ppxscal/embedding_network huggingface dataset:
Mathematical models for mycobacterium tuberculosis complex genotyping and patient data
Authors: Kristin P. Bennett
Venue:  (2006)

The goal of this project was to develop biologically appropriate mathematical models for genotyping and patient data and use them to analyze and exploit the information in heterogeneous genotyping and epidemiological databases. These databases can be used to address fundamental questions in public health, particularly dynamics of emerging infectious diseases. This work focuses on Mycobacterium tuberculosis complex (MTC) because tuberculosis (TB) presents a reemerging serious health threat worldwide; the most optimistic scenarios predict in excess of 80 million new cases and 20 million deaths in the coming decade. Moreover, mycobacteria are one of the most widely sequenced pathogenic groups, and global TB databases currently exist. Advances in molecular methods contribute significantly to our understanding of the spread of TB. Differentiating between various patent isolates and using the data to guide the efforts of TB control programs are major applications for MTC genotyping. Our research develops mathematical models for spacer oligonucleotide typing (spoligotyping) and demographic data on TB patients. The spoligotyping method exploits polymorphism in the direct repeat locus of chromosome of the MTC bacteria. Spoligotyping produces a simple binary pattern for each TB isolate and is widely used for MTC strain discrimination. We present SPOTCLUST, a novel mixture modeling approach to advance global studies of MTC genotyping data. SPOTCLUST incorporates biological information on spoligotype evolution without attempting to derive the full phylogeny of MTC. The algorithm is applied to spoligotyping data identified among strains isolated between 1996 and 2004, primarily from New York State TB patients. Our results both confirm previously defined families of MTC strains and suggest certain new families. We demonstrate on New York City demographic data how the resulting models can potentially form the basis of TB control tools using genotyping. Several alternative methods of analysis of MTC genotype and patient data are explored. Improvements to the current method are suggested. Future work will concentrate on developing methods for merging probabilistic models for spoligotypes and results from other TB genotyping methods with traditional epidemiological data.
Switching Attention without Shifting the Spotlight: Object-Based Attentional Modulation of Brain Potentials
Authors: Mitchell Valdes-Sosa, Maria A. Bobes, Valia Rodriguez, Tupac Pinilla
Venue: Journal of Cognitive Neuroscience (1998)

Although psychophysical evidence for object-based attention has been reported, corresponding studies with eventrelated potentials (ERPs) are scarce. Here subjects were presented with perceptual fields containing two superimposed objects (transparent surfaces generated by two sets of dots in rigid rotation around fixation, each set of a different color and direction of motion) or only one object (the same dots but either at rest or all rotating in the same direction). Brief (150- msec) rectilinear displacements affected either of the sets at random ISIs of 350 to 550 msec. Attention was directed to one set of dots, guided by color, in order to discriminate the direction of their displacement. Motion-onset ERPs elicited by these displacements were compared for attended and unattended dots.When the perceptual field consisted of two objects,strong suppression of P1 and N1 was obtained in the ERPs associated with the unattended object. No suppression was found with the field containing a single object, although an enhanced selection negativity was found in ERPs associated with attended dots (selected by color). Since the two objects occupied the same region of visual space, the suppression of P1/N1 cannot be explained by the space-based mechanisms but is consistent with object-based attentional selection at early stages of vision. The results highlight the role of perceptual organization in enabling alternative attentional mechanisms.
Implications of link range and (In)stability on sensor network architecture
Authors: Bhaskaran Raman, Kameswari Chebrolu, Naveen Madabhushi, Dattatraya Y. Gokhale, Phani K. Valiveti, Dheeraj Jain
Venue: Proceedings of the 1st international workshop on Wireless network testbeds, experimental evaluation characterization (2006)

