INESC-ID

About: INESC-ID is a nonprofit organization based out in Lisbon, Portugal. It is known for research contribution in the topics: Computer science & Context (language use). The organization has 932 authors who have published 2618 publications receiving 37658 citations.

KiMoSys: a web-based repository of experimental data for KInetic MOdels of biological SYStems.

Abstract: The kinetic modeling of biological systems is mainly composed of three steps that proceed iteratively: model building, simulation and analysis. In the first step, it is usually required to set initial metabolite concentrations, and to assign kinetic rate laws, along with estimating parameter values using kinetic data through optimization when these are not known. Although the rapid development of high-throughput methods has generated much omics data, experimentalists present only a summary of obtained results for publication, the experimental data files are not usually submitted to any public repository, or simply not available at all. In order to automatize as much as possible the steps of building kinetic models, there is a growing requirement in the systems biology community for easily exchanging data in combination with models, which represents the main motivation of Ki MoSys development. Ki MoSys is a user-friendly platform that includes a public data repository of published experimental data, containing concentration data of metabolites and enzymes and flux data. It was designed to ensure data management, storage and sharing for a wider systems biology community. This community repository offers a web-based interface and upload facility to turn available data into publicly accessible, centralized and structured-format data files. Moreover, it compiles and integrates available kinetic models associated with the data. Ki MoSys also integrates some tools to facilitate the kinetic model construction process of large-scale metabolic networks, especially when the systems biologists perform computational research. Ki MoSys is a web-based system that integrates a public data and associated model(s) repository with computational tools, providing the systems biology community with a novel application facilitating data storage and sharing, thus supporting construction of ODE-based kinetic models and collaborative research projects. The web application implemented using Ruby on Rails framework is freely available for web access at http://kimosys.org , along with its full documentation.

New Normalized LMS Algorithms Based on the Kalman Filter

Abstract: While the LMS algorithm and its normalized version (NLMS), have been thoroughly used and studied. Connections between the Kalman filter and the RLS algorithm have been established however, the connection between the Kalman filter and the LMS algorithm has not received much attention. By linking these two algorithms, a new normalized Kalman based LMS (KLMS) algorithm can be derived that has some advantages to the classical one. Their stability is guaranteed since they are a special case of the Kalman filter. More, they suggests a new way to control the step size, that results in good convergence properties for a large range of input signal powers, that occur in many applications. They prevent high measurement noise sensitivity that may occur in the NLMS algorithm for low order filters, like the ones used in OFDM equalization systems. In these paper, different algorithms based on the correlation form, information form and simplified versions of these are presented. The simplified form maintain the good convergence properties of the KLMS with slightly lower computational complexity.

On QBF Proofs and Preprocessing

Abstract: QBFs (quantified boolean formulas), which are a superset of propositional formulas, provide a canonical representation for PSPACE problems. To overcome the inherent complexity of QBF, significant effort has been invested in developing QBF solvers as well as the underlying proof systems. At the same time, formula preprocessing is crucial for the application of QBF solvers. This paper focuses on a missing link in currently-available technology: How to obtain a certificate (e.g. proof) for a formula that had been preprocessed before it was given to a solver? The paper targets a suite of commonly-used preprocessing techniques and shows how to reconstruct certificates for them. On the negative side, the paper discusses certain limitations of the currently-used proof systems in the light of preprocessing. The presented techniques were implemented and evaluated in the state-of-the-art QBF preprocessor bloqqer.

Developing a Deep Linguistic Databank Supporting a Collection of Treebanks: the CINTIL DeepGramBank

Abstract: Corpora of sentences annotated with grammatical information have been deployed by extending the basic lexical and morphological data with increasingly complex information, such as phrase constituency, syntactic functions, semantic roles, etc. As these corpora grow in size and the linguistic information to be encoded reaches higher levels of sophistication, the utilization of annotation tools and, above all, supporting computational grammars appear no longer as a matter of convenience but of necessity. In this paper, we report on the design features, the development conditions and the methodological options of a deep linguistic databank, the CINTIL DeepGramBank. In this corpus, sentences are annotated with fully fledged linguistically informed grammatical representations that are produced by a deep linguistic processing grammar, thus consistently integrating morphological, syntactic and semantic information. We also report on how such corpus permits to straightforwardly obtain a whole range of past generation annotated corpora (POS, NER and morphology), current generation treebanks (constituency treebanks, dependency banks, propbanks) and next generation databanks (logical form banks) simply by means of a very residual selection/extraction effort to get the appropriate ""views"" exposing the relevant layers of information.

Wiki Supported Collaborative Requirements Engineering

Abstract: The high number of unsuccessful IT projects, due to the inconsistent and ambiguous requirements speciflcations, justifles the proposal of new socio-technical approaches to overcome these software quality issues. To address these problems it is required a platform that simultaneously fosters stakeholders’ involvement to capture their tacit knowledge, but also to enforce Requirements Engineering best practices. In this paper, we present our approach for enhancing the quality and rigor of requirements speciflcations by combining emergent Web 2.0 concepts with CASE tools for requirements speciflcation and validation. This approach provides a ∞exible platform for collaborative Requirements Engineering: non-technical stakeholders are assisted during the elicitation process and requirements engineers beneflt from the seamlessly integration with a broader CASE tool.