OpenRaiser/Intern-Atlas huggingface dataset:
The Threshold for Random k-SAT is 2^k ln2 - O(k)
Venue: arXiv cs.CC 2003
Year: 2003

Let F be a random k-SAT formula on n variables, formed by selecting uniformly and independently m = rn out of all possible k-clauses. It is well-known that if r>2^k ln 2, then the formula F is unsatisfiable with probability that tends to 1 as n tends to infinity. We prove that there exists a sequence t_k = O(k) such that if r < 2^k ln 2 - t_k, then the formula F is satisfiable with probability that tends to 1 as n tends to infinity. Our technique yields an explicit lower bound for the random k-SAT threshold for every k. For k>3 this improves upon all previously known lower bounds. For example, when k=10 our lower bound is 704.94 while the upper bound is 708.94.
Cluster-based Specification Techniques in Dempster-Shafer Theory
Venue: arXiv cs.AI 2003
Year: 2003

When reasoning with uncertainty there are many situations where evidences are not only uncertain but their propositions may also be weakly specified in the sense that it may not be certain to which event a proposition is referring. It is then crucial not to combine such evidences in the mistaken belief that they are referring to the same event. This situation would become manageable if the evidences could be clustered into subsets representing events that should be handled separately. In an earlier article we established within Dempster-Shafer theory a criterion function called the metaconflict function. With this criterion we can partition a set of evidences into subsets. Each subset representing a separate event. In this article we will not only find the most plausible subset for each piece of evidence, we will also find the plausibility for every subset that the evidence belongs to the subset. Also, when the number of subsets are uncertain we aim to find a posterior probability distribution regarding the number of subsets.
Cluster-based Specification Techniques in Dempster-Shafer Theory for an Evidential Intelligence Analysis of MultipleTarget Tracks (Thesis Abstract)
Venue: arXiv cs.AI 2003
Year: 2003

In Intelligence Analysis it is of vital importance to manage uncertainty. Intelligence data is almost always uncertain and incomplete, making it necessary to reason and taking decisions under uncertainty. One way to manage the uncertainty in Intelligence Analysis is Dempster-Shafer Theory. This thesis contains five results regarding multiple target tracks and intelligence specification.
Simultaneous Dempster-Shafer clustering and gradual determination of number of clusters using a neural network structure
Venue: arXiv cs.AI 2003
Year: 2003

In this paper we extend an earlier result within Dempster-Shafer theory ["Fast Dempster-Shafer Clustering Using a Neural Network Structure," in Proc. Seventh Int. Conf. Information Processing and Management of Uncertainty in Knowledge-Based Systems (IPMU'98)] where several pieces of evidence were clustered into a fixed number of clusters using a neural structure. This was done by minimizing a metaconflict function. We now develop a method for simultaneous clustering and determination of number of clusters during iteration in the neural structure. We let the output signals of neurons represent the degree to which a pieces of evidence belong to a corresponding cluster. From these we derive a probability distribution regarding the number of clusters, which gradually during the iteration is transformed into a determination of number of clusters. This gradual determination is fed back into the neural structure at each iteration to influence the clustering process.
Applications of Intuitionistic Logic in Answer Set Programming
Venue: arXiv cs.LO 2003
Year: 2003

We present some applications of intermediate logics in the field of Answer Set Programming (ASP). A brief, but comprehensive introduction to the answer set semantics, intuitionistic and other intermediate logics is given. Some equivalence notions and their applications are discussed. Some results on intermediate logics are shown, and applied later to prove properties of answer sets. A characterization of answer sets for logic programs with nested expressions is provided in terms of intuitionistic provability, generalizing a recent result given by Pearce. It is known that the answer set semantics for logic programs with nested expressions may select non-minimal models. Minimal models can be very important in some applications, therefore we studied them; in particular we obtain a characterization, in terms of intuitionistic logic, of answer sets which are also minimal models. We show that the logic G3 characterizes the notion of strong equivalence between programs under the semantic induced by these models. Finally we discuss possible applications and consequences of our results. They clearly state interesting links between ASP and intermediate logics, which might bring research in these two areas together.
2D Electrophoresis Gel Image and Diagnosis of a Disease
Venue: arXiv cs.CC 2003
Year: 2003

