OpenRaiser/Intern-Atlas huggingface dataset:
Open Access, Intellectual Property, and How Biotechnology Becomes a New Software Science
Venue: arXiv cs.CY 2009
Year: 2009

Innovation is slowing greatly in the pharmaceutical sector. It is considered here how part of the problem is due to overly limiting intellectual property relations in the sector. On the other hand, computing and software in particular are characterized by great richness of intellectual property frameworks. Could the intellectual property ecosystem of computing come to the aid of the biosciences and life sciences? We look at how the answer might well be yes, by looking at (i) the extent to which a drug mirrors a software program, and (ii) what is to be gleaned from trends in research publishing in the life and biosciences.
Measuring the Knowledge Base: A Program of Innovation Studies
Venue: arXiv cs.CY 2009
Year: 2009

Organized knowledge production can then be considered as the codification of communication. Communications leave traces that can be studied as indicators. Institutions can be considered as retention mechanisms functional for the reproduction of ever more complex, that is, scientific and knowledge-based, communications. The focus on communication enables us to operationalize the research questions in terms of indicators by using the mathematical theory of communication. The combination of two theories with a very different status--i.e., a combination of theory and methods--enables us to update and inform empirical hypotheses about how the knowledge base transforms the institutional relations of an increasingly knowledge-based society. Policy implications are specified.
'Interaction' versus 'action' in Luhmann's sociology of communication
Venue: arXiv cs.CY 2009
Year: 2009

Both 'actions' and 'interactions' can be considered as micro-operations that can be aggregated from a systemic perspective. Whereas actions operate historically, interactions provide the events retrospectively with meaning. Luhmann's sociology of communication systems adds to the approach of symbolic interactionism the question of what global dimensions of communication mean for local interactions. When communication is functionally differentiated--for example, in terms of media--tensions can be expected to develop between local organizations and global developments of communication structures. Interfaces enable us to translate selectively among (provisionally) stabilized representations, for example, in professional practices. 'Big science' and 'high tech' can be considered as organizational acculturations of an emerging level of sophistication in global communications. The global dimension remains a hypothesis, but entertaining this hypothesis of 'globalization' restructures the local expectations.
A study of seismology as a dynamic, distributed area of scientific research
Venue: arXiv cs.DL 2009
Year: 2009

Seismology has several features that suggest it is a highly internationalized field: the subject matter is global, the tools used to analyse seismic waves are dependent upon information technologies, and governments are interested in funding cooperative research. We explore whether an emerging field like seismology has a more internationalised structure than the older, related field of geophysics. Using aggregated journal-journal citations, we first show that, within the citing environment, seismology emerged from within geophysics as its own field in the 1990s. The bibliographic analysis, however, does not show that seismology is more internationalised than geophysics: in 2000, seismology had a lower percentage of all articles co-authored on an international basis. Nevertheless, social network analysis shows that the core group of cooperating countries within seismology is proportionately larger and more distributed than that within geophysics. While the latter exhibits an established network with a hierarchy, the formation of a field in terms of new partnership relations is ongoing in seismology.
Comment on "New Results on Frame-Proof Codes and Traceability Schemes"
Venue: arXiv cs.IT 2009
Year: 2009

In the paper "New Results on Frame-Proof Codes and Traceability Schemes" by Reihaneh Safavi-Naini and Yejing Wang [IEEE Trans. Inform. Theory, vol. 47, no. 7, pp. 3029-3033, Nov. 2001], there are lower bounds for the maximal number of codewords in binary frame-proof codes and decoders in traceability schemes. There are also existence proofs using a construction of binary frame-proof codes and traceability schemes. Here it is found that the main results in the referenced paper do not hold.
On the achievable improvement by the linear minimum mean square error detector
Venue: arXiv cs.IT 2009
Year: 2009

Linear minimum mean square error (MMSE) detector has been shown to alleviate the noise amplification problem, resulting in the conventional zero-forcing (ZF) detector. In this paper, we analyze the performance improvement by the MMSE detector in terms of the condition number of its filtering matrix, and in terms of the post-precessing signal to noise ratio (SNR) improvement. To this end, we derive explicit formulas for the condition numbers of the filtering matrices and the post-processing SNRs. Analytical and simulation results demonstrate that the improvement achieved by the MMSE detector over the ZF detector is not only dependent on the noise variance and the condition number of the channel matrix, but also on how close the smallest singular values are to the noise variance.
An evaluation of Flickrs distributed classification system, from the perspective of its members, and as an image retrieval tool in comparison with a controlled vocabulary
Venue: arXiv cs.DL 2009
Year: 2009

