ppxscal/embedding_network huggingface dataset:
Cancer informatics by prototype networks in mass spectrometry
Authors: Frank-Michael Schleif, Thomas Villmann, Markus Kostrzewa, Barbara Hammer, Alexander Gammerman
Venue: Artificial Intelligence in Medicine (2009)

Objective: Mass spectrometry has become a standard technique to analyze clinical samples in cancer research. The obtained spectrometric measurements reveal a lot of information of the clinical sample at the peptide and protein level. The spectra are high dimensional and, due to the small number of samples a sparse coverage of the population is very common. In clinical research the calculation and evaluation of classification models is important. For classical statistics this is achieved by hypothesis testing with respect to a chosen level of confidence. In clinical proteomics the application of statistical tests is limited due to the small number of samples and the high dimensionality of the data. Typically soft methods from the field of machine learning are used to generate such models. However for these methods no or only few additional information about the safety of the model decision is available. In this contribution the spectral data are processed as functional data and conformal classifier models are generated. The obtained models allow the detection of potential biomarker candidates and provide confidence measures for the classification decision. Methods: First, wavelet-based techniques for the efficient processing and encoding of mass spectrometric measurements from clinical samples are presented. A prototype-based classifier is extended by a functional metric and combined with the concept of conformal prediction to classify the clinical proteomic spectra and to evaluate the results. Results: Clinical proteomic data of a colorectal cancer and a lung cancer study are used to test the performance of the proposed algorithm. The prototype classifiers are evaluated with respect to prediction accuracy and the confidence of the classification decisions. The adapted metric parameters are analyzed and interpreted to find potential biomarker candidates. Conclusions: The proposed algorithm can be used to analyze functional data as obtained from clinical mass spectrometry, to find discriminating mass positions and to judge the confidence of the obtained classifications, providing robust and interpretable classification models.
Life Assistance Protocols (LAP) - A Model for the Personalization of Lifestyle Support for Health and Wellbeing
Authors: Teresa Meneu, Vicente Traver, Carlos Fernández, Riccardo Serafin, David Domínguez, Sergio Guillén
Venue: Proceedings of the 2009 International Conference on eHealth, Telemedicine, and Social Medicine (2009)

The WHO Report 2002 describes in detail how a few major risk factors account for a significant proportion of all deaths and diseases in most countries. Those risk factors are directly related with lifestyle and unhealthy habits. Thus, population based approaches addressing lifestyle factors have huge potential for the prevention of severe morbidity and mortality. The best therapeutic choice is guided by correct risk stratification for the individual, taking into account all the risk factors, not only the physio-pathological ones, but also the genetic, environmental, socio-cultural, behavioural and personal factors, in order to personalize health-hygiene measures on the basis of the risk profile. Health risk management programs address the identified risk levels of each individual and the action strategy proposed to elaborate a complete comprehensive program of life which should lead him from the current status towards the optimal one. Therefore, the objective of our proposed model has been to develop an intelligent system for the planning of personalized health risk management processes considering both the health strategies and the personal preferences: The Life Assistance Protocols (LAPs).
Approximating maximum weight K-colorable subgraphs in chordal graphs
Authors: Venkatesan T. Chakaravarthy, Sambuddha Roy
Venue: Information Processing Letters (2009)

We present a 2-approximation algorithm for the problem of finding the maximum weight K-colorable subgraph in a given chordal graph with node weights. The running time of the algorithm is O(K(n+m)), where n and m are the number of vertices and edges in the given graph.
Conferencing, Paging, Voice Mailing via Asterisk EPBX
Authors: Ale Imran, Mohammed A. Qadeer
Venue: Proceedings of the 2009 International Conference on Computer Engineering and Technology - Volume 01 (2009)

This paper is intended to present theoretical and implementation details of various important features that are generally associated with an Asterisk based Voice Exchange i.e. Conferencing, Paging and Voice mailing. Besides this we will be concentrating on the web based approach for the configuration of the hard phones that will be used at the clients end. Our approach follows the client server model for all subsidiary procedures. The application is developed in C language and is compatible with all the versions of Linux, essentially providing PC to PC data and voice communications.
Scalable stream join processing with expensive predicates: workload distribution and adaptation by time-slicing
Authors: Song Wang, Elke Rundensteiner
Venue: Proceedings of the 12th International Conference on Extending Database Technology: Advances in Database Technology (2009)