The process of diagnosing a disease from the 2D gel electrophoresis image is a challenging problem. This is due to technical difficulties of generating reproducible images with a normalized form and the effect of negative stain. In this paper, we will discuss a new concept of interpreting the 2D images and overcoming the aforementioned technical difficulties using mathematical transformation. The method makes use of 2D gel images of proteins in serums and we explain a way of representing the images into vectors in order to apply machine-learning methods, such as the support vector machine.
Goodness-of-fit of the Heston model
Venue: arXiv cs.CE 2003
Year: 2003

An analytical formula for the probability distribution of stock-market returns, derived from the Heston model assuming a mean-reverting stochastic volatility, was recently proposed by Dragulescu and Yakovenko in Quantitative Finance 2002. While replicating their results, we found two significant weaknesses in their method to pre-process the data, which cast a shadow over the effective goodness-of-fit of the model. We propose a new method, more truly capturing the market, and perform a Kolmogorov-Smirnov test and a Chi Square test on the resulting probability distribution. The results raise some significant questions for large time lags -- 40 to 250 days -- where the smoothness of the data does not require such a complex model; nevertheless, we also provide some statistical evidence in favour of the Heston model for small time lags -- 1 and 5 days -- compared with the traditional Gaussian model assuming constant volatility.
ATLAS and CMS applications on the WorldGrid testbed
Venue: arXiv cs.DC 2003
Year: 2003

WorldGrid is an intercontinental testbed spanning Europe and the US integrating architecturally different Grid implementations based on the Globus toolkit. It has been developed in the context of the DataTAG and iVDGL projects, and successfully demonstrated during the WorldGrid demos at IST2002 (Copenhagen) and SC2002 (Baltimore). Two HEP experiments, ATLAS and CMS, successful exploited the WorldGrid testbed for executing jobs simulating the response of their detectors to physics eve nts produced by real collisions expected at the LHC accelerator starting from 2007. This data intensive activity has been run since many years on local dedicated computing farms consisting of hundreds of nodes and Terabytes of disk and tape storage. Within the WorldGrid testbed, for the first time HEP simulation jobs were submitted and run indifferently on US and European resources, despite of their underlying different Grid implementations, and produced data which could be retrieved and further analysed on the submitting machine, or simply stored on the remote resources and registered on a Replica Catalogue which made them available to the Grid for further processing. In this contribution we describe the job submission from Europe for both ATLAS and CMS applications, performed through the GENIUS portal operating on top of an EDG User Interface submitting to an EDG Resource Broker, pointing out the chosen interoperability solutions which made US and European resources equivalent from the applications point of view, the data management in the WorldGrid environment, and the CMS specific production tools which were interfaced to the GENIUS portal.
A Secure Infrastructure For System Console and Reset Access
Venue: arXiv cs.DC 2003
Year: 2003

During the last years large farms have been built using commodity hardware. This hardware lacks components for remote and automated administration. Products that can be retrofitted to these systems are either costly or inherently insecure. We present a system based on serial ports and simple machine controlled relays. We report on experience gained by setting up a 50-machine test environment as well as current work in progress in the area.
The CMS Integration Grid Testbed
Venue: arXiv cs.DC 2003
Year: 2003