The profusion of online digital images presents new challenges for image indexing. Images have always been problematic to describe and catalogue due to lack of inherent textual data and ambiguity of meaning. An alternative to time-consuming professionally-applied metadata has been sought in the form of tags, simple keywords that form a flat structure known as distributed classification, or more popularly as a folksonomy. This research aims to increase understanding of why people tag and how effective they find it for searching, using as the focus. Open-ended questionnaires were sent out to members of the photo-sharing website Flickr, with the opportunity to post comments to an online discussion space. There is also a systematic comparison between a tag-based system and a more traditional controlled vocabulary, to test out the claims made regarding the suitability of tagging for searching and browsing. For this purpose Flickr has been compared with Getty Images using a series of test themes. The small number of people who replied to the questionnaire gave detailed answers that confirmed several assertions made about tags: they are accepted despite their flaws (sloppiness and potential for inaccuracy) because they serve their purpose to a satisfactory level. Some answers challenged the assumption that tagging is only done for personal benefit. The search comparison found that while Getty allows highly specific queries and logical semantic links, Flickr is more flexible and better placed to deal with subtle concepts. The overall conclusion is that tags achieve most when used in conjunction with groupings of people with a shared interest.
On the Optimality of a Class of LP-based Algorithms
Venue: arXiv cs.CC 2009
Year: 2009

In this paper we will be concerned with a class of packing and covering problems which includes Vertex Cover and Independent Set. Typically, one can write an LP relaxation and then round the solution. In this paper, we explain why the simple LP-based rounding algorithm for the \\VC problem is optimal assuming the UGC. Complementing Raghavendra's result, our result generalizes to a class of strict, covering/packing type CSPs.
iSSEE: IMS Sensors Search Engine Enabler for Sensors Mashups Convergent Application
Venue: arXiv cs.NI 2009
Year: 2009

Integrating the sensing capabilities in Internet Protocol network will open the opportunities to build a wide range of novel multimedia applications. The problem when using sensors (e.g. temperature sensor, camera, audio, humidity, etc.) connected to the network is to know dynamically at any time if they are always connected or not, what type of data they can transmit and where they are geographically located. This paper describes an application enabler: IMS Sensor Search Engine Enabler (iSSEE), which allows IMS applications using sensors and IMS based devices, to get information about the sensor availability, its location and the type of the sensor. Using data collected by sensors and from the web, mash-ups convergent applications use cases are proposed by combining the contents from heterogeneous data.
Modelling Clock Synchronization in the Chess gMAC WSN Protocol
Venue: arXiv cs.LO 2009
Year: 2009

We present a detailled timed automata model of the clock synchronization algorithm that is currently being used in a wireless sensor network (WSN) that has been developed by the Dutch company Chess. Using the Uppaal model checker, we establish that in certain cases a static, fully synchronized network may eventually become unsynchronized if the current algorithm is used, even in a setting with infinitesimal clock drifts.
Enterprise Multi-Branch Database Synchronization with MSMQ
Venue: arXiv cs.DB 2009
Year: 2009

When we talk about databases there have always been problems concerning data synchronization. The latter is a technique for maintaining consistency among different copies of data (often called replicas). In general, there is no universal solution to this problem and often a particular situation requires a particular approach driven by specific conditions. This paper presents an approach tackling the issue of data synchronization in a distributed multi-branch enterprise database. The proposed solution is based on MSMQ (Microsoft Message Queue), a mechanism for asynchronous messaging.
Evaluation of Varrying Mobility Models & Network Loads on DSDV Protocol of MANETs
Venue: arXiv cs.NI 2009
Year: 2009

A mobile ad-hoc network (MANET) is collection of intercommunicating mobile hosts forming a spontaneous network without using established network infrastructure. Unlike the cellular or infrastructure networks who have a wired backbone connecting the base-station, the MANETs have neither fixed routers nor fixed locations. Their performance largely depend upon the routing mechanism & nature of mobility. Earlier research hints that the Destination Sequenced Distance Vector (DSDV) routing protocol is one of the most efficient and popular protocols, as far as general parameters have been concerned.[1,6] We have experimentally evaluated, the performance metrics for network load, packet delivery fraction and end-to-end delay with DSDV Protocol using NS2 Simulator.This paper presents, the performance of DSDV protocol for four different mobility models namely: Random Waypoint, Reference Point Group Mobility, Gauss Markov & Manhattan Mobility Model having varying network load & speed. The experimental results suggest that DSDV protocol with RPGM mobility model has optimized results for varying network load and speed.
A QoS-Aware Intelligent Replica Management Architecture for Content Distribution in Peer-to-Peer Overlay Networks
Venue: arXiv cs.NI 2009
Year: 2009