Multi-way stream joins with expensive join predicates lead to great challenge for real-time (or close to real-time) stream processing. Given the memory- and CPU-intensive nature of such stream join queries, scalable processing on a cluster must be employed. This paper proposes a novel scheme for distributed processing of generic multi-way joins with window constraints, called Pipelined State Partitioning (PSP). We target generic joins with arbitrarily join conditions, which are used in non-trivial stream applications such as image matching and biometric recognizing. The PSP scheme partitions the states into disjoint slices in the time domain, and then distributes the fine-grained states in the cluster, forming a virtual computation ring. Compared to replication-based distribution of non-equi-joins, PSP scheme is superior since: (1) zero state duplication and thus no repeated computations, (2) pipelined processing of every input tuple on multiple nodes to achieve low response time, and (3) cost-based adaptive workload distribution. We have implemented the proposed PSP schemes within the CAPE DSMS. Our experimental study demonstrates the significant performance improvements compared to the state-of-the-art generic distributed stream join algorithms.
C++ concepts as institutions: a specification view on concepts
Authors: Marcin Zalewski, Sibylle Schupp
Venue: Proceedings of the 2007 Symposium on Library-Centric Software Design (2007)

With the recent developments in the C++ language, concepts are mostly discussed as a form of constrained polymorphism. Yet, concepts also allow for an alternative, implementation-independent view that comes from their origin in (algebraic) specification languages. In this paper, we return to this specification view on concepts and formalize C++ concepts as institutions, a well-established notion for precise specifications of software components. We argue that institutions form a suitable theoretical framework for software systems like libraries where the different parts establish relations that are captured by different logics, or no formal logic at all. Assuming the C++ concept descriptions, concept maps, and axioms as in the draft currently accepted by the C++ standardization committee, we show that concept descriptions and axioms form an institution (with equational logic) but also, and perhaps surprisingly, that concept descriptions and concept maps form an institution (with no formal logic).
Parameterized Graph Cleaning Problems
Authors: Dániel Marx, Ildikó Schlotter
Venue: Graph-Theoretic Concepts in Computer Science: 34th International Workshop, WG 2008, Durham, UK, June 30 --- July 2, 2008. Revised Papers (2008)

We investigate the Induced Subgraph Isomorphism problem with non-standard parametrization, where the parameter is the difference |V(G)| ¿ |V(H)| with H and G being the smaller and the larger input graph, respectively. Intuitively, we can interpret this problem as "cleaning" the graph G, regarded as a pattern containing extra vertices indicating errors, in order to obtain the graph H representing the original pattern. We show fixed-parameter tractability of the cases where both H and G are planar and H is 3-connected, or H is a tree and G is arbitrary.
Why Eliciting and Managing Legal Requirements Is Hard
Authors: Nadzeya Kiyavitskaya, Albeta Krausová, Nicola Zannone
Venue: Proceedings of the 2008 Requirements Engineering and Law (2008)

The increasing complexity of IT systems and the growing demand for regulation compliance are main issues for the design of IT systems. Addressing these issues requires the developing of effective methods to support the analysis of regulations and the elicitation of any organizational and system requirements from them. This work investigates the problem of designing regulation-compliant systems and, in particular, the challenges in eliciting and managing legal requirements.
A generalized data windowing scheme for adaptive conjugate gradient algorithms
Authors: Shengkui Zhao, Zhihong Man, Suiyang Khoo
Venue: Signal Processing (2009)

The performance of the modified adaptive conjugate gradient (CG) algorithms based on the iterative CG method for adaptive filtering is highly related to the ways of estimating the correlation matrix and the cross-correlation vector. The existing approaches of implementing the CG algorithms using the data windows of exponential form or sliding form result in either loss of convergence or increase in misadjustment. This paper presents and analyzes a new approach to the implementation of the CG algorithms for adaptive filtering by using a generalized data windowing scheme. For the new modified CG algorithms, we show that the convergence speed is accelerated, the misadjustment and tracking capability comparable to those of the recursive least squares (RLS) algorithm are achieved. Computer simulations demonstrated in the framework of linear system modeling problem show the improvements of the new modifications.
Future trends in distributed simulation and distributed virtual environments: results of a peer study
Authors: Steffen Strassburger, Thomas Schulze, Richard Fujimoto
Venue: Proceedings of the 40th Conference on Winter Simulation (2008)

This paper reports main results of a peer study on future trends in distributed simulation and distributed virtual environments (Strassburger et al. 2008). The peer study was based on the opinions of more than 60 experts which were collected by means of a survey and personal interviews. The survey collected opinions concerning the current state-of-the-art, relevance, and research challenges that must be addressed to advance and strengthen these technologies to a level where they are ready to be applied in day-to-day business in industry. Most important result of this study is the observation that as research areas, both distributed simulation and distributed virtual environments are attributed a high future practical relevance and a high economic potential. At the same time the study shows that the current adoption of these technologies in the industrial sector is rather low. The study analyses reasons for this observation and identifies open research challenges.
Interoperating Logic Engines
Authors: Paul Tarau, Arun Majumdar
Venue: Proceedings of the 11th International Symposium on Practical Aspects of Declarative Languages (2009)

