5228937
Merging and Aligning Ontologies in dl-Programs
The language of dl-programs is a latest effort in developing an expressive representation for Web-based ontologies. It allows to build answer set programming (ASP) on top of description logic and thus some attractive features of ASP can be employed in the design of the Semantic Web architecture. In this paper we first generalize dl-programs by allowing multiple knowledge bases and then accordingly, define the answer set semantics for the dl-programs. A novel technique called forgetting is developed in the setting of dl-programs and applied to ontology merging and aligning.
15783530
A Top-Down Procedure for Disjunctive Well-Founded Semantics
Skepticism is one of the most important semantic intuitions in artificial intelligence. The semantics formalizing skeptical reasoning in (disjunctive) logic programming is usually named well-founded semantics. However, the issue of defining and computing the well-founded semantics for disjunctive programs and databases has proved to be far more complex and difficult than for normal logic programs. The argumentation-based semantics WFDS is among the most promising proposals that attempts to define a natural well-founded semantics for disjunctive programs. In this paper, we propose a top-down procedure for WFDS called D-SLS Resolution, which naturally extends the Global SLS-resolution and SLI-resolution. We prove that D-SLS Resolution is sound and complete with respect to WFDS. This result in turn provides a further yet more powerful argument in favor of the WFDS.
1885288
A Theory of Forgetting in Logic Programming
The study of forgetting for reasoning has attracted considerable attention in AI. However, much of the work on forgetting, and other related approaches such as independence, irrelevance and novelty, has been restricted to the classical logics. This paper describes a detailed theoretical investigation of the notion of forgetting in the context of logic programming. We first provide a semantic definition of forgetting under the answer sets for extended logic programs. We then discuss the desirable properties and some motivating examples. An important result of this study is an algorithm for computing the result of forgetting in a logic program. Furthermore, we present a modified version of the algorithm and show that the time complexity of the new algorithm is polynomial with respect to the size of the given logic program if the size of certain rules is fixed. We show how the proposed theory of forgetting can be used to characterize the logic program updates.
31845675
Alternating Fixpoint Theory for Logic Programs with Priority
van Gelder's alternating fixpoint theory has proven to be a very useful tool for unifying and characterizing various semantics for logic programs without priority. In this paper we propose an extension of van Gelder's alternating fixpoint theory and show that it can be used as a general semantic framework for logic programs with priority. Specifically, we define three declarative and model-theoretic semantics in this framework for prioritied logic programs: prioritized answer sets, prioritized regular extensions and prioritized well-founded model. We show that all of these semantics are natural generalizations of the corresponding semantics for logic programs without priority. We also show that these semantics have some other desirable properties. In particular, they can handle conflicts caused indirectly by the priorities.
2566357
Nested Epistemic Logic Programs
Nested logic programs and epistemic logic programs are two important extensions of answer set programming. However, the relationship between these two formalisms is rarely explored. In this paper we first introduce the epistemic HT-logic, and then propose a more general extension of logic programs called nested epistemic logic programs. The semantics of this extension – named equilibrium views – is defined on the basis of the epistemic HT-logic. We prove that equilibrium view semantics extends both the answer sets of nested logic programs and the world views of epistemic logic programs. Therefore, our work establishes a unifying framework for both nested logic programs and epistemic logic programs. Furthermore, we also provide a characterization of the strong equivalence of two nested epistemic logic programs.
30385305
Genome-Wide Discovery of Modulators of Transcriptional Interactions in Human B Lymphocytes
Transcriptional interactions in a cell are modulated by a variety of mechanisms that prevent their representation as pure pairwise interactions between a transcription factor and its target(s). These include, among others, transcription factor activation by phosphorylation and acetylation, formation of active complexes with one or more co-factors, and mRNA/protein degradation and stabilization processes. 
