ppxscal/embedding_network huggingface dataset:
A HIDDEN MARKOV MODEL THAT FINDS GENES IN E. COLI DNA
Authors: Anders Krogh, I. S Mian, David Haussler
Venue:  (1994)

A hidden Markov model (HMM) has been developed to find protein coding genes in E. coli DNA using E. coli genome DNA sequence from the EcoSeq6 database maintained by Kenn Rudd. This HMM includes states that model the codons and their frequencies in E. coli genes, as well as the patterns found in the intergenic region, including repetitive extragenic palindromic sequences and the Shine-Delgarno motif. To account for potential sequencing errors and or frameshifts in raw genomic DNA sequence, it allows for the (very unlikely) possiblity of insertions and deletions of individual nucleotides within a codon. The parameters of the HMM are estimated using approximately one million nucleotides of annotated DNA in EcoSeq6 and the model tested on a disjoint set of contigs containing about 325,000 nucleotides. The HMM finds the exact locations of about 80% of the known E. coli genes, and approximate locations for about 10%. It also finds several potentially new genes, and locates several places were insertion or deletion errors and or frameshifts may be present in the contigs. Based on further examination and analysis of the results from the parser, we describe a new putative S-adenosyl-L-methionine methyltransferase domain that appears to be present in proteins from a variety of phylogenetically diverse organisms and organelles.
Dynamic Load Sharing within Workstation Clusters
Authors: Paul S Williams, Roberto Togneri
Venue:  (1994)

Workstation clusters make a collection of computing resources appear to be a single entity, resulting in a high level of service transparency. Although services and resources seem to be fully distributed, processes still operate on a single machine, causing the potential for a load imbalance. An analysis is conducted to determine the general characteristics and behaviour of the networked environment, in an attempt to discover how various system resources interact with respect to job throughput and user interaction time. The concept of matching a set of user task requirements to the most suitable machine is presented. In order to effectively achieve this, the factors affecting job completion time and user interaction delays are examined in depth. Quantitative and qualitative analyses of theoretical load sharing methods and issues are examined in order to produce an effective and well engineered load sharing system. The system is configurable, robust and reliable, offering a standard interface. It performs load sharing based on numerous types of system loads and outperforms other, more common, load sharing methods. Finally, it is determined that in order to make an optimal initial placement decision, the system must take into account the user job characteristics as well as the long term load statistics of each applicable workstation within the cluster.
Design and Analysis of a Multimedia Network Architecture
Authors: Robert Christie
Venue:  (1995)

A paradigm shift is underway in how computer networks are used. The new breed of applications that incorporate multimedia add a new dimension of complexity to network management because their service requirements are quite different from those of older applications. The problem lies in the service discipline of the network, where routers generally use a single queue which operates in a first-come-first-served manner. As traffic through the router increases, packet delays become longer to the point where the router''s internal queue overflows and packets are dropped. This project addresses the design of a packet-switched network that can support soft real-time applications such as multimedia. We focus on the communications protocol, the router design, and the resource reservation and admission control policies that will allow the overall system to operate. We provide a survey of related work on design issues concerning network service paradigms, traffic policing mechanisms, resource administration mechanisms, and resource reservation protocols. We then discuss the design and implementation of our router, end-systems, and admission control policies. We show that with the proper choice of protocols, traffic policing, and resource reservation within the router, a packet-switched network can support guaranteed quality-of-service for multimedia communications. The ACM Portal is published by the Association for Computing Machinery. Copyright © 2010 ACM, Inc. Terms of Usage Privacy Policy Code of Ethics Contact Us Useful downloads: Adobe Acrobat QuickTime Windows Media Player Real Player
Sparse LU Factorization with Partial Pivoting on Distributed Memory Machines
Authors: Cong Fu, Tao Yang
Venue:  (1996)

Sparse LU factorization with partial pivoting is important to many scientific applications, but the effective parallelization of this algorithm is still an open problem. The main difficulty is that partial pivoting operations make structures of $L$ and $U$ factors unpredictable beforehand. This paper presents a novel approach called $S^*$ for parallelizing this problem on distributed memory machines. $S^*$ incorporates static symbolic factorization to avoid run-time control overhead and uses nonsymmetric L/U supernode partitioning and amalgamation strategies to maximize the use of BLAS-3 routines. The irregular task parallelism embedded in sparse LU is exploited using the RAPID run-time system which optimizes asynchronous communication, overlaps computation with communication and balances processor loads. The experimental results on the Cray-T3D with a set of Harwell-Boeing nonsymmetric matrices are very encouraging and good scalability has been achieved. Even compared to a highly optimized sequential code, the parallel speedups are still impressive considering the current status of sparse LU research.
Specification of Realtime Systems Using ASTRAL
Authors: Alberto Coen-Porisini, Carlo Ghezzi, Richard A. Kemmerer
Venue:  (1997)

