ppxscal/embedding_network huggingface dataset:
Integrating Brain Data Spatially: Spatial Data Infrastructure and Atlas Environment for Online Federation and Analysis of Brain Images
Authors: Ilya Zaslavsky, Haiyun He, Joshua Tran, Maryann E. Martone, Amarnath Gupta
Venue: Proceedings of the Database and Expert Systems Applications, 15th International Workshop (2004)

Numerous digital atlases of the brain have been developed for different species through the efforts of researchers around the world. For a comprehensive picture of brain morphology and function, it is important to discover and bring together various images, segmentations and markup, generated within different projects, and juxtapose them within a single federated atlas interface. This paper describes strategies and tools for integrating distributed sources of brain data spatially. We focus on the organization of web-enabled spatial data sources which include ArcIMS feature and image services and distributed grid sources, and on the Smart Atlas, a GIS-based atlas environment enabling users to discover, access, visualize and query heterogeneous images and image markup. We demonstrate construction of spatial databases from unorganized vector and raster brain data based on ontological relationships between anatomical features from the Unified Medical Language System, spatial registration mechanisms, and tools and user interfaces for federated brain data visualization and analysis.
Some progress on (v, 4, 1) difference families and optical orthogonal codes
Authors: R. Julian R. Abel, Marco Buratti
Venue: Journal of Combinatorial Theory Series A (2004)

Some new classes of optimal (v, 4, 1) optical orthogonal codes are constructed. First, mainly by using perfect difference families, we establish that such an optimal OOC exists for v ≤ 408, v ≠ 25. We then look at larger (p, 4, 1) OOCs with p prime; some of these codes have the nice property that the missing differences are the (r - 1)th roots of unity in Zp, (r being the remainder of the Euclidean division of p by 12) and we prove that for r = 5 or 7 they give rise to (rp, 4,1) difference families. In this way we are able to give a strong indication about the existence of (5p,4,1) and (7p,4, 1) difference families with p a prime ≡ 5, 7 mod 12 respectively. In particular, we prove that for a given prime p ≡ 7 mod 12, the existence of a (7p,4, 1) difference family is assured (1) if p < 10,000 or (2) if ω is a given primitive root unity in Zp and we have 3 ≡ ωi (mod p) with gcd(i, p-1/6) < 20.Finally, we remove all undecided values of v ≤ 601 for which a cyclic (v, 4, 1) difference family exists, and we give a few cyclic pairwise balanced designs with minimum block size 4.
Low distortion maps between point sets
Authors: Claire Kenyon, Yuval Rabani, Alistair Sinclair
Venue: Proceedings of the thirty-sixth annual ACM symposium on Theory of computing (2004)

We initiate the study of the minimum distortion problem: given as input two n-point metric spaces, find a bijection between them with minimum distortion. This is an abstraction of certain geometric problems in shape and image matching, and is also a natural variation and extension of the fundamental problems of graph isomorphism and bandwidth. Our focus is on algorithms that find an optimal (or near-optimal) bijection when the distortion is fairly small. We present a polynomial time algorithm that finds an optimal bijection between two line metrics, provided the distortion is less than 3+2√2. We also give a parameterized polynomial time algorithm that finds an optimal bijection between an arbitrary unweighted graph metric and a bounded-degree tree metric.
A Game Theoretic Approach to Dynamic Energy Minimization in Wireless Transceivers
Authors: Ali Iranli, Hanif Fatemi, Massoud Pedram
Venue: Proceedings of the 2003 IEEE/ACM international conference on Computer-aided design (2003)

Adaptive transceivers can significantly reduce the energyconsumption of a mobile, battery-powered node by capturing real-timechanges in the communication channel. This paper proposes agame-theoretic solution to the optimization of the energy consumptionin wireless transceivers. This is accomplished by dynamicallyadapting the modulation level of the transmitter modulator and theerror correction aptitude of the receiver decoder with respect tochannel conditions subject to specified average bit-error-rate andthroughput constraints. Experimental results demonstrate energysavings of up to 15%.
Polynomiality of an inexact infeasible interior point algorithm for semidefinite programming
Authors: Guanglu Zhou, Kim-Chuan Toh
Venue: Mathematical Programming: Series A and B (2004)

