ppxscal/embedding_network huggingface dataset:
The Blueprint for Life?
Authors: Dror G. Feitelson, Millet Treinin
Venue: Computer (2002)

One of the greatest scientific discoveries of the twentieth century is the structure of DNA and how it encodes proteins. Current genome projects, especially the Human Genome Project, have sparked interest in the information encoded in DNA, which is often referred to as "the blueprint for life,"implying that it contains all the information needed to create life. But this interpretation ignores the complex interactions between DNA and its cellular environment--interactions that regulate and control the spatial and temporal patterns of gene expression. Moreover, the particulars of many cellular structures seem not to be encoded in DNA, and they are never created from scratch--rather,each cell inherits templates for these structures from its parent cell. Thus, it is not clear that DNAdirectly or indirectly encodes all life processes, casting doubt on the belief that we can understand them solely by studying DNA sequences.
Increasing Reliability in Cable-Free Radio LANs Low Level Forwarding in HIPERLAN
Authors: Philippe Jacquet, Pascale Minet, Paul Mühlethaler, Nicolas Rivierre
Venue: Wireless Personal Communications: An International Journal (1997)

Radio LANs are emerging in the computing world. They are supported by distinct configurations: on the one hand radio LANs with base stations and a wired backbone, on the other hand radio LANs implementing Intra-forwarding. Adding a new node in a radio LAN with Intra-forwarding, increases the reliability, while this reliability decreases with ad hoc or hub configurations. This advantage of Intra-forwarding is quantified. Intra-forwarding, as defined in the HIPERLAN standard, is based on a hop-by-hop policy and link check procedures. It is shown how point-to-point packets and broadcast packets are forwarded. The three basic components of Intra-forwarding needed to build and update the Intra-forwarding database are described. The originality of this approach is the use of multipoint relays which enable better scalability. The correctness of the Intra-forwarding protocol is proved and its cost is evaluated.
Numerical Analysis of Strategic Contingent Claims Models
Authors: Ronald W. Anderson, Cheng Tu
Venue: Computational Economics (1998)

We study the numerical properties of a class of models recently introduced to calculate the values of corporate bonds and other corporate liabilities. Starting from a discrete-time extensive form game representing the consequences of financial distress, these &rsquo;&rsquo;strategic contingent claims models" are associated with a particular free-boundary problem. Here we consider the properties of alternative solution techniques applied to this problem. We discuss four solution techniques of the finite difference type: explicit solutions, explicit solutions of the log transformed model, implicit solutions on a regular grid, and dynamically remeshed implicit solutions. To our knowledge this last method has not previously been employed in financial applications. We find that the use of dynamic remeshing can speed calculation solutions enormously. This opens the way to applying strategic contingent claims models in practical applications.
Open Source Software Adoption: A Status Report
Authors: Huaiqing Wang, Chen Wang
Venue: IEEE Software (2001)

Because of many misgivings and myths regarding open source's state of maturity, organizations often struggle to make informed software adoption decisions. The authors systematically apply a generally accepted set of requirements-oriented criteria to a representative set of open source software. Their approach and the data they collected offer a practical roadmap to navigating this new landscape.
Agent Programming in 3APL
Authors: Koen V. Hindriks, Frank S. De Boer, Wiebe Van Der Hoek, John-Jules Ch. Meyer
Venue: Autonomous Agents and Multi-Agent Systems (1999)

An intriguing and relatively new metaphor in the programming community is that of an intelligent agent. The idea is to view programs as intelligent agents acting on our behalf. By using the metaphor of intelligent agents the programmer views programs as entities which have a mental state consisting of beliefs and goals. The computational behaviour of an agent is explained in terms of the decisions the agent makes on the basis of its mental state. It is assumed that this way of looking at programs may enhance the design and development of complex computational systems.To support this new style of programming, we propose the agent programming language 3APL. 3APL has a clear and formally defined semantics. The operational semantics of the language is defined by means of transition systems. 3APL is a combination of imperative and logic programming. From imperative programming the language inherits the full range of regular programming constructs, including recursive procedures, and a notion of state-based computation. States of agents, however, are belief or knowledge bases, which are different from the usual variable assignments of imperative programming. From logic programming, the language inherits the proof as computation model as a basic means of computation for querying the belief base of an agent. These features are well-understood and provide a solid basis for a structured agent programming language. Moreover, on top of that 3APL agents use so-called practical reasoning rules which extend the familiar recursive rules of imperative programming in several ways. Practical reasoning rules can be used to monitor and revise the goals of an agent, and provide an agent with reflective capabilities.Applying the metaphor of intelligent agents means taking a design stance. From this perspective, a program is taken as an entity with a mental state, which acts pro-actively and reactively, and has reflective capabilities. We illustrate how the metaphor of intelligent agents is supported by the programming language. We also discuss the design of control structures for rule-based agent languages. A control structure provides a solution to the problem of which goals and which rules an agent should select. We provide a concrete and intuitive ordering on the practical reasoning rules on which such a selection mechanism can be based. The ordering is based on the metaphor of intelligent agents. Furthermore, we provide a language with a formal semantics for programming control structures. The main idea is not to integrate this language into the agent language itself, but to provide the facilities for programming control structures at a meta level. The operational semantics is accordingly specified at the meta level, by means of a meta transition system.
An Icon-Based Design Method for Prolog
Authors: Gerald M. Karam
Venue: IEEE Software (1988)

