solutions, (3) BDDs are used to compute all solutions below intermediate points in the SAT decision tree, (4) a ne-grained variable quanti cation schedule is used for each BDD subproblem, based on the CNF representation of the Boolean relation. These enhancements coupled with more engineering heuristics lead to an overall algorithm that can potentially handle larger problems. This is supported by our preliminary results on exact reachability analysis of ISCAS benchmark circuits.
854648
Approximation algorithms for low-distortion embeddings into low-dimensional spaces
We present several approximation algorithms for the problem of embedding metric spaces into a line, and into the two-dimensional plane. Among other results, we give an O(√n)-approximation algorithm for the problem of finding a line embedding of a metric induced by a given unweighted graph, that minimizes the (standard) multiplicative distortion. We give an improved Õ(n1/3) approximation for the case of metrics generated by unweighted trees. This is the first result of this type.
11387042
Predicate learning and selective theory deduction for a difference logic solver
Design and verification of systems at the register-transfer (RT) or behavioral level require the ability to reason at higher levels of abstraction. Difference logic consists of an arbitrary Boolean combination of propositional variables and difference predicates and therefore provides an appropriate abstraction. In this paper, we present several new optimization techniques for efficiently deciding difference logic formulas. We use the lazy approach by combining a DPLL Boolean SAT procedure with a dedicated graph-based theory solver, which adds transitivity constraints among difference predicates on a "need-to" basis. Our new optimization techniques include flexible theory constraint propagation, selective theory deduction, and dynamic predicate learning. We have implemented these techniques in our lazy solver. We demonstrate the effectiveness of the proposed techniques on public benchmarks through a set of controlled experiments