ppxscal/embedding_network huggingface dataset:
Protein Classification into Domains of Life Using Markov Chain Models
Authors: Francisca Zanoguera, Massimo de Francesco
Venue: Proceedings of the 2004 IEEE Computational Systems Bioinformatics Conference (2004)

It has recently been shown that oligopeptide composition allows clustering proteomes of different organisms into the main domains of life. In this paper, we go a step further by showing that, given a single protein, it is possible to predict whether it has a bacterial or eukaryotic origin with 85% accuracy, and we obtain this result after ensuring that no important homologies exist between the sequences in the test set and the sequences in the training set. To do this, we model the sequence as a Markov chain. A bacterial and an eukaryote model are produced using the training sets. Each input sequence is then classified by calculating the log-odds ratio of the sequence probability for each model. By analyzing the models obtained we extract a set of most discriminant oligopeptides, many of which are part of known functional motifs.
Real-Time Rendering of Soap Bubbles Taking into Account Light Interference
Authors: Kei Iwasaki, Keichi Matsuzawa, Tomoyuki Nishita
Venue: Proceedings of the Computer Graphics International (2004)

In the field of computer graphics, simulation of physicalphenomena is of great interest. We focus on the opticaleffects of soap bubbles. Soap bubbles have fascinating colorationand interesting physical properties. Therefore theyare useful for the entertainment such as movies and games.Soap bubbles change their shapes by surface tension andexternal forces, and therefore their surface thickness alsochanges. Since the thickness of the soap bubble is severalhundred nanometers, interference of the light occurs. Thispaper proposes a fast rendering method for the soap bubblestaking into account light interference and dynamics.In our method, the reflectivities of the thin film that is thecause of the light interference are calculated in advance andstored as textures. This makes it possible to render the deformablesoap bubbles in real-time.
Computational Methods for Predicting Intramolecular G-Quadruplexes in Nucleotide Sequences
Authors: Lawrence D'Antonio, Paramjeet Bagga
Venue: Proceedings of the 2004 IEEE Computational Systems Bioinformatics Conference (2004)

Guanine-rich sequences, including those that form G-quadruplexes, are abundant in regions of biological significance. In order to map putative G-quadruplex elements within mammalian genes we have created a suite of computational tools. This suite contains algorithms to search genes for occurrences of the G-quadruplex motif and determine their distribution near RNA processing sites.
A Synthesis Method for MVL Reversible Logic
Venue: Proceedings of the 34th International Symposium on Multiple-Valued Logic (2004)

An r-valued m-variable reversible logic functionmaps each of the r^m input patters to a unique outputpattern. The synthesis problem is to realize a reversiblefunction by a cascade of primitive reversible gates.In this paper, we present a simple heuristic algorithmthat exploits the bidirectional synthesis possibilityinherent in the reversibility of the specification. Theprimitive reversible gates considered here are onepossible extension of the well-known binary Toffoligates.We present exhaustive results for the 9! 2-variable 3-valued reversible functions comparing the results of our algorithm to optimal results found by breadth-firstsearch. The approach can be applied to general m-variable,r-valued reversible specifications. Further, weshow how the presented technique can be applied toirreversible specifications. The synthesis of a 3-input,3-valued adder is given as a specific case.
National Museum of American Jewish History
Venue: ACM SIGGRAPH 2003 video review on Animation theater program: part 2 - Volume 146 (2003)

A fundraising video for the new National Museum of American Jewish History, on the mall in Philadelphia, Pennsylvania. Due to a very preliminary architectural design scheme at the time of production, IOMEDIA was challenged to develop a rendering style that would not look computer generated, so that the design would not seem too "real". IOMEDIA produced extensive hand painted watercolors of the building elevations, surrounding site and interiors in order to achieve this soft, impressionistic look. Copyright held by creator.
Impact of Path Diversity on Multi-homed and Overlay Networks
Authors: Junghee Han, Farnam Jahanian
Venue: Proceedings of the 2004 International Conference on Dependable Systems and Networks (2004)