In this work, we consider sensor networks used for scientific instrumentation, where we have a set of nodes collecting data and relaying the same to a central base node. From the point of view of deploying such networks,we re-look at the design choices available for the network architecture and protocol design. A design choice which has not received in-depth attention thus far is the use of external antennas for improving the communication range. We present extensive measurements to quantify the use of external antennas. We show that this is a simple yet effective mechanism, in many cases allowing the use of just a single-hop network architecture. Such an approach of course, also greatly simplifies protocol design. Related to the range studies, we also look at the time variability of RSSI and the packet error rate. We find variability at time scales as small as a single packet and also at several hours. Given this, we argue that dynamic metric based routing becomes highly questionable, and a centralized protocol design becomes a serious alternative.
Pragmatic text mining: minimizing human effort to quantify many issues in call logs
Authors: George Forman, Evan Kirshenbaum, Jaap Suermondt
Venue: Proceedings of the 12th ACM SIGKDD international conference on Knowledge discovery and data mining (2006)

We discuss our experiences in analyzing customer-support issues from the unstructured free-text fields of technical-support call logs. The identification of frequent issues and their accurate quantification is essential in order to track aggregate costs broken down by issue type, to appropriately target engineering resources, and to provide the best diagnosis, support and documentation for most common issues. We present a new set of techniques for doing this efficiently on an industrial scale, without requiring manual coding of calls in the call center. Our approach involves (1) a new text clustering method to identify common and emerging issues; (2) a method to rapidly train large numbers of categorizers in a practical, interactive manner; and (3) a method to accurately quantify categories, even in the face of inaccurate classifications and training sets that necessarily cannot match the class distribution of each new month's data. We present our methodology and a tool we developed and deployed that uses these methods for tracking ongoing support issues and discovering emerging issues at HP.
Pattern categories: a mathematical approach for organizing design patterns
Authors: Saluka R. Kodituwakku, Peter Bertok
Venue: Proceedings of the 2002 conference on Pattern languages of programs - Volume 13 (2003)

We describe mathematical structures in existing pattern or ganization methods and introduce a new organization method based on those mathematical structures. This method organizes patterns into related groups called pattern categories by structuring them according to mathematical structures. Our method assists users to find a set of patterns that can be collectively applied to solve complex design problems. Furthermore, it assists to find alternatives for such patterns. Thus this method facilitates the selection of most appropriate patterns to solve the problem at hand. A second aspect of this method is that it provides the details of patterns and relationships between them. The users can select all or some of the patterns in a category according to their requirements.
A Relation-Based Search Engine in Semantic Web
Authors: Yufei Li, Yuan Wang, Xiaotao Huang
Venue: IEEE Transactions on Knowledge and Data Engineering (2007)

With the development of the Web, an information "Big Bang” has taken place on the Internet. Search engines have become one of the most helpful tools for obtaining useful information from the Internet. However, instead of caring about the semantics of information, the machine on the current Web cares about the location and display of information only. Because of this shortcoming of the current Web, the search results by even the most popular search engines cannot produce satisfactory results. The development of the next generation Web, Semantic Web, will turn the situation around completely. This paper proposes a prototype relation-based search engine, "OntoLook,” which has been implemented in a virtual Semantic Web environment in our lab. We also present its system architecture and analyze the key algorithm.
Nonself-adjoint operators with almost Hermitian spectrum: matrix model. I
Authors: Alexander V. Kiselev, Serguei N. Naboko
Venue: Journal of Computational and Applied Mathematics (2006)

Nonself-adjoint, nondissipative perturbations of bounded self-adjoint operators with real purely singular spectrum are considered. Using a functional model of a nonself-adjoint operator as a principal tool, spectral properties of such operators are investigated. In particular, in the case of rank two perturbations the pure point spectral component is completely characterized in terms of matrix elements of the operators' characteristic function.
SMIL to MPEG-4 BIFS Conversion
Authors: Beilu Shao, Laureano Moro Velazquez, Nicolas Scaringella, Neha Singh, Marco Mattavelli
Venue: Proceedings of the Second International Conference on Automated Production of Cross Media Content for Multi-Channel Distribution (2006)

