ppxscal/embedding_network huggingface dataset:
Ab initio Tertiary Structure Prediction of Proteins
Authors: J. L. Klepeis, C. A. Floudas
Venue: Journal of Global Optimization (2003)

A daunting challenge in the area of computational biology has been to develop a method to theoretically predict the correct three-dimensional structure of a protein given its linear amino acid sequence. The ability to surmount this challenge, which is known as the protein folding problem, has tremendous implications. We introduce a novel ab initio approach for the protein folding problem. The accurate prediction of the three-dimensional structure of a protein relies on both the mathematical model used to mimic the protein system and the technique used to identify the correct structure. The models employed are based solely on first principles, as opposed to the myriad of techniques relying on information from statistical databases. The framework integrates our recently proposed methods for the prediction of secondary structural features including helices and strands, as well as &beta;-sheet and disulfide bridge formation. The final stage of the approach, which culminates in the tertiary structure prediction of a protein, utilizes search techniques grounded on the foundations of deterministic global optimization, powerful methods which can potentially guarantee the correct identification of a protein's structure. The performance of the approach is illustrated with bovine pancreatic trypsin inhibitor protein and the immunoglobulin binding domain of protein G.
A Systolic, Linear-Array Multiplier for a Class of Right-Shift Algorithms
Authors: P. Kornerup
Venue: IEEE Transactions on Computers (1994)

A very simple multiplier cell is developed for use in a linear, purely systolic array forming a digit-serial multiplier for unsigned or 2'complement operands. Each cell produces two digit-product terms and accumulates these into a previous sum of the same weight, developing the product least significant digit first. Grouping two terms per cell, the ratio of active elements to latches is low, and only upper bound [n]/2 cells are needed for a full n by n multiply. A module-multiplier is then developed by incorporating a Montgomery type of module-reduction. Two such multipliers interconnect to form a purely systolic module exponentiator, capable of performing RSA encryption at very high clock frequencies, but with a low gate count and small area. It is also shown how the multiplier, with some simple back-end connections, can compute modular inverses and perform modular division for a power of two as modulus.
Semantic Modeling and Knowledge Representation in Multimedia Databases
Authors: Wasfi Al-Khatib, Y. Francis Day, Arif Ghafoor, P. Bruce Berra
Venue: IEEE Transactions on Knowledge and Data Engineering (1999)

In this paper, we present the current state of the art in semantic data modeling of multimedia data. Semantic conceptualization can be performed at several levels of information granularity, leading to multilevel indexing and searching mechanisms. Various models at different levels of granularity are compared. At the finest level of granularity, multimedia data can be indexed based on image contents, such as identification of objects and faces. At a coarser level of granularity, indexing of multimedia data can be focused on events and episodes, which are higher level abstractions. In light of the above, we also examine modeling and indexing techniques of multimedia documents.
Information filtering using bayesian networks: effective user interfaces for aviation weather data
Authors: Corinne Clinton Ruokangas, Ole J. Mengshoel
Venue: Proceedings of the 8th international conference on Intelligent user interfaces (2003)

Weather is a complex, dynamic process with tremendous impact on aviation. While pilots often have access to large amounts of aviation weather data, they find it difficult and time-consuming to identify weather hazards, due to the sheer amount and cryptic formatting of the data. To address this challenge, we have developed information filtering concepts based on a unified Bayesian network model, integrating text and graphical weather data in the context of specific mission, equipment and personal profiles. Based on these concepts, we have implemented three applications, all of which were to existing technology. Using one of the applications, the AWARE Preflight system, pilots found significantly more hazards in about half the time compared to using the current technology
Range Sensing by Projecting Multiple Slits with Random Cuts
Authors: M. Maruyama, S. Abe
Venue: IEEE Transactions on Pattern Analysis and Machine Intelligence (1993)

