ppxscal/embedding_network huggingface dataset:
A Two-Step Approach for Clustering Proteins Based on Protein Interaction Profile
Authors: Pengjun Pei, Aidong Zhang
Venue: Proceedings of the Fifth IEEE Symposium on Bioinformatics and Bioengineering (2005)

High-throughput methods for detecting protein-protein interactions (PPI) have given researchers an initial global picture of protein interactions on a genomic scale. The huge data sets generated by such experiments pose new challenges in data analysis. Though clustering methods have been successfully applied in many areas in bioinformatics, many clustering algorithms cannot be readily applied on protein interaction data sets. One main problem is that the similarity between two proteins cannot be easily defined. This paper proposes a probabilistic model to define the similarity based on conditional probabilities. We then propose a two-step method for estimating the similarity between two proteins based on protein interaction profile. In the first step, the model is trained with proteins with known annotation. Based on this model, similarities are calculated in the second step. Experiments show that our method improves performance.
Computing Moments of First Passage Times to a Subset of States in Markov Chains
Authors: Tugrul Dayar, Nail Akar
Venue: SIAM Journal on Matrix Analysis and Applications (2005)

This paper presents a relatively efficient and accurate method to compute the moments of first passage times to a subset of states in finite ergodic Markov chains. With the proposed method, the moment computation problem is reduced to the solution of a linear system of equations with the right-hand side governed by a novel recurrence for computing the higher-order moments. We propose using a form of the Grassmann--Taksar--Heyman (GTH) algorithm to solve these linear equations. Due to the form of the linear systems involved, the proposed method does not suffer from the drawbacks associated with GTH in a row-wise sparse implementation.
Summarization — Compressing Data into an Informative Representation
Authors: Varun Chandola, Vipin Kumar
Venue: Proceedings of the Fifth IEEE International Conference on Data Mining (2005)

In this paper, we formulate the problem of summarization of a dataset of transactions with categorical attributes as an optimization problem involving two objective functions - compaction gain and information loss. We propose metrics to characterize the output of any summarization algorithm. We investigate two approaches to address this problem. The first approach is an adaptation of clustering and the second approach makes use of frequent itemsets from the association analysis domain. We illustrate one application of summarization in the field of network data where we show how our technique can be effectively used to summarize network traffic into a compact but meaningful representation. Specifically, we evaluate our proposed algorithms on the 1998 DARPA Off-line Intrusion Detection Evaluation data and network data generated by SKAION Corp for the ARDA information assurance program.
Channel-Aware Weighted Proportional Fair Medium Access Control in Wireless LANs with MIMO links
Authors: Dong Zheng, Junshan Zhang
Venue: Proceedings of the Second International Conference on Quality of Service in Heterogeneous Wired/Wireless Networks (2005)

MIMO techniques using multiple antennas for both transmitting and receiving have recently manifested themselves to be very promising for future broadband wireless networks. Aiming to leverage the impact of these MIMO techniques on network protocol design in wireless LANs (WLANs), we take a utility approach to study channelaware weighted proportional fair medium access control (WPF MAC) for QoS provisioning. Simply put, in this utility based approach, every user in a WLAN attempts to maximize its own utility, and the optimization procedure takes place in two stages: a channel contention phase that arbitrates fair channel access across the users via combining adaptive persistence mechanism with random backoff, and a data transmission phase that determines the transmission duration based on the channel conditions in each transmission round. Furthermore, adaptive beamforming is carried out by using the training signals embedded in the RTS/CTS handshake to enhance the spectral efficiency of the MIMO links. Using a stochastic approximation method, together with the Lyapunov stability theorems, we establish the stability of the adaptive persistence mechanism in the proposed WPF MAC and analyze the fairness across the users therein.
Developing Mobile Services: Balancing Customer and Network Value
Authors: Harry Bouwman, Timber Haaker, Edward Faber
Venue: Proceedings of the Second IEEE International Workshop on Mobile Commerce and Services (2005)

Designing mobile services and the business models behind them is a complex undertaking. A business model can be seen as a blueprint of four interrelated components: service offering, technical architecture, and organizational and financial arrangements. How these different components are related to one another, is hardly been object of research. In this paper the connections between these components are explored by analyzing the critical design issues, e.g. targeting, branding and customer retention in the service domain, security, quality of service and system integration in the technology domain, network governance in the organization domain, and revenue sharing in the finance domain. These critical design issues are linked to each other and to expected customer value and expected network value in a conceptual model.
3D Object Modeling Method for Multimedia Using Cellular Structured Space
Authors: Nat Charussuriyong, Pizzanu Kanongchaiyos
Venue: Proceedings of the Sixth International Conference on Computational Intelligence and Multimedia Applications (2005)