Traditional media, such as text, image, audio and video, have long been the main media resources and granted full support of standard desktop tools and applications. Interactive rich multimedia documents, adding resources such as video or synthetic animations and relying on complex synchronization among objects, are now making their entrance into the world as new multimedia formats emerge. In this context, the Synchronized Multimedia Integration Language (SMIL) is receiving more and more attention from content authors due to its fine property of multimedia synchronization and authoring interactivity for the content production. At the same time, MPEG-4 is designed to address the requirement of new generation of highly interactive multimedia applications, while simultaneously maintaining the support of traditional applications. MPEG-4 provides facilities (XMT and BIFS) to integrate and synchronize, spatially and temporally, many different media objects together. However, these facilities lack appropriate authoring tools to widen its audience and subsequently limit the application. In this paper, we present a comparative analysis between SMIL and XMT, the textual description of MPEG-4, to illustrate the pros and cons of these two major interactive media. And then we propose a conversion scheme from SMIL to the Binary Format for Scenes (BIFS) of MPEG-4 to take advantage of both formats. According to this scheme, we design the real implementation method using the current available tools and discuss the purpose and significance of such conversion.
A subband adaptive filter with the optimum analysis filter bank
Authors: H. Ochi, Y. Higa, S. Kinjo
Venue: Proceedings of the Acoustics, Speech, and Signal Processing, 1995. on International Conference - Volume 02 (1995)

Conventional subband ADFs (adaptive digital filters) using filter banks have shown degradation in performance because of the non-ideal nature of filters. For this problem, we propose a new type of subband ADF incorporating two types of analysis filter bank. In this paper, we show that we can design the optimum filter bank which minimizes the LMSE (least mean squared error). In other words, we can design a subband ADF with less MSE than that of conventional subband ADFs.
Digital Rights Management for Video Sensor Network
Authors: Taojun Wu, Liang Dai, Yuan Xue, Yi Cui
Venue: Proceedings of the Eighth IEEE International Symposium on Multimedia (2006)

Video sensor network is evolving from an isolated system to an integral component of the global information infrastructure. In this paper, we argue that when video sensor network becomes a public information source on the Internet, DRM (Digital Rights Management) must be enforced, due to the sensitivity and the privacy natures of sensor content. Moreover, existing DRM solutions do not suffice because the explicit one-to-one mapping between content producer and consumer does not apply in the sensor network domain. We propose a DRM-enabled content service architecture for video sensor network. Within this architecture, we propose a binary-tree-based hierarchical key generation scheme for data encryption, and adopt a label-guided watermarking strategy to address the unique challenges of video sensor content. We present the evaluation results of our solution based on a preliminary video sensor testbed system.
A Practical Multipurpose Watermarking Scheme for Visual Content Copyright Protection and Authentication
Authors: Zhifang Wang, Bian Yang, Xiamu Niu, Yijia Zhang
Venue: Proceedings of the 2006 International Conference on Intelligent Information Hiding and Multimedia (2006)

A practical multipurpose watermarking scheme is proposed for color image and video's copyright protection and authentication, which embeds a robust watermark and a reversible fragile watermark into different color components of a color image or video original frame. The robust watermark is constructed utilizing the method of square deviation modulation on image block coefficient distribution; and the reversible fragile watermark is employed utilizing a scrambled LSB embedding scheme for lossless authentication of copy-watermarked image. Simulation results show that the reversible fragile watermark has a bit-exact tampering detection ability while the robust watermark has a strong robustness to common distortions in practical applications such as small rotation, JPEG, filtering, brightness and contrast enhancement and additive Gaussian noise, etc.
Dynamic provisioning of lightpath services for radio astronomy applications
Authors: Jerry Sobieski, Tom Lehman, Bijan Jabbari, Chester Ruszczyk, Rick Summerhill, Alan Whitney
Venue: Future Generation Computer Systems (2006)

