ppxscal/embedding_network huggingface dataset:
Edit distance between two RNA structures
Authors: Guo-Hui Lin, Bin Ma, Kaizhong Zhang
Venue: Proceedings of the fifth annual international conference on Computational biology (2001)

Arc-annotated sequences are useful in representiug the structural information of RNA sequences. Typically, RNA secondary and tertiary structures could be represented by a set of nested arcs and a set of crossing arcs, respectively. As the specified RNA functions are determined by the specified molecular confirmation and therefore the specified secondary and tertiary structures, the comparison between RNA secondary and tertiary structures have received much attention recently. In this paper, we propose the notion of edit distance to measure the similarity between two RNA secondary and tertiary structures, by incorporating the various edit operations performing on both bases and arcs (base-pairs). Several algorithms are presented to compute the edit distance two RNA sequences with various arc structures and under various score schemes, either exactly or approximately. Preliminary experimental tests confirm that our definition of edit distance and the computation model are among the most reasonable ones ever studied in the literature.
An Axiomatic Approach to Information Flow in Programs
Authors: Gregory R. Andrews, Richard P. Reitman
Venue: ACM Transactions on Programming Languages and Systems (TOPLAS) (1980)

A new approach to information flow in sequential and parallel programs is presented. Flow proof rules that capture the information flow semantics of a variety of statements are given and used to construct program flow proofs. The method is illustrated by examples. The applications of flow proofs to certifying information flow policies and to solving the confinement problem are considered. It is also shown that flow rules and correctness rules can be combined to form an even more powerful proof system.
Time Constrained Push Strategies in Client-Server Databases
Authors: Vinay Kanitkar, Alex Delis
Venue: Distributed and Parallel Databases (2001)

The widespread availability of networked environments and the arrival of high-speed networks have rekindled interest in the area of automatic data refresh/update mechanisms. In many application areas, the updated information has a limited period of usefulness. Therefore, the development of systems and protocols that can handle such update tasks within predefined deadlines is required. In this paper, we propose and evaluate two real-time update-propagation mechanisms in a client-server environment. The fundamental difference in these two time-constrained techniques, Client&ndash;Push and Server-Push, is in the location where the push-transactions are generated. In both these techniques, and in contrast to conventional methods, we propose the transport of the scripts of updating transactions in order to make client-cached data current. This avoids unnecessary shipments of data over the network. Instead, messages are used to maintain the consistency of cached data. In addition, the propagation of update transaction scripts to client sites is neither periodic nor mandatory, but is instead based on client-specific criteria. These criteria depend on the content of the database objects being updated. We carry out a comprehensive experimental evaluation of the suggested methods as we examine the following aspects: (a) time constrained push scheduling issues, (b) effects of various workloads on real-time push-transaction completion rates (efficiency), and (c) overheads imposed by push-transactions on the regular transaction processing. Our experiments show that Client&ndash;Push outperforms Server-Push only for a small number of clients. The opposite is true once the load is increased by attaching a large number of sites per server. The efficiency of the update push protocols is, as expected, dependent on the load on the system as well as the percentage of updates to the database. Surprisingly, the percentage of successfully completed real-time push-transactions is not affected very much by the strategy used to schedule them.
Scaling Up the TREC Collection
Authors: David Hawking, Paul Thistlewaite, Donna Harman
Venue: Information Retrieval (1999)

Due to the popularity of Web search engines, a large proportion of real text retrieval queries are now processed over collections measured in tens or hundreds of gigabytes. A new Very Large test Collection (VLC) has been created to support qualification, measurement and comparison of systems operating at this level and to permit the study of the properties of very large collections. The VLC is an extension of the well-known TREC collection and has been distributed under the same conditions. A simple set of efficiency and effectiveness measures have been defined to encourage comparability of reporting. The 20 gigabyte first-edition of the VLC and a representative 10% sample have been used in a special interest track of the 1997 Text Retrieval Conference (TREC-6). The unaffordable cost of obtaining complete relevance assessments over collections of this scale is avoided by concentrating on early precision and relying on the core TREC collection to support detailed effectiveness studies. Results obtained by TREC-6 VLC track participants are presented here. All groups observed a significant increase in early precision as collection size increased. Explanatory hypotheses are advanced for future empirical testing. A 100 gigabyte second edition VLC (VLC2) has recently been compiled and distributed for use in TREC-7 in 1998.
A regularity-driven fast gridless detailed router for high frequency datapath designs
Authors: Sabyasachi Das, Sunii P. Khatri
Venue: Proceedings of the 2001 international symposium on Physical design (2001)