The CMS Integration Grid Testbed (IGT) comprises USCMS Tier-1 and Tier-2 hardware at the following sites: the California Institute of Technology, Fermi National Accelerator Laboratory, the University of California at San Diego, and the University of Florida at Gainesville. The IGT runs jobs using the Globus Toolkit with a DAGMan and Condor-G front end. The virtual organization (VO) is managed using VO management scripts from the European Data Grid (EDG). Gridwide monitoring is accomplished using local tools such as Ganglia interfaced into the Globus Metadata Directory Service (MDS) and the agent based Mona Lisa. Domain specific software is packaged and installed using the Distrib ution After Release (DAR) tool of CMS, while middleware under the auspices of the Virtual Data Toolkit (VDT) is distributed using Pacman. During a continuo us two month span in Fall of 2002, over 1 million official CMS GEANT based Monte Carlo events were generated and returned to CERN for analysis while being demonstrated at SC2002. In this paper, we describe the process that led to one of the world's first continuously available, functioning grids.
The Clarens web services architecture
Venue: arXiv cs.DC 2003
Year: 2003

Clarens is a uniquely flexible web services infrastructure providing a unified access protocol to a diverse set of functions useful to the HEP community. It uses the standard HTTP protocol combined with application layer, certificate based authentication to provide single sign-on to individuals, organizations and hosts, with fine-grained access control to services, files and virtual organization (VO) management. This contribution describes the server functionality, while client applications are described in a subsequent talk.
The first deployment of workload management services on the EU DataGrid Testbed: feedback on design and implementation
Venue: arXiv cs.DC 2003
Year: 2003

Application users have now been experiencing for about a year with the standardized resource brokering services provided by the 'workload management' package of the EU DataGrid project (WP1). Understanding, shaping and pushing the limits of the system has provided valuable feedback on both its design and implementation. A digest of the lessons, and "better practices", that were learned, and that were applied towards the second major release of the software, is given.
Virtual Data in CMS Production
Venue: arXiv cs.DC 2003
Year: 2003

Initial applications of the GriPhyN Chimera Virtual Data System have been performed within the context of CMS Production of Monte Carlo Simulated Data. The GriPhyN Chimera system consists of four primary components: 1) a Virtual Data Language, which is used to describe virtual data products, 2) a Virtual Data Catalog, which is used to store virtual data entries, 3) an Abstract Planner, which resolves all dependencies of a particular virtual data product and forms a location and existence independent plan, 4) a Concrete Planner, which maps an abstract, logical plan onto concrete, physical grid resources accounting for staging in/out files and publishing results to a replica location service. A CMS Workflow Planner, MCRunJob, is used to generate virtual data products using the Virtual Data Language. Subsequently, a prototype workflow manager, known as WorkRunner, is used to schedule the instantiation of virtual data products across a grid.
On multiple connectedness of regions visible due to multiple diffuse reflections
Venue: arXiv cs.CG 2003
Year: 2003

It is known that the region $V(s)$ of a simple polygon $P$, directly visible (illuminable) from an internal point $s$, is simply connected. Aronov et al. \cite{addpp981} established that the region $V_1(s)$ of a simple polygon visible from an internal point $s$ due to at most one diffuse reflection on the boundary of the polygon $P$, is also simply connected. In this paper we establish that the region $V_2(s)$, visible from $s$ due to at most two diffuse reflections may be multiply connected; we demonstrate the construction of an $n$-sided simple polygon with a point $s$ inside it so that and the region of $P$ visible from $s$ after at most two diffuse reflections is multiple connected.
Grid Data Management in Action: Experience in Running and Supporting Data Management Services in the EU DataGrid Project
Venue: arXiv cs.DC 2003
Year: 2003

In the first phase of the EU DataGrid (EDG) project, a Data Management System has been implemented and provided for deployment. The components of the current EDG Testbed are: a prototype of a Replica Manager Service built around the basic services provided by Globus, a centralised Replica Catalogue to store information about physical locations of files, and the Grid Data Mirroring Package (GDMP) that is widely used in various HEP collaborations in Europe and the US for data mirroring. During this year these services have been refined and made more robust so that they are fit to be used in a pre-production environment. Application users have been using this first release of the Data Management Services for more than a year. In the paper we present the components and their interaction, our implementation and experience as well as the feedback received from our user communities. We have resolved not only issues regarding integration with other EDG service components but also many of the interoperability issues with components of our partner projects in Europe and the U.S. The paper concludes with the basic lessons learned during this operation. These conclusions provide the motivation for the architecture of the next generation of Data Management Services that will be deployed in EDG during 2003.
Relational databases for data management in PHENIX
Venue: arXiv cs.DB 2003
Year: 2003