Multi-homed and overlay networks are two widely studiedapproaches aimed at leveraging the inherent redundancyof the Internet's underlying routing infrastructure toenhance end-to-end application performance and availability.However, the effectiveness of these approaches dependson the natural diversity of redundant paths between twoendhosts in terms of physical links, routing infrastructure,administrative control and geographical distribution. Thispaper quantitatively analyzes the impact of path diversityon multi-homed and overlay networks and highlights severalinherent limitations of these architectures in exploitingthe full potential redundancy of the Internet. We basedour analysis on traceroutes and routing table data collectedfrom several vantage points in the Internet including: lookingglasses at ten major Internet Service Providers (ISPs),RouteViews servers from twenty ISPs, and more than fiftyPlanetLab nodes globally distributed across the Internet.Our study motivates new research directions-constructingtopology-aware multi-homing and overlay networks for better availability.
Energy conservation techniques for disk array-based servers
Authors: Eduardo Pinheiro, Ricardo Bianchini
Venue: Proceedings of the 18th annual international conference on Supercomputing (2004)

In this paper, we study energy conservation techniques for disk array-based network servers. First, we introduce a new conservation technique, called Popular Data Concentration (PDC), that migrates frequently accessed data to a subset of the disks. The goal is to skew the load towards a few of the disks, so that others can be transitioned to low-power modes. Next, we introduce a user-level file server that takes advantage of PDC. In the context of this server, we compare PDC to the Massive Array of Idle Disks (MAID). Using a validated simulator, we evaluate these techniques for conventional and two-speed disks and a wide range of parameters. Our results for conventional disks show that PDC and MAID can only conserve energy when the load on the server is extremely low. When two-speed disks are used, both PDC and MAID can conserve significant energy with only a small fraction of delayed requests. Overall, we find that PDC achieves more consistent and robust energy savings than MAID.
Refining term weights of documents using term dependencies
Authors: Hee-soo Kim, Ikkyu Choi, Minkoo Kim
Venue: Proceedings of the 27th annual international ACM SIGIR conference on Research and development in information retrieval (2004)

When processing raw documents in Information Retrieval (IR) System, a term-weighting scheme is used to calculate the importance of each term which occurs in a document. However, most term-weighting schemes assume that a term is independent of the other terms. Term dependency is an indispensable consequence of language use [1]. Therefore, this assumption can make the information of a document being lost. In this paper, we propose new approach to refine term weights of documents using term dependencies discovered from a set of documents. Then, we evaluate our method with two experiments based on the vector space model [2] and the language model [3].
A Compression Approach to Support Vector Model Selection
Authors: Ulrike von Luxburg, Olivier Bousquet, Bernhard Schölkopf
Venue: The Journal of Machine Learning Research (2004)

In this paper we investigate connections between statistical learning theory and data compression on the basis of support vector machine (SVM) model selection. Inspired by several generalization bounds we construct "compression coefficients" for SVMs which measure the amount by which the training labels can be compressed by a code built from the separating hyperplane. The main idea is to relate the coding precision to geometrical concepts such as the width of the margin or the shape of the data in the feature space. The so derived compression coefficients combine well known quantities such as the radius-margin term R2/&rho;2, the eigenvalues of the kernel matrix, and the number of support vectors. To test whether they are useful in practice we ran model selection experiments on benchmark data sets. As a result we found that compression coefficients can fairly accurately predict the parameters for which the test error is minimized.
Semantic Interoperability of Field-based Thematic Geographic Information
Authors: Toni Navarrete, Josep Blat, Maurici Ruiz
Venue: Proceedings of the Database and Expert Systems Applications, 15th International Workshop (2004)