Modeling method for three-dimensional objects in computer graphics usually starts from geometry level. For using in multimedia or database system, such methods can display on screen but lack essential properties of the models such as shape equivalence, shape invariant, topological equivalence and features. We propose a valid shape modeling using topology features for checking validity of the model called cellular structured space, starting from inductively compose a finite structure via attaching map. By this method, invariant and some topological properties are preserved and used for finding similarity of the 3D objects in multimedia database.
Efficient simulation of nondeterministic weighted finite automata
Authors: Mark G. Eramian
Venue: Journal of Automata, Languages and Combinatorics (2004)

Simulation of nondeterministic automata is often required in algorithms for string matching and image compression. We give three algorithms for NWFA simulation and compare them with known methods. When we consider the problem of computing the acceptance weight of all words of a given finite length, we find that the best of the three algorithms is comparable with a recursive version of a known sparse matrix based algorithm with respect to time, but offers an implementation with simpler data structures.
The essence of command injection attacks in web applications
Authors: Zhendong Su, Gary Wassermann
Venue: Conference record of the 33rd ACM SIGPLAN-SIGACT symposium on Principles of programming languages (2006)

Web applications typically interact with a back-end database to retrieve persistent data and then present the data to the user as dynamically generated output, such as HTML web pages. However, this interaction is commonly done through a low-level API by dynamically constructing query strings within a general-purpose programming language, such as Java. This low-level interaction is ad hoc because it does not take into account the structure of the output language. Accordingly, user inputs are treated as isolated lexical entities which, if not properly sanitized, can cause the web application to generate unintended output. This is called a command injection attack, which poses a serious threat to web application security. This paper presents the first formal definition of command injection attacks in the context of web applications, and gives a sound and complete algorithm for preventing them based on context-free grammars and compiler parsing techniques. Our key observation is that, for an attack to succeed, the input that gets propagated into the database query or the output document must change the intended syntactic structure of the query or document. Our definition and algorithm are general and apply to many forms of command injection attacks. We validate our approach with SqlCheckS, an implementation for the setting of SQL command injection attacks. We evaluated SqlCheckS on real-world web applications with systematically compiled real-world attack data as input. SqlCheckS produced no false positives or false negatives, incurred low runtime overhead, and applied straightforwardly to web applications written in different languages.
Teaching ethics and computer forensics: the Markkula center for applied ethics approach
Authors: Thomas S. J. Schwarz
Venue: Proceedings of the 2nd annual conference on Information security curriculum development (2005)

I claim that we teach Ethics in Information Assurance courses because we want to install the importance of ethical behavior right at the beginning of our students' professional career and because we need to give them tools to deal with newly arising situations, for example those that are not dealt with in codes of conduct or that straddle the lines. Since fact finding and evaluation of facts are important aspects of ethical decision making, part of ethics education needs to be done within technical courses with the goal of complementing the philosophical foundations or generic applied ethics discussions left best to the general education curriculum. Teaching ethics well is hard. A basic problem -- an instance of living in a post-modern world -- is the lack of a common foundation to make ethical judgments. In addition, gaining and maintaining technical expertise is a full-time job that an instructor might not want to supplement by gaining expertise in the challenging fields of business or applied ethics; thus, any method for teaching ethics needs to be simple.A group of philosophers at the Markkula Center for Ethics at Santa Clara University developed a simple framework for business ethics that distills various philosophical approaches towards Ethics in simple questions. The resulting procedure consists in "simply" answering these questions and thereby approaching a difficult situation from various perspectives. While the framework cannot solve certain thorny issues, it is quite successful at elucidating ethical problems and -- possibly more importantly -- it gives those exposed to it a common language. In my opinion, this framework allows us to teach ethics in Information Assurance classes in a manner that (1) is not biased by the personal views of the instructor, that (2) does not involve a large sacrifice of class room time, that is (3) reasonably culturally and gender neutral, that (4) is quite successful helping elucidating new ethical issues and (5) that allows someone with a technical background but no or limited philosophical background to successfully teach ethics.
A System for Indian Postal Automation
Authors: K. Roy, S. Vajda, A. Belaid, U. Pal, B. B. Chaudhuri
Venue: Proceedings of the Eighth International Conference on Document Analysis and Recognition (2005)

In this paper, we present a system towards Indian postal automation based on the recognition of pin-code and city name of the postal document. In the proposed system, at first, non-text blocks (postal stamp, postal seal etc.) are detected and Destination Address Block (DAB) is identified from the document. Next, lines and words of the DAB are segmented. Since India is a multi-lingual and multi-script country, the address part may be written by combination of two scripts. To identify the script by which a word is written, we propose a water reservoir based technique. It is very difficult to identify the script by which the pin-code portion is written. So we have used two-stage artificial Neural Network (NN) based general classifiers for the recognition of pin-code digits written in English/Bangla. For recognition of city names we propose an NSHP-HMM (Non-Symmetric Half Plane- Hidden Markov Model) based technique.
An adaptive middleware framework for context-aware applications
Authors: C. Huebscher, A. McCann
Venue: Personal and Ubiquitous Computing (2005)