A method for range sensing that projects a single pattern of multiple slits is described. Random dots are used to identify each slit. The random dots are given as randomly distributed cuts on each slit. Thus, each slit is divided into many small line segments. Segment matching between the image and the pattern is performed to obtain 3-D data. Using adjacency relations among slit segments, the false matches are reduced, and segment pairs whose adjacent segments correspond with each other are extracted and considered to be correct matches. Then, from the resultant matches, the correspondence is propagated by exploiting the adjacency relationships to get an entire range image.
Distributed network computing over local ATM networks
Authors: Mengjou Lin, Jenwei Hsieh, David H. C. Du, Joseph P. Thomas, James A. MacDonald
Venue: Proceedings of the 1994 ACM/IEEE conference on Supercomputing (1994)

Communication between processors has long been the bottleneck of distributed network computing. However, recent progress in switch-based high-speed Local Area Networks (LANs) may be changing this situation. Asynchronous Transfer Mode (ATM) is one of the most widely-accepted and emerging high-speed network standards which can potentially satisfy the communication needs of distributed network computing. In this paper, we investigate distributed network computing over local ATM networks. We first study the performance characteristics involving end-to-end communication in an environment that includes several types of workstations interconnected via a Fore Systems' ASX-100 ATM Switch. We then compare the communication performance of four different Application Programming Interfaces (APIs). The four APIs were Fore Systems ATM API, BSD socket programming interface, Sun's Remote Procedure Call (RPC), and the Parallel Virtual Machine (PVM) message passing library. Each API represents distributed programming at a different communication protocol layer. We evaluate parallel Matrix Multiplication over the local ATM network. The experimental results show that network computing is promising over local ATM networks.
Ces&#x00E0;ro asymptotics for orthogonal polynomials on the unit circle and classes of measures
Authors: Leonid Golinskii, Sergei Khrushchev
Venue: Journal of Approximation Theory (2002)

The convergence in L2(T) of the even approximants of the Wall continued fractions is extended to the Cesàro-Nevai class CN, which is defined as the class of probability measures σ with limn → ∞ 1/nΣk=0n-1 |ak|=0, {an}n ≥ 0 being the Geronimus parameters of σ. We show that CN contains universal measures, that is, probability measures for which the sequence {|φn|2 dσ}n ≥ 0 is dense in the set of all probability measures equipped with the weak-* topology. We also consider the "opposite" Szegö class which consists of measures with Σn=0∞ (1-|an|2)1/2 < ∞ and describe it in terms of Hessenberg matrices.
An Integrated Network Component Architecture
Authors: Israel Ben-Shaul, James W. Gish, William Robinson
Venue: IEEE Software (1998)

To deploy large-scale, interactive, distributed systems, we need architectures that support integration of new and existing components and allow dynamic configuration of component connections. The architecture presented in this article builds connection mechanisms into the components, which facilitates composition and the construction of flexible, scalable systems.
When Good Enough Software Is Best
Authors: Edward Yourdon
Venue: IEEE Software (1995)

There¿s a sign that my printer displays prominently on his wall. ¿You can getit fast; you can have it cheap; you can get it right. Pick two!¿ That samesign could be displayed on the wall of every software¿development organization.And yet most of our customers want all three. Ed Yourdon tackles that dilemmain this issue¿s column. He contends that we don¿t rationally establish properbalance among the critical project parameters: cost, schedule, staffing,functionality, and quality. Our customers want us to optimize all theseparameters, even when this is clearly impossible. The purists among you mayfind Ed¿s comments grating. But I suspect that those of you who¿ve been bloodied in the project wars will find wisdom in his words. ¿ Roger Pressman
Software's Future: Managing Evolution
Authors: M. m. Lehman
Venue: IEEE Software (1998)

