ppxscal/embedding_network huggingface dataset:
A NMR-spectra-based scoring function for protein docking
Authors: O. Kohlbacher, A. Burchardt, A. Moll, A. Hildebrandt, P. Bayer, H.-P Lenhof
Venue: Proceedings of the fifth annual international conference on Computational biology (2001)

A well studied problem in the area of Computational Molecular Biology is the so-called Protein-Protein Docking problem (PPD) that can be formulated as follows: Given two proteins A and B that form a protein complex, compute the 3D-structure of the protein complex AB. Protein docking algorithms can be used to study the driving forces and reaction mechanisms of docking processes. They are also able to speed up the lenghty process of experimental structure elucidation of protein complexes by proposing potential structures. In this paper, we are discussing a variant of the PPD-problem where the input consists of the tertiary structures of A and B plus an unassigned 1H-NMR spectrum of the complex AB. We present a new scoring function for evaluating and ranking potential complex structures produced by a docking algorithm. The scoring function computes a &ldquo;theoretical&rdquo; 1H-NMR spectrum for each tentative complex structure and subtracts the calculated spectrum from the experimental spectrum. The absolute areas of the difference spectra are then used to rank the potential complex structures. In contrast to formerly published approaches (e.g. Morelli et. al. [38]) we do not use distance constraints (intermolecular NOE constraints). We have tested the approach with the bound conformations of four protein complexes whose three-dimensional structures are stored in the PDB data bank [5] and whose 1H-NMR shift assignments are available from the BMRB database (BioMagResBank [47]). In all examples, the new scoring function produced very good rankings of the structures. The best result was obtained for an example, where all standard scoring functions failed completely. Here, our new scoring function achieved an almost perfect separation between good approximations of the true complex structure and false positives. Unfortunately, the number of complexes with known structure and available spectra is very small. Nevertheless, these experiments indicate that scoring functions based on comparisons of one- or multi-dimensional NMR spectra might be a good instrument to improve the reliability and accuracy of docking predictions and perhaps also of protein structure predictions (threading).
Disturbance Decoupling for Descriptor Systems by State Feedback
Authors: Delin Chu, Volker Mehrmann
Venue: SIAM Journal on Control and Optimization (2000)

We study the disturbance decoupling problem for linear time invariant descriptor systems. We give necessary and sufficient conditions for the existence of a solution to the disturbance decoupling problem with or without stability via a proportional and/or derivative feedback that also makes the resulting closed-loop system regular and/or of index at most one. All results are proved constructively based on condensed forms that can be computed using orthogonal matrix transformations, i.e., transformations that can be implemented in a numerically stable way.
On optimum switch box designs for 2-D FPGAs
Authors: Hongbing Fan, Jiping Liu, Yu-Liang Wu, Chak-Chung Cheung
Venue: Proceedings of the 38th annual Design Automation Conference (2001)

An FPGA switch box is said to be universal (hyper-universal) if it can detailed route all possible surrounding 2-pin (multi-pin) net topologies satisfying the global routing density constraints. A switch box is optimum if it is hyper-universal and the switches inside is minimum. It has been shown that if the net topology is restricted to 2-pin nets, then a 2-D (4-way) switch box can be built to be universal with only 6Wswitches, whereWis the global routing channel density. As the routing resource is relatively expensive in FPGA chips, study of the optimum switch box designs is clearly a topic with theoretical and commercial value of reducing silicon cost. A previous work has constructed a formal mathematical model of this optimum design problem for switch boxes with arbitrary dimensions, and gave a scheme to produce hyper-universal designs with less than 6.7W switches for 4-way FPGA switch boxes. In this paper, we will further investigate this most common 4-way switch box case, and will give new theoretical results followed by extensive experimental justification. The results seem to be quite attractive. We show that such an optimum switch box can be built with a very low number of additional switches beyond 6W for today's practical range of lowW's (e.g. just 6Wplus 1 or 2 additional switches forW's up to 7). Even for arbitrary largeW's, the bound can be shown to be under 6.34W. To make experimental comparison, we run today's published best FPGA router VPR on large benchmarks for the popular Disjoint structure and our proposed designs. The results are quite encouraging.
Reusable embedded in-circuit emulator
Authors: Ing-Jer Huang, Hsin-Ming Chen, Chung-Fu Kao
Venue: Proceedings of the 2001 Asia and South Pacific Design Automation Conference (2001)