ASTRAL is a formal specification language for realtime systems. It is intended to support formal software development and, therefore, has been formally defined. The structuring mechanisms in ASTRAL allow one to build modularized specifications of complex systems with layering. A realtime system is modeled by a collection of state machine specifications and a single global specification. This paper discusses the rationale of ASTRAL''s design. ASTRAL''s specification style is illustrated by discussing a telephony example. Composability of one or more ASTRAL system specifications is also discussed by the introduction of a composition section, which provides the needed information to combine two or more ASTRAL system specifications into a single new one. Finally, this paper discusses the current status of the ASTRAL software development environment.
Finite element predictions of the dynamic effects on a adjacent structure
Authors: A. Rouaiguia, I. Jefferson
Venue: Proceedings of the eighth international conference on The application of artificial intelligence to civil and structural engineering computing (2001)

Dynamic compaction is a well-established soil improvement method, used to densify loose deposits of cohesionless soil by means of high energy impact. This heavy tamping is achieved by dropping a heavy mass of 10-40 tonnes from a height generally varying between 10 and 25 m onto predetermined grid points on the ground. This paper describes numerical simulation study of dynamic compaction process by using LUSAS©[1] to generate a full axisymmetric elasto-platic finite element representation of soils. Examples show the analysis of a pounder dynamically impacting the soil. The cylindrical pounder is of 1 m in length and has a diameter of 2.5 m. Computed results such as pounder penetration during impact, drop mass effect, height of drop, horizontal and vertical displacements, and peak particle velocity attenuation from different distances of the impact point are presented. The numerical results were quite consistent with published data.
Integrity Constraints in Federated Database Design
Authors: Stefan Conrad, Hö, Michael ding, S. Jannsen, Gunter Saake, Ingo Schmitt, T&uuml, Can rker
Venue:  (1996)

In this paper we demonstrate the application of a methodology for federated database design. Federated database design includes the transformation of heterogeneous local schemata from the native data models of the component database systems into a common data model, the integration of these homogenized schemata into the federated schema, and the derivation of external schemata for global applications. Our methodology seamlessly captures all phases from schema transformation and integration up to derivation of external schemata. Our approach differs from other recently proposed methodologies because we consider integrity constraints throughout all phases and use them for resolving conflicts. Therefore, the main focus of this paper is the treatment of integrity constraints and their evolution in the federated database design process. For resolving conflicts which arise during the transformation and integration process the consideration of integrity constraints can be useful, although the process becomes more complicated. Taking constraints into account provides a better understanding of conflicts. The constraints can be used to judge possible resolutions of conflicts. For certain kinds of conflicts we have to add new global constraints, but often there is not a unique and predictable choice of additional global constraints. The way of resolving such conflicts also depends on the intended semantics of the federated schema and, thereby, on the intended global applications. Sometimes, situations arise where there is even not a consistent solution for all conflicts together. Therefore, a methodology for federated database design must be prepared to make compromises.
Fast Content-Based Packet Handling for Intrusion Detection
Authors: Mike Fisk, George Varghese
Venue:  (2001)

It is becoming increasingly common for network devices to handle packets based on the contents of packet payloads. Example applications include intrusion detection, firewalls, web proxies, and layer seven switches. This paper analyzes the problem of intrusion detection and its reliance on fast string matching in packets. We show that the problem can be restructured to allow the use of more efficient string matching algorithms that operate on sets of patterns in parallel. We then introduce and analyze a new string matching algorithm that has average-case performance that is better than the best theoretical algorithm (Aho-Corasick) and much better than the currently deployed algorithm (multiple iterations of Boyer-Moore). Finally, we implement these algorithms in the popular intrusion detection platform Snort and analyze their relative performance on actual packet traces. Our results provide lessons on the structuring of content-based handlers, string matching algorithms in general, and the importance of performance to security.
Analysis of Function Component Complexity for Hypercube Homotopy Algorithms
Authors: Amal Chakraborty, Donald C. S. Allison, Calvin J. Ribbens, Layne T. Watson
Venue:  (1991)

Probability-one homotopy algorithms are a class of methods for solving nonlinear systems of equations that are globally convergent from an arbitrary starting point with probability one. The essence of these homotopy algorithms is the construction of a homotopy map ra and the subsequent tracking of a smooth curve g in the zero set ra-1 (0) of ra . Tracking the zero curve g requires repeated evaluation of the map ra its n x (n + 1) Jacobian matrix Dra , and numerical linear algebra for calculating the kernel of Dra . This paper analyzes parallel homotopy algorithms on a hypercube, briefly reviewing the numerical linear algebra, several communication topologies and problem decomposition strategies, and concentrating on function component complexity, problem size, and the effect of different component complexity distributions. These parameters interact in complicated ways, but some general principles can be inferred based on empirical results. Implications for developing reliable and efficient parallel mathematical software packages for this problem area are also discussed.
Simplifying annotation support for real-world-settings: a comparative study of active reading
Authors: Hartmut Obendorf
Venue: Proceedings of the fourteenth ACM conference on Hypertext and hypermedia (2003)