In his essay, Ed Yourdon expresses, justifies, and leaves unresolved two well-founded questions: What is the future of software? What does the future hold for the software professional? His prognosis is evasive, incomplete, and unsatisfying: the future will be good for some, not so for others. Given Yourdon's extensive experience in the real world of computer usage, as proven by the problems he has observed, it is easy to see why he feels that soft-ware's future is uncertain. But he does not point to a solution to this uncertainty, nor does he indicate what can be done to achieve the best possible outcome for software professionals. More importantly, Yourdon's analysis does not indicate what should be done to ensure the security, well being, and survival of society, which depends increasingly on software. For more than a decade now, there have been those in the software engineering community who have accepted that the need to continually change and evolve software is a fact-a fact addressed through activity that is planned, executed, and controlled by humans. Thus, the software development and maintenance processes, which I prefer to unify and call software evolution, are key to managing computerization. In my view it is key to our survival in this computer age.
Evaluating the Effectiveness of Independent Verification and Validation
Authors: James D. Arthur, Markus K. Gröner, Kelly J. Hayhurst, C. Michael Holloway
Venue: Computer (1999)

The complexity of today's software systems mandates a structured approach to development and a verification and validation process that ensure that the right product is built and that it is built right. A V&V process is critical for those high-consequence systems in which a software failure can result in injury or death or where live testing isn't feasible. NASA Langley Research Center funded a study to examine the effectiveness of the Army's Software Engineering Evaluation System (SEES). The project led to a study designed to examine the benefits of using SEES as an independent V&V methodology. The study consisted of two independent development groups. Each was given an identical set of requirements that outlined a solution to a particular problem. The authors asked both groups to design, code, and test their software. The results indicate that IV&V provides a significant value-added component to the software development process.
On a Pattern-Oriented Model for Intrusion Detection
Authors: Shiuh-Pyng Shieh, Virgil D. Gligor
Venue: IEEE Transactions on Knowledge and Data Engineering (1997)

Operational security problems, which are often the result of access authorization misuse, can lead to intrusion in secure computer systems. We motivate the need for pattern-oriented intrusion detection, and present a model that tracks both data and privilege flows within secure systems to detect context-dependent intrusions caused by operational security problems. The model allows the uniform representation of various types of intrusion patterns, such as those caused by unintended use of foreign programs and input data, imprudent choice of default privileges, and use of weak protection mechanisms. As with all pattern-oriented models, this model cannot be used to detect new, unanticipated intrusion patterns that could be detected by statistical models. For this reason, we expect that this model will complement, not replace, statistical models for intrusion detection.
An Algebraic Theory of Object-Oriented Systems
Authors: X. -M. Yu, T. S. Dillon
Venue: IEEE Transactions on Knowledge and Data Engineering (1994)

The paper presents an algebraic specification of net objects. By net objects we mean those that are defined in object-oriented paradigms and those defined with nested relations in complex database models. An algebraic specification is set up that involves structures of net objects, accesses of net objects, and some features of object-oriented programming, such as multiple inheritance and polymorphism. Objects and their relationships are then characterized formally in the modeling, which utilizes the hierarchical approach in the algebraic theory of abstract data types, and is further developed by adding mechanisms from existing object systems. Categories of net objects are presented with the properties of accesses among them.
High-Speed Electrical Signaling: Overview and Limitations
Authors: Mark Horowitz, Chih-Kong Ken Yang, Stefanos Sidiropoulos
Venue: IEEE Micro (1998)

As IC speeds and integration levels increase with advances in fabrication technology, so must off-chip data bandwidth. Although this goal is challenging, circuit design techniques will enable bandwidth to scale.
The Least Action and the Metric of an Organized System
Authors: Georgi Georgiev, Iskren Georgiev
Venue: Open Systems Information Dynamics (2002)