We introduce a new programming language construct, Interactors, supporting the agent-oriented view that programming is a dialog between simple, self-contained, autonomous building blocks.We define Interactors as an abstraction of answer generation and refinement in Logic Engines resulting in expressive language extension and metaprogramming patterns.As a first step toward a declarative semantics, we sketch a pure Prolog specification showing that Interactors can be expressed at source level, in a relatively simple and natural way.Interactors extend language constructs like Ruby, Python and C#'s multiple coroutining block returns through yield statements and they can emulate the action of fold operations and monadic constructs in functional languages.Using the Interactor API, we describe at source level, language extensions like dynamic databases and algorithms involving generation of infinite answer streams.
A simultaneous learning framework for clustering and classification
Authors: Weiling Cai, Songcan Chen, Daoqiang Zhang
Venue: Pattern Recognition (2009)

Traditional pattern recognition generally involves two tasks: unsupervised clustering and supervised classification. When class information is available, fusing the advantages of both clustering learning and classification learning into a single framework is an important problem worthy of study. To date, most algorithms generally treat clustering learning and classification learning in a sequential or two-step manner, i.e., first execute clustering learning to explore structures in data, and then perform classification learning on top of the obtained structural information. However, such sequential algorithms cannot always guarantee the simultaneous optimality for both clustering and classification learning. In fact, the clustering learning in these algorithms just aids the subsequent classification learning and does not benefit from the latter. To overcome this problem, a simultaneous learning framework for clustering and classification (SCC) is presented in this paper. SCC aims to achieve three goals: (1) acquiring the robust classification and clustering simultaneously; (2) designing an effective and transparent classification mechanism; (3) revealing the underlying relationship between clusters and classes. To this end, with the Bayesian theory and the cluster posterior probabilities of classes, we define a single objective function to which the clustering process is directly embedded. By optimizing this objective function, the effective and robust clustering and classification results are achieved simultaneously. Experimental results on both synthetic and real-life datasets show that SCC achieves promising classification and clustering results at one time.
A trace-based framework for verifiable GALS composition of IPs
Authors: Syed Suhaib, Deepak A. Mathaikutty, Sandeep K. Shukla
Venue: IEEE Transactions on Very Large Scale Integration (VLSI) Systems (2008)

Composing intellectual property (IP) blocks running at different clock speeds over asynchronous communication links for a system-on-chip (SoC) design is a challenging task, especially for ensuring the functional correctness of the overall design. In this paper, we propose a trace-based framework that helps in identifying a class of IPs that can be composed to "correct-by-construction" globally asynchronous locally synchronous (GALS) designs, and their correctness is maintained with respect to their synchronous compositions. Our notion of correctness is latency equivalence. Latency equivalence means that the order of valid values is same on the corresponding signals in the synchronous as well as asynchronous compositions. We also provide a description of the protocol to be inserted between the IPs to obtain this equivalence.
Latency Estimation for Time-Sensitive Applications under Wireless Network Coding Scheme
Authors: Kui Xu, Bin Dai, Fan Zhang, Benxiong Huang, Bo Zhang
Venue: Proceedings of the 2009 WRI International Conference on Communications and Mobile Computing - Volume 02 (2009)

Network coding has been designed for wireless networks to improve the capabilities of throughput, reliability, and routing by mixing information from different flows and conveying more information in each transmission. If packets are coded by blocks with large sizes, time-sensitive applications in wireless network will suffer from high latency between blocks caused by intrasession coding scheme. In this paper, a block latency model in coding scheme is derived, and then four latency estimation algorithms are introduced which are used for choosing a proper block size to satisfy the need of time-sensitive applications. Simulations results show that Kalman filter has a better performance than the others.
Enabling Cross-Disciplinary E-Science by Integrating Geoscience Ontologies with Dolce
Authors: Boyan Brodaric, Florian Probst
Venue: IEEE Intelligent Systems (2009)

E-Science is increasingly being used to address scientific problems that require cross-disciplinary knowledge, such as climate change, natural disasters, and environmental health. However, the ontologies used to represent scientific knowledge are largely unidisciplinary and need to be integrated to enable big e-Science. The authors investigate the potential of the Dolce foundational ontology to aid the integration of two geoscientific knowledge representations, the Sweet ontology and the GeoSciML schema, to meet the requirements of a cross-disciplinary use case focused on groundwater pollution estimation. They connected the domain ontologies via the foundational ontology, leading to new and improved relations between the domain ontologies that enabled satisfaction of the use case. Although the integrated ontology, called Dolce Rocks, contains some semantic inconsistencies resulting from incompatibilities among the ontologies, the overall results suggest that foundational ontologies can play an important role in cross-disciplinary e-Science.
Key Estimation Using Circle of Fifths
Authors: Takahito Inoshita, Jiro Katto
Venue: Proceedings of the 15th International Multimedia Modeling Conference on Advances in Multimedia Modeling (2009)

