ppxscal/embedding_network huggingface dataset:
Output perturbation with query relaxation
Authors: Xiaokui Xiao, Yufei Tao
Venue: Proceedings of the VLDB Endowment (2008)

Given a dataset containing sensitive personal information, a statistical database answers aggregate queries in a manner that preserves individual privacy. We consider the problem of constructing a statistical database using output perturbation, which protects privacy by injecting a small noise into each query result. We show that the state-of-the-art approach, &epsilon;-differential privacy, suffers from two severe deficiencies: it (i) incurs prohibitive computation overhead, and (ii) can answer only a limited number of queries, after which the statistical database has to be shut down. To remedy the problem, we develop a new technique that enforces &epsilon;-different privacy with economical cost. Our technique also incorporates a query relaxation mechanism, which removes the restriction on the number of permissible queries. The effectiveness and efficiency of our solution are verified through experiments with real data.
Annotation of metagenome short reads using proxygenes
Authors: Daniel Dalevi, Natalia N. Ivanova, Konstantinos Mavromatis, Sean D. Hooper, Ernest Szeto, Philip Hugenholtz, Nikos C. Kyrpides, Victor M. Markowitz
Venue: Bioinformatics (2008)

Motivation: A typical metagenome dataset generated using a 454 pyrosequencing platform consists of short reads sampled from the collective genome of a microbial community. The amount of sequence in such datasets is usually insufficient for assembly, and traditional gene prediction cannot be applied to unassembled short reads. As a result, analysis of such datasets usually involves comparisons in terms of relative abundances of various protein families. The latter requires assignment of individual reads to protein families, which is hindered by the fact that short reads contain only a fragment, usually small, of a protein. Results: We have considered the assignment of pyrosequencing reads to protein families directly using RPS-BLAST against COG and Pfam databases and indirectly via proxygenes that are identified using BLASTx searches against protein sequence databases. Using simulated metagenome datasets as benchmarks, we show that the proxygene method is more accurate than the direct assignment. We introduce a clustering method which significantly reduces the size of a metagenome dataset while maintaining a faithful representation of its functional and taxonomic content. Contact: vmmarkowitz@lbl.gov
The WAMI toolkit for developing, deploying, and evaluating web-accessible multimodal interfaces
Authors: Alexander Gruenstein, Ian McGraw, Ibrahim Badr
Venue: Proceedings of the 10th international conference on Multimodal interfaces (2008)

Many compelling multimodal prototypes have been developed which pair spoken input and output with a graphical user interface, yet it has often proved difficult to make them available to a large audience. This unfortunate reality limits the degree to which authentic user interactions with such systems can be collected and subsequently analyzed. We present the WAMI toolkit, which alleviates this difficulty by providing a framework for developing, deploying, and evaluating Web-Accessible Multimodal Interfaces in which users interact using speech, mouse, pen, and/or touch. The toolkit makes use of modern web-programming techniques, enabling the development of browser-based applications which rival the quality of traditional native interfaces, yet are available on a wide array of Internet-connected devices. We will showcase several sophisticated multimodal applications developed and deployed using the toolkit, which are available via desktop, laptop, and tablet PCs, as well as via several mobile devices. In addition, we will discuss resources provided by the toolkit for collecting, transcribing, and annotating usage data from multimodal user interactions.
Knowledge discovery standards
Authors: Sarabjot Singh Anand, Marko Grobelnik, Frank Herrmann, Mark Hornick, Christoph Lingenfelder, Niall Rooney, Dietrich Wettschereck
Venue: Artificial Intelligence Review (2007)