In this paper, we formulate the least action principle for organized system as the minimum of the total sum of the actions of all of the elements. This allows us to see how this most basic law of physics determines the development of the system towards states with less action &mdash; organized states. Also we state that the metric tensor can describe the specific state of the constraints of the system, which is its actual organization. With this the organization is defined in two ways: 1. quantitative: the action I; 2. qualitative: the metric tensor gmn. These two measures can describe the level of development and the specifics of the organization of a system. We consider closed and open systems.
Segmenting Simply Connected Moving Objects in a Static Scene
Authors: M. Bichsel
Venue: IEEE Transactions on Pattern Analysis and Machine Intelligence (1994)

A new segmentation algorithm is derived, based on an object-background probability estimate exploiting the experimental fact that the statistics of local image derivatives show a Laplacian distribution. The objects' simple connectedness is included directly into the probability estimate and leads to an iterative optimization approach that can be implemented efficiently. This new approach avoids early thresholding, explicit edge detection, motion analysis, and grouping.
A timing-constrained algorithm for simultaneous global routing of multiple nets
Authors: Jiang Hu, Sachin S. Sapatnekar
Venue: Proceedings of the 2000 IEEE/ACM international conference on Computer-aided design (2000)

In this paper, we propose a new approach for VLSI interconnect global routing that can optimize both congestion and delay, which are often competing objectives. Our approach provides a general framework that may use any single-net routing algorithm and any delay model in global routing. It is based on the observation that there are several routing topology flexibilities under timing constraints. These flexibilities are exploited for congestion reduction through a network flow based hierarchical bisection and assignment process. Experimental results on benchmark circuits are quite promising.
Applying game design theory to virtual heritage environments
Authors: Erik Champion
Venue: Proceedings of the 1st international conference on Computer graphics and interactive techniques in Australasia and South East Asia (2003)

Much literature has argued that interactive engagement in a computer medium is best demonstrated by games. With this in mind, this paper suggests certain techniques that virtual environments (especially cultural heritage ones) can learn from game design.
Access Graphs: A Model for Investigating Memory Consistency
Authors: D. H. Linder, J. C. Harden
Venue: IEEE Transactions on Parallel and Distributed Systems (1994)

Computer architectures supporting shared memory continue to increase in complexity asdesigners seek to improve memory performance. This is especially true of proposals formassively parallel systems with distributed, yet shared, memory. The need to maintain areasonably simple memory model for programmers, in spite of enhancements like cachesand access pipelining, is responsible for many of the complications. We develop a novelgraph model, access graphs, for visualizing processor/memory interaction. Access graphssymbolically represent the causal relationships between load, store, and synchronizationevents. The focus is on two classes of access graphs: pseudo and real. A pseudo accessgraph describes an execution in terms of abstract events familiar to the programmer. Ifthe pseudo access graph is acyclic, then memory consistency is preserved during theexecution. A real access graph describes an execution in terms of physical events knownto the hardware designer. A real access graph must be acyclic since hardware cannotviolate causality. Memory consistency can be verified for a given computer system byproving that for any acyclic real access graph describing a program's execution on thatcomputer, an acyclic pseudo access graph can be derived describing the same execution.
On a 2-factor with a specified edge in a graph satisfying the Ore condition
Authors: Atsushi Kaneko, Kiyoshi Yoshimoto
Venue: Discrete Mathematics (2002)

Let k be an integer greater than one, and let G be a simple graph with at least 4k + 1 vertices. In this article, we prove that if σ2(G) ≥ |V(G)|, then for an edge e of G, there exists a 2-factor with k cycles that contains e, or |V(G)| is even and G has a vertex cover of size |V(G)|/2 containing the endpoints of e. Here σ2(G) is the minimum degree sum for a pair of nonadjacent vertices.
PREPARE: A Tool for Knowledge Base Verification
Authors: D. Zhang, D. Nguyen
Venue: IEEE Transactions on Knowledge and Data Engineering (1994)