An icon-based design method that combines a module-oriented Prolog design model, graphical software design, and software engineering principles is presented. It is based on a dataflow-driven decomposition that is guided by design principles, followed by evaluation. Its purpose is to enable Prolog applications to be developed in accordance with the general principles of software engineering: modifiability, efficiency, reliability, and understandability. The design model and procedure are described. The design of a Lisp interpreter is considered to illustrate the method.
Interactive visualization of complex plant ecosystems
Authors: Oliver Deussen, Carsten Colditz, Marc Stamminger, George Drettakis
Venue: Proceedings of the conference on Visualization '02 (2002)

We present a method for interactive rendering of large outdoor scenes. Complex polygonal plant models and whole plant populations are represented by relatively small sets of point and line primitives. This enables us to show landscapes faithfully using only a limited percentage of primitives. In addition, a hierarchical data structure allows us to smoothly reduce the geometrical representation to any desired number of primitives. The scene is hierarchically divided into local portions of geometry to achieve large reduction factors for distant regions. Additionally, the data reduction is adapted to the visual importance of geometric objects. This allows us to maintain the visual fidelity of the representation while reducing most of the geometry drastically. With our system, we are able to interactively render very complex landscapes with good visual quality.
The Great Term Robbery
Authors: Neville Holmes
Venue: Computer (2001)

The computing profession's subtle Newspeak blurs the distinction between human and machine.
An Expectation-Driven Response Understanding Paradigm
Authors: D. -G. Shin
Venue: IEEE Transactions on Knowledge and Data Engineering (1994)

This paper describes a model that can account for ad hoc user-responses to argument interrogative type of system-initiated questions. Successful implementation of the model can provide an alternative solution that is more effective than the menu-driven approach that has been proposed as a meager solution to enable the system to ask a question to the user. The proposed model assumes that when the system asks a question, it maintains an expectation of the potential answers. The system then uses the expectation as the focus to perform the most likely interpretation of the user's response. Without using such a focus the interpretation process could be unbounded. The interpretation process is mapped into a heuristic search problem. The interpretation process results in identifying a particular expectation-response relationship type, which the system can use to tailor its response strategy with respect to the given user-response. A prototype has been constructed to demonstrate the soundness of the proposed model.
Program Comprehension During Software Maintenance and Evolution
Authors: Anneliese von Mayrhauser, A. Marie Vans
Venue: Computer (1995)

How well programmers comprehend programs is key to effective software maintenance and evolution. But how exactly do programmers understand code? Over the years, several code-comprehension models have been developed to help researchers answer this question. Five types of tasks are commonly associated with software maintenance and evolution: adaptive, perfective, and corrective maintenance; reuse; and code leverage. Each type has its own set of typical activities. Some of them, such as understanding a system or problem, are common to several tasks. Code comprehension models describe the cognitive processes involved in these tasks. Experiments support some, but not all of these models. The authors analyze six comprehension models and their validation experiments to determine the current state of knowledge program comprehension offers. They begin by describing some common elements of cognition models. Programmer knowledge plays a key role in the understanding process. The mental model--an internal, working representation of the software under consideration--includes both static and dynamic elements. Static elements include text-structure knowledge, "chunks," plans, hypotheses, beacons, and rules of discourse. Dynamic elements include strategies, actions, episodes, and processes. The authors compare the six models in this light and identify a need for more experimental studies with experienced software engineers working on specific maintenance tasks and large-scale code in state-of-the-art computing environments.
A road map to ARPA involvement in electronic packaging
Authors: Lance A. Glasser
Venue: Computer (1993)

The application of advanced electronic packaging and interconnect (EP/I) technology by US Department of Defense's Advance Research Projects Agency are discussed. The EP/I domain includes packages, multichip modules (MCMs), connectors, printed circuit boards (PCBs), boxes, backplanes, and cages. The EP/I physical technologies, including diamond substrates, superconductors, and metal matrix packages, are discussed, and information technologies are described.
EPIC: Explicitly Parallel Instruction Computing
Authors: Michael S. Schlansker, B. Ramakrishna Rau
Venue: Computer (2000)