As knowledge discovery (KD) matures and enters the mainstream, there is an onus on the technology developers to provide the technology in a deployable, embeddable form. This transition from a stand-alone technology, in the control of the knowledgeable few, to a widely accessible and usable technology will require the development of standards. These standards need to be designed to address various aspects of KD ranging from the actual process of applying the technology in a business environment, so as to make the process more transparent and repeatable, through to the representation of knowledge generated and the support for application developers. The large variety of data and model formats that researchers and practitioners have to deal with and the lack of procedural support in KD have prompted a number of standardization efforts in recent years, led by industry and supported by the KD community at large. This paper provides an overview of the most prominent of these standards and highlights how they relate to each other using some example applications of these standards.
Instance-Based Ontology Matching Using Regular Expressions
Authors: Katrin Zaiß, Tim Schlüter, Stefan Conrad
Venue: Proceedings of the OTM Confederated International Workshops and Posters on On the Move to Meaningful Internet Systems: 2008 Workshops: ADI, AWeSoMe, COMBEK, EI2N, IWSSA, MONET, OnToContent + QSI, ORM, PerSys, RDDS, SEMELS, and SWWS (2008)

Many algorithms dealing with thematching task have been proposed in the past, most of them not considering instances. Only a few existing systems like [EM07] or [DMDH04] use the information provided by instances in their matching algorithms. Due to the fact that ontologies offer the possibility to model instances within the ontology, these should definitely be used to increase the accuracy of the matching results. Additionally, the set of instances probably provides more information about the meaning of a concept than its label. Thus, we propose a new instance-based ontology matcher which should extend existing libraries to enhance the matching quality.
New methods to access scientific content
Authors: Stefan Geißler
Venue: Information Services and Use (2008)

The availability of systems capable to perform accurate and large-scale analysis and indexing of scientific content has a profound effect on the scientific publishing sector. Many scenarios about the extension of existing products or the definition of new ones that would have otherwise resulted in significant or even prohibitive costs, now become feasible. The present paper introduces several case studies of the application of methods of Text Mining in the scientific publishing sector and outlines the motivation and additional benefits that arise from such approaches.
Steganography of VoIP Streams
Authors: Wojciech Mazurczyk, Krzysztof Szczypiorski
Venue: Proceedings of the OTM 2008 Confederated International Conferences, CoopIS, DOA, GADA, IS, and ODBASE 2008. Part II on On the Move to Meaningful Internet Systems (2008)

The paper concerns available steganographic techniques that can be used for creating covert channels for VoIP (Voice over Internet Protocol) streams. Apart from characterizing existing steganographic methods we provide new insights by presenting two new techniques. The first one is network steganography solution which exploits free/unused protocols' fields and is known for IP, UDP or TCP protocols but has never been applied to RTP (Real-Time Transport Protocol) and RTCP (Real-Time Control Protocol) which are characteristic for VoIP. The second method, called LACK (Lost Audio Packets Steganography), provides hybrid storage-timing covert channel by utilizing delayed audio packets. The results of the experiment, that was performed to estimate a total amount of data that can be covertly transferred during typical VoIP conversation phase, regardless of steganalysis, are also included in this paper.
A general framework for parallel BDI agents in dynamic environments
Authors: Huiliang Zhang, Shell Ying Huang
Venue: Web Intelligence and Agent Systems (2008)

In this paper, a general framework for the parallel BDI model suitable for dynamic environments is proposed. It is a parallel agent architecture that supports the following agent abilities at architecture level: (1) the ability to monitor the environment at all times and respond to emergencies timely; (2) the ability to reconsider and re-schedule goals, intentions and actions in reaction to unexpected or new information; (3) the ability to perform multiple actions at once; (4) the ability to perceive, deliberate and act simultaneously; (5) the ability to prioritize the deliberations and intention executions. We define the functions and the operations of the processing units in the agent and how these units interact, cooperate and synchronize with each other. With the advances in semiconductor technology which allow multiple processing units to be implemented on the same silicon chip, a parallel BDI agent will be an effective way to enable it to perform in a dynamically changing environment when the arrival rate of events is high. We illustrate the working of a parallel agent under the general framework with an agent simulating the behaviour of a vessel captain navigating in sea. Then the performance of a parallel agent is evaluated against several versions of sequential agents. The issue of how much parallelism and how to configure a parallel agent based on the general framework are studied by experiments with different configurations of the parallel agent.
Analytical and numerical investigations of a batch crystallization model
Authors: Shamsul Qamar, Gerald Warnecke
Venue: Journal of Computational and Applied Mathematics (2008)