A demonstration at iGRID 2005 used dynamic, deterministic, and dedicated LightPath network services to link radio telescopes from around the world with computational facilities at the MIT Haystack Observatory to create a single coherent instrument for real-time astronomical and geodetic research. The "electronic Very Long Baseline Interferometry" (e-VLBI) application provides ultra-high resolution images of very faint and very distant objects in the universe. The application-specific network topology carried 2 Gbps of VLBI data from radio telescopes in Europe, North America, and Japan to Haystack for real-time correlation processing. This paper describes the application, the network technologies employed for the demonstration, the results, challenges and future work.
Simulation analysis of correlation and credit migration models for credit portfolios
Authors: William J. Morokoff
Venue: Proceedings of the 37th conference on Winter simulation (2005)

The market for derivatives such as first-to-default baskets and CDO tranches on portfolios of corporate credit exposures (bonds, loans, default swaps, etc.) has grown rapidly in recent years. Various models for capturing portfolio correlation effects have been introduced, with Default Time models becoming the most widely used. While attractive for their relative simplicity and ability, in some cases, to allow fast computation of hedge ratios, there is increasing concern around the limitations and implications of these models. This paper uses simulation to study the effects of credit migration and correlation assumptions underlying the models for valuation of derivatives on credit portfolios.
A Semi-Automatic Video Annotation tool with MPEG-7 Content Collections
Authors: Roberto Vezzani, Costantino Grana, Daniele Bulgarelli, Rita Cucchiara
Venue: Proceedings of the Eighth IEEE International Symposium on Multimedia (2006)

In this work, we present a general purpose system for hierarchical structural segmentation and automatic annotation of video clips, by means of standardized low level features. We propose to automatically extract some prototypes for each class with a context based intra-class clustering. Clips are annotated following the MPEG-7 standard directives to provide easier portability. Results of automatic annotation and semi-automatic metadata creation are provided.
CTL* model checking on a shared-memory architecture
Authors: Cornelia P. Inggs, Howard Barringer
Venue: Formal Methods in System Design (2006)

In this article we present the parallelisation of an explicit-state CTL* model checking algorithm for a virtual shared-memory high-performance parallel machine architecture. The algorithm uses a combination of private and shared data structures for implicit and dynamic load balancing with minimal synchronisation overhead. The performance of the algorithm and the impact that different design decisions have on the performance are analysed using both mathematical cost models and experimental results. The analysis shows not only the practicality and effective speedup of the algorithm, but also the main pitfalls of parallelising model checking for shared-memory architectures.
Ontology-based multi-agent system to multi-site software development
Authors: P. Wongthongtham, E. Chang, T. S. Dillon
Venue: Proceedings of the 2004 workshop on Quantitative techniques for software agile process (2004)

The disadvantages associated with remote communication rather than face-to-face communication is a key problem in the multi-site distributed software development environment. Awareness of what work has been done, what task has been misunderstood, what problems have been raised, what issues have been clarified, and understanding of why a team or a software engineer does not follow the project plan, and how to carry out a discussion over a multi-site distributed environment and to make a just-in-time decision are difficult parts in software engineering and project management. Consequently, these problems cause project delay and anxiety among teams and managers. Ontologies coupled with a multi-agents systems allow greater shall ease of communication by aggregating the agreed knowledge about the project, the domain knowledge, the concepts of software engineering and project management into a shared information resource platform and allow them to be shared among the distributed teams across the sites and enable the intelligent agents use the ontology as its knowledge repository to brain to carry out initial communication and classification with developers when the problem is raised in the first instance. We estimate that over 50% of issues can be ironed out by Agents. In this paper, we present the key challenges in multi-site software engineering and the ontology representation of common issues in software development. We demonstrate the agent communication with developers and the great potential of such a system to be used in the future of software engineering in multi-site environments.
Angular Voronoi Diagram with Applications
Authors: Tetsuo Asano, Hisao Tamaki
Venue: Proceedings of the 3rd International Symposium on Voronoi Diagrams in Science and Engineering (2006)