PHENIX is one of the two large experiments at the Relativistic Heavy Ion Collider (RHIC) at Brookhaven National Laboratory (BNL) and archives roughly 100TB of experimental data per year. In addition, large volumes of simulated data are produced at multiple off-site computing centers. For any file catalog to play a central role in data management it has to face problems associated with the need for distributed access and updates. To be used effectively by the hundreds of PHENIX collaborators in 12 countries the catalog must satisfy the following requirements: 1) contain up-to-date data, 2) provide fast and reliable access to the data, 3) have write permissions for the sites that store portions of data. We present an analysis of several available Relational Database Management Systems (RDBMS) to support a catalog meeting the above requirements and discuss the PHENIX experience with building and using the distributed file catalog.
The Redesigned BaBar Event Store: Believe the Hype
Venue: arXiv cs.DB 2003
Year: 2003

As the BaBar experiment progresses, it produces new and unforeseen requirements and increasing demands on capacity and feature base. The current system is being utilized well beyond its original design specifications, and has scaled appropriately, maintaining data consistency and durability. The persistent event storage system has remained largely unchanged since the initial implementation, and thus includes many design features which have become performance bottlenecks. Programming interfaces were designed before sufficient usage information became available. Performance and efficiency were traded off for added flexibility to cope with future demands. With significant experience in managing actual production data under our belt, we are now in a position to recraft the system to better suit current needs. The Event Store redesign is intended to eliminate redundant features while adding new ones, increase overall performance, and contain the physical storage cost of the world's largest database.
An Abstract Programming System
Venue: arXiv cs.SE 2003
Year: 2003

The system PL permits the translation of abstract proofs of program correctness into programs in a variety of programming languages. A programming language satisfying certain axioms may be the target of such a translation. The system PL also permits the construction and proof of correctness of programs in an abstract programming language, and permits the translation of these programs into correct programs in a variety of languages. The abstract programming language has an imperative style of programming with assignment statements and side-effects, to allow the efficient generation of code. The abstract programs may be written by humans and then translated, avoiding the need to write the same program repeatedly in different languages or even the same language. This system uses classical logic, is conceptually simple, and permits reasoning about nonterminating programs using Scott-Strachey style denotational semantics.
Installing, Running and Maintaining Large Linux Clusters at CERN
Venue: arXiv cs.DC 2003
Year: 2003

Having built up Linux clusters to more than 1000 nodes over the past five years, we already have practical experience confronting some of the LHC scale computing challenges: scalability, automation, hardware diversity, security, and rolling OS upgrades. This paper describes the tools and processes we have implemented, working in close collaboration with the EDG project [1], especially with the WP4 subtask, to improve the manageability of our clusters, in particular in the areas of system installation, configuration, and monitoring. In addition to the purely technical issues, providing shared interactive and batch services which can adapt to meet the diverse and changing requirements of our users is a significant challenge. We describe the developments and tuning that we have introduced on our LSF based systems to maximise both responsiveness to users and overall system utilisation. Finally, this paper will describe the problems we are facing in enlarging our heterogeneous Linux clusters, the progress we have made in dealing with the current issues and the steps we are taking to gridify the clusters
The Use of HepRep in GLAST
Venue: arXiv cs.GR 2003
Year: 2003

