ppxscal/embedding_network huggingface dataset:
Creating the backbone for the virtual cell (abstract only): cell mapping projects on the run
Authors: Matthias Wilm
Venue: Proceedings of the fifth annual international conference on Computational biology (2001)

The ability to identify proteins with mass spectrometry has a profound impact on biological research. Its long term effects can only be compared with the significance PCR enzyme had for the advancement of biological science. Suddenly proteins can be identified having only minute quantities available. The efforts invested in to the technology lead to a constant increase in throughput - comparable to the development of DNA sequencing technology. Biological mechanisms can be studied directly on the protein level. There are two research directions: protein expression based proteomics and cell mapping or functional proteomics. Protein expression based proteomics is focussing on the understanding of cellular states by analyzing the protein expression level of as many proteins as possible. In cell mapping experiments the protein - protein interaction network within a cell is analyzed. At the EMBL a protein complex purification technique, called tandem affinity purification (TAP), was developed which allows to rapidly purify very specifically non covalently interacting proteins which can be subsequently analyzed with mass spectrometry (cell mapping approach). The complexes assemble in vivo, are purified as such and characterized. The technique had been developed in yeast and efforts are under way to establish similar methods in higher eukaryotes. The comparison of this technique with similar experiments based on two hybrid screens demonstrate that the protein based approach is more specific and functional data suggest that it is more complete. This may be due to the fact that the complexes assemble first in their native environment and are then pulled out for characterization. The organization of all the proteins into groups of physically in teracting proteins is an important step towards understanding their functional role within a cell. To a large degree cellular processes organize themselves based on the non-covalent affinity of proteins. Protein based approaches as exemplified by the tandem affinity purification method in conjunction with mass spectrometry are very important in analyzing this functional infra structure. The identification of all the proteins involved in a particular biological mechanism and the characterization of their interaction constants may provide the physical data to simulate the process by a computer.
A study of errors, error-proneness, and error diagnosis in Cobol
Authors: Charles R. Litecky, Gordon B. Davis
Venue: Communications of the ACM (1976)

This paper provides data on Cobol error frequency for correction of errors in student-oriented compilers, improvement of teaching, and changes in programming language. Cobol was studied because of economic importance, widespread usage, possible error-inducing design, and lack of research. The types of errors were identified in a pilot study; then, using the 132 error types found, 1,777 errors were classified in 1,400 runs of 73 Cobol students. Error density was high: 20 percent of the types contained 80 percent of the total frequency, which implies high potential effectiveness for software-based correction of Cobol. Surprisingly, only four high-frequency errors were error-prone, which implies minimal error inducing design. 80 percent of Cobol misspellings were classifiable in the four error categories of previous researchers, which implies that Cobol misspellings are correctable by existent algorithms. Reserved word usage was not error-prone, which implies minimal interference with usage of reserved words. Over 80 percent of error diagnosis was found to be inaccurate. Such feedback is not optimal for users, particularly for the learning user of Cobol.
Independent Motion Detection in 3D Scenes
Authors: Harpreet S. Sawhney, Yanlin Guo, Rakesh Kumar
Venue: IEEE Transactions on Pattern Analysis and Machine Intelligence (2000)

This paper presents an algorithmic approach to the problem of detecting independently moving objects in 3D scenes that are viewed under camera motion. There are two fundamental constraints that can be exploited for the problem: 1) two/multiview camera motion constraint (for instance, the epipolar/trilinear constraint) and 2) shape constancy constraint. Previous approaches to the problem either use only partial constraints, or rely on dense correspondences or flow. We employ both the fundamental constraints in an algorithm that does not demand a priori availability of correspondences or flow. Our approach uses the plane-plus-parallax decomposition to enforce the two constraints. It is also demonstrated that for a class of scenes, called sparse 3D scenes in which genuine parallax and independent motions may be confounded, how the plane-plus-parallax decomposition allows progressive introduction, and verification of the fundamental constraints. Results of the algorithm on some difficult sparse 3D scenes are promising.
Majorization of Weighted Trees: A New Tool to Study Correlated Stochastic Systems
Authors: Susan H. Xu, Haijun Li
Venue: Mathematics of Operations Research (2000)