In this paper we present a primal-dual inexact infeasible interior-point algorithm for semidefinite programming problems (SDP). This algorithm allows the use of search directions that are calculated from the defining linear system with only moderate accuracy, and does not require feasibility to be maintained even if the initial iterate happened to be a feasible solution of the problem. Under a mild assumption on the inexactness, we show that the algorithm can find an &#x03b5;-approximate solution of an SDP in O(n2ln(1/&#x03b5;)) iterations. This bound of our algorithm is the same as that of the exact infeasible interior point algorithms proposed by Y. Zhang.
Holistic UDAFs at streaming speeds
Authors: Graham Cormode, Theodore Johnson, Flip Korn, S. Muthukrishnan, Oliver Spatscheck, Divesh Srivastava
Venue: Proceedings of the 2004 ACM SIGMOD international conference on Management of data (2004)

Many algorithms have been proposed to approximate holistic aggregates, such as quantiles and heavy hitters, over data streams. However, little work has been done to explore what techniques are required to incorporate these algorithms in a data stream query processor, and to make them useful in practice.In this paper, we study the performance implications of using user-defined aggregate functions (UDAFs) to incorporate selection-based and sketch-based algorithms for holistic aggregates into a data stream management system's query processing architecture. We identify key performance bottlenecks and tradeoffs, and propose novel techniques to make these holistic UDAFs fast and space-efficient for use in high-speed data stream applications. We evaluate performance using generated and actual IP packet data, focusing on approximating quantiles and heavy hitters. The best of our current implementations can process streaming queries at OC48 speeds (2x 2.4Gbps).
A Hybrid Shape Representation for Free-Form Modelling
Venue: Proceedings of the Shape Modeling International 2004 (2004)

In this paper, we introduce a hybrid modeling frameworkfor creating complex objects. Our system relies on an extendedCSG tree that assembles skeletal implicit surfacesand polygonal meshes in a coherent fashion: we call thisstructure the HybridTree. Editing operations are performedby exploiting the complementary abilities of both implicitand parametric surface representations. Implicit surfacesare powerful for combining shapes with Boolean and blendingoperations, while polygonal meshes are well-suited forlocal deformations such as FFD and fast visualization. Theevaluation of the HybridTree is performed on the fly eitherthrough field function queries when the implicit form is required,or through a mesh creation process which is specificand optimized for every kind of node. Both types of queriesare achieved in a complete transparent way for the user.
Process optimization and characterization of deep metal-junction contact
Authors: Junghwan Lee, Jaehan Cha
Venue: Microelectronic Engineering (2004)

In this paper, we elaborate a process optimization of deep metal contact in 0.25 µm embedded DRAM technology and investigate its electrical characteristic. The contact size is 0.32 µm and its height is varied between 2.1 and 3.8 µm which give aspect ratio from 6.7 to 11.9. It appears that both Ti thickness and aspect ratio play important role on contact resistance. Especially, P+ contact resistance is more sensitive to these parameters. P+ contact resistance in contact array is increased from 1 to 4 KΩ per contact when Ti thickness decreases from 900 to 500 Å, while N+ contact resistance is just increased from 300 to 400 Ω. TEM image reveals that the degree of Ti silicidation depends on the Ti thickness. The boundary between silicon and TiSi2 is non-uniform with Ti thickness of 500 Å, however, it becomes uniform and flat with Ti thickness of 900 Å. To characterize the behavior of current flow in various contacts, both contact array and Kelvin resistor patterns are used. It appears that Schottky barrier plays major role at low voltage region, while the spreading resistance dominates at high voltage region and thus contact resistance approaches to 220 Ω at high voltage region regardless of process condition. The Schottky barrier evaluated by thermionic emission model increases with decreasing Ti thickness and increasing aspect ratio. It appears that a relationship between Schottky barrier and process parameters is given by Schottky barrier energy = (Ti thickness)-0.26 × (aspect ratio)0.53.
An Operational Data Store for Reporting Clinical Practice Guideline Adherence in Chronic Disease Patients
Authors: Carolyn K. Hamm, Matthew R. Kennedy, Timothy T. Wu, Jill S. Phillips
Venue: Proceedings of the 17th IEEE Symposium on Computer-Based Medical Systems (2004)