The large scale content distribution systems were improved broadly using the replication techniques. The demanded contents can be brought closer to the clients by multiplying the source of information geographically, which in turn reduce both the access latency and the network traffic. The system scalability can be improved by distributing the load across multiple servers which is proposed by replication. If a copy of the requested object (e.g., a web page or an image) is located in its closer proximity then the clients would feel low access latency. Depending on the position of the replicas, the effectiveness of replication tends to a large extent. A QoS based overlay network architecture involving an intelligent replica placement algorithm is proposed in this paper. Its main goal is to improve the network utilization and fault tolerance of the P2P system. In addition to the replica placement, it also has a caching technique, to reduce the search latency. We are able to show that our proposed architecture attains less latency and better throughput with reduced bandwidth usage, through the simulation results.
Prediction-Based Data Transmission for Energy Conservation in Wireless Body Sensors
Venue: arXiv cs.NI 2009
Year: 2009

Wireless body sensors are becoming popular in healthcare applications. Since they are either worn or implanted into human body, these sensors must be very small in size and light in weight. The energy consequently becomes an extremely scarce resource, and energy conservation turns into a first class design issue for body sensor networks (BSNs). This paper deals with this issue by taking into account the unique characteristics of BSNs in contrast to conventional wireless sensor networks (WSNs) for e.g. environment monitoring. A prediction-based data transmission approach suitable for BSNs is presented, which combines a dual prediction framework and a low-complexity prediction algorithm that takes advantage of PID (proportional-integral-derivative) control. Both the framework and the algorithm are generic, making the proposed approach widely applicable. The effectiveness of the approach is verified through simulations using real-world health monitoring datasets.
Markov Modeling of Cooperative Multiplayer Coupon Collectors' Problems
Venue: arXiv cs.DM 2009
Year: 2009

The paper introduces a modified version of the classical Coupon Collector's Problem entailing exchanges and cooperation between multiple players. Results of the development show that, within a proper Markov framework, the complexity of the Cooperative Multiplayer Coupon Collectors' Problem can be attacked with an eye to the modeling of resource harvesting and sharing within the context of Next Generation Network. The cost of cooperation is computed in terms of exchange protocol burden and found to be dependent on only ensemble parameters such as the number of players and the number of coupons but not on the detailed collection statistics. The benefits of cooperation are quantified in terms of reduction of the average number of actions before collection completion.
Tarmo: A Framework for Parallelized Bounded Model Checking
Venue: arXiv cs.LO 2009
Year: 2009

This paper investigates approaches to parallelizing Bounded Model Checking (BMC) for shared memory environments as well as for clusters of workstations. We present a generic framework for parallelized BMC named Tarmo. Our framework can be used with any incremental SAT encoding for BMC but for the results in this paper we use only the current state-of-the-art encoding for full PLTL. Using this encoding allows us to check both safety and liveness properties, contrary to an earlier work on distributing BMC that is limited to safety properties only. Despite our focus on BMC after it has been translated to SAT, existing distributed SAT solvers are not well suited for our application. This is because solving a BMC problem is not solving a set of independent SAT instances but rather involves solving multiple related SAT instances, encoded incrementally, where the satisfiability of each instance corresponds to the existence of a counterexample of a specific length. Our framework includes a generic architecture for a shared clause database that allows easy clause sharing between SAT solver threads solving various such instances. We present extensive experimental results obtained with multiple variants of our Tarmo implementation. Our shared memory variants have a significantly better performance than conventional single threaded approaches, which is a result that many users can benefit from as multi-core and multi-processor technology is widely available. Furthermore we demonstrate that our framework can be deployed in a typical cluster of workstations, where several multi-core machines are connected by a network.
QR Factorization of Tall and Skinny Matrices in a Grid Computing Environment
Venue: arXiv cs.DC 2009
Year: 2009

Previous studies have reported that common dense linear algebra operations do not achieve speed up by using multiple geographical sites of a computational grid. Because such operations are the building blocks of most scientific applications, conventional supercomputers are still strongly predominant in high-performance computing and the use of grids for speeding up large-scale scientific problems is limited to applications exhibiting parallelism at a higher level. We have identified two performance bottlenecks in the distributed memory algorithms implemented in ScaLAPACK, a state-of-the-art dense linear algebra library. First, because ScaLAPACK assumes a homogeneous communication network, the implementations of ScaLAPACK algorithms lack locality in their communication pattern. Second, the number of messages sent in the ScaLAPACK algorithms is significantly greater than other algorithms that trade flops for communication. In this paper, we present a new approach for computing a QR factorization -- one of the main dense linear algebra kernels -- of tall and skinny matrices in a grid computing environment that overcomes these two bottlenecks. Our contribution is to articulate a recently proposed algorithm (Communication Avoiding QR) with a topology-aware middleware (QCG-OMPI) in order to confine intensive communications (ScaLAPACK calls) within the different geographical sites. An experimental study conducted on the Grid'5000 platform shows that the resulting performance increases linearly with the number of geographical sites on large-scale problems (and is in particular consistently higher than ScaLAPACK's).
Data management in Systems biology II - Outlook towards the semantic web
Venue: arXiv cs.DB 2009
Year: 2009