In this paper, we o introduce the Reusable Embedded In-Circuit Emulator (EICE) and Reusable EICE development system. The main function in EICE we design are testing and debugging. The architecture of EICE is reusable and based on IEEE 1149.1 boundary scan architecture. The EICE development system can help EICE to reduce developing time while developing a microcontroller/microprocessor. We implemented EICE by ASIC and FPGA way and the development system had been demonstrated in two microcontroller.
Real-Time Disk Scheduling for Multimedia Applications withDeadline-Modification-Scan Scheme
Authors: Ray-I Chang, Wei-Kuan Shih, Ruei-Chuan Chang
Venue: Real-Time Systems (2000)

Real-time disk scheduling (RTDS) is important for time-critical multimedia applications. In conventional approaches of real-time disk scheduling, such as SCAN-EDF, the seek-optimizing SCAN scheme is applied to reduce the disk service time of the real-time EDF schedule. Since only tasks with the same deadline are seek-optimized, the obtained improvement of SCAN-EDF is limited. In this paper, based on the maximum-scannable-group (MSG) concept, a deadline-modification-scan (DMS or DM-SCAN) algorithm is proposed. Our algorithm uses MSG to automatically decide the suitable task groups for seek-optimizing. Based on the MSG concept, we repeatedly apply DMS to further increase disk throughput to support more tasks. We have implemented the proposed algorithm on UnixWare 2.01. The appropriate problem behaviors and parameter values to yield good solutions are investigated. Experiments show that DMS is better than conventional approaches in both the obtained disk throughput and the supported tasks. Moreover, our proposed approach can schedule task sets that are not schedulable by EDF and SCAN-EDF.
Effective information retrieval using term accuracy
Authors: C. T. Yu, G. Salton
Venue: Communications of the ACM (1977)

The performance of information retrieval systems can be evaluated in a number of different ways. Much of the published evaluation work is based on measuring the retrieval performance of an average user query. Unfortunately, formal proofs are difficult to construct for the average case. In the present study, retrieval evaluation is based on optimizing the performance of a specific user query. The concept of query term accuracy is introduced as the probability of occurrence of a query term in the documents relevant to that query. By relating term accuracy to the frequency of occurrence of the term in the documents of a collection it is possible to give formal proofs of the effectiveness with respect to a given user query of a number of automatic indexing systems that have been used successfully in experimental situations. Among these are inverse document frequency weighting, thesaurus construction, and phrase generation.
Building a user-derived interface
Authors: Michael D. Good, John A. Whiteside, Dennis R. Wixon, Sandra J. Jones
Venue: Communications of the ACM (1984)

Many human-computer interfaces are designed with the assumption that the user must adapt to the system, that users must be trained and their behavior altered to fit a given interface. The research presented here proceeds from the alternative assumption: Novice behavior is inherently sensible, and the computer system can be made to adapt to it. Specifically, a measurably easy-to-use interface was built to accommodate the actual behavior of novice users. Novices attempted an electronic mail task using a command-line interface containing no help, no menus, no documentation, and no instruction. A hidden operator intercepted commands when necessary, creating the illusion of an interactive session. The software was repeatedly revised to recognize users' new commands; in essence, the interface was derived from user behavior. This procedure was used on 67 subjects. The first version of the software could recognize only 7 percent of all the subjects' spontaneously generated commands; the final version could recognize 76 percent of these commands. This experience contradicts the idea that user input is irrelevant to the design of command languages. Through careful observation and analysis of user behavior, a mail interface unusable by novices evolved into one that let novices do useful work within minutes.
User-defined music sequence retrieval
Authors: Masoud Alghoniemy, Ahmed H. Tewfik
Venue: Proceedings of the eighth ACM international conference on Multimedia (2000)

A system for retrieving a sequence of music excerpts or songs based on users and producers requirements is proposed in this paper. Our system provides a flexible way to retrieve music pieces based on its contents as well as user-defined constraints. The proposed system allows online users to extract a sequence of songs whose first and last tracks are known and at the same time the in-between songs have minimum inter-track differences and satisfy predefined requirements. We model the problem as a constrained minimum cost flow problem which leads to a binary integer linear program (BILP) that can be solved in a reasonable amount of time.
Using types to analyze and optimize object-oriented programs
Authors: Amer Diwan, Kathryn S. McKinley, J. Eliot B. Moss
Venue: ACM Transactions on Programming Languages and Systems (TOPLAS) (2001)

