INESC-ID

About: INESC-ID is a nonprofit organization based out in Lisbon, Portugal. It is known for research contribution in the topics: Field-programmable gate array & Control theory. The organization has 932 authors who have published 2618 publications receiving 37658 citations.

DegreeCox – a network-based regularization method for survival analysis

Abstract: Modeling survival oncological data has become a major challenge as the increase in the amount of molecular information nowadays available means that the number of features greatly exceeds the number of observations. One possible solution to cope with this dimensionality problem is the use of additional constraints in the cost function optimization. Lasso and other sparsity methods have thus already been successfully applied with such idea. Although this leads to more interpretable models, these methods still do not fully profit from the relations between the features, specially when these can be represented through graphs. We propose DegreeCox, a method that applies network-based regularizers to infer Cox proportional hazard models, when the features are genes and the outcome is patient survival. In particular, we propose to use network centrality measures to constrain the model in terms of significant genes. We applied DegreeCox to three datasets of ovarian cancer carcinoma and tested several centrality measures such as weighted degree, betweenness and closeness centrality. The a priori network information was retrieved from Gene Co-Expression Networks and Gene Functional Maps. When compared with Ridge and Lasso, DegreeCox shows an improvement in the classification of high and low risk patients in a par with Net-Cox. The use of network information is especially relevant with datasets that are not easily separated. In terms of RMSE and C-index, DegreeCox gives results that are similar to those of the best performing methods, in a few cases slightly better. Network-based regularization seems a promising framework to deal with the dimensionality problem. The centrality metrics proposed can be easily expanded to accommodate other topological properties of different biological networks.

Execution of data mappers

Abstract: Data mappers are essential operators for implementing data transformations supporting schema mapping and integration scenarios such as legacy data migration, ETL processes for data warehousing, data cleaning activities, and business integration initiatives. Despite their widespread use, no formalization of this important operation has been proposed so far. In this paper we propose the data mapper operator as an extension to the relational algebra. We supply a set of algebraic rewriting rules for optimizing queries that combine standard relational operators with data mappers. Finally, we propose algorithms for their efficient physical execution.

Blobby: how to guide a blind person

Abstract: For the majority of blind people, walking in unknown places is a very difficult, or even impossible, task to perform, when without help. The adoption of the white cane is the main aid to a blind user's mobility. However, the major difficulties arise in the orientation task. The lack of reference points and the inability to access visual cues are its main causes. We aim to overcome this issue allowing users to walk through unknown places, by receiving a familiar and easily understandable feedback. Our preliminary contributions are in understanding, through user studies, how blind users explore an unknown place, their difficulties, capabilities and needs. We also analyzed how these users create their own mental maps, verbalize a route and communicate with each other. Structuring and generalizing this information, we were able to create a prototype that generates familiar and adequate instructions, behaving like a blind companion, one with similar capabilities that understands his "friend" and speaks the same language. We evaluated the system with the target population, validating our approach and orientation guidelines, while gathering overall user satisfaction.

Multiresponse Optimization and Pareto Frontiers

Abstract: Methods that can capture evenly distributed solutions along the Pareto frontier are useful for multiresponse optimization problems because they provide a large variety of alternative solutions to the decision maker from among a set of nondominated solutions. However, methods often used for optimizing dual and multiple dual response problems have been rarely evaluated in terms of their ability to capture those solutions. This article provides this information by evaluating a global criterion–based method and the popular weighted mean square error method. Convex and nonconvex response surfaces were considered, and results of the methods were compared with those of a lexicographic approach on the basis of two examples from the literature. Regarding the results, it is shown that the user can be successful in capturing Pareto solutions in convex and nonconvex regions using the global criterion–based method. Moreover, it is shown that the starting point affects the distribution of solutions along the Pareto frontier but is not pivotal to obtain a complete representation of the Pareto frontier. For this purpose, it is necessary to decrease the weight increment and to compute for more solutions. Copyright © 2011 John Wiley & Sons, Ltd.

Manage Risks through the Enterprise Architecture

Abstract: The goal of Risk Management activities is to define prevention and control mechanisms to address the risks attached to specify activities and valuable assets. Many Risk Management efforts operate in silos with narrowly focused, functionally driven, and disjointed activities. That fact leads to a fragmented view of risks, where each activity uses its own language, customs and metrics. The lack of interconnection and holistic view of risks limits an organization-wide perception of risks, where interdependent risks are not anticipated, controlled or managed. In order to address the Risk Management interoperability and standardization issues, this paper proposes an alignment between Risk Management, Governance and Enterprise Architecture activities, providing a systematic support to map and trace identified risks to enterprise artifacts modeled within the Enterprise Architecture, supporting the overall strategy of any organization. We discuss the main relationships between Risk Management and Enterprise Architecture and propose an architecture to integrate risks concerns into the overall organization environment.