Over the past two and a half decades, the computer industry has grown accustomed to the spectacular rate of increase in microprocessor performance. The industry accomplished this without fundamentally rewriting programs in parallel form, without changing algorithms or languages, and often without even recompiling programs. Instruction-level parallel processing achieves high performance without major changes to software. However, computers have thus far achieved this goal at the expense of tremendous hardware complexity--a complexity that has grown so large as to challenge the industry's ability to deliver ever-higher performance. The authors developed the Explicitly Parallel Instruction Computing (EPIC) style of architecture to enable higher levels of instruction-level parallelism without unacceptable hardware complexity. They focus on the broader concept of EPIC as embodied by HPL-PD (formerly known as HPL PlayDoh) architecture, which encompasses a large space of possible EPIC ISAs (instruction set architectures). In this article, the authors focus on HPL-PD because it represents the essence of the EPIC philosophy while avoiding the idiosyncracies of a specific ISA.
Analytical transmission electron microscopy observation of Aluminium-Tungsten interaction in thermally stressed Al/Ti/W/TiN interconnections
Authors: R. Pantel, H. Wehbe-Alause, S. Jullian, L. F. Tz. Kwakman
Venue: Microelectronic Engineering (2002)

In this communication, we used a modern analytical TEM-STEM fully equipped to carry out a complete physical and chemical study of Al/Ti/W/TiN interconnection evolution after 450 °C annealing. Using energy filtered TEM, compositional mapping, scanning TEM (STEM) Z contrast imaging, EDX and EELS spectrum imaging and micro-diffraction, we evidence at the Al/W top contacts interface a reaction between Al and W leading to the growth of AlxW inclusions inside the Al grains.
Shape-based features for cat ganglion retinal cells classification
Authors: Regina C&#x00E9;lia Coelho Vito Di Ges&#x00F9; Giosu&#x00E8; Lo Bosco J&#x00FA;lia Sawaki Tanaka Cesare Valenti
Venue: Real-Time Imaging (2002)

This article presents a quantitative and objective approach to cat ganglion cell characterization and classification. The combination of several biologically relevant features such as diameter, eccentricity, fractal dimension, influence histogram, influence area, convex hull area, and convex hull diameter are derived from geometrical transforms and then processed by three different clustering methods (Ward's hierarchical scheme, K-means and genetic algorithm), whose results are then combined by a voting strategy. These experiments indicate the superiority of some features and also suggest some possible biological implications.
Uncertainty Management in Expert Systems Using Fuzzy Petri Nets
Authors: Amit Konar, Ajit K. Mandal
Venue: IEEE Transactions on Knowledge and Data Engineering (1996)

The paper aims at developing new techniques for uncertainty management in expert systems for two generic class of problems using fuzzy Petri net that represents logical connectivity among a set of imprecise propositions. One class of problems addressed in the paper deals with the computation of fuzzy belief of any proposition from the fuzzy beliefs of a set of independent initiating propositions in a given network. The other class of problems is concerned with the computation of steady-state fuzzy beliefs of the propositions embedded in the network, from their initial fuzzy beliefs through a process called belief-revision. During belief-revision, a fuzzy Petri net with cycles may exhibit "limitcycle behavior" of fuzzy beliefs for some propositions in the network. No decisions can be arrived at from a fuzzy Petri net with such behavior. To circumvent this problem, techniques have been developed for the detection and elimination of limitcycles. Further, an algorithm for selecting one evidence from each set of mutually inconsistent evidences, referred to as nonmonotonic reasoning, has also been presented in connection with the problems of belief-revision. Finally, the concepts proposed for solving the problems of belief-revision have been applied successfully for tackling imprecision, uncertainty, and nonmonotonicity of evidences in an illustrative expert system for criminal investigation.
Integrating Online and Offline Testing of a Switching Memory
Authors: Stefano Barbagallo, Davide Medina, Fulvio Corno, Paolo Prinetto, Matteo Sonza Reorda
Venue: IEEE Design Test (1998)

The article describes the architecture of a circuit used in a telephone switching unit and focuses on its on-line and off-line test features. Several techniques have been exploited: BIST is adopted to test some embedded memories, Partial Scan allows the test of the remaining logic, and Boundary Scan is used to activate the test and gather the results. Data are reported, concerning the obtained fault coverage, the hardware overhead and the performance penalties introduced by the approach. By sharing the same circuitry for both on-line and off-line testing we succeeded in minimizing the additional logic.
Communication-Based Power Management
Authors: Kanishka Lahiri, Sujit Dey, Anand Raghunathan
Venue: IEEE Design Test (2002)