We present a new detailed routing methodology specifically designed for datapath layouts. In typical state-of-the-art microprocessor designs, datapaths comprise about 70\% of the logic (excluding caches). Although research on datapath placement and global routing has been reported, very little research has been reported in the area of detailed routing for datapaths.Datapaths typically comprise regular {\em bit-slices} which are replicated. We define anet-cluster, which is collection of similarly structured nets present across different bit-slices. We introduce two clustering schemes (Footprint-driven clusteringandInstance-driven clustering) to extract such net-clusters. Then, we perform astrap-basedrouting on exactly one member net of each net-cluster (in a single representative bit-slice). Next, for each net, wepropagateits route to all other nets in its net-cluster. Our algorithm is unique in that it performs the detailed routing on asinglebit-slice, and infers the routing for all bit-slices using the notion of net clusters.We demonstrate at least 6$\times$ speed gains for industrial 32 and 64-bit datapath designs. The regularity of the routes across the bit-slices results in more predictable timing characteristics for the resulting datapath layout.
Logic optimization and code generation for embedded control applications
Authors: Yunjian Jiang, Robert K. Brayton
Venue: Proceedings of the ninth international symposium on Hardware/software codesign (2001)

We address software optimization for embedded control systems. The Esterel language is used as the front-end specification; Esterel compiler v6 is used to partition the control circuit and data path; the resulting intermediate representation of the design is a control-data network. This paper emphasizes the optimization of the control circuit portion and the code generation of the logic network. The new control-data network representation has four types of nodes: control, multiplexer, predicate and data expression; the control portion is a multi-valued logic network (MV-network). We use an effective multi-valued logic network optimization package called MVSIS for the control optimization. It includes algebraic methods to perform multi-valued algebraic division, factorization and decomposition and logic simplification methods based on observability don't cares. We have developed methods to evaluate a control-data network based on both an MDD and sum-of-products representation of the multi-valued logic functions. The MDD-based approach uses multi-valued intermediate variables and generates code according to the internal BDD structure. The SOP-based code is proportional to the number of cubes in the logic network. Preliminary results compare the two approaches and the optimization effectiveness.
Modelling and visualizing agent conversations
Authors: Marisuz Nowostawski, Martin Purvis, Stephen Cranefield
Venue: Proceedings of the fifth international conference on Autonomous agents (2001)

Although the notion of conversations has been discussed for some time as a way in which to provide an abstract representation of extended agent message exchange, there is still no consensus established concerning how to use these abstractions effectively. This paper describes a layered approach based on coloured Petri Nets that can be used for modelling complex, concurrent conversations among agents in a multi-agent system. The approach can be used both to define simple conversation protocols and to define more complex conversation protocols composed of a number of simpler conversations. With this method it is possible (a) to capture the concurrent characteristics of a conversation, (b) to capture the state of a conversation at runtime, and (c) to reuse conversation structures for the processing of multiple concurrent messages.
Multiple ways to incorporate Oracle's database and tools into the entire curriculum (tutorial presentation)
Authors: Catherine C. Bareiss
Venue: Proceedings of the fourteenth annual consortium on Small Colleges Southeastern conference (2000)

It is not uncommon for students to view the curriculum as pieces instead of an integrated whole. This can hinder them from applying knowledge learned previously in one course to the course they are currently taking. In addition there are a number of recurring concepts in computer science that students need to recognize. The concepts associated with the management of large amounts of information is one such area.
A user-friendly software environment for the novice programmer
Authors: Marc Eisenstadt
Venue: Communications of the ACM (1983)

SOLO, a nonnumerical programming language, was developed at The Open University in the U.K. to support a course on Cognitive Psychology. It was designed to acquaint students as painlessly as possible with the computing fundamentals necessary both to grasp AI principles as applied in Cognitive Psychology and to actually initiate fairly sophisticated exercises on their own. The language has been used successfully by more than 2500 social science students.
An Intelligent Human-Computer Interface for Provisionof On-Line Help
Authors: Jennifer Jerrams-Smith
Venue: Artificial Intelligence Review (2000)

Some user interfaces, such as that of Unix, are difficult for novices to use, and this paper suggests a possible solution to such problems. The results of a study of Unix users enabled the development of a taxonomy of error types so that users' errors can be classified. This information is encapsulated as production rules within a knowledge base and forms the basis for the design and development of an intelligent interface to Unix. The prototype makes inferences about users' mental models and uses these to select appropriate tutorial advice. Performance of users of the prototype intelligent interface was compared with that of users of the usual Unix interface. The prototype users were found to make fewer errors, exhibit fewer misconceptions and take less time to complete a standard set of tasks.
A practical approach to managing resources and avoiding deadlocks
Authors: Dennis J. Frailey
Venue: Communications of the ACM (1973)