An operational data store was designed to extract, load and transform data contained in atransactional outcomes management database. The system was designed to be easilyupdatable from the production environment, and provide rapid, widely accessible reportingcapabilities. Clinical practice guideline success data, patient-reported outcomes measures,and clinical patient data were collected from many systems to populate the data warehouseand data store. Five years of patient data in the Walter Reed Health Care System have beenloaded, and refreshed on an on-going periodic basis. Reporting tools enabled users to drilldown from the hospital, to clinic, to provider level for compliance measures, success rates, and various other metrics. The operational data store helped the Walter Reed Health Care System achieve certification in six disease-specific care Certifications of Distinction from the Joint Commission on Accreditation of Healthcare Organizations.
Navigating through the Biological Maze
Authors: Zoe Lacroix, Kaushal Parekh, Louiqa Raschid, Maria Esther Vidal
Venue: Proceedings of the 2004 IEEE Computational Systems Bioinformatics Conference (2004)

Advances in genome science have created a surge of data. These data critical to scientific discovery are made available in thousands of heterogeneous public resources. Each of these resources provides biological data with a specific data organization, format, and quality, object identification, and a variety of capabilities that allow scientists to access, analyze, cluster, visualize and navigate through the datasets. The heterogeneity of biological resources and their increasing number make it difficult for scientists to exploit and understand them. Learning the properties of a new resource is a tedious and time-consuming process, often made more difficult by the many changes made on the resources (new or changed information, capabilities) that stress scientists keeping their knowledge up-to-date. Therefore many scientists master a few resources while ignoring others that may provide additional data and useful capabilities.
The Evolution of Composition Framework in a Distributed System Toolkit
Authors: Casey K. Fung, Stephen A. Uczekaj, Guijun Wang, Scott A. Moody
Venue: Proceedings of the IEEE International Conference on Web Services (2004)

Network Centric Information Infrastructure (NCII) is atoolkit of prefabricated software components together witha composition framework for integration andexperimentation. Typical distributed system applicationsof a toolkit such as NCII can be applied to air trafficmanagement, shop floor control and in-flight connectionto Internet. The composition framework has gone thoughthrough three generations of changes in the past five yearsand it is a good illustration of a paradigm shift fromObject-Oriented Architecture, through Component-BasedArchitecture to Service-Based Architecture.
Subwebs for specialized search
Authors: Raman Chandrasekar, Harr Chen, Simon Corston-Oliver, Eric Brill
Venue: Proceedings of the 27th annual international ACM SIGIR conference on Research and development in information retrieval (2004)

We describe a method to define and use subwebs, user-defined neighborhoods of the Internet. Subwebs help improve search performance by inducing a topic-specific page relevance bias over a collection of documents. Subwebs may be automatically identified using a simple algorithm we describe, and used to provide highly-relevant topic-specific information retrieval. Using subwebs in a Help and Support topic, we see marked improvements in precision compared to generic search engine results.
Adaptive reservations in a Linux environment
Venue: Proceedings of the 10th IEEE Real-Time and Embedded Technology and Applications Symposium (2004)

In this paper, we address the problem of adaptively reservingthe CPU to concurrent soft real-time tasks, in orderto meet target Quality of Service requirements. First, wepresent two new techniques inspired to the idea of stochasticcontrol. Then, we present a flexible and modular softwarearchitecture suitable for adaptive scheduling, realisedas a minimally invasive set of modifications to the LinuxKernel. Finally, we show experimental results that validateour approach and prove its effectiveness in the context ofmultimedia applications.
Comparison of resonant tunneling currents in double gate MOS diodes with metal and Poly-Silicon gates
Authors: Bogdan Majkusiak
Venue: Microelectronic Engineering (2004)

A purpose of this work is to investigate theoretically the electron resonant tunneling current through the gate - SiO2- Si-SiO2-gate system. The resonant tunneling current is calculated and analyzed in dependence on bias voltage for two kinds of the gate material: metal (aluminum) gate and n+-poly-silicon gate.
Runtime Verification of Timing and Probabilistic Properties using WMI and .NET
Authors: Jane Jayaputera, Iman Poernomo, Heinz Schmidt
Venue: Proceedings of the 30th EUROMICRO Conference (2004)