The benefit of using ontologies, defined by the respective data standards, is shown. It is presented how ontologies can be used for the semantic enrichment of data and how this can contribute to the vision of the semantic web to become true. The problems existing today on the way to a true semantic web are pinpointed, different semantic web standards, tools and development frameworks are overlooked and an outlook towards artificial intelligence and agents for searching and mining the data in the semantic web are given, paving the way from data management to information and in the end true knowledge management systems.
Multi-valued Action Languages in CLP(FD)
Venue: arXiv cs.AI 2009
Year: 2009

Action description languages, such as A and B, are expressive instruments introduced for formalizing planning domains and planning problem instances. The paper starts by proposing a methodology to encode an action language (with conditional effects and static causal laws), a slight variation of B, using Constraint Logic Programming over Finite Domains. The approach is then generalized to raise the use of constraints to the level of the action language itself. A prototype implementation has been developed, and the preliminary results are presented and discussed. To appear in Theory and Practice of Logic Programming (TPLP)
Zone Diagrams in Euclidean Spaces and in Other Normed Spaces
Venue: arXiv cs.CG 2009
Year: 2009

Zone diagram is a variation on the classical concept of a Voronoi diagram. Given n sites in a metric space that compete for territory, the zone diagram is an equilibrium state in the competition. Formally it is defined as a fixed point of a certain "dominance" map. Asano, Matousek, and Tokuyama proved the existence and uniqueness of a zone diagram for point sites in Euclidean plane, and Reem and Reich showed existence for two arbitrary sites in an arbitrary metric space. We establish existence and uniqueness for n disjoint compact sites in a Euclidean space of arbitrary (finite) dimension, and more generally, in a finite-dimensional normed space with a smooth and rotund norm. The proof is considerably simpler than that of Asano et al. We also provide an example of non-uniqueness for a norm that is rotund but not smooth. Finally, we prove existence and uniqueness for two point sites in the plane with a smooth (but not necessarily rotund) norm.
Breaking a modified substitution-diffusion image cipher based on chaotic standard and logistic maps
Venue: arXiv cs.CR 2009
Year: 2009

Recently, an image encryption scheme based on chaotic standard and logistic maps was proposed by Patidar et al. It was later reported by Rhouma et al. that an equivalent secret key can be reconstructed with only one known/chosen-plaintext and the corresponding ciphertext. Patidar et al. soon modified the original scheme and claimed that the modified scheme is secure against Rhouma et al.'s attack. In this paper, we point out that the modified scheme is still insecure against the same known/chosen-plaintext attack. In addition, some other security defects existing in both the original and the modified schemes are also reported.
Random Access: An Information-Theoretic Perspective
Venue: arXiv cs.IT 2009
Year: 2009

This paper considers a random access system where each sender can be in two modes of operation, active or not active, and where the set of active users is available to a common receiver only. Active transmitters encode data into independent streams of information, a subset of which are decoded by the receiver, depending on the value of the collective interference. The main contribution is to present an information-theoretic formulation of the problem which allows us to characterize, with a guaranteed gap to optimality, the rates that can be achieved by different data streams. Our results are articulated as follows. First, we exactly characterize the capacity region of a two-user system assuming a binary-expansion deterministic channel model. Second, we extend this result to a two-user additive white Gaussian noise channel, providing an approximate characterization within $\sqrt{3}/2$ bit of the actual capacity. Third, we focus on the symmetric scenario in which users are active with the same probability and subject to the same received power constraint, and study the maximum achievable expected sum-rate, or throughput, for any number of users. In this case, for the symmetric binary expansion deterministic channel (which is related to the packet collision model used in the networking literature), we show that a simple coding scheme which does not employ superposition coding achieves the system throughput. This result also shows that the performance of slotted ALOHA systems can be improved by allowing encoding rate adaptation at the transmitters. For the symmetric additive white Gaussian noise channel, we propose a scheme that is within one bit of the system throughput for any value of the underlying parameters.
A simple and efficient explicit parallelization of logic programs using low-level threading primitives
Venue: arXiv cs.PL 2009
Year: 2009

In this work, we present an automatic way to parallelize logic programs for finding all the answers to queries using a transformation to low level threading primitives. Although much work has been done in parallelization of logic programming more than a decade ago (e.g., Aurora, Muse, YapOR), the current state of parallelizing logic programs is still very poor. This work presents a way for parallelism of tabled logic programs in XSB Prolog under the well founded semantics. An important contribution of this work relies in merging answer-tables from multiple children threads without incurring copying or full-sharing and synchronization of data-structures. The implementation of the parent-children shared answer-tables surpasses in efficiency all the other data-structures currently implemented for completion of answers in parallelization using multi-threading. The transformation and its lower-level answer merging predicates were implemented as an extension to the XSB system.