ppxscal/embedding_network huggingface dataset:
On the predictive power of sequence similarity in yeast
Authors: Yonatan Bilu, Michal Linial
Venue: Proceedings of the fifth annual international conference on Computational biology (2001)

Perhaps the most direct way to infer functional linkage of proteins is through structural similarity. However, structure determination lags behind DNA sequencing. Here we show that sequence similarity based on nucleotide sequences alone between ORFs in yeast is indicative of the corresponding genes being of the same functional group, having a similar gene expression pattern or of being involved in a protein-protein interaction. In particular, we compare the nucleotide sequences corresponding to the 6280 yeast ORFs using BLAST, and then cluster them together using a simple neighbor-joining algorithm. This, in effect, gives us hierarchical clustering of 53 levels, where higher levels have bigger clusters. We compare the clustering to large databases that are not based a-priori on sequence information to get a notion of how well our clustering is correlated with this data. For functional annotation we use the SGD database that gives one of 540 annotations for about half the yeast genes. For all pairs that appear within a cluster, we test the hypothesis that almost all genes within the same cluster have the same function. We get very high percentage rates of correct annotation at the lower levels of the hierarchy, which decreases gradually at higher ones. From the results of the large scale gene expression experiments we generate a list of pairs of genes, whose expression is highly correlated (&nge;0.9). We then go over this list of pairs, and count how many of them are contained within a cluster as opposed to the expected number by a random model. We estimate the significance of our results using simulation, and get for all levels p-value&nle;&nle;0.001. The third type of data obtained from the protein-protein interaction database that is given as a list of airs of proteins involved in interaction. As before, we count how many pairs are contained within a cluster, and get much better results than expected by a random model, with p-values&nle;0.001 for almost all levels. In summary, we show that successful functional predictions and functional annotations can be applied at a genomic scale. This can be achieved by combining a naive hierarchical clustering method that creates sets of clusters at different levels of granularity with statistical validation tools.
Symbolic analysis methods for information systems
Authors: Ned Chapin
Venue: Communications of the ACM (1961)

The purpose of this research in the area of information systems is basically twofold: (1) to produce new techniques of systems analysis and systems design that will be free of many of the defects of present techniques, and (2) to program a general purpose computer to enable it to apply at least major parts of these new techniques, in a way that will enable a linkage with automatic coding techniques. The major defects of the present techniques are high cost, low validity, low reliability, heavy reliance upon intuition and experience, and slow speed of effective application.
Performance modeling and tuning of an unstructured mesh CFD application
Authors: William D. Gropp, Dinesh K. Kaushik, David E. Keyes, Barry Smith
Venue: Proceedings of the 2000 ACM/IEEE conference on Supercomputing (CDROM) (2000)

This paper describes performance tuning experiences with a three-dimensional unstructured grid Euler flow code from NASA, which we have reimplemented in the PETSc framework and ported to several large-scale machines, including the ASCI Red and Blue Pacific machines, the SGI Origin, the Cray T3E and Beowulf clusters. The code achieves a respectable level of performance for sparse problems, typical of scientific and engineering codes based on partial differential equations, and scales well up to thousands of processors. Since the gap between CPU speed and memory access rate is widening, the code is analyzed from a memory-centric perspective (in contrast to traditional flop-orientation) to understand its sequential and parallel performance. Performance tuning is approached on three fronts: data layouts to enhance locality of reference, algorithmic parameters and parallel programming model. This effort was guided partly by some simple performance models developed for the sparse matrix-vector product operation.
Decision Diagram Method for Calculation of Pruned Walsh Transform
Authors: Dragan Jankovic, Radomir S. Stankovic, Rolf Drechsler
Venue: IEEE Transactions on Computers (2001)