 
This paper presents a first step towards the systematic, genome-wide computational inference of genes that modulate the interactions of specific transcription factors at the post-transcriptional level. The method uses a statistical test based on changes in the mutual information between a transcription factor and each of its candidate targets, conditional on the expression of a third gene. The approach was first validated on a synthetic network model, and then tested in the context of a mammalian cellular system. By analyzing 254 microarray expression profiles of normal and tumor related human B lymphocytes, we investigated the post transcriptional modulators of the MYC proto-oncogene, an important transcription factor involved in tumorigenesis. Our method discovered a set of 100 putative modulator genes, responsible for modulating 205 regulatory relationships between MYC and its targets. The set is significantly enriched in molecules with function consistent with their activities as modulators of cellular interactions, recapitulates established MYC regulation pathways, and provides a notable repertoire of novel regulators of MYC function. The approach has broad applicability and can be used to discover modulators of any other transcription factor, provided that adequate expression profile data are available.
38950979
Behavior Profiling of Email
This paper describes the forensic and intelligence analysis capabilities of the Email Mining Toolkit (EMT) under development at the Columbia Intrusion Detection (IDS) Lab. EMT provides the means of loading, parsing and analyzing email logs, including content, in a wide range of formats. Many tools and techniques have been available from the fields of Information Retrieval (IR) and Natural Language Processing (NLP) for analyzing documents of various sorts, including emails. EMT, however, extends these kinds of analyses with an entirely new set of analyses that model "user behavior". EMT thus models the behavior of individual user email accounts, or groups of accounts, including the "social cliques" revealed by a user's email behavior.
11784167
An access control language for web services
This paper presents an approach for formally specifying and enforcing security policies on web service implementations. Networked services in general, and web services in particular, require extensive amounts of code to ensure that clients respect site-integrity constraints. We provide a language by which these constraints can be expressed and enforced automatically, portably and efficiently. Security policies in our system are specified in a language based on temporal logic, and are processed by an enforcement engine to yield site and platform-specific access control code. This code is integrated with a web server and platform-specific libraries to enforce the specified policy on a given web service. Our approach decouples the security policy specification from service implementations, provides a mandatory access control model for web services, and achieves good performance. We show that up to 22% of the code in a traditional web service module is dedicated to security checking functionality, including checks for client sequencing and parameter validation. We show that our prototype language implementation, WebGuard, enables web programmers to significantly reduce the amount of security checking code they need to develop manually. The quality of the code generated by WebGuard from formal policy specifications is competitive with the latency of handcrafted code to within a few percent.
2992297
Global and localized parallel preconditioning techniques for large scale solid Earth simulations
We investigate and compare a few parallel preconditioning techniques in the iterative solution of large sparse linear systems arising from solid Earth simulation with and without using contact information in the domain partitioning process. Previous studies are focused on using static or matrix pattern-based incomplete LU (ILU) preconditioners in a localized preconditioner implementation. Our current studies are concerned about preconditioner performance for solving two different problem configurations with and without known contact information. For the cases with contact information, we use localized threshold value-based ILU (ILUT) preconditioner to improve efficiency. For the cases without contact information, we use a global sparse approximate inverse preconditioner with a static sparsity pattern to achieve robustness. Numerical results from simulating ground motion on a parallel supercomputer are given to compare the effectiveness of these parallel preconditioning techniques.
12496214
Anomaly Detection in Computer Security and an Application to File System Accesses
We present an overview of anomaly detection used in computer security, and provide a detailed example of a host-based Intrusion Detection System that monitors file systems to detect abnormal accesses. The File Wrapper Anomaly Detector (FWRAP) has two parts, a sensor that audits file systems, and an unsupervised machine learning system that computes normal models of those accesses. FWRAP employs the Probabilistic Anomaly Detection (PAD) algorithm previously reported in our work on Windows Registry Anomaly Detection. FWRAP represents a general approach to anomaly detection. The detector is first trained by operating the host computer for some amount of time and a model specific to the target machine is automatically computed by PAD. The model is then deployed to a real-time detector. In this paper we describe the feature set used to model file system accesses, and the performance results of a set of experiments using the sensor while attacking a Linux host with a variety of malware exploits. The PAD detector achieved impressive detection rates in some cases over 95% and about a 2% false positive rate when alarming on anomalous processes.