Object-oriented programming languages provide many software engineering benefits, but these often come at a performance cost. Object-oriented programs make extensive use of method invocations and pointer dereferences, both of which are potentially costly on modern machines. We show how to use types to produce effective, yet simple, techniques that reduce the costs of these features in Modula-3, a statically typed, object-oriented language. Our compiler performs type-based alias analysis to disambiguate memory references. It uses the results of the type-based alias analysis to eliminate redundant memory references and to replace monomorphic method invocation sites with direct calls. Using limit, static, and running time evaluation, we demonstrate that these techniques are effective, and sometimes perfect for a set of Modula-3 benchmarks.
Adaptive-Scale Filtering and Feature Detection Using Range Data
Authors: Clark F. Olson
Venue: IEEE Transactions on Pattern Analysis and Machine Intelligence (2000)

In edge and corner detection applications, it is typical to examine a single scale without knowing which scale is appropriate for each location in the image. However, many images contain a wide variation in the distance to the scene pixels and, thus, features of the same size can appear at greatly differing scales in the image. We present a method where the scale of the filtering and feature detection is varied locally according to the distance to the scene pixel, which we estimate through stereoscopy. The features that are detected are, thus, at the same scale in the world, rather than at the same scale in the image. This method has been implemented efficiently by filtering the image at a discrete set of scales and performing interpolation to estimate the response at the correct scale for each pixel. The application of this technique to an ordnance recognition problem has resulted in a considerable improvement in performance.
A ticket-based access control architecture for object systems
Authors: John Hale, Jody Threet, Sujeet Shenoi
Venue: Journal of Computer Security (2000)

The design and implementation of authorization services for distributed object systems are hindered by the semantic diversity of object models, the brittleness of access control mechanisms, and the lack of design and analysis tools. This paper presents a primitive ticket-based access control architecture that can model a variety of authorization policies. The access control architecture is integrated within a primitive distributed object model that can capture most distributed object languages and systems. The integration provides a common foundation for access control in heterogeneous distributed object systems, instrumental to achieving high assurance secure interoperability.
An assessment of the prototyping approach to information systems development
Authors: Maryam Alavi
Venue: Communications of the ACM (1984)

A two-phased research project comparing the prototyping approach with the more traditional life cycle approach finds that prototyping facilitates communication between users and designers during the design process. However, the findings also indicate that designers who used prototyping experienced difficulties in managing and controlling the design process.
A framework for symmetric band reduction
Authors: Christian H. Bischof, Bruno Lang, Xiaobai Sun
Venue: ACM Transactions on Mathematical Software (TOMS) (2000)

We develop an algorithmic framework for reducing the bandwidth of symmetric matrices via orthogonal similarity transformations. This framework includes the reduction of full matrices to banded or tridiagonal form and the reduction of banded matrices to narrower banded or tridiagonal form, possibly in multiple steps. Our framework leads to algorithms that require fewer floating-point operations than do standard algorithms, if only the eigenvalues are required. In addition, it allows for space-time tradeoffs and enables or increases the use of blocked transformations.
Mechanical program analysis
Authors: Ben Wegbreit
Venue: Communications of the ACM (1975)

One means of analyzing program performance is by deriving closed-form expressions for their execution behavior. This paper discusses the mechanization of such analysis, and describes a system, Metric, which is able to analyze simple Lisp programs and produce, for example, closed-form expressions for their running time expressed in terms of size of input. This paper presents the reasons for mechanizing program analysis, describes the operation of Metric, explains its implementation, and discusses its limitations.
Computational challenges in simulating large DNA over long times
Authors: Tamar Schlick, Daniel A. Beard, Jing Huang, Daniel A. Strahs, Xiaoliang Qian
Venue: Computing in Science and Engineering (2000)

Simulating DNA's dynamics requires a sophisticated array of algorithms appropriate for DNA's impressive spectrum of spatial and temporal levels. The authors describe computational challenges, solution approaches, and applications that their group has performed in DNA dynamics.
Organization and retrieval of continuous media
Authors: Yasuo Ariki
Venue: Proceedings of the 2000 ACM workshops on Multimedia (2000)

Because of the media digitization, a large amount of information such as speech, audio and video data is produced everyday. In order to retrieve data quickly and precisely from these databases, multimedia technologies for organizing and retrieving of speech, audio and video data are strongly required. In this paper, we overview the multimedia technologies such as organization and retrieval of speech, audio and video data, speaker indexing, audio summarization and cross media retrieval existing today. The main purpose of the organization is to produce tables of contents and indices from audio and video data automatically. In order to make these technologies feasible, first, processing units such as words on audio data and shots on video data are extracted. On a second step, they are meaningfully integrated into topics. Furthermore, the units extracted from different types of media are integrated for higher functions.
Application-level scheduling on distributed heterogeneous networks
Authors: Francine D. Berman, Rich Wolski, Silvia Figueira, Jennifer Schopf, Gary Shao
Venue: Proceedings of the 1996 ACM/IEEE conference on Supercomputing (CDROM) (1996)