Discrete Walsh transform is an orthogonal transform often used in spectral methods for different applications in signal processing and logic design. FFT-like algorithms make it possible to efficiently calculate the discrete Walsh spectrum. However, for their exponential complexity, these algorithms are practically unsuitable for large functions. For this reason, a Binary Decision Diagram (BDD) based recursive method for Walsh spectrum calculation has been introduced in [4]. A disadvantage of this algorithm is that the resulting Multi-Terminal Binary Decision Diagram (MTBDD) representing the Walsh spectrum for $f$ can be large for some functions. Another disadvantage turns out if particular Walsh coefficients are to be computed separately. The algorithm always calculates the entire spectrum and, therefore, it is rather inefficient for applications where a subset of Walsh spectral coefficients, i.e., the pruned Walsh spectrum, is required. In this paper, we propose another BDD-based method for Walsh spectrum calculation adapted for application where the pruned Walsh spectrum is needed. The method takes advantage of the property that, for most switching functions, the size of a BDD for $f$ is usually quite a bit smaller than the size of the MTBDD for the Walsh spectrum. In our method, a MTBDD representing the Walsh spectrum is not constructed. Instead, two additional fields are assigned to each node in the BDD for the processed function $f$. These fields are used to store the results of intermediate calculations. Pairs of spectral coefficients are calculated and stored in the fields assigned to the root node. Therefore, the calculation complexity of the proposed algorithm is proportional to the size of the BDD for $f$ whose spectrum is calculated. Experimental results demonstrate the efficiency of the approach.
Sampling from the gamma distribution on a computer
Authors: George S. Fishman
Venue: Communications of the ACM (1976)

This paper describes a method of generating gamma variates that appears to be less costly than Wallace's recently suggested method. For large shape parameter &agr;; the cost of computation is proportional to &radic;&agr;, whereas Wallace's method is proportional to &agr;. Experimentation by Robinson and Lewis indicates that for small &agr; the method suggested here also dominates methods recently suggested by Dieter and Ahrens, albeit those methods dominate for large &agr;. The method suggested here uses the rejection technique.
Some social implications of ubiquitous wireless networks
Authors: Marc A. Smith
Venue: ACM SIGMOBILE Mobile Computing and Communications Review (2000)

Wireless computer networks and the devices to communicate with them are about to become ubiquitous. A profusion of devices is likely to emerge quickly in specialized form factors, from handhelds to cheap, disposable sensors. Groups of people using these tools will gain new forms of social power, ways to organize and coordinate their interactions and exchanges just in time and just in place. Using these tools, people will be able to collectively construct a range of resources that were too difficult or expensive, or simply impossible to provide before. Simultaneously, these tools will gather a constellation of intimate data about each of us. Wireless devices will penetrate every nook and cranny of the social world, bringing the efficiency of information technology to the production of panoptic power. In the following, two sociological concepts, Power/Knowledge and social dilemmas, are used as a guide to the kinds of social institutions and relationships that are likely to emerge from the use of these tools.
A methodology for teaching object-oriented programming concepts in an advanced programming course
Authors: Essam M. Arif
Venue: ACM SIGCSE Bulletin (2000)

I have been teaching an advanced programming course for undergraduate students for four years. My intention is that object-oriented programming principles and concepts could be easily simplified and taught to the students in this course. In this paper we will discusses a step by step methodology that I use in this course to teach my students how to understand and apply these concepts. The paper also attempts to determine the attribute of students to OOP and their reaction towards the methodology. It reports the result of a survey conducted to students after taking two introductory computer programming courses using a structural programming language.
The Graphic-Linguistic DistinctionExploring Alternatives
Authors: Atsushi Shimojima
Venue: Artificial Intelligence Review (2001)

What properties, if any, distinguish graphical representations from linguistic representations? This paper looks for answers in the literature of philosophy, logic, artificial intelligence, and cognitive psychology, and extracts seven alternative binary classifications of representations that may characterize the graphic-linguistic boundary. We assess each alternative by two standards: (a) whether it extensionally fits the graphic-linguistic distinction, and (b) how far it explains the properties commonly attributed to graphic representations but not to linguistic ones.
Combining multiple sources for short query translation in Chinese-English cross-language information retrieval
Authors: Aitao Chen, Hailing Jiang, Fredric Gey
Venue: Proceedings of the fifth international workshop on on Information retrieval with Asian languages (2000)