Given a set of line segments in the plane, we define an angular Voronoi diagram as follows: a point belongs to a Voronoi region of a line segment if the visual angle of the line segment from the point is smallest among all line segments. The Voronoi diagram is interesting in itself and different from an ordinary Voronoi diagram for a point set. After introducing interesting properties, we present an efficient algorithms for finding a point to maximize the smallest visual angle. Some applications to mesh improvement are also mentioned.
Covering Problems with Hard Capacities
Authors: Julia Chuzhoy
Venue: SIAM Journal on Computing (2006)

We consider the classical vertex cover and set cover problems with hard capacity constraints. This means that a set (vertex) can cover only a limited number of its elements (adjacent edges), and the number of available copies of each set (vertex) is bounded. This is a natural generalization of the classical problems which also captures resource limitations in practical scenarios.We obtain the following results. For the unweighted vertex cover problem with hard capacities we give a 3-approximation algorithm that is based on randomized rounding with alterations. We prove that the weighted version is at least as hard as the set cover problem, yielding an interesting separation between the approximability of weighted and unweighted versions of a "natural" graph problem. A logarithmic approximation factor for both the set cover and the weighted vertex cover problem with hard capacities follows from the work of Wolsey [Combinatorica, 2 (1982), pp. 385-393] on submodular set cover. We provide here a simple and intuitive proof for this bound.
You must be joking...: should the internet have an ON/OFF switch?
Authors: Michalis Faloutsos
Venue: ACM SIGCOMM Computer Communication Review (2006)

If despite your better judgment you decide to read this article, keep in mind that it was written during the summer, and this has been the hottest summer ever. To avoid such articles in the future, respond to the call below:Request for Contributions: Do you have a news-item of interest? Social gossip? Do you have a pressing question that needs a serious answer? Don't procrastinate: send me an email with "CCR" in the subject.
Facilitating inquiry using technology and teams in exercise physiology: the FITT project
Authors: Darla M. Castelli, Ellen M. Evans, Mark M. Misic
Venue: Proceedings of the 7th international conference on Learning sciences (2006)

The link between physical inactivity and disease has become a major public health priority. The aim of this project was to reform Exercise Physiology laboratory instruction through curriculum mapping and the implementation of inquiry-based modules. Use of a quasi-experimental design, content knowledge, interviews, modules, and a questionnaire provided evidence of student performance. There was a significant knowledge difference between groups and increased comfort with the majority of course content resulting from inquiry-based versus traditional instruction.
Novel Modulo 2^n + 1 Multipliers
Authors: H. T. Vergos, C. Efstathiou
Venue: Proceedings of the 9th EUROMICRO Conference on Digital System Design (2006)

A new modulo 2^n+1 multiplier architecture is proposed for operands in the normal representation. The novel architecture is derived by showing that all required correction factors can be merged into a single constant one and by treating this, partly as a partial product and partly by the final parallel adder. The proposed architecture utilizes a total of (n+1) partial products, each n bits wide and is built using an inverted end-around-carry, carry-save adder tree and a final parallel adder.
Optimization of filter banks using cyclostationary spectral analysis
Authors: S. Ohno, H. Sakai
Venue: Proceedings of the Acoustics, Speech, and Signal Processing, 1995. on International Conference - Volume 02 (1995)

Generally, the output of a filter bank for a stationary input signal is not stationary but cyclostationary. In this paper, by using cyclostationary spectral analysis, the spectral correlation density of this output is derived. Using this result we derive a criterion to construct an optimal 2-band perfect reconstruction filter bank which minimizes the averaged mean squared reconstruction error when the high pass band signal is dropped. By adding constrains to the filter coefficients, the biorthogonal filter bank, the conjugate quadrature filter bank and the biorthogonal linear phase filter bank are respectively obtained. Some numerical results are also presented for optimal biorthogonal and PR linear phase filter banks which are compared in terms of some performance measures.