Battery-Powered Systems account for a significant and rapidly expanding segment of the electronics and semiconductor industries. Unfortunately, projections of the complexity, functionality, and performance of such systems far exceed expected improvements in battery technologies, leading to a widening "battery gap", Bridging this gap is a challenge that system designers must face for the foreseeable future. The need to improve battery life has, in large
Fundamentals of Distributed System Observation
Authors: Colin Fidge
Venue: IEEE Software (1996)

It's difficult to determine event order in distributed systems because of the problem of observability. The author discusses this problem and evaluates different strategies for determining arrival order.
New Strategies for Assigning Real-Time Tasks to Multiprocessor Systems
Authors: Jörg Liebeherr, Almut Burchard, Yingfeng Oh, Sang H. Son
Venue: IEEE Transactions on Computers (1995)

Optimal scheduling of real-time tasks on multiprocessor systems is known to be computationally intractable for large task sets. Any practical scheduling algorithm for assigning real-time tasks to a multiprocessor system presents a trade-off between its computational complexity and its performance. In this study, new schedulability conditions are presented for homogeneous multiprocessor systems where individual processors execute the rate-monotonic scheduling algorithm. The conditions are used to develop new strategies for assigning real-time tasks to processors. The performance of the new strategies is shown to be significantly better than suggested by the existing literature. Under the realistic assumption that the load of each real-time task is small compared to the processing speed of each processor, it is shown that the processors can be almost fully utilized.
XML and the new design regime: disputes between designers, application developers, authors, and readers in changing technological conditions and perceptions of social and professional need
Authors: Gilbert Vanburen Wilkes,  IV
Venue: ACM Journal of Computer Documentation (JCD) (2002)

In this study I attempt (a) to specify a theory that explains the historical character of change or transition in the production of written artifacts, and (b) use that theory to cast light on a particular instance of change or transition in the production of written artifacts, that of the Web, principally, the issue of structured markup and discussions about precisely what a structured Web should look like, the work it should do, and so forth. What I attempt to identify, describe, and analyze, are the norms and conventions that govern the production of written discourse.
CLARANS: A Method for Clustering Objects for Spatial Data Mining
Authors: Raymond T. Ng, Jiawei Han
Venue: IEEE Transactions on Knowledge and Data Engineering (2002)

Spatial data mining is the discovery of interesting relationships and characteristics that may exist implicitly in spatial databases. To this end, this paper has three main contributions. First, we propose a new clustering method called CLARANS, whose aim is to identify spatial structures that may be present in the data. Experimental results indicate that, when compared with existing clustering methods, CLARANS is very efficient and effective. Second, we investigate how CLARANS can handle not only points objects, but also polygon objects efficiently. One of the methods considered, called the IR-approximation, is very efficient in clustering convex and nonconvex polygon objects. Third, building on top of CLARANS, we develop two spatial data mining algorithms that aim to discover relationships between spatial and nonspatial attributes. Both algorithms can discover knowledge that is difficult to find with existing spatial data mining algorithms.
Building a high-performance collective communication library
Authors: Mike Barnett, Satya Gupta, David G. Payne, Lance Shuler, Robert van de Geijn, Jerrell Watts
Venue: Proceedings of the 1994 ACM/IEEE conference on Supercomputing (1994)

In this paper, we report on a project to develop a unified approach for building a library of collective communication operations that performs well on a cross-section of problems encountered in real applications. The target architecture is a two-dimensional mesh with worm-hole routing, but the techniques are more general. The approach differs from traditional library implementations in that we address the need for implementations that perform well for various sized vectors and grid dimensions, including non-power-of-two grids. We show how a general approach to hybrid algorithms yields performance across the entire range of vector lengths. Moreover, many scalable implementations of application libraries require collective communication within groups of nodes. Our approach yields the same kind of performance for group collective communication. Results from the Intel Paragon system are included. To obtain this library for Intel systems contact intercom&copy;cs.utexas.edu.
Query Relaxation by Structure and Semantics for Retrieval of Logical Web Documents
Authors: Wen-Syan Li, K. Selçuk Candan, Quoc Vu, Divyakant Agrawal
Venue: IEEE Transactions on Knowledge and Data Engineering (2002)

Since the Web encourages hypertext and hypermedia document authoring (e.g., HTML or XML), Web authors tend to create documents that are composed of multiple pages connected with hyperlinks. A Web document may be authored in multiple ways, such as, 1) all information in one physical page, or 2) a main page and the related information in separate linked pages. Existing Web search engines, however, return only physical pages containing keywords. In this paper, we introduce the concept of information unit, which can be viewed as a logical Web document consisting of multiple physical pages as one atomic retrieval unit. We present an algorithm to efficiently retrieve information units. Our algorithm can perform progressive query processing. These functionalities are essential for information retrieval on the Web and large XML databases. We also present experimental results on synthetic graphs and real Web data.