In this paper, we examine various factors that affect the retrieval performance of Chinese-English cross-language retrieval. The factors include segmentation dictionary coverage, segmentation algorithm, transfer dictionary coverage, transfer dictionary quality, and translation disambiguation. The paper introduces an idea of recovering the original English names for the transliterated Chinese words, mainly the proper name, using search engine. We used two transfer dictionaries and a Chinese search engine to transfer short Chinese queries into English. The majority of the Chinese words were translated into English, but the overall precision of the Chinese to English cross-language retrieval is only about 56% of the overall precision for the monolingual retrieval.1
Digital simulation of discrete flow systems0
Authors: C. J. Moore, T. S. Lewis
Venue: Communications of the ACM (1960)

The discrete flow systems discussed are characterized by the movement of randomly arriving items along interacting channels. Programming a digital computer to simulate such systems utilizes some techniques not common in other approaches to physical problems. The principal portion of the paper is a discussion of two simulation studies that illustrate some of the programming problems involved. One is of an extensive package-handling plant, with the objective being optimization of parameters such as storage capacities and processing rates. In the other, air traffic flow and control procedures are simulated to compare the effects of alternative control decisions.
Competitive on-line stream merging algorithms for media-on-demand
Authors: Amotz Bar-Noy, Richard E. Ladner
Venue: Proceedings of the twelfth annual ACM-SIAM symposium on Discrete algorithms (2001)

We consider the problem of minimizing the bandwidth needed by media-on-demand servers that use stream merging. We consider the on-line case where client requests are not known ahead of time. To facilitate stream merging, clients have the ability to receive data from two streams simultaneously and can buffer up to half of a full stream. We present a new family of on-line stream merging algorithms called dynamic tree algorithms. The bandwidth requirements of the best of these, the dynamic Fibonacci tree algorithms, are within a factor of the minimum between log&oslash;(n) + &Ogr;(1) and log&oslash;(1/(2D)) + &Ogr;(1) from the off-line optimal, where n is the number of requests, D is the guaranteed maximum startup delay measured as a fraction of the time for a full stream, and &oslash; = (1 + &radic;5)/2. Empirical studies show that the dynamic Fibonacci tree algorithms perform much better than indicated by the analysis.
The SMOOTH video DB - demonstration of an integrated generic indexing approach
Authors: Alexander Bachlechner, László Böszörményi, Bernhard Döflinger, Christian Hofbauer, Harald Kosch, Carmen Riedler, Roland Tusch
Venue: Proceedings of the eighth ACM international conference on Multimedia (2000)

The SMOOTH Video DB is a distributed system proposing an integral query, browsing, and annotation software framework in common with an index database for video media material.
Tears and fears: modeling emotions and emotional behaviors in synthetic agents
Authors: Jonathan Gratch, Stacy Marsella
Venue: Proceedings of the fifth international conference on Autonomous agents (2001)

Emotions play a critical role in creating engaging and believable characters to populate virtual worlds. Our goal is to create general computational models to support characters that act in virtual environments, make decisions, but whose behavior also suggests an underlying emotional current. In service of this goal, we integrate two complementary approaches to emotional modeling into a single unified system. Gratch's &Eacute;mile system focuses on the problem of emotional appraisal: how emotions arise from an evaluation of how environmental events relate to an agent's plans and goals. Marsella et al. 's IPD system focuses more on the impact of emotions on behavior, including the impact on the physical expressions of emotional state through suitable choice of gestures and body language. This integrated model is layered atop Steve, a pedagogical agent architecture, and exercised within the context of the Mission Rehearsal Exercise, a prototype system designed to teach decision- making skills in highly evocative situations.
Key Agreement in Dynamic Peer Groups
Authors: Michael Steiner, Gene Tsudik, Michael Waidner
Venue: IEEE Transactions on Parallel and Distributed Systems (2000)