Stochastic models with simultaneous arrivals arise naturally in the areas such as synchronized communication networks, flexible manufacturing systems, production/inventory systems, reliability modeling in random environment, etc., with a wide variety of interpretations. Simultaneous arrivals introduce dependence among various components of the system and make the explicit solutions of joint system performance measures either computationally intensive or intractable. This calls for structural analysis of dependence natures of such systems so that the insight gained from the analysis can suggest plausible approaches to develop tight bounds and efficient approximations to key system performance measures.The usual majorization order on a totally ordered index set and Schur convexity are powerful tools for establishing inequalities, in particular, for stochastic systems. However, the investigation on stochastic systems with simultaneous arrivals leads naturally to the comparison of distributions of parameter values on a tree-structured index set. In this paper, we introduce the notion ofmajorization with respect to weighted trees. The fundamental strength of tree majorization lies in its ability to make versatile comparisons over two parameter sets defined on a partially ordered index set. We identify several classes of transformations that provide simple characterizations of tree majorization orders. Finally, we apply the new notion to an assemble-to-order system and to a shock model with simultaneous subsystem failures and study the dependence structure of these systems. Our results show that tree majorization and its interplay with various notions of stochastic orders are useful tools to study the dependency of stochastic systems with multivariate, synchronized input processes.
Some ideas on data types in high-level languages
Authors: David Gries, Narain Gehani
Venue: Communications of the ACM (1977)

A number of issues are explored concerning the notion that a data type is a set of values together with a set of primitive operations on those values. Among these are the need for a notation for iterating over the elements of any finite set (instead of the more narrow for i := 1 to n notation), the use of the domain of an array as a data type, the need for a simple notation for allowing types of parameters to be themselves parameters (but in a restrictive fashion), and resulting problems with conversion of values from one type to another.
Expected time bounds for selection
Authors: Robert W. Floyd, Ronald L. Rivest
Venue: Communications of the ACM (1975)

A new selection algorithm is presented which is shown to be very efficient on the average, both theoretically and practically. The number of comparisons used to select the ith smallest of n numbers is n + min(i,n-i) + o(n). A lower bound within 9 percent of the above formula is also derived.
Binary summation
Authors: R. J. Walker
Venue: Communications of the ACM (1971)

In discussing his binary summation method [1] Linz mentions two defects: &ldquo;It is more difficult to program than the standard method, and it is difficult to use unless all numbers are available at the start of the summation.&rdquo; A defect not mentioned is the extra storage space (approximately N words) required for the Sij. The last two of these three defects can be removed by proper combination of partial sums. In the adjacent PL/I program, the only storage needed is for the M-component vector T, where M &gE; [log2 N]. N must be even, and B is a number not expressible as a sum of A(I)'s, e.g. B = -1 if A(I) &ge; 0, or B = 1E + 75 for reasonably sized A(I).
Communication Reduction in Multiple Multicasts Based on Hybrid Static-Dynamic Scheduling
Authors: David R. Surma, Edwin H.-M. Sha
Venue: IEEE Transactions on Parallel and Distributed Systems (2000)

This paper presents a novel approach to reducing the communication costs incurred when performing multiple multicasts on wormhole routed two-dimensional mesh multiprocessor systems. Both unicast and path-based implementations of multicasting incur communication costs due to the inherent message passing and contention for network resources. The start-up time dominates the transmission time when the data volume is small. However, in the presence of multiple multicasts when the data volume is very large, the communication delays due to message blocking and resource contention become very significant. Because of this, we present a hybrid static-dynamic technique to reduce the communication costs incurred when performing multiple multicasts on worm-hole routed direct networks. This technique requires a focus on ordering and routing information for the individual message transmissions. At compile time, each message is assigned a priority using the recently developed collision graph model. Then at run-time these priorities are used to arbitrate the message transmissions. As a base, dimension-ordered routing is used. However, to further reduce the communication costs, some messages will be rerouted. This technique is useful either as a stand-alone algorithm or as an embedded procedure into existing algorithms. Furthermore, the techniques can be applied to higher dimension direct networks. For a single multicast, our work performs as well as conventional methods. For multiple multicasts, results show that our approach provides significant improvement over baseline techniques.
Isomorph-Redundancy in Sequential Circuits
Authors: Debesh K. Das, Uttam K. Bhattacharya, Bhargab B. Bhattacharya
Venue: IEEE Transactions on Computers (2000)

Design of irredundant and fully testable nonscan sequential circuits is a major concern of logic synthesis, as the presence of undetectable faults may render an ATPG intractable. This paper outlines some intriguing properties of isomorph faults, which are sequentially undetectable as well as redundant. An isomorph fault in a sequential circuit makes the state diagram of the faulty machine identical to that of the fault-free machine under certain renaming of states. Examples of reduced sequential machines whose circuit realization is combinationally irredundant, but isomorph-redundant, are hard to construct and very little is known about them. In this paper, many curious examples of such sequential circuits are presented wherein a single stuck-at fault causes isomorphic faulty machines. An infinite family of such circuits may, in fact, be constructed. It is shown that even two-level irredundant circuits obtained by synthesis tools may admit isomorph-redundancy under multiple stuck-at faults. Various classifications and related properties of isomorph faults are also reported. These results reveal new insight and understanding of redundancy in sequential circuits.
A framework for efficient reuse of binary code in Java
Authors: Pramod G. Joisha, Samuel P. Midkiff, Mauricio J. Serrano, Manish Gupta
Venue: Proceedings of the 15th international conference on Supercomputing (2001)