Reliability and availability are key issues to distributed service-oriented systems. In this paper, we present a methodology for run-time verification of reliability and availability properties for distributed architectures. Our approach generalizes the concept of design-by-contract to contracts involving time and probabilities. We define a language for contracts based on Probabilistic real time Computational Tree Logic (PCTL). We provide a formal semantics for this language based on possibile execution traces of a system. Then we describe a .NET-based system for monitoring contracts, built upon the Windows Management Instrumentation (WMI) framework.
Development of a Knowledge-Based Multi-Scheme Cancer Microarray Data Analysis System
Authors: John H. Phan, Chang F. Quo, Kejiao Guo, Weimin Feng, Geoffrey Wang, May D. Wang
Venue: Proceedings of the 2004 IEEE Computational Systems Bioinformatics Conference (2004)

Comparing genes expressed in normal and diseased states assists the understanding of cancer pathophysiology, detection, prognosis, and therapeutic target study. Many existing expression analysis papers show that microarray data are usually case dependent, have small sample (patients) sizes, and have large gene dimensions. Thus, we have been developing a robust multi-parameter, multi-scheme knowledge-based optimization system that integrates the strengths of statistics, pattern-recognition, and support vector machines (SVM). The optimization logic identifies optimal cancer signature genes by utilizing different analysis models based on unsupervised and supervised clustering. Our system is being finalized by testing over public and in-house datasets with the intention of validation through clinical knowledge feedback.
IP Traffic Modeling: Most Relevant Time-Scale and Local Poisson Property
Authors: Tetsuya Takine, Kentaro Okazaki, Hiroyuki Masuyama
Venue: Proceedings of the International Conference on Informatics Research for Development of Knowledge Society Infrastructure (2004)

This paper considers IP traffic modeling to evaluate thepacket loss probability. It is well-known that IP traffic showslong-range dependence or self-similarity in a long time-scale,whereas it looks random in a short time-scale. Thuswe consider the branching Poisson process that has sucha multiple time-scale feature. We focus on a queue fed bybranching Poisson input and briefly discuss the local Poissonproperty in a short time-scale. Further we construct anequivalent MMPP input in such a sense that the packet lossprobability can be predicted by evaluating the queue fed bythe MMPP input.
A Finite Model Theory for Biological Hypotheses
Authors: Stephen Racunas, Christopher Griffin, Nigam Shah
Venue: Proceedings of the 2004 IEEE Computational Systems Bioinformatics Conference (2004)

We have designed and implemented a set of software tools for the composition and evaluation of hypotheses about gene regulation in biological systems. Our software uses a unified formal grammar for the representation of both diagram-based and text-based hypotheses. The objective of this paper is to show how to use this grammar as the basis for an effective logic for specifying hypotheses about biological systems in precise model-theoretic terms. To accomplish this, we take inspiration from inflationary extensions to fixed point logics and define a new type of logic: a deflationary logic for describing the effects of experiments upon models of biological systems. We present results that characterize decidability, satisfiability, and inflationary/deflationary properties of this logic. We formally define what it means for a set of assertions to be discoverable under this new logic, and show that our software generates discoverable queries. Thus, we lay the groundwork for a formal treatment of machine-aided experimental design under the conceptual framework we have developed for our hypothesis evaluation software.
Extreme re-balancing for SVMs: a case study
Authors: Bhavani Raskutti, Adam Kowalczyk
Venue: ACM SIGKDD Explorations Newsletter (2004)