A model for semantic interoperability among a repository of geographic datasets from different providers is proposed in this article. Specifically, this approach focuses on qualified field-based geographic information. Our solution is based on an ontology describing geographic themes. We present a method to build up this ontology from the data schemas of each dataset in the repository. We have developed a tool, which is currently being evaluated by users, to support this process.
A Portable Implementation Framework for Intrusion-Resilient Database Management Systems
Authors: Alexey Smirnov, Tzi-cker Chiueh
Venue: Proceedings of the 2004 International Conference on Dependable Systems and Networks (2004)

An intrusion-resilient database management system isthe one that is capable of restoring its consistency after being compromised by a malicious attack or a human error. More specifically, an intrusion-resilient mechanism helps toquickly repair a database by nullifying the damage causedby malicious or erroneous transactions, while preservingthe effects of unaffected legitimate transactions that takeplace between intrusions/errors and their detection. Thegoal of this project is to develop a portable implementation framework that can augment a commercial database management system with intrusion resilience without requiring any modifications to its internals. The intrusion resilience mechanism described in this paper significantly improves the availability of modern DBMSs by facilitatingand sometimes even automating the post-intrusion damage repair process. In addition, it can be embodied in a reusable implementation framework, whose portability isdemonstrated by its successful application to three different DBMSs: PostgreSQL, Oracle, and Sybase. Performance measurements on the fully operational prototypes under theTPC-C benchmark show that the run-time overhead of theintrusion-resilience mechanism is between 6% and 13%.
Unifying business objects and system dynamics as a paradigm for developing decision support systems
Authors: Andreas Gregoriades, Bill Karakostas
Venue: Decision Support Systems (2004)

Due to the market-driven nature of modem organisations, it is important that they can easily adapt to changing business needs. In order to be able to do so, organisations need to employ information systems that exhibit the important characteristic of adaptability. Change, however, is risky because it encompasses unpredictable behaviours. Organisations, in order to minimise this risk, employ decision support systems (DSS) techniques that enable predictions to be made. This paper describes a simulation methodology, based on the combination of business objects and system dynamics that assists organisations in predicting future behaviours. The methodology eliminates the need for duplicate models of enterprise operation and simulation, and introduces a framework that enables the unification of the two in a single model.
A Framework for Automatic and Secure Cycle Stealing
Authors: Wayne Kelly, Paul Roe
Venue: Proceedings of the High Performance Computing and Grid in Asia Pacific Region, Seventh International Conference (2004)

Cycle stealing systems use idle PCs to create virtual supercomputers. Utilizing third party PCs in this way is very attractive but one fraught with problems. Firstly writing applications is difficult without supporting middleware, the cycle stealing environment is highly volatile with machines coming and going at random. Secondly cycle stealing applications and data need to be deployed and installed on third party machines. This requires considerable trust from third party users, if they are to donate their machines. Reports of file sharing programs such as Kazzaa carrying Trojan horses have made users understandably wary of running unknown third party code. This second problem is the focus of this paper; we describe the G2 middleware and how it is able to automatically and securely deploy and run code and associated data with minimal trust required from the user. This is achieved by leverage the security and deployment features of Microsoft .NET and extending them to a cycle stealing system.
Excluding any graph as a minor allows a low tree-width 2-coloring
Authors: Matt DeVos, Guoli Ding, Bogdan Oporowski, Daniel P. Sanders, Bruce Reed, Paul Seymour, Dirk Vertigan
Venue: Journal of Combinatorial Theory Series B (2004)

This article proves the conjecture of Thomas that, for every graph G, there is an integer k such that every graph with no minor isomorphic to G has a 2-coloring of either its vertices or its edges where each color induces a graph of tree-widlh at most k. Some generalizations are also proved.
Integrating collective I/O and cooperative caching into the "clusterfile" parallel file system
Authors: Florin Isaila, Guido Malpohl, Vlad Olaru, Gabor Szeder, Walter Tichy
Venue: Proceedings of the 18th annual international conference on Supercomputing (2004)