Heterogeneous networks are increasingly being used as platforms for resource-intensive distributed parallel applications. A critical contributor to the performance of such applications is the scheduling of constituent application tasks on the network. Since often the distributed resources cannot be brought under the control of a single global scheduler, the application must be scheduled by the user. To obtain the best performance, the user must take into account both application-specific and dynamic system information in developing a schedule which meets his or her performance criteria. In this paper, we define a set of principles underlying application-level scheduling and describe our work-in-progress building AppLeS (application-level scheduling) agents. We illustrate the application-level scheduling approach with a detailed description and results for a distributed 2D Jacobi application on two production heterogeneous platforms.
Reaching movements to augmented and graphic objects in virtual environments
Authors: Andrea H. Mason, Masuma A. Walji, Elaine J. Lee, Christine L. MacKenzie
Venue: Proceedings of the SIGCHI conference on Human factors in computing systems (2001)

This work explores how the availability of visual and haptic feedback affects and kinematics of reaching performance in a tabletop virtual environment. Eight subjects performed reach-to-grasp movements toward target objects of various sites in conitions where visual and haptic feedback were either present or absent. It was found that movement time was slower when visual feedback of the moving limb was not available. Further MT varied systematically with target size when haptic feedback was available (i.e. augmented targets), and thus followed Fitts' law. However, movement times were constant regardless of target size when haptic feedback was removed. In depth analysis of the reaching kinematics revealed that subjects spent longer decelerating toward smaller targets in conditions where haptic feedback was available. In contrast, deceleration time was constant when haptic feedback was absent. These results suggest that visual feedback about the moving limb and veridical haptic feedback about object contract are extremely important for humans to effectively work in virtual environments.
A statistical study of the accuracy of floating point number systems
Authors: H. Kuki, W. J. Cody
Venue: Communications of the ACM (1973)

This paper presents the statistical results of tests of the accuracy of certain arithmetic systems in evaluating sums, products and inner products, and analytic error estimates for some of the computations. The arithmetic systems studied are 6-digit hexadecimal and 22-digit binary floating point number representations combined with the usual chop and round modes of arithmetic with various numbers of guard digits, and with a modified round mode with guard digits. In a certain sense, arithmetic systems differing only in their use of binary or hexadecimal number representations are shown to be approximately statistically equivalent in accuracy. Further, the usual round mode with guard digits is shown to be statistically superior in accuracy to the usual chop mode in all cases save one. The modified round mode is found to be superior to the chop mode in all cases.
Out-of-core build of a topological data structure from polygon soup
Authors: Sara McMains, Joseph M. Hellerstein, Carlo H. Séquin
Venue: Proceedings of the sixth ACM symposium on Solid modeling and applications (2001)

Many solid modeling applications require information not only about the geometry of an object but also about its topology. Most interchange formats do not provide this information, which the application must then derive as it builds its own topological data structure from unordered, &ldquo;polygon soup&rdquo; input. For very large data sets, the topological data structure itself can be bigger than core memory, so that a naive algorithm for building it that doesn't take virtual memory access patterns into account can become prohibitively slow due to thrashing. In this paper, we describe a new out-of-core algorithm that can build a topological data structure efficiently from very large data sets, improving performance by two orders of magnitude over a naive approach.
The Structure of Automorphism Groups of Cayley Graphs and Maps
Authors: Robert Jajcay
Venue: Journal of Algebraic Combinatorics: An International Journal (2000)

The automorphism groups i>Aut(i>C(i>G, i>X)) and i>Aut(i>CM(i>G, i>X, i>p)) of a Cayley graph i>C(i>G, i>X) and a Cayley map i>CM(i>G, i>X, i>p) both contain an isomorphic copy of the underlying group i>G acting via left translations. In our paper, we show that both automorphism groups are rotary extensions of the group i>G by the stabilizer subgroup of the vertex 1i>G. We use this description to derive necessary and sufficient conditions to be satisfied by a finite group in order to be the (full) automorphism group of a Cayley graph or map and classify all the finite groups that can be represented as the (full) automorphism group of some Cayley graph or map.