We describe a middleware framework for the adaptive delivery of context information to context-aware applications. The framework abstracts the applications from the sensors that provide context. Further applications define utility functions on the quality of context attributes that describe the context providers. Then, given multiple alternatives for providing the same type of context, the middleware applies the utility function to each alternative and choose the one with maximum utility. By allowing applications to delegate the selection of context source to the middleware, our middleware can implement autonomic properties, such as self-configuration when new context providers appear and resilience to failures of context providers.
Trust and reputation in peer-to-peer networks
Authors: Hector Garcia-Molina
Venue:  (2005)

The increasing availability of high bandwidth Internet connections and low-cost, commodity computers in people's homes has stimulated the use of resource sharing peer-to-peer networks. These systems employ scalable mechanisms that allow anyone to offer content and services to other system users. However, the open accessibility of these systems make them vulnerable to malicious users wishing to poison the system with corrupted data or harmful services and worms. Because of this danger, users must be wary of the quality or validity of the resources they access. To mitigate the adverse behavior of unreliable or malicious peers in a network, researchers have suggested using reputation systems. Yet our understanding of how to incorporate an effective reputation system into an autonomous network is limited. This thesis categorizes and evaluates the components and mechanisms necessary to build robust, effective reputation systems for use in decentralized autonomous networks. Borrowing techniques from game theory and economic analysis, we begin with high-level models in order to understand general trends and properties of reputation systems and their effect on a user's behavior and experience. We then closely examine the effects of limited reputation sharing through simulations based on large-scale measurements from actual, operating P2P networks. Finally, we propose new mechanisms for improving message routing throughput in decentralized networks of untrusted peers: one geared towards structured DHTs (SPROUT) and two other complementary mechanisms for mobile ad hoc networks (Watchdog and Pathrater).
Fast Block Matching Algorithm Using Spatial Intensity Distribution
Authors: Jik-Han Jung, Hwal-Suk Lee, Byung-Gyu Kim, Dong-Jo Park
Venue: Proceedings of the Sixth International Conference on Computational Intelligence and Multimedia Applications (2005)

Block matching algorithm is useful in many applications such as stereo vision, visual tracking and so on. And the heavy computational burden of the full-search algorithm induces many faster algorithms, which can be classified into two. One class reduces the search area where the other reduces the unnecessary computation of each candidate block. In this paper, a new matching algorithm, which reduces the computational burden by using vote strategy, is proposed. With the observation of the property that the best match also has the similar spatial intensity distribution, block matching algorithm is described. The proposed matching algorithm is fast and robust to speckle noise or object occlusion.
A Dynamical Multi-level Scheme for the Burgers Equation: Wavelet and Hierarchical Finite Element
Authors: A. Debussche, J. Laminie, E. Zahrouni
Venue: Journal of Scientific Computing (2005)

Algorithms issued from the NonLinear Galerkin method have been used in many situations and with different discretizations for the resolution of evolutionary nonlinear equations. The main idea of these methods is to use a splitting of the solution in order to model the equation. According to the splitting of the solution, a splitting of the equation is obtained. The modeling principle is to freeze terms which have a small time variation. In this work we use wavelet discretizations of the 2-D Burgers equations and compare the results with the hierarchical finite elements method. The numerical tests indicate that wavelets give better results than finite elements
Fluid-Based Analysis of a Network with DCCP Connections and RED Routers
Authors: Hiroyuki Hisamatsu, Hiroyuki Ohsaki, Masayuki Murata
Venue: Proceedings of the International Symposium on Applications on Internet (2006)

In this paper, we model DCCP congestion control mechanism and RED as independent discrete-time systems using fluid-flow approximation. By interconnecting DCCP connections and RED routers, we model the entire network as a feedback system called DCCP/RED. We then analyze the steady state performance and the transient state performance of DCCP/RED. Specifically, we derive the packet transmission rate of DCCP connections, the packet transmission rate, the packet loss probability, and the average queue length of the RED router in steady state. Moreover, we investigate the parameter region where DCCP/RED operates stably by linearizing DCCP/RED around its equilibrium point. We also evaluate the transient state performance of DCCP/RED in terms of ramp-up time, overshoot, and settling time. Consequently, we show that the stability and the transient state performance of DCCP/RED degrade when the weight of the exponential weighted moving average, which is one of RED control parameters, is small. To solve this problem, by adding changes to the function with which RED determines the packet loss probability, we propose RED-IQI (RED with Immediate Queue Information). We analyze the transient state performance of the feedback system DCCP/RED-IQI where DCCP connections and RED-IQI routers are interconnected. Consequently, we show that DCCP/RED-IQI has significantly better transient state performance than DCCP/RED.
Off-Line Handwritten Character Recognition by SVM on the Virtual Examples Synthesized from On-Line Characters
Authors: Hidetoshi Miyao, Minoru Maruyama, Yasuaki Nakano, Toshihiro Hananoi
Venue: Proceedings of the Eighth International Conference on Document Analysis and Recognition (2005)