This paper presents the integration of two collective I/O techniques into the Clusterfile parallel file system: disk-directed I/O and two-phase I/O. We show that global cooperative cache management improves the collective I/O performance. The solution focuses on integrating disk parallelism with other types of parallelism: memory (by buffering and caching on several nodes), network (by parallel I/O scheduling strategies) and processors (by redistributing the I/O related computation over several nodes). The performance results show considerable throughput increases over ROMIO's extended two-phase I/O.
Cache-oblivious shortest paths in graphs using buffer heap
Authors: Rezaul Alam Chowdhury, Vijaya Ramachandran
Venue: Proceedings of the sixteenth annual ACM symposium on Parallelism in algorithms and architectures (2004)

We present the Buffer Heap (BH), a cache-oblivious priority queue that supports Delete-Min, Delete, and Decrease-Key operations in O(1overB log2 NoverB) amortized block transfers from external memory, where B is the (unknown) block-size and N is the maximum number of elements in the queue. As is common in cache-oblivious algorithms, we assume a 'tall cache' (i.e., M = Ω(B1 + ε), where M is the size of the main memory). We also assume the Decrease-Key operation only verifies that the element does not exist in the priority queue with a smaller key value, hence it also supports the insert operation in the same amortized bound. The amortized time bound for each operation is O(log N). We also present a Cache-Oblivious Tournament Tree (COTT), which is simpler than the Buffer Heap, but has weaker bounds.Using the Buffer Heap we present cache-oblivious algorithms for undirected and directed single-source shortest path (SSSP) problems for graphs with non-negative edge-weights. On a graph with V vertices and E edges, our algorithm for the undirected case performs O(V + EoverB log2 VoverB) block transfers and for the directed case performs O((V + EoverB) . log2 VoverB) block transfers. The running time of both algorithms is O((V + E). log V).For both priority queues with Decrease-Key operation, and for shortest path problems on general graphs, our results appear to give the first non-trivial cache-oblivious bounds.
COSIMAB2B " Sales Automation for E-Procurement
Authors: Werner Kiesling, Stefan Fischer, Sven Doring
Venue: Proceedings of the IEEE International Conference on E-Commerce Technology (2004)

We present a fully automated electronic sales agent for e-procurement portals. The key technologies for this breakthrough are based on preferences modeled as strict partial orders, enabling a deep personalization of the B2B sales process. The interplay of several novel middleware components achieves to automate skills that so far could be executed only by a human vendor. As personalized search engine for XML based e-catalogs we use Preference XPath; the Preference Presenter implements a sales psychology based presentation of search results, supporting various human sales strategies; the Preference Repository provides the management of situated long-term preferences; the flexible Personalized Price Offer and the multi-objective Preference Bargainer provide a personalized price fixing and the opportunity to bargain about the price of an entire product bundle, applying up/cross and down selling techniques. Our prototype COSIMA^B2B, supported by industrial partners, has been successfully demonstrated at a large computer fair.
Mining with rarity: a unifying framework
Authors: Gary M. Weiss
Venue: ACM SIGKDD Explorations Newsletter (2004)

Rare objects are often of great interest and great value. Until recently, however, rarity has not received much attention in the context of data mining. Now, as increasingly complex real-world problems are addressed, rarity, and the related problem of imbalanced data, are taking center stage. This article discusses the role that rare classes and rare cases play in data mining. The problems that can result from these two forms of rarity are described in detail, as are methods for addressing these problems. These descriptions utilize examples from existing research. So that this article provides a good survey of the literature on rarity in data mining. This article also demonstrates that rare classes and rare cases are very similar phenomena---both forms of rarity are shown to cause similar problems during data mining and benefit from the same remediation methods.
Leveraging the "Multi" in secure multi-party computation
Authors: Jaideep Vaidya, Chris Clifton
Venue: Proceedings of the 2003 ACM workshop on Privacy in the electronic society (2003)