Despite the multitude of existing interfaces for annotation, little is known about their influence on the created annotations. In this paper, first findings of a comparative video-supported study of active reading are presented. The support for active reading offered by traditional paper-and-pencil vs. two existing annotation tools for the World Wide Web is examined and possible implications for annotation systems are drawn.An immediate conclusion is the existence of a strong need for simplicity and the importance of generic tools that can be adapted to the user's task at hand.
A Smooth Subdivision Scheme for Hexahedral Meshes
Authors: Chandrajit L. Bajaj, Joe Warren, Guoliang Xu
Venue:  (2001)

In a landmark paper, Catmull and Clark described a simple generalization of the subdivision rules for bi-cubic B-splines to arbitrary quadrilateral surface meshes. This smooth subdivision scheme has become a mainstay of surface modeling systems. Joy and MacCracken described a generalization of this surface scheme to volume meshes. Unfortunately, little is known about the smoothness and regularity of this scheme due to the complexity of the subdivision rules. This paper presents an alternative subdivision scheme for hexahedral volume meshes that consists of a simple split and average algorithm. Along extraordinary edges of the volume mesh, the scheme provably converges to a smooth limit volume. At extraordinary vertices, the authors supply strong experimental evidence that the scheme also converges to a smooth limit volume. The scheme automatically produces reasonable rules for non-nianifold topology and can easily be extended to incorporate boundaries and embedded creases expressed as Catmull-Clark surfaces and
Complexity, Gratuitous and Otherwise
Authors: Christopher deSilva, Michael Alder, Yianni Attikiouzel
Venue:  (1991)

Abstract unavailable.
Definitive Principles and the Specification of Software
Authors: W. M. Beynon, S. B. Russ, M. Slade, Y. P. Yung, Y. W. Yung
Venue:  (1989)

We investigate a novel approach to programming and specification that aims to support both incremental development and interactive validation. The specification of the behaviour of several agents interacting in a room is viewed as a process of design and simulation. The resemblance between state changes in design (such as moving a shelf) and those in simulation (such as opening a door) motivates a unified representation. The distinction between design and simulation is conventionally reflected in the representation (cf the editing and execution of a program), but it can be better understood in terms of the privileges for action of agents. The action of an agent in a state is expressed within a definitive (definition-based) programming paradigm by a system of definitions specifying systems within an appropriate abstract family of variables. Such use of definitive systems within an appropriate abstract machine model facilitates the representation of the actions associated with each agent and the formalisation of a design in terms of possible agent interactions. The paper concludes with a brief review of the progress to date on the definitive programming project.
Photometric Method for Radiometric Dorrection of Multispectral Scanner Data
Authors: R. J. Woodham, T. K. Lee
Venue:  (1984)

Radiometric correction of multispectral scanner data requires physical models of image formation in order to deal with variations in topography, scene irradiance, atmosphere and viewing conditions. The scene radiance equation is more complex for rugged terrain than for flat terrain since it must model elevation, slope and aspect dependent effects. A simple six parameter model is presented to account for differential amounts of solar irradiance, sky irradiance and path radiance across a scene. The model uses the idea of a reflectance map to represent scene radiance as a function of surface orientation. Scene radiance is derived from the bidirectional reflectance distribution function (BRDF) of the surface material and a distribution of light sources. The sun is treated as a collimated source and the sky is treated as a uniform hemispherical source. The atmosphere adds further complication and is treated as an optically thin, horizontally uniform layer. The required six parameters account for atmospheric effects and can be estimated when a suitable digital terrain model (DTM) is available. This is demonstrated for Landsat MSS images using a test site near St. Mary Lake in southeastern British Columbia. An intrinsic surface albedo is estimated at each point, independent of how that point is illuminated and viewed. It is argued that earlier conclusions about the usefulness of the Lambertian assumption for the radiometric correction of multispectral scanner data were premature. Correction methods proposed in the literature fail even if the surface is Lambertian. This is because sky irradiance is significant and must be dealt with explicitly, especially for slopes approaching the grazing angle of solar incidence.
Quantum Signal Propagation in Depolarizing Channels
Authors: Nicholas Pippenger
Venue:  (2001)