This paper proposes a method to improve the off-line character classifiers which are learned from examples by using the virtual examples synthesized from on-line character database. To obtain the good classifiers, usually a large database which contains enough number of variations of handwritten characters is required. However, in practice collecting enough number of data is time-consuming and costly. In this paper, we propose a method to train SVM for off-line character recognition based on the artificially augmented examples using on-line characters. In our method, a virtual example is synthesized from an on-line character by applying affine transformation to each stroke. SVM classifiers are trained by using the artificially generated patterns. To reject inappropriate artificial examples, a preliminary SVM is learned from the original set of samples, and then used for data selection. Using the augmented training samples, the final SVM is obtained. We examine the effectiveness of the proposed method by experiments of handwritten Japanese Hiragana character classi- fication.
Identity Boxing: A New Technique for Consistent Global Identity
Authors: Douglas Thain
Venue: Proceedings of the 2005 ACM/IEEE conference on Supercomputing (2005)

Today, users of the grid may easily authenticate themselves to computing resources around the world using a public key security infrastructure. However, users are forced to employ a patchwork of local identities, each assigned by a different local authority. This forces each grid system to provide a mapping from global to local identities, creating a significant administrative burden and inhibiting many possibilities of data sharing. To remedy this, we introduce the technique of identity boxing. This technique allows a high-level identity to be attached directly to each process and resource that a user employs, rendering the local account name irrelevant. This allows a grid user to be known by the same name consistently at all sites, thus reducing administrative burdens and enabling new forms of sharing. We have implemented identity boxing at the user level within a secure system-call interposition agent and applied it to a distributed storage and execution system. The performance overhead of this implementation is only 0.7 to 6.5 percent for a selection of scientific applications, but as high as 35 percent for a metadata-intensive software build. We conclude with some reflections on how the operating system might be modified to better support grid computing.
Automatic Metadata Generation forWeb Pages Using a Text Mining Approach
Authors: Hsin-Chang Yang, Chung-Hong Lee
Venue: Proceedings of the International Workshop on Challenges in Web Information Retrieval and Integration (2005)

The Semantic Web has emerged to replace the World Wide Web (WWW or the Web) as the unique platform for information sharing. Applications such as e-commerce will be and could be plausible only if we can annotate the Web pages with their semantics. For newly developed Semantic Web resources, such annotation can be done manually or by help of some authoring tools. However, it is not practical to semantically annotating existing Web pages due to the gigantic amount of them. To overcome this difficulty, we propose a machine learning approach to automatically generate semantic metadata for Web pages. The proposed automated process adopts the self-organizing map algorithm to cluster training Web pages and conducts a text mining process to discover some semantic descriptions about the Web pages. Preliminary experiments show that our method may generate semantically relevant metadata for the Web pages.
Real-time volume graphics
Authors: Klaus Engel, Markus Hadwiger, Joe M. Kniss, Aaron E. Lefohn, Christof Rezk Salama, Daniel Weiskopf
Venue: ACM SIGGRAPH 2004 Course Notes (2004)

The tremendous evolution of programmable graphics hardware has made high-quality real-time volume graphics a reality. In addition to the traditional application of rendering volume data in scientific visualization, the interest in applying these techniques for real-time rendering of atmospheric phenomena and participating media such as fire, smoke, and clouds is growing rapidly. This course covers both applications in scientific visualization, e.g., medical volume data, and real-time rendering, such as advanced effects and illumination in computer games, in detail. Course participants will learn techniques for harnessing the power of consumer graphics hardware and high-level shading languages for real-time rendering of volumetric data and effects. Beginning with basic texture-based approaches including hardware ray casting, the algorithms are improved and expanded incrementally, covering local and global illumination, scattering, pre-integration, implicit surfaces and non-polygonal isosurfaces, transfer function design, volume animation and deformation, dealing with large volumes, high-quality volume clipping, rendering segmented volumes, higher-order filtering, and non-photorealistic volume rendering. Course participants are provided with documented source code covering details usually omitted in publications.