17573600
Two-way Web service: from interface design to interface verification
In this paper, we introduce a theoretical framework for two-way Web service (WS) interaction and interface design based on the concepts of operation reversal and XML type generalization. Under this theoretical framework, two generic types of interface solutions in two-way WS interaction, i.e. tightly coupled (TC) interface and loosely coupled (LC) interface, are formally defined and studied. The proposed theoretical framework is used to design, derive and verify WS interface for full duplex two-way WS interaction. An algorithm of interface verification is described that allows effective WS interface design and verification to support asynchronous two-way WS operation and event notification. The interface verification algorithm in our approach utilizes verification by derivation and verification by content to validate the client interface in two-way WS interaction. Use case studies are performed for both TC and LC interface solutions. A generic infrastructure based on two-way Web service application proxy (2SAP) is described and implemented. The proposed approach is applied to applications of realizing ECMA-348 for WS enablement of telecommunication.
11582687
Web service enablement of communication services
In this paper, we introduce Web service application session services, WS-session, for Web service based application session management in communication. A two-way Web service framework is described. It supports the use of Web service in the situation of telecommunication where the communication endpoint can be both a client and a peer-to-peer server. We describe the interface design in two-way Web service interaction based on the concept of tightly coupled interface and loosely coupled interface solutions. The proposed approach provides full support of asynchronous outbound operations and event notifications in communication services. It is implemented in a research prototype system that provides both standard based (ECMA-348) services and Avaya service extensions. In addition, we investigated the integration of our proposed approach with BPEL4WS. It allows the user to create new services through a drag-n-drop based service creation environment (ECLIPSE/BPEL4WS). It leads to a paradigm of service creation through Web service composition. More sophisticated telecommunication services are created from composing the basic services.
21164331
Optimization model of internet protocols
Layered architecture is one of the most fundamental and influential structures of network design. Can we integrate the various protocol layers into a single coherent theory by regarding them as carrying out an asynchronous distributed primal-dual computation over the network to implicitly solve a global optimization problem? Different layers iterate on different subsets of the decision variables using local information to achieve individual optimalities, but taken together, these local algorithms attempt to achieve a global objective. Such a theory will expose the interconnection between protocol layers and can be used to study rigorously the performance tradeoff in protocol layering as different ways to distribute a centralized computation. In this talk, we describe some preliminary work towards this goal and discuss some of the difficulties of this approach.
20793791
Longitudinal data model selection
In longitudinal data with correlated errors, we apply the likelihood and residual likelihood approaches to obtain the corrected Akaike information criterion (AICc) and the residual information criterion (RIC), respectively. Simulation studies show that AICc outperforms the Akaike information criterion (AIC) when the numbers of subjects and repeated observations are small, and RIC is superior to the Bayesian information criterion (BIC) when the signal-to-noise ratio is moderate to large. We illustrate the practical use of these selection criteria with an empirical example for modeling the serum cholesterol measured at six time occasions.
15147687
GAPWM: a genetic algorithm method for optimizing a position weight matrix
MOTIVATION
Position weight matrices (PMWs) are simple models commonly used in motif-finding algorithms to identify short functional elements, such as cis-regulatory motifs, on genes. When few experimentally verified motifs are available, estimation of the PWM may be poor. The resultant PWM may not reliably discriminate a true motif from a false one. While experimentally identifying such motifs remains time-consuming and expensive, low-resolution binding data from techniques such as ChIP-on-chip and ChIP-PET have become available. We propose a novel but simple method to improve a poorly estimated PWM using ChIP data.


METHODOLOGY
Starting from an existing PWM, a set of ChIP sequences, and a set of background sequences, our method, GAPWM, derives an improved PWM via a genetic algorithm that maximizes the area under the receiver operating characteristic (ROC) curve. GAPWM can easily incorporate prior information such as base conservation. We tested our method on two PMWs (Oct4/Sox2 and p53) using three recently published ChIP data sets (human Oct4, mouse Oct4 and human p53).


RESULTS
GAPWM substantially increased the sensitivity/specificity of a poorly estimated PWM and further improved the quality of a good PWM. Furthermore, it still functioned when the starting PWM contained a major error. The ROC performance of GAPWM compared favorably with that of MEME and others. With increasing availability of ChIP data, our method provides an alternative for obtaining high-quality PWMs for genome-wide identification of transcription factor binding sites.


AVAILABILITY
The C source code and all data used in this report are available at http://dir.niehs.nih.gov/dirbb/gapwm.


SUPPLEMENTARY INFORMATION
Supplementary data are available at Bioinformatics online.
32109138
Rewriting Queries for XML Integration Systems
A data integration system typically creates a target XML schema to represent an application domain and source schemas are mapped to the target schema. A user poses a query over the target schema, and the system rewrites the query into a set of queries over the data sources. Existing algorithms generate a set of static rules based on the target schema and mappings, and rewrite the target query using these rules. We design a flexible and dynamic approach that rewrites XML queries directly based on the mappings between the target and source schemas. Theoretical analysis and experiments on both synthetic and real-world datasets indicate that the proposed approach is efficient and scalable.
5737470
A pragmatic approach to dealing with high-variability in network measurements
The Internet is teeming with high variability phenomena, from measured IP flow sizes to aspects of inferred router-level connectivity, but there still exists considerable debate about how best to deal with this encountered high variability and model it. While one popular approach favors modeling highly variable event sizes with conventional, finite variance distributions such as lognormal or Weibull distributions, Mandelbrot has argued for the last 40 years that there are compelling mathematical, statistical, and practical reasons for why infinite variance distributions are natural candidates for capturing the essence behind high variability phenomena. In this paper, we elaborate on Mandelbrot's arguments and present a methodology that often allows for a clear distinction between the two approaches. In particular, by requiring the resulting models to be resilient to ambiguities (i.e., robust to real-world deficiencies in the underlying network measurements) and internally self-consistent (i.e., insensitive with respect the duration, location, or time of the data collection), we provide a rigorous framework for a qualitative assessment of the observed high variability. We apply the proposed framework to assess previously reported findings about measured Internet traffic and inferred router- and AS-level connectivity. In the process, we also discuss what our approach has to say about recent discussions concerning network traffic being Poisson or self-similar and router-level or AS-level connectivity graphs of the Internet being scale-free or not.