Secure Multi-Party Computation enables parties with private data to collaboratively compute a global function of their private data, without revealing that data. The increase in sensitive data on networked computers, along with improved ability to integrate and utilize that data, make the time ripe for practical secure multi-party computation. This paper surveys approaches to secure multi-party computation, and gives a method whereby an efficient protocol for two parties using an untrusted third party can be used to construct an efficient peer-to-peer secure multi-party protocol.
Flexible bones for the haptic prototyping of deformable objects
Authors: L. Blanding, M. Turkiyyah
Venue: Virtual Reality (2004)

Accurate modelling of the compliance characteristics of solid models is an important rendering task for increasing the realism of virtual environments. The ability to feel the force and moment stress resultants that cause the bending, twisting, shearing and/or fracture of physically-based models is useful for a large number of application areas including medical training, CAD environments, computer animation and games. An important element of compliance rendering is the mechanics engine that solves the equations governing the deformations and stresses in solid models. The development of such engines has to carefully balance the needs for haptic (not just graphical) realism with the needs for real time processing at rates in the range of 500-1000&#x00a0;Hz. In this paper we describe methods and techniques we have developed for such an engine, and demonstrate their characteristics in a number of applications including design of compliant mechanisms, animation and solid modelling.
Porting DPPX from the IBM 8100 to the IBM ES/9370: migration
Authors: C. Goodrich, M. B. Loughlin
Venue: IBM Systems Journal (1990)

This paper explains the development of the migration process by which applications running on a network of DPPX/SP systems would migrate to a network of DPPX/370 systems. DPPX/SP is a centrally managed, distributed processing system designed to run on the IBM 8100 family of processors. DPPX/370 is the DPPX/SP system ported to the IBM ES/9370 family of processors. The paper outlines the strategies, the technical problems encountered and their solutions, customer participation, and testing. Finally, it provides recommendations on how the process might have been improved.
Speeding up String Matching over Compressed Text on Handheld Devices using Tagged Sub-optimal Code (TSC)
Venue: Proceedings of the 10th IEEE Real-Time and Embedded Technology and Applications Symposium (2004)

Tagged Sub-optimal code (TSC) is a new codingtechnique presented in this paper to speed up stringmatching over compressed databases on PDAs. TSCis a variable-length sub-optimal code that supportsminimal prefix property. It always determines itscodeword boundary without traversing a tree orlookup table. TSC technique may be beneficial inmany types of applications: speeding up stringmatching over compressed text, speeding decodingprocess, as well as any general-purpose integerrepresentation code. Experimental results show thatTSC is 8.9 times faster than string matching overcompressed text using Huffman encoding, and 3times faster in the decoding process. On the otherhand, the compression ratio of TSC is 6% less thanthat of Huffman encoding. Additionally, TSC is 14times faster than Byte Pair Encoding (BPE)compression process, and achieves betterperformance than searching over compressed textusing BPE scheme on handheld devices.
Routing with Confidence: Supporting Discretionary Routing Requirements in Policy Based Networks
Venue: Proceedings of the Fifth IEEE International Workshop on Policies for Distributed Systems and Networks (2004)

We propose a novel policy-based secure routingframework that extends the mandatory nature of networkaccess-control policies and allows users to exercise discretionarycontrol on what routes they choose in a givennetwork. In contrast to existing research that focusesmainly on restricting network access based on user credentials,we present a model that allows users to specifydiscretionary constraints on path characteristics anddiscover routes based on situational trust attributes ofrouters in a network. In this context, we present threelevels of trust-attribute certification based on inherent,consensus based, and inferred characteristics of routers.We also define a "confidence" measure that captures the"quality of protection" of a route with regard to variousdynamic trust relationships that arise from this interactionbetween user preferences and network policy.Based on this measure, we show how to generate pathsof highest confidence efficiently by using shortest pathalgorithms. We show how our model generalizes thenotion of Quality of Protection (QoP) for secure routingand discuss how it can be applied to anonymousand privacy-aware routing, intrusion tolerant communication,and secure resource discovery for ubiquitouscomputing, high performance, and peer-to-peer environments.