As a result of the increased popularity of group-oriented applications and protocols, group communication occurs in many different settings: from network multicasting to application layer tele- and videoconferencing. Regardless of the application environment, security services are necessary to provide communication privacy and integrity. This paper considers the problem of key agreement in dynamic peer groups. (Key agreement, especially in a group setting, is the stepping stone for all other security services.) Dynamic peer groups require not only initial key agreement (IKA) but also auxiliary key agreement (AKA) operations, such as member addition, member deletion, and group fusion. We discuss all group key agreement operations and present a concrete protocol suite, CLIQUES, which offers complete key agreement services. CLIQUES is based on multiparty extensions of the well-known Diffie-Hellman key exchange method. The protocols are efficient and provably secure against passive adversaries.
Detailed routing architectures for embedded programmable logic IP cores
Authors: Peter Hallschmid, Steven J. E. Wilton
Venue: Proceedings of the 2001 ACM/SIGDA ninth international symposium on Field programmable gate arrays (2001)

As the complexity of integrated circuits increases, the ability to make post-fabrication changes to fixed ASIC chips will become more and more attractive. This ability can be realized using programmable logic cores. These cores are blocks of programmable logic that can be embedded into a fixed-function ASIC or a custom chip. Such cores differ from stand-alone FPGAs in that they can take on a variety of shapes and sizes. With this in mind, we investigate the detailed routing characteristics of rectangular programmable logic cores. We quantify the effects of having different x and y channel capacities, and show that the optimum ratio between the x and y channel widths for a rectangular core is between 1.2 and 1.5. We also present a new switch block family optimized for rectangular cores. Compared to a simple extension of an existing switch block, our new architecture leads to an 8.7% improvement in density with little effect on speed. Finally, we show that if the channel widths and switch block are chosen carefully the penalty for using a rectangular core (compared to a square core with the same logic capacity) is small; for a core with an aspect ratio of 2:1, the area penalty is 1.6% and the speed penalty is 1.1%.
Pagination of B*-trees with variable-length records
Authors: Edward M. McCreight
Venue: Communications of the ACM (1977)

A strategy is presented for pagination of B*-trees with variable-length records. If records of each length are uniformly distributed within the file, and if a wide distribution of record lengths exists within the file, then this strategy results in shallow trees with fast access times. The performance of this strategy in an application is presented, compared with that of another strategy, and analyzed.
Computation's development critical to our society
Authors: Alan J. Perlis
Venue: Communications of the ACM (1963)

The ACM's growth continues: we are now at 13,000 members; expenses also grow. Our professional membership does not spring from a uniformly trained group as in mathematics or physics or even economics. Instead, our increasing membership comes from what I might call intellectual adventures&mdash;pioneers in an over-organized society&mdash;who see great futures in computing at all levels of aspiration.
Simulating frequency-dependent current distribution for inductance modeling of on-chip copper interconnects
Authors: L.-F. Chang, K.-J. Chang, R. Mathews
Venue: Proceedings of the 2000 international conference on Computer-aided design (2001)

500+ MHz designs using deep-submicron (DSM) copper interconnects require accurate and efficient modeling of cladding-metals' frequency-dependent impedance [1]. In this paper, for the first time, we simulate and describe the current distribution inside a copper-based interconnect in a rich set of multi-line structures. The difference of the resistivities of copper alloy and the cladding metals causes a non-monotonic current density versus cross-wire axis relation. The same situation does not occur for the state-of-the-art aluminum processes. It enlarges the inductance by more than 12 percent. Simulating the frequency dependence of the inductance with this property, we find that PEEC [2][3] can simulate cladded wire profile to achieve accurate inductance extraction. Other approximate methods result in inaccurate and lower inductance values. A new modeling methodology based on library look-up is then proposed to make an efficient field-solver based extraction flow for realistic DSM designs.
Separating access control policy, enforcement, and functionality in extensible systems
Authors: Robert Grimm, Brian N. Bershad
Venue: ACM Transactions on Computer Systems (TOCS) (2001)