This article is concerned with the analytical and numerical investigations of a one-dimensional population balance model for batch crystallization processes. We start with a one-dimensional batch crystallization model and prove the local existence and uniqueness of the solution of this model. For this purpose Laplace transformation is used as a basic tool. A semi-discrete high resolution finite volume scheme is proposed for the numerical solution of the current model. The issues of positivity (monotonicity), consistency, stability and convergence of the proposed scheme for the current model are analyzed and proved. Finally, we give a numerical test problem. The numerical results of the proposed high resolution scheme are compared with the solution of the reduced four-moments model and the first-order upwind scheme.
Soft computing-based gait planners for a dynamically balanced biped robot negotiating sloping surfaces
Authors: Pandu Ranga Vundavilli, Dilip Kumar Pratihar
Venue: Applied Soft Computing (2009)

Dynamically balanced gait generation problems of a biped robot moving up and down the sloping surface have been solved utilizing soft computing-based approaches. The gait generation problem of a biped robot is difficult to model due to its inherent complexity, imprecision in the collected data of the environment, which are the characteristics that can be the best modeled using soft computing. Two different approaches, namely genetic-neural (GA-NN) and genetic-fuzzy (GA-FLC) systems have been developed to solve the ascending and descending gait generation problems of a two-legged robot negotiating the sloping surface. Two modules of neural network (NN)/fuzzy logic controller (FLC) have been used to model the gait generation problem of a biped robot using the GA-NN/GA-FLC system. The weights of the NNs in the GA-NN and knowledge bases of the FLCs in the GA-FLC systems are optimized offline, utilizing a genetic algorithm (GA). Once the GA-NN/GA-FLC system is optimized, it will be able to generate the dynamically balanced gaits of the two-legged robot in the optimal sense.
Reliability testing of nano-particle system packaging
Authors: James E. Morris
Venue: Microsystem Technologies (2008)

Metal nanoparticle applications in nanoelectronics are based on single nanodots or 1-D nanodot chains (both for single electron transistors), or 2-D discontinuous metal thin film (DMTF) arrays (e.g. for sensors), or 3-D polymer or ceramic &#x201c;cermets,&#x201d; (for high resistivity resistors and high-k dielectrics). DMTF fabrication relies upon weak substrate adhesion for discrete island formation, which promotes long-term instability and reliability problems. Past work on DMTF nanodot stability is applicable to future nanoelectronics and nanopackaging.
HCI Research for E-Learning: Adaptability and Adaptivity to Support Better User Interaction
Authors: Vlado Glavinić, Andrina Granić
Venue: Proceedings of the 4th Symposium of the Workgroup Human-Computer Interaction and Usability Engineering of the Austrian Computer Society on HCI and Usability for Education and Work (2008)

The paper provides an overview of our research being performed in the area of interfaces for e-learning, with the emphasis on application of intelligent methods. We especially address the efforts being done in providing a suitable interaction for a class of intelligent e-learning systems --- Intelligent Tutoring Systems (ITSs), within the research framework of our home institutions. The specific issues being thus studied include adaptivity topics related to knowledge representation, interaction style as well as mobility support, along with related usability assessment methods. The dependence on intelligent handling of the former stems from the expected more efficient and effective solution of problems related to the diversity of users of Information and Communication Technology (ICT) supported education. In this respect we also shortly tackle and comment on a number of adaptable and adaptive interfaces for e-learning, which are in this context being conceptualized, implemented, and assessed both in vitro and in vivo.
Using Clustering Technique for Students' Grouping in Intelligent E-Learning Systems
Authors: Danuta Zakrzewska
Venue: Proceedings of the 4th Symposium of the Workgroup Human-Computer Interaction and Usability Engineering of the Austrian Computer Society on HCI and Usability for Education and Work (2008)