This paper presents a compilation framework that enables efficient sharing of executable code across distinct Java Virtual Machine (JVM) instances. High-performance JVMs rely on run-time compilation, since static compilation cannot handle many dynamic features of Java. These JVMs suffer from large memory footprints and high startup costs, which are serious problems for embedded devices (such as hand held personal digital assistants and cellular phones) and scalable servers. A recently proposed approach called quasi-static compilation overcomes these difficulties by reusing precompiled binary images after performing validation checks and stitching on them (i.e., adapting them to a new execution context), falling back to interpretation or dynamic compilation whenever necessary. However, the requirement in our previous design to duplicate and modify the executable binary image for stitching is a major drawback when targeting embedded systems and scalable servers. In this paper, we describe a new approach that allows stitching to be done on an indirection table, leaving the executable code unmodified and therefore writable to read-only memory. On embedded devices, this saves precious space in writable memory. On scalable servers, this allows a single image of the executable to be shared among multiple JVMs, thus improving scalability. Furthermore, we describe a novel technique for dynamically linking classes that uses traps to detect when a class should be linked and initialized. Like back-patching, the technique allows all accesses after the first to proceed at full speed, but unlike back-patching, it avoids the modification of running code. We have implemented this approach in the Quicksilver quasi-static compiler for the Jalape~ no JVM. On the SPECjvm98 benchmark suite, our approach obtains code space savings, in writable memory, of between 82% to 89% of that from our previous quasi-static compiler, while delivering performance that is typically within 1% to 7% of that approach, and which is competitive with the performance of the Jalape&ntilde;o adaptive optimization system.
Design patterns for sorting
Authors: Dung “Zung” Nguyen, Stephen B. Wong
Venue: ACM SIGCSE Bulletin (2001)

Drawing on Merritt's divide-and-conquer sorting taxonomy [1], we model comparison-based sorting as an abstract class with a template method to perform the sort by relegating the splitting and joining of arrays to its concrete subclasses. Comparison on objects is carried out via an abstract ordering strategy. This reduces code complexity and simplifies the analyses of the various concrete sorting algorithms. Performance measurements and visualizations can be added without modifying any code by utilizing the decorator design pattern. This object-oriented design not only provides the student a concrete way of unifying seemingly disparate sorting algorithms but also help him/her differentiate them at the proper level of abstraction.
Reversible execution
Authors: M. V. Zelkowitz
Venue: Communications of the ACM (1973)

The ability to backtrack, or retrace, the execution of a computer program has gained wider acceptance recently as a desired feature within a programming language. This is particularly useful in two different applications: (1) In debugging systems where the trace output is saved and can be interrogated under programmer control [1, 3]; (2) In artificial intelligence applications where one is trying to prove a certain result. It is frequently necessary to backup the proof and try some alternative path [2].
Automatic text summarization based on relevance feedback with query splitting (poster session)
Authors: Kyoung-Soo Han, Dae-Ho Baek, Hae-Chang Rim
Venue: Proceedings of the fifth international workshop on on Information retrieval with Asian languages (2000)

This paper describes a method of text summarization using a query expansion technique. Generally, summarization systems using query expansion have the problem that feedback query gets biased during a query expansion process. We can alleviate this problem by expanding the initial query into several split feedback queries. Experimental results show that our query splitting method is superior to other methods using query expansion.
A System Design Methodology for Analog Feed Forward Artificial Neural Networks
Authors: Mario Costa, Davide Palmisano, Eros Pasero
Venue: Analog Integrated Circuits and Signal Processing (1999)

Today Feed Forward Neural Networks (FFNs) use paradigms tied to mathematical frameworks more than to actual electronic devices. This fact makes analog neural integrated circuits heavy to design. Here we propose an alternative model that can use the native computational properties of the basic electronic circuits. A practical framework is described to train analog FFNs in compliance with the model. This is especially useful whenever the weight storage elements cannot be re-programmed on the fly at a high rate. To show how the capability of such framework can be applied to neural systems with non conventional architectures two cases are presented. The first one is a neural signal processor named NESP which has sigmoidal neurons and the other is an innovative architecture named N-LESS.
Chain mulitplication of matrices of approximately or exactly the same size
Authors: Nicola Santoro
Venue: Communications of the ACM (1984)

We present a different approach to finding an optimal computation order; it exploits both the difference between the size of the matrices and the difference between the number of nonzero elements in the matrices. Therefore, this technique can be usefully applied where the matrices are almost or exactly the same size. We show that using the proposed technique, an optimal computation order can be determined in time O(n) if the matrices have the same size, and in time O(n3) otherwise.
Automatically tracking and analyzing the behavior of live insect colonies
Authors: Tucker Balch, Zia Khan, Manuela Veloso
Venue: Proceedings of the fifth international conference on Autonomous agents (2001)