Resource scheduling and allocation can be expensive with regard to time and space in multiprogramming or time-sharing environments involving large numbers of tasks and resources with conflicting requirements. Detection and/or prevention of deadlocks can require massive amounts of additional overhead if efficient usage of resources is to be maintained. A resource management program is described which uses linked lists along with other techniques to overcome a large portion of this overhead. The program, which is currently running as part of a large scale general purpose operating system, keeps resources relatively active but does not detect or prevent all deadlocks in its implemented state. Certain changes, which would permit more comprehensive levels of deadlock prevention/detection at additional cost, have not been incorporated in the running system due to the infrequency of deadlock situations.
An efficient and lightweight embedded Web server for Web-based network element management
Authors: Hong-Taek Ju, Mi-Joung Choi, James W. Hong
Venue: International Journal of Network Management (2000)

An Embedded Web Server &lpar;EWS&rpar; is a Web server which runs on an embedded system with limited computing resources to serve embedded Web documents to a Web browser. By embedding a Web server into a network device, it is possible to provide a Web&hyphen;based management user interface, which are user&hyphen;friendly, inexpensive, cross&hyphen;platform, and network&hyphen;ready. This article explores the topic of an efficient and lightweight embedded Web server for Web&hyphen;based network element management. Copyright &copy; 2000 John Wiley Sons, Ltd.
Development of an information kiosk with a sign language recognition system
Authors: Hirohiko Sagawa, Masaru Takeuchi
Venue: Proceedings on the 2000 conference on Universal Usability (2000)

An information kiosk with a JSL (Japanese sign language) recognition system that allows hearing-impaired people to easily search for various kinds of information and services was tested in a government office. This kiosk system was favorably received by most users.
A Low Power 8 &times; 8 Direct 2-D DCT Chip Design
Authors: Hao-Chieh Chang, Jiun-Ying Jiu, Li-Lin Chen, Liang-Gee Chen
Venue: Journal of VLSI Signal Processing Systems (2000)

This paper presents the design and implementation of a low power 8 &times; 8 2-D DCT chip based on a computation-effective algorithm. Computational complexity can be reduced by simplifying the direct 2-D algorithm. Thus, the low power consumption is achieved due to complexity reduction. Besides, the parallel distributed-arithmetic (DA) technique is used to realize constant multiplication due to the low-power consideration. Additionally, the 2 V-power supply is practiced in circuit implementation for now and future battery operated applications. By using the TSMC 0.6 &mu;m single-poly double-metal technology, 133 mW power consumption at 100 MHz and the 133 MHz maximum operation speed are achieved by critical path simulation.
Designing computer system messages
Authors: Ben Shneiderman
Venue: Communications of the ACM (1982)

tive computer systems and studies of their users, we have become increasingly aware of the importance of system messages. Novice users are unimpressed with CPU speeds, disk storage capabilities, or elegant file structures. For them, the system appears only in the form of the messages on their screens or printers. So when novices encounter violent messages such as &ldquo;FATAL ERROR, RUN ABORTED&rdquo;, vague phases like &ldquo;ILLEGAL CMD&rdquo;, or obscure codes such as &ldquo;OC7&rdquo; or &ldquo;IEH2191&rdquo;, they are understandably shaken, confused, dismayed, and discouraged from continuing. The negative image that computer systems sometimes generate is, we believe, largely due to the difficulties users experience when they make mistakes or are unsure about what to do next.
Proof of a program: FIND
Authors: C. A. R. Hoare
Venue: Communications of the ACM (1971)

A proof is given of the correctness of the algorithm &ldquo;Find.&rdquo; First, an informal description is given of the purpose of the program and the method used. A systematic technique is described for constructing the program proof during the process of coding it, in such a way as to prevent the intrusion of logical errors. The proof of termination is treated as a separate exercise. Finally, some conclusions relating to general programming methodology are drawn.
Comparing sequence scaffolds
Authors: Gene Myers
Venue: Proceedings of the fifth annual international conference on Computational biology (2001)

The DNA sequence assembler we built for the whole genome shotgun assembly of the human genome, utilizes end-reads of inserts to order and orient assembled contigs into scaffolds for which the distances between consecutive contigs are statistically characterized. We consider the problem of comparing two such scaffolds. Applications include comparison of two distinct assemblies for mutual confirmation, and comparison of scaffold assemblies of BACs to determine a whole genome tiling of the BACs. We formalize the problem and develop efficient algorithms for a number of variations of the problem, the essential result being a sparse algorithm that refines gap estimates based on the overlap evidence.
Scalable Hardware-Algorithms for Binary Prefix Sums
Authors: R. Lin, K. Nakano, S. Olariu, M. C. Pinotti, J. L. Schwing, A. Y. Zomaya
Venue: IEEE Transactions on Parallel and Distributed Systems (2000)