This paper presents a novel key estimation method of sound sources based on the music theory known as "circle of fifths". We firstly overview music theory and formulate the musical key analysis by vector operations. In detail, we separate music sources into small pieces and calculate FFT-based chroma vectors. They are converted to tonality vectors and COF (circle-of-fifth) vectors are calculated from the tonality vectors, which are mapped onto the circle of fifths coordinate. As a result, each music source can be represented by traces of COF vectors, which usually stay inside a single key region on the circle of fifths. Finally, HMM is applied to the traces of COF vectors in order to detect keys and their boundaries. Experiments using music databases are also carried out.
A Classification Method of Images Based on Composition and Its Application to Image Retrieval
Authors: Shigenori Maeda, Masayuki Mukunoki, Katsuo Ikeda
Venue: Proceedings of the 1999 IEEE International Conference on Multimedia Computing and Systems - Volume 02 (1999)

We propose a visual query method for image retrieval, in which the user expresses the composition of the target image by selecting one of the composition types presented by the system, and also propose an image classification method to derive composition types from an image database. From the viewpoint of communication between the system and its user, we point out the problem of visual query methods using concrete images as queries. Though suited to convey visual image properties, they grow the ambiguity in the system's interpretation of queries. To manage this tradeoff, we implemented our methods in a prototype system and derived composition types from an image database to show how our query method works in image retrieval.
Spectral Characterisation of Spontaneous Parametric-Down Conversion Entangled Photons Source in Femtosecond Pulsed Regime
Authors: G. Brida, V. Caricato, M. Genovese, M. Gramegna, S. P. Kulik, M. V. Fedorov, L. A. Krivitsky
Venue: Proceedings of the 2009 Third International Conference on Quantum, Nano and Micro Technologies (2009)

We report on experimental measurements of coincidence and single particle spectral shapes of biphoton signals when frequency entangled states are generated by SPDC crystals pumped by short pulses.It is shown evidence for biphoton coincidence spectrum narrower and single-particle one wider than the pump spectrum, with a large contrast between coincidence and singles distributions.The investigation of biphoton correlations has been performed by fixing one monochromator at the maximal transmission wavelength on down-converted signal gate and scanning the one placed in the idler branch in order to observe the spectral distribution of single counts and coincidences.The degree of entanglement is evaluated by the ratio of the FWHM of single particle and coincidence distributions: the greater the ratio, the greater is the entanglement.The degree of entanglement in frequency variables can be very high: it increases linearly with the length of the crystal, and decreases with the growing pump pulse.
Finding causes of program output with the Java Whyline
Authors: Andrew J. Ko, Brad A. Myers
Venue: Proceedings of the 27th international conference on Human factors in computing systems (2009)

Debugging and diagnostic tools are some of the most important software development tools, but most expect developers choose the right code to inspect. Unfortunately, this rarely occurs. A new tool called the Whyline is described which avoids such speculation by allowing developers to select questions about a program's output. The tool then helps developers work backwards from output to its causes. The prototype, which supports Java programs, was evaluated in an experiment in which participants investigated two real bug reports from an open source project using either the Whyline or a breakpoint debugger. Whyline users were successful about three times as often and about twice as fast compared to the control group, and were extremely positive about the tool's ability to simplify diagnostic tasks in software development work.
Automatic pre-tessellation culling
Authors: Jon Hasselgren, Jacob Munkberg, Tomas Akenine-Möller
Venue: ACM Transactions on Graphics (TOG) (2009)

Graphics processing units supporting tessellation of curved surfaces with displacement mapping exist today. Still, to our knowledge, culling only occurs after tessellation, that is, after the base primitives have been tessellated into triangles. We introduce an algorithm for automatically computing tight positional and normal bounds on the fly for a base primitive. These bounds are derived from an arbitrary vertex shader program, which may include a curved surface evaluation and different types of displacements, for example. The obtained bounds are used for backface, view frustum, and occlusion culling before tessellation. For highly tessellated scenes, we show that up to 80&percnt; of the vertex shader instructions can be avoided, which implies an &ldquo;instruction speedup&rdquo; of 5&times;. Our technique can also be used for offline software rendering.
Pruning an ensemble of classifiers via reinforcement learning
Authors: Ioannis Partalas, Grigorios Tsoumakas, Ioannis Vlahavas
Venue: Neurocomputing (2009)

This paper studies the problem of pruning an ensemble of classifiers from a reinforcement learning perspective. It contributes a new pruning approach that uses the Q-learning algorithm in order to approximate an optimal policy of choosing whether to include or exclude each classifier from the ensemble. Extensive experimental comparisons of the proposed approach against state-of-the-art pruning and combination methods show very promising results. Additionally, we present an extension that allows the improvement of the solutions returned by the proposed approach over time, which is very useful in certain performance-critical domains.