We introduce the study of {\it live} social insect colonies as a relevant and exciting domain for the development and application of multi-agent systems modeling tools. Social insects provide a rich source of {\it traceable} social behavior for testing multi-agent tracking, prediction and modeling algorithms. An additional benefit of this research is the potential for contributions to experimental biology --- the principled techniques developed for analyzing artificial multi-agent systems can be applied to advance the state of knowledge of insect behavior. We contribute a novel machine vision system that addresses the challenge of tracking hundreds of small animals simultaneously. Fast color-based tracking is combined with movement-based tracking to locate ants in a real-time video stream. We also introduce new methods for analyzing the spatial activity of ant colonies. The system was validated in experiments with laboratory colonies of {\it Camponotus festinatus} and several example analyses of the colonies' spatial behavior are provided.
Restoration by path concatenation: fast recovery of MPLS paths
Authors: Anat Bremler-Barr, Yehuda Afek, Haim Kaplan, Edith Cohen, Michael Merritt
Venue: Proceedings of the twentieth annual ACM symposium on Principles of distributed computing (2001)

A new general theory about restoration of network paths is first introduced. The theory pertains to restoration of shortest paths in a network following failure, e.g., we prove that a shortest path in a network after removing k edges is the concatenation of at most k + 1 shortest paths in the original network. The theory is then combined with efficient path concatenation techniques in MPLS (multi-protocol label switching), to achieve powerful schemes for restoration in MPLS based networks. We thus transform MPLS into a flexible and robust method for forwarding packets in a network. Finally, the different schemes suggested are evaluated experimentally on three large networks (a large ISP, the AS graph of the Internet, and the full Internet topology). These experiments demonstrate that the restoration schemes perform well in actual topologies.
Automating the linking of content and concept
Authors: Robert Tansley, Colin Bird, Wendy Hall, Paul Lewis, Mark Weal
Venue: Proceedings of the eighth ACM international conference on Multimedia (2000)

In previous work we have described a multimedia system, MAVIS 2, supporting content and concept based retrieval and navigation. A central component of the system is a multimedia thesaurus in which media content is associated with appropriate concepts in a semantic layer. A major challenge is identifying and constructing these associations in a particular application without requiring a huge amount of manual effort. In this paper we propose a two phase approach to the problem. In the first phase, latent semantic analysis is used to associate metadata available for some media objects with concept class descriptions. This facilitate automatic associations to be made with the concept layer of the those media objects. In the second phase, media content matching is used to classify media objects without metadata through their similarity to media objects classified in phase 1.
Eliminating Exception Handling Errors with Dependability Cases: A Comparative, Empirical Study
Authors: Roy A. Maxion, Robert T. Olszewski
Venue: IEEE Transactions on Software Engineering (2000)

Programs fail mainly for two reasons: logic errors in the code and exception failures. Exception failures can account for up to two-thirds of system crashes [1], hence, are worthy of serious attention. Traditional approaches to reducing exception failures, such as code reviews, walkthroughs, and formal testing, while very useful, are limited in their ability to address a core problem: The programmer's inadequate coverage of exceptional conditions. The problem of coverage might be rooted in cognitive factors that impede the mental generation (or recollection) of exception cases that would pertain in a particular situation, resulting in insufficient software robustness. This paper describes controlled experiments for testing the hypothesis that robustness for exception failures can be improved through the use of various coverage-enhancing techniques: N-version programming, group collaboration, and dependability cases. N-version programming and collaboration are well known. Dependability cases, derived from safety cases, comprise a new methodology based on structured taxonomies and memory aids for helping software designers think about and improve exception handling coverage. All three methods showed improvements over control conditions in increasing robustness to exception failures but dependability cases proved most efficacious in terms of balancing cost and effectiveness. A controlled experiment conducted with 119 subjects revealed a statistically significant 34 percent increase (p
General Interior-Point Maps and Existence of Weighted Paths for Nonlinear Semidefinite Complementarity Problems
Authors: Renato D. C. Monteiro, Paulo R. Zanjácomo
Venue: Mathematics of Operations Research (2000)

Extending the previous work of Monteiro and Pang (1998), this paper studies properties of fundamental maps that can be used to describe the central path of the monotone nonlinear com-plementarity problems over the cone of symmetric positive semidefinite matrices. Instead of focusing our attention on a specific map as was done in the approach of Monteiro and Pang (1998), this paper considers a general form of a fundamental map and introduces conditions on the map that allow us to extend the main results of Monteiro and Pang (1998) to this general map. Each fundamental map leads to a family of "weighted" continuous trajectories which include the central trajectory as a special case. Hence, for complementarity problems over the cone of symmetric positive semidefinite matrices, the notion of weighted central path depends on the fundamental map used to represent the central path.