In this work, we address the problem of designing efficient and scalable hardware-algorithms for computing the sum and prefix sums of a $w^k\hbox{-}{\rm{bit}}$, $(k\geq 2)$, sequence using as basic building blocks linear arrays of at most $w^2$ shift switches, where $w$ is a small power of $2$. An immediate consequence of this feature is that in our designs broadcasts are limited to buses of length at most $w^2$. We adopt a VLSI delay model where the ¿length¿ of a bus is proportional with the number of devices on the bus. We begin by discussing a hardware-algorithm that computes the sum of a $w^k\hbox{-}{\rm{bit}}$ binary sequence in the time of $2k-2$ broadcasts, while the corresponding prefix sums can be computed in the time of $3k-4$ broadcasts. Quite remarkably, in spite of the fact that our hardware-algorithm uses only linear arrays of size at most $w^2$, the total number of broadcasts involved is less than three times the number required by an ¿ideal¿ design. We then go on to propose a second hardware-algorithm, operating in pipelined fashion, that computes the sum of a $kw^k\hbox{-}{\rm{bit}}$ binary sequence in the time of $3k+\lceil\log_w k\rceil -3$ broadcasts. Using this design, the corresponding prefix sums can be computed in the time of $4k+\lceil\log_w k\rceil -5$ broadcasts.
Reflections on an operating system design
Authors: Butler W. Lampson, Howard E. Sturgis
Venue: Communications of the ACM (1976)

The main features of a general purpose multiaccess operating system developed for the CDC 6400 at Berkeley are presented, and its good and bad points are discussed as they appear in retrospect. Distinctive features of the design were the use of capabilities for protection, and the organization of the system into a sequence of layers, each building on the facilities provided by earlier ones and protecting itself from the malfunctions of later ones. There were serious problems in maintaining the protection between layers when levels were added to the memory hierarchy; these problems are discussed and a new solution is described.
Internet protocol version 6 (student paper)
Authors: Gregory R. Scholz, Clint Evans, Jaime Flores, Mustafa Rahman
Venue: Proceedings of the seventh annual consortium for computing in small colleges central plains conference on The journal of computing in small colleges (2001)

Many students, educators, and other professionals are increasingly finding that they need to become familiar with networking protocols. While the technical details are more complex than most professionals need, an understanding of the basic uses, features, terminology, and configurations is essential for any technical decision-maker or computer professional. Because of the Internet's dominance, computer professionals need to be, at least, familiar with its basic functionality. Currently, Internet Protocol version 4, IPv4, is the standard for Internet communications. However, with the tremendous expansion of the Internet, IPv4 is proving to be incapable of handling the coming demand. A new standard will be accepted to allow the Internet to continue to grow in size as well as function. Internet Protocol version 6, or IPv6, is the next currently proposed standard for Internet communications. While the basic function of IPv6 is similar to IPv4, IPv6 is drastically different in form. Differences fall into the categories of addressing, security, and configuration. Already, many large organizations, including Microsoft and Cisco, are developing and testing the new protocol. Beta software that allows construction of IPv6 networks has also been released to the general public. Because of the significant enhancements IPv6 provides and the shortage of IPv4 addresses, many organizations have begun implementing Internet Protocol version 6. The many differences between IPv4 and IPv6 make this preliminary testing an absolute necessity for the eventual migration to IPv6 to be successful. There are many methods available for transitioning to IPv6. One tool, however, is by far a greater necessity than any other. Knowledge of IPv6 is an essential element to the success of the next generation of Internet communication. Whether you are an educator, student, technician, or manager, if you need to know network communication, you will need to know Internet Protocol version 6.
New upper bounds for selection
Authors: Chee K. Yap
Venue: Communications of the ACM (1976)

The worst-case, minimum number of comparisons complexity Vi(n) of the i-th selection problem is considered. A new upper bound for Vi(n) improves the bound given by the standard Hadian-Sobel algorithm by a generalization of the Kirkpatrick-Hadian-Sobel algorithm, and extends Kirkpatrick's method to a much wider range of application. This generalization compares favorably with a recent algorithm by Hyafil.
Experience with Performance Testing of Software Systems: Issues, an Approach, and Case Study
Authors: Elaine J. Weyuker, Filippos I. Vokolos
Venue: IEEE Transactions on Software Engineering (2000)

An approach to software performance testing is discussed. A case study describing the experience of using this approach for testing the performance of a system used as a gateway in a large industrial client/server transaction processing application is presented.
Completeness in formal specification language design for process-control systems
Authors: Nancy Leveson
Venue: Proceedings of the third workshop on Formal methods in software practice (2000)

This paper examines the issue of completeness in specification language design. In the mid-80s we identified a set of 26 formal criteria to identify missing, incorrect, and ambiguous requirements for process-control systems. Experimental validation of the criteria on NASA and NASDA spacecraft systems have supported their usefulness in detecting commonly omitted but important information and engineers have been using them in checklist form on real systems. At the same time, we have extended the criteria and now have over 60. This paper shows how most of the criteria can be embedded in a formal specification language in ways that potentially allow automated checking or assist in manual reviews.