12588315
The Many Faces of Process Interaction Graphs: A Data Management Perspective
WE USE THE EXPRESSION “process interaction graph” (PIG) as a general purpose term to cover instances of network-like structures with specific semantics, including signal transduction networks, gene regulatory networks, metabolic pathways and so forth, because we believe that despite the differences in biological significance, they can be treated in a uniform data management framework. Aside from the fact that they are all graph-like entities, PIGs share a few common characteristics, such as follows:
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.
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.
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.
2332293
Using predators to combat worms and viruses: a simulation-based study
Large-scale attacks generated by fast-spreading or stealthy malicious mobile code, such as flash worms and e-mail viruses, demand new approaches to patch management and disinfection. Currently popular centralized approaches suffer from distribution bottlenecks which cannot be solved by merely increasing the number of servers, as the number of servers required to eliminate all bottlenecks is impractically large. Recently, predators were proposed as a technique for eliminating automated mobile malware from computer networks. Predators are benevolent, self-propagating mobile programs which have the ability to clean up systems infected by malignant worms/viruses. We propose a number of extensions to the original predator model, including immunizing predators, persistent predators, and seeking predators. We report on a set of simulations which explore the effects of predators on small-scale (800 to 1600 node) networks. Our results indicate that predators hold significant promise as an alternative to the centralized patch distribution mechanism. The results show that predators can be used to disinfect systems and distribute patches rapidly across the network, without suffering from bottlenecks or causing network congestion. The results also show that the new predator models provide significant benefits over the original predator model. The simulation tool is also useful for tuning predator behavior, so that an optimal tradeoff between the peak virus/worm infection rate and the overhead generated by the predator can be chosen before a predator is released.
2840997
A survey of recent advances in SAT-based formal verification
Dramatic improvements in SAT solver technology over the last decade and the growing need for more efficient and scalable verification solutions have fueled research in verification methods based on SAT solvers. This paper presents a survey of the latest developments in SAT-based formal verification, including incomplete methods such as bounded model checking and complete methods for model checking. We focus on how the surveyed techniques formulate the verification problem as a SAT problem and how they exploit crucial aspects of a SAT solver, such as application-specific heuristics and conflict-driven learning. Finally, we summarize the noteworthy achievements in this area so far and note the major challenges in making this technology more pervasive in industrial design verification flows.
13088866
Specification-based anomaly detection: a new approach for detecting network intrusions
Unlike signature or misuse based intrusion detection techniques, anomaly detection is capable of detecting novel attacks. However, the use of anomaly detection in practice is hampered by a high rate of false alarms. Specification-based techniques have been shown to produce a low rate of false alarms, but are not as effective as anomaly detection in detecting novel attacks, especially when it comes to network probing and denial-of-service attacks. This paper presents a new approach that combines specification-based and anomaly-based intrusion detection, mitigating the weaknesses of the two approaches while magnifying their strengths. Our approach begins with state-machine specifications of network protocols, and augments these state machines with information about statistics that need to be maintained to detect anomalies. We present a specification language in which all of this information can be captured in a succinct manner. We demonstrate the effectiveness of the approach on the 1999 Lincoln Labs intrusion detection evaluation data, where we are able to detect all of the probing and denial-of-service attacks with a low rate of false alarms (less than 10 per day). Whereas feature selection was a crucial step that required a great deal of expertise and insight in the case of previous anomaly detection approaches, we show that the use of protocol specifications in our approach simplifies this problem. Moreover, the machine learning component of our approach is robust enough to operate without human supervision, and fast enough that no sampling techniques need to be employed. As further evidence of effectiveness, we present results of applying our approach to detect stealthy email viruses in an intranet environment.
6212306
Constraint checking with partial information
Constraints are a valuable tool for managing information across multiple databases, as well as for general purposes of assuring data integrity. However, efficient implementation of constraint checking is difficult. In this paper we explore techniques for assuring constraint satisfaction without performing a complete evaluation of the constraints. We consider methods that use only constraint definitions, methods that use constraints and updates, and methods that use constraints, updates, and “local” data.
17407466
Point-Based Approaches to Qualitative Temporal Reasoning
We are interested in the problem of qualitative, point-based temporal reasoning. That is, given a set of assertions concerning the relative positions of points in time, we are interested in compiling the assertions into a representation that supports efficient reasoning, determining consistency, computing the strongest entailed relation between any two points and updating the set of assertions. We begin by considering a general set of operations and their corresponding algorithms, applicable to general point-based temporal domains. We also consider special-purpose reasoners, which may be expected to perform well in an application domain with a restricted structure. Lastly we consider reasoners which incorporate restricted structures into a more general reasoning framework. Finally, we present instances of each such approach and give a comparison of their performance on random data sets.