The knowledge base is the most important component in a knowledge-based system. Because a knowledge base is often built in an incremental, piecemeal fashion, potential errors may be inadvertently brought into it. One of the critical issues in developing reliable knowledge-based systems is how to verify the correctness of a knowledge base. The paper describes an automated tool called PREPARE for detecting potential errors in a knowledge base. PREPARE is based on modeling a knowledge base by using a predicate/transition net representation. Inconsistent, redundant, subsumed, circular, and incomplete rules in a knowledge base are then defined as patterns of the predicate/transition net model, and are detected through a syntactic pattern recognition method. The research results to date have indicated that: the methodology ran be adopted in knowledge-based systems where logic is used as knowledge representation formalism; the tool can be invoked at any stage of the system's development, even without a fully functioning inference engine; the predicate/transition net model of knowledge bases is easy to implement and provides a clear and understandable display of the knowledge to be used by the system.
Feedback&ndash;Feedforward Scheduling of Control Tasks
Authors: Anton Cervin, Johan Eker, Bo Bernhardsson, Karl-Erik Årzén
Venue: Real-Time Systems (2002)

A scheduling architecture for real-time control tasks is proposed. The scheduler uses feedback from execution-time measurements and feedforward from workload changes to adjust the sampling periods of the control tasks so that the combined performance of the controllers is optimized. The performance of each controller is described by a cost function. Based on the solution to the optimal resource allocation problem, explicit solutions are derived for linear and quadratic approximations of the cost functions. It is shown that a linear rescaling of the nominal sampling frequencies is optimal for both of these approximations. An extensive inverted pendulum example is presented, where the performance obtained with open-loop, feedback, combined feedback and feedforward scheduling, and earliest-deadline first scheduling are compared. The performance under earliest-deadline first scheduling is explained by studying the behavior of periodic tasks under overload conditions. It is shown that the average values of the sampling periods equal the nominal periods, rescaled by the processor utilization.
Multiresolution Color Image Segmentation
Authors: J. Liu, Y. H. Yang
Venue: IEEE Transactions on Pattern Analysis and Machine Intelligence (1994)

Image segmentation is the process by which an original image is partitioned into some homogeneous regions. In this paper, a novel multiresolution color image segmentation (MCIS) algorithm which uses Markov random fields (MRF's) is proposed. The proposed approach is a relaxation process that converges to the MAP (maximum a posteriori) estimate of the segmentation. The quadtree structure is used to implement the multiresolution framework, and the simulated annealing technique is employed to control the splitting and merging of nodes so as to minimize an energy function and therefore, maximize the MAP estimate. The multiresolution scheme enables the use of different dissimilarity measures at different resolution levels. Consequently, the proposed algorithm is noise resistant. Since the global clustering information of the image is required in the proposed approach, the scale space filter (SSF) is employed as the first step. The multiresolution approach is used to refine the segmentation. Experimental results of both the synthesized and real images are very encouraging. In order to evaluate experimental results of both synthesized images and real images quantitatively, a new evaluation criterion is proposed and developed.
Estimating and Optimizing Performance for Parallel Programs
Authors: Thomas Fahringer
Venue: Computer (1995)

P3T, a Parameter-based Performance Prediction Tool, is an interactive performance estimator that helps users tune scientific Fortran programs. It detects bottlenecks in the program, identifies the causes of performance problems, and guides users in selecting effective program transformations to gain performance. Four of the most critical aspects of parallel programs are automatically estimated: load balance, data locality, communication, and computation overhead. Operating as an integrated tool of the Vienna Fortran Compilation System, P3T is enabled to aggressively exploit considerable knowledge about the compiler's analysis information and code restructuring strategies. The author evaluates existing features and describes substantial en-hancements in three key areas: the graphical user interface, performance parameters, and input programs. The tool's graphical user interface directs the user to bottlenecks in a computation that prevent the program from performing well. In addition, it allows performance data to be filtered and visualized at various levels of detail. The author discusses a new performance parameter that models computation time. Experiments show how P3T can successfully guide the user in performance tuning of parallel programs. The results demonstrate the feasibility of automatic performance prediction for parallel programs.