HepRep is a generic, hierarchical format for description of graphics representables that can be augmented by physics information and relational properties. It was developed for high energy physics event display applications and is especially suited to client/server or component frameworks. The GLAST experiment, an international effort led by NASA for a gamma-ray telescope to launch in 2006, chose HepRep to provide a flexible, extensible and maintainable framework for their event display without tying their users to any one graphics application. To support HepRep in their GUADI infrastructure, GLAST developed a HepRep filler and builder architecture. The architecture hides the details of XML and CORBA in a set of base and helper classes allowing physics experts to focus on what data they want to represent. GLAST has two GAUDI services: HepRepSvc, which registers HepRep fillers in a global registry and allows the HepRep to be exported to XML, and CorbaSvc, which allows the HepRep to be published through a CORBA interface and which allows the client application to feed commands back to GAUDI (such as start next event, or run some GAUDI algorithm). GLAST's HepRep solution gives users a choice of client applications, WIRED (written in Java) or FRED (written in C++ and Ruby), and leaves them free to move to any future HepRep-compliant event display.
Distributed Offline Data Reconstruction in BaBar
Venue: arXiv cs.DC 2003
Year: 2003

The BaBar experiment at SLAC is in its fourth year of running. The data processing system has been continuously evolving to meet the challenges of higher luminosity running and the increasing bulk of data to re-process each year. To meet these goals a two-pass processing architecture has been adopted, where 'rolling calibrations' are quickly calculated on a small fraction of the events in the first pass and the bulk data reconstruction done in the second. This allows for quick detector feedback in the first pass and allows for the parallelization of the second pass over two or more separate farms. This two-pass system allows also for distribution of processing farms off-site. The first such site has been setup at INFN Padova. The challenges met here were many. The software was ported to a full Linux-based, commodity hardware system. The raw dataset, 90 TB, was imported from SLAC utilizing a 155 Mbps network link. A system for quality control and export of the processed data back to SLAC was developed. Between SLAC and Padova we are currently running three pass-one farms, with 32 CPUs each, and nine pass-two farms with 64 to 80 CPUs each. The pass-two farms can process between 2 and 4 million events per day. Details about the implementation and performance of the system will be presented.
AliEnFS - a Linux File System for the AliEn Grid Services
Venue: arXiv cs.DC 2003
Year: 2003

Among the services offered by the AliEn (ALICE Environment http://alien.cern.ch) Grid framework there is a virtual file catalogue to allow transparent access to distributed data-sets using various file transfer protocols. $alienfs$ (AliEn File System) integrates the AliEn file catalogue as a new file system type into the Linux kernel using LUFS, a hybrid user space file system framework (Open Source http://lufs.sourceforge.net). LUFS uses a special kernel interface level called VFS (Virtual File System Switch) to communicate via a generalised file system interface to the AliEn file system daemon. The AliEn framework is used for authentication, catalogue browsing, file registration and read/write transfer operations. A C++ API implements the generic file system operations. The goal of AliEnFS is to allow users easy interactive access to a worldwide distributed virtual file system using familiar shell commands (f.e. cp,ls,rm ...) The paper discusses general aspects of Grid File Systems, the AliEn implementation and present and future developments for the AliEn Grid File System.
Data Management for Physics Analysis in Phenix (BNL, RHIC)
Venue: arXiv cs.DC 2003
Year: 2003

Every year the PHENIX collaboration deals with increasing volume of data (now about 1/4 PB/year). Apparently the more data the more questions how to process all the data in most efficient way. In recent past many developments in HEP computing were dedicated to the production environment. Now we need more tools to help to obtain physics results from the analysis of distributed simulated and experimental data. Developments in Grid architectures gave many examples how distributed computing facilities can be organized to meet physics analysis needs. We feel that our main task in this area is to try to use already developed systems or system components in PHENIX environment. We are concentrating here on the followed problems: file/replica catalog which keep names of our files, data moving over WAN, job submission in multicluster environment. PHENIX is a running experiment and this fact narrowed our ability to test new software on the collaboration computer facilities. We are experimenting with system prototypes at State University of New York at Stony Brook (SUNYSB) where we run midrange computing cluster for physics analysis. The talk is dedicated to discuss some experience with Grid software and achieved results.