In the paper, application of cluster analysis for students' grouping in intelligent e-learning systems is considered. It is proposed the system architecture, in which teaching paths as well as proper layouts are adjusted to groups of students according to their learning styles and usability preferences. Considered student models are built on the basis of Felder and Silverman model, together with student color choices. It is considered usage of two versions of two-phase hierarchical clustering algorithm for students' grouping. Experimental results for both of the approaches are compared and discussed.
Maintaining dynamic channel profiles on the web
Authors: Haggai Roitman, David Carmel, Elad Yom-Tov
Venue: Proceedings of the VLDB Endowment (2008)

This work addresses a novel problem of maintaining channel proflies on the Web. Such channel maintenance is essential for next generation of Web 2.0 applications that provide sophisticated search and discovery services over Web information channels. Maintaining a fresh channel profile is extremely difficult due to the the dynamic nature of the channel, especially under the constraint of a limited monitoring budget. We propose a novel monitoring scheme that learns the channels' monitoring rates. The monitoring scheme is further extended to consider the content that is published on the channels. We describe a novelty detection filter that refines the monitoring rate according to the expected rate of novel content published on the channels. We further show how inter-channel profile similarities can be utilized to refine the channel monitoring rates. Using real-world data of Web feeds we study the performance of the monitoring scheme. We experiment with several monitoring policies over a large set of Web feeds and show that a policy based on learning the monitoring rate of the channels, combined with novelty detection, outperforms alternative channel monitoring policies. Our results show that the suggested content-based policy is able to maintain high quality channel profiles under limited monitoring resources.
E-science: Where Are We and Where Should We Go
Authors: Daniel E. Atkins
Venue: Proceedings of the OTM 2008 Confederated International Conferences, CoopIS, DOA, GADA, IS, and ODBASE 2008. Part I on On the Move to Meaningful Internet Systems: (2008)

Grid computing, high-performance and distributed applications --- the GADA environment --- provides much of the platform for transformative approaches to the conduct of scientific and engineering research and associated education that are now being called e-science or cyberinfrastructure (CI)-enhanced science. This talk will review progress in this area with reference to initiatives of the U.S. National Science Foundation and similar European agencies over the last decade. The speaker will provide his assessment of where we now stand and highlight some remaining challenges and opportunities.
Traceroute probe method and forward IP path inference
Authors: Matthew Luckie, Young Hyun, Bradley Huffaker
Venue: Proceedings of the 8th ACM SIGCOMM conference on Internet measurement (2008)

Several traceroute probe methods exist, each designed to perform better in a scenario where another fails. This paper examines the effects that the choice of probe method has on the inferred forward IP path by comparing the paths inferred with UDP, ICMP, and TCP-based traceroute methods to (1) a list of routable IP addresses, (2) a list of known routers, and (3) a list of well-known websites. We further compare methods by examining seven months of macroscopic Internet topology data collected by CAIDA's Archipelago infrastructure. We found significant differences in the topology observed using different probe methods. In particular, we found that ICMP-based traceroute methods tend to successfully reach more destinations, as well as collect evidence of a greater number of AS links. UDP-based methods infer the greatest number of IP links, despite reaching the fewest destinations. We hypothesise that some per-flow load balancers implement different forwarding policies for TCP and UDP, and run a specific experiment to confirm this hypothesis.
Detection of 3D atomic similarities and their use in the discrimination of small molecule protein-binding sites
Authors: Rafael Najmanovich, Natalja Kurbatova, Janet Thornton
Venue: Bioinformatics (2008)

