A Probabilistic Approach for Integrating Heterogeneous Knowledge Sources

Open Information Extraction (OIE) systems like Nell and ReVerb have achieved impressive results by harvesting massive amounts of machine-readable knowledge with minimal supervision. However, the knowledge bases they produce still lack a clean, explicit semantic data model. This, on the other hand, could be provided by full-fledged semantic networks like DBpedia or Yago, which, in turn, could benefit from the additional coverage provided by Web-scale IE. In this paper, we bring these two strains of research together, and present a method to align terms from Nell with instances in DBpedia. Our approach is unsupervised in nature and relies on two key components. First, we automatically acquire probabilistic type information for Nell terms given a set of matching hypotheses. Second, we view the mapping task as the statistical inference problem of finding the most likely coherent mapping – i.e., the maximum a posteriori (MAP) mapping – based on the outcome of the first component used as soft constraint. These two steps are highly intertwined: accordingly, we propose an approach that iteratively refines type acquisition based on the output of the mapping generator, and vice versa. Experimental results on gold-standard data indicate that our approach outperforms a strong baseline, and is able to produce ever-improving mappings consistently across iterations

UvA-DARE (Digital Academic Repository) Uncertain Data Integration Using Functional Dependencies

Abstract. Data integration systems are crucial for applications that need to provide a uniform interface to a set of autonomous and heterogeneous data sources. However, setting up a full data integration system for many application contexts, e.g. web and scientific data management, requires significant human effort which prevents it from being really scalable. In this paper, we propose IFD (Integration based on Functional Dependencies), a pay-as-you-go data integration system that allows integrating a given set of data sources, as well as incrementally integrating additional sources. IFD takes advantage of the background knowledge implied within functional dependencies for matching the source schemas. Our system is built on a probabilistic data model that allows capturing the uncertainty in data integration systems. Our performance evaluation results show significant performance gains of our approach in terms of recall and precision compared to the baseline approaches. They confirm the importance of functional dependencies and also the contribution of using a probabilistic data model in improving the quality of schema matching. The analytical study and experiments show that IFD scales well

Integrating heterogeneous knowledges for understanding biological behaviors: a probabilistic approach

Despite recent molecular technique improvements, biological knowledge remains incomplete. Reasoning on living systems hence implies to integrate heterogeneous and partial informations. Although current investigations successfully focus on qualitative behaviors of macromolecular networks, others approaches show partial quantitative informations like protein concentration variations over times. We consider that both informations, qualitative and quantitative, have to be combined into a modeling method to provide a better understanding of the biological system. We propose here such a method using a probabilistic-like approach. After its exhaustive description, we illustrate its advantages by modeling the carbon starvation response in Escherichia coli. In this purpose, we build an original qualitative model based on available observations. After the formal verification of its qualitative properties, the probabilistic model shows quantitative results corresponding to biological expectations which confirm the interest of our probabilistic approach.Comment: 10 page

Integrating and Ranking Uncertain Scientific Data

Mediator-based data integration systems resolve exploratory queries by joining data elements across sources. In the presence of uncertainties, such multiple expansions can quickly lead to spurious connections and incorrect results. The BioRank project investigates formalisms for modeling uncertainty during scientific data integration and for ranking uncertain query results. Our motivating application is protein function prediction. In this paper we show that: (i) explicit modeling of uncertainties as probabilities increases our ability to predict less-known or previously unknown functions (though it does not improve predicting the well-known). This suggests that probabilistic uncertainty models offer utility for scientific knowledge discovery; (ii) small perturbations in the input probabilities tend to produce only minor changes in the quality of our result rankings. This suggests that our methods are robust against slight variations in the way uncertainties are transformed into probabilities; and (iii) several techniques allow us to evaluate our probabilistic rankings efficiently. This suggests that probabilistic query evaluation is not as hard for real-world problems as theory indicates

PTOMSM: A modified version of Topological Overlap Measure used for predicting Protein-Protein Interaction Network

A variety of methods are developed to integrating diverse biological data to predict novel interaction relationship between proteins. However, traditional integration can only generate protein interaction pairs within existing relationships. Therefore, we propose a modified version of Topological Overlap Measure to identify not only extant direct PPIs links, but also novel protein interactions that can be indirectly inferred from various relationships between proteins. Our method is more powerful than a naïve Bayesian-network-based integration in PPI prediction, and could generate more reliable candidate PPIs. Furthermore, we examined the influence of the sizes of training and test datasets on prediction, and further demonstrated the effectiveness of PTOMSM in predicting PPI. More importantly, this method can be extended naturally to predict other types of biological networks, and may be combined with Bayesian method to further improve the prediction