Extensible systems, such as Java or the SPIN extensible operating system, allow for units of code, or extensions, to be added to a running system in almost arbitrary fashion. Extensions closely interact through low-latency but type-safe interfaces to form a tightly integrated system. As extensions can come from arbitrary sources, not all of whom can be trusted to conform to an organization's security policy, such structuring raises the question of how security constraints are enforced in an extensible system. In this paper, we present an access control mechanism for extensible systems to address this problem. Our access control mechanism decomposes access control into a policy-neutral enforcement manager and a security policy manager, and it is transparent to extensions in the absence of security violations. It structures the system into protection domains, enforces protection domains through access control checks, and performs auditing of system operations. The access control mechanism works by inspecting extensions for their types and operations to determine which abstractions require protection and by redirecting procedure or method invocations to inject access control operations into the system. We describe the design of this access control mechanism, present an implementation within the SPIN extensible operating systems, and provide a qualitative as well as quantitative evaluation of the mechanism.
New Sinusoidal Oscillators with Fully Uncoupled Control of Oscillation Frequency and Condition Using Three CCII+s
Authors: Muhammad Taher Abuelma’atti
Venue: Analog Integrated Circuits and Signal Processing (2000)

Using Sedra-Smith gyrator (IEEE Transactions on Circuit Theory 17, pp. 132&ndash;134, 1970) new realizations for grounded-resistor controlled sinusoidal oscillators using the plus-type second-generation current-conveyor (CCII&plus;) can be systemically derived. Some of the new circuits enjoy the attractive feature of totally uncoupled frequency and condition of oscillation. Experimental and simulation results obtained using PSPICE are included.
Colored Tutte polynomials and Kaufman brackets for graphs of bounded tree width
Authors: J. A. Makowsky
Venue: Proceedings of the twelfth annual ACM-SIAM symposium on Discrete algorithms (2001)

Jones polynomials and Kauffman polynomials are the most prominent invariants of knot theory. For alternating links, they are easily computable from the Tutte polynomials by a result of Thistlethwaite (1988), but in general one needs Kauffman's Tutte polynomials for signed graphs (1989), further generalized to colored Tutte polynomials, as introduced by Bollobas and Riordan (1999). Knots and links can be presented as labeled planar graphs. The tree width of a link L is defined as the minimal tree width of its graphical presentations D(L) as crossing diagrams. We show that the colored Tutte polynomial can be computed in polynomial time for graphs of tree width at most k. Hence, for (not necessarily alternating) knots and links of tree width at most k, even the Kauffman square bracket [L] introduced by Bollobas and Riordan can be computed in polynomial time. In particular, the classical Kauffman bracket (L) and the Jones polynomial of links of tree width at most k are computable in polynomial time.
Proving monitors
Authors: John H. Howard
Venue: Communications of the ACM (1976)

Interesting scheduling and sequential properties of monitors can be proved by using state variables which record the monitors' history and by defining extended proof rules for their wait and signal operations. These two techniques are defined, discussed, and applied to examples to prove properties such as freedom from indefinitely repeated overtaking or unnecessary waiting, upper bounds on queue lengths, and historical behavior.
Construction of rational and negative powers of a formal series
Authors: R. A. Broucke
Venue: Communications of the ACM (1971)

Some methods are described for the generation of fractional and negative powers of any formal series, such as Poisson series or Chebyshev series. It is shown that, with the use of the three elementary operations of addition, subtraction, and multiplication, all rational (positive and negative) powers of a series can be constructed. There are basically two approaches: the binomial theorem and the iteration methods. Both methods are described here, and the relationship between them is pointed out. Some well-known classical formulas are obtained as particular cases, and it is shown how the convergence properties of these formulas can be improved with very little additional computations. Finally, at the end of the article, some numerical experiments are described with Chebyshev series and with Fourier series.