Motivation: Current computational methods for the prediction of function from structure are restricted to the detection of similarities and subsequent transfer of functional annotation. In a significant minority of cases, global sequence or structural (fold) similarities do not provide clues about protein function. In these cases, one alternative is to detect local binding site similarities. These may still reflect more distant evolutionary relationships as well as unique physico-chemical constraints necessary for binding similar ligands, thus helping pinpoint the function. In the present work, we ask the following question: is it possible to discriminate within a dataset of non-homologous proteins those that bind similar ligands based on their binding site similarities? Methods: We implement a graph-matching-based method for the detection of 3D atomic similarities introducing some simplifications that allow us to extend its applicability to the analysis of large allatom binding site models. This method, called IsoCleft, does not require atoms to be connected either in sequence or space. We apply the method to a cognate-ligand bound dataset of non-homologous proteins. We define a family of binding site models with decreasing knowledge about the identity of the ligand-interacting atoms to uncouple the questions of predicting the location of the binding site and detecting binding site similarities. Furthermore, we calculate the individual contributions of binding site size, chemical composition and geometry to prediction performance. Results: We find that it is possible to discriminate between different ligand-binding sites. In other words, there is a certain uniqueness in the set of atoms that are in contact to specific ligand scaffolds. This uniqueness is restricted to the atoms in close proximity of the ligand in which case, size and chemical composition alone are sufficient to discriminate binding sites. Discrimination ability decreases with decreasing knowledge about the identity of the ligand-interacting binding site atoms. The decrease is quite abrupt when considering size and chemical composition alone, but much slower when including geometry. We also observe that certain ligands are easier to discriminate. Interestingly, the subset of binding site atoms belonging to highly conserved residues is not sufficient to discriminate binding sites, implying that convergently evolved binding sites arrived at dissimilar solutions. Availability: IsoCleft can be obtained from the authors. Contact: rafael.najmanovich@ebi.ac.uk
EQOWSN: Evolutionary-based query optimization over self-organized wireless sensor networks
Authors: Sherin M. Youssef, Meer A. Hamza, Salma F. Fayed
Venue: Expert Systems with Applications: An International Journal (2009)

In this paper, a new approach has been introduced that integrates an evolutionary-based mechanism with a distributed query sensor cover algorithm for optimal query execution in self-organized wireless sensor networks (WSN). An algorithm based on an evolutionary technique is proposed, with problem-specific genetic operators to improve computing efficiency. Redundancy within a sensor network can be exploited to reduce the communication cost incurred in execution of spatial queries. Any reduction in communication cost would result in an efficient use of battery energy, which is very limited in sensors. Our objective is to self-organize the network, in response to a query, into a topology that involves an optimal subset of sensors that is sufficient to process the query subject to connectivity, coverage, energy consumption, cover size and communication overhead constraints. Query processing must incorporate energy awareness into the system by reducing the total energy consumption and hence increasing the lifetime of the sensor cover, which is beneficial for large long running queries. Experiments have been carried out on networks with different sensors Transmission radius, different query sizes, and different network configurations. Through extensive simulations, we have shown that our designed technique result in substantial energy savings in a sensor network. Compared with other techniques, the results demonstrated a significant improvement of the proposed technique in terms of energy-efficient query cover with lower communication cost and lower size.
Separation of sets and Wolfe duality
Authors: F. Giannessi, G. Mastroeni
Venue: Journal of Global Optimization (2008)

Lagrangian duality can be derived from separation in the Image Space, namely the space where the images of the objective and constraining functions of the given extremum problem run. By exploiting such a result, we analyse the relationships between Wolfe and Mond-Weir duality and prove their equivalence in the Image Space under suitable generalized convexity assumptions.
Properties of General Semantic Operators Determined by Logic-Based Systems
Authors: Máire Lane, Anthony Karel Seda
Venue: Electronic Notes in Theoretical Computer Science (ENTCS) (2009)

We discuss a very general semantic operator arising within logic-based programming systems from an algebraic point of view, and show how it connects four interesting aspects of computation: neural networks, conventional logic programming, constraint logic programming, and simple models of uncertainty in logic-based systems.