There are many practical applications where learning from single class examples is either, the only possible solution, or has a distinct performance advantage. The first case occurs when obtaining examples of a second class is difficult, e.g., classifying sites of "interest" based on web accesses. The second situation is exemplified by the gene knock-out experiments for understanding Aryl Hydrocarbon Receptor signalling pathway that provided the data for the second task of the KDD 2002 Cup, where minority one-class SVMs significantly outperform models learnt using examples from both classes.This paper explores the limits of supervised learning of a two class discrimination from data with heavily unbalanced class proportions. We focus on the case of supervised learning with support vector machines. We consider the impact of both sampling and weighting imbalance compensation techniques and then extend the balancing to extreme situations when one of the classes is ignored completely and the learning is accomplished using examples from a single class.Our investigation with the data for KDD 2002 Cup as well as text benchmarks such as Reuters Newswire shows that there is a consistent pattern of performance differences between one and two-class learning for all SVMs investigated, and these patterns persist even with aggressive dimensionality reduction through automated feature selection. Using insight gained from the above analysis, we generate synthetic data showing similar pattern of performance.
A note on the 29-th Smarandache's problem
Authors: Liu Hongyan, Lou Yuanbing
Venue: Smarandache Notions Journal (2004)

Let n be a positive integer, ak(n) be the k-th complement number of n. In this paper, we study the mean value properties of the k-th complement number sequences, and give an interesting asymptotic formula.
SPIDER: Software for Protein Identification from Sequence Tags with De Novo Sequencing Error
Authors: Yonghua Han, Bin Ma, Kaizhong Zhang
Venue: Proceedings of the 2004 IEEE Computational Systems Bioinformatics Conference (2004)

For the identification of novel proteins using MS/MS, de novo sequencing software computes one or several possible amino acid sequences (called sequence tags) for each MS/MS spectrum. Those tags are then used to match, accounting amino acid mutations, the sequences in a protein database. If the de novo sequencing gives correct tags, the homologs of the proteins can be identified by this approach and software such as MS-BLAST is available for the matching. However, de novo sequencing very often gives only partially correct tags. The most common error is that a segment of amino acids is replaced by another segment with approximately the same masses. We developed a new efficient algorithm to match sequence tags with errors to database sequences for the purpose of protein and peptide identification. A software package, SPIDER, was developed and made available on Internet for free public use. This paper describes the algorithms and features of the SPIDER software.
Guest Editor's Introduction: Wired on Wireless
Authors: William A. Arbaugh
Venue: IEEE Security and Privacy (2004)

In the past few years, weýve seen wireless keyboards, mice, headsets, broadband networking, and even high-fidelity speakers. Radio frequency-based productsý move toward the consumer space has greatly reduced the equipmentýs price, and this in turn has caused a groundswell of new consumer- and enterpriseoriented products that use wireless technology. This, however, creates the potential for security and privacy problems--the focus of this special issue. The articles in this issue aim to have frank and open debates on the problems as well as advantages so that the results benefit everyone.
Toponym resolution in text (abstract only): "which sheffield is it?"
Authors: Jochen L. Leidner
Venue: Proceedings of the 27th annual international ACM SIGIR conference on Research and development in information retrieval (2004)

Named entity tagging comprises the sub-tasks of identifying a text span and classifying it, but this view ignores the relationship between the entities and the world. Spatial and temporal entities ground events in space-time, and this relationship is vital for applications such as question answering and event tracking. There is much recent work regarding the temporal dimension (Setzer and Gaizauskas 2002, Mani and Wilson 2000), but no detailed study of the spatial dimension.I propose to investigate how spatial named entities (which are often referentially ambiguous) can be automatically resolved with respect to an extensional coordinate model (toponym resolution). To this end, various information sources including linguistic cue patterns, co-occurrence information, discourse/positional information, world knowledge (such as size and population) as well as minimality heuristics (Leidner et al. 2003) will be combined in a supervised machine learning regime.The major contributions of this research project will be a corpus of text manually annotated for spatial named entities with their model correlates as a training and evaluation resource, a novel method to spatially ground toponyms in text and a component-based evaluation based on this new reference corpus.
Reachable Regions for Spiral Segments and Applications in Geometric Modelling
Authors: Zulfiqar Habib, Manabu Sakai
Venue: Proceedings of the International Conference on Computer Graphics, Imaging and Visualization (2004)

We obtain a G^2 fair curve by adding a spiral segment to one end of an existing curve. The added segments are cubic and Pythagorean hodograph quintic spirals. We derive the more explicit reachable regions for the end points of the added spirals. Spiral segments are useful in the design of fair curves. The advantage of our technique is its more flexible control of the curvature and inflection points of a designed curve.