Quantum Signal Propagation in Depolarizing Channels Nicholas Pippenger Abstract: Let X be an unbiassed random bit, let Y be a qubit whose mixed state depends on X, and let the qubit Z be the result of passing Y through a depolarizing channel, which replaces Y with a completely random qubit with probability p. We measure the quantum mutual information between X and Y by T(X; Y) = S(X) + S(Y) - S(X,Y), where S(...) denotes von Neumann''s entropy. (Since X is a classical bit, the quantity T(X; Y) agrees with Holevo''s bound chi(X; Y) to the classical mutual information between X and the outcome of any measurement of Y.) We show that T(X;Z) >= (1-p)^2 T(X;Y). This generalizes an analogous bound for classical mutual information due to Evans and Schulman, and provides a new proof of their result.
Design and Analysis of Embedded Real-Time Systems: An Elevator Case Study
Authors: Yang Zhang, Alan K. Mackworth
Venue:  (1993)

Constraint Nets have been developed as an algebraic on-line computational model of robotic systems. Timed forall-automata have been studied as a logical specification language of real-time behaviors. A general verification method has been proposed for checking whether a constraint net model satisfies a timed forall-automaton specification. In this paper, we illustrate constraint net modeling and timed forall-automata analysis using an elevator example. We start with a description of the functions and user interfaces of a simple elevator system, and then model the complete system in Constraint Nets. The analysis of a well-designed elevator system should guarantee that any request will be served within some bounded time. We specify such requirements in timed forall-automata, and show that the constraint net model of the elevator system satisfies the timed forall-automaton specification.
Cluster Algebra: A Query Language for Heterogeneous Databases
Authors: Bharat Bhasker, Csaba J. Egyhazy, Konstantinos Triantis
Venue:  (1992)

This report describes a query language based on algebra for heterogeneous databases. The database logic is used as a uniform framework for studying the heterogeneous databases. The data model based on the database logic is referred to as cluster data model in this report. Generalized Structured Query Language (GSQL) is used for expressing ad-hoc queries over the relational, hierarchical and network database uniformly. For the purpose of query optimization, a query language that can express the primitive heterogeneous database operations is required. This report describes such a query language for the clusters (i.e., heterogeneous databases). The cluster algebra consists of (a) generalized relational operations such as selection, union, intersection, difference, semi-join, rename and cross-product; (b) modified relational operations such as normal projection and normal join; and (c) new operations such as normalize, embed, and unembed.
Enhanced web document summarization using hyperlinks
Authors: J.-Y. Delort, B. Bouchon-Meunier, M. Rifqi
Venue: Proceedings of the fourteenth ACM conference on Hypertext and hypermedia (2003)

This paper addresses the issue of Web document summarization. As textual content of Web documents is often scarce or irrelevant and existing summarization techniques are based on it, many Web pages and websites cannot be suitably summarized. We consider the context of a Web document by the textual content of all the documents linking to it. To summarize a target Web document, a context-based summarizer has to perform a preprocessing task, during which it will be decided which pieces of information in the source documents are relevant to the content of the target. Then a context-based summarizer faces two issues: first, the selected elements may partially deal with the topic of the target, second they may be related to the target and yet not contain any clues about the content of the target.In this paper we put forward two new summarization by context algorithms. The first one uses both the content and the context of the document and the second one is based only on the elements of the context. It is shown that summaries taking into account the context are usually much more relevant than those made only from the content of the target document. Optimal conditions of the proposed algorithms with respect to the sizes of the content and the context of the document to summarize are studied.
Positivity Conditions for Quartic Polynomials
Authors: Gary Ulrich, Layne T. Watson
Venue:  (1990)

Simple necessary and sufficient conditions that a quartic polynomial f(z) be non-negative for z greater than or equal to 0 or a is less than or equal to z and z is less than or equal to b are derived, and illustrated geometrically. The geometry provides considerable insight and suggests various approximations and computational simplifications. The theory is applied to monotone quintic spline interpolations, giving necessary and sufficient conditions and an algorithm for monotone Hermite quintic interpolation.
Space-Efficient Data Cubes for Dynamic Environments
Authors: M. Riedewald, D. Agrawal, A. E Abbadi, R. Pajarola
Venue:  (2000)

Data cubes provide aggregate information to support the analysis of the contents of data warehouses and databases. An important tool to analyze data in data cubes is the range query. For range queries that summarize large regions of massive data cubes, computing the query result on the fly can result in non-interactive response times (e.g. in the order of minutes). To speed up range queries, values that summarize regions of the data cube are pre-computed and stored. This faster response time results in more expensive updates and/or space overhead. While the emphasis is typically on low query and update costs, growing data collections increase the demand for space-efficient approaches. In this paper two techniques are presented that have the same update and query costs as earlier approaches, without introducing any space overhead.