Semantic processing of EHR data for clinical research

There is a growing need to semantically process and integrate clinical data from different sources for clinical research. This paper presents an approach to integrate EHRs from heterogeneous resources and generate integrated data in different data formats or semantics to support various clinical research applications. The proposed approach builds semantic data virtualization layers on top of data sources, which generate data in the requested semantics or formats on demand. This approach avoids upfront dumping to and synchronizing of the data with various representations. Data from different EHR systems are first mapped to RDF data with source semantics, and then converted to representations with harmonized domain semantics where domain ontologies and terminologies are used to improve reusability. It is also possible to further convert data to application semantics and store the converted results in clinical research databases, e.g. i2b2, OMOP, to support different clinical research settings. Semantic conversions between different representations are explicitly expressed using N3 rules and executed by an N3 Reasoner (EYE), which can also generate proofs of the conversion processes. The solution presented in this paper has been applied to real-world applications that process large scale EHR data.Comment: Accepted for publication in Journal of Biomedical Informatics, 2015, preprint versio

Deverbal semantics and the Montagovian generative lexicon

We propose a lexical account of action nominals, in particular of deverbal nominalisations, whose meaning is related to the event expressed by their base verb. The literature about nominalisations often assumes that the semantics of the base verb completely defines the structure of action nominals. We argue that the information in the base verb is not sufficient to completely determine the semantics of action nominals. We exhibit some data from different languages, especially from Romance language, which show that nominalisations focus on some aspects of the verb semantics. The selected aspects, however, seem to be idiosyncratic and do not automatically result from the internal structure of the verb nor from its interaction with the morphological suffix. We therefore propose a partially lexicalist approach view of deverbal nouns. It is made precise and computable by using the Montagovian Generative Lexicon, a type theoretical framework introduced by Bassac, Mery and Retor\'e in this journal in 2010. This extension of Montague semantics with a richer type system easily incorporates lexical phenomena like the semantics of action nominals in particular deverbals, including their polysemy and (in)felicitous copredications.Comment: A revised version will appear in the Journal of Logic, Language and Informatio

Computing Possible and Certain Answers over Order-Incomplete Data

This paper studies the complexity of query evaluation for databases whose relations are partially ordered; the problem commonly arises when combining or transforming ordered data from multiple sources. We focus on queries in a useful fragment of SQL, namely positive relational algebra with aggregates, whose bag semantics we extend to the partially ordered setting. Our semantics leads to the study of two main computational problems: the possibility and certainty of query answers. We show that these problems are respectively NP-complete and coNP-complete, but identify tractable cases depending on the query operators or input partial orders. We further introduce a duplicate elimination operator and study its effect on the complexity results.Comment: 55 pages, 56 references. Extended journal version of arXiv:1707.07222. Up to the stylesheet, page/environment numbering, and possible minor publisher-induced changes, this is the exact content of the journal paper that will appear in Theoretical Computer Scienc

WEB SEMANTICS DATA

Data Semantics is a wide area that continuously faces new challenges arising from the invention of new infor- mation formats and novel applications. An area that is partic- ularly challenging with respect to identifying, representing and using data semantics is the Web. This paper attempts to characterize the nature and challenges of Data Semantics on the Web as an interesting research area to be covered by the Journal on Data Semantics

Challenges for the multilingual Web of Data

Garcia J, Montiel-Ponsoda E, Cimiano P, Gómez-Pérez A, Buitelaar P, McCrae J. Challenges for the multilingual Web of Data. Journal of Web Semantics: Science, Services and Agents on the World Wide Web. 2012;11:63-71

A Study of Actor and Action Semantic Retention in Video Supervoxel Segmentation

Existing methods in the semantic computer vision community seem unable to deal with the explosion and richness of modern, open-source and social video content. Although sophisticated methods such as object detection or bag-of-words models have been well studied, they typically operate on low level features and ultimately suffer from either scalability issues or a lack of semantic meaning. On the other hand, video supervoxel segmentation has recently been established and applied to large scale data processing, which potentially serves as an intermediate representation to high level video semantic extraction. The supervoxels are rich decompositions of the video content: they capture object shape and motion well. However, it is not yet known if the supervoxel segmentation retains the semantics of the underlying video content. In this paper, we conduct a systematic study of how well the actor and action semantics are retained in video supervoxel segmentation. Our study has human observers watching supervoxel segmentation videos and trying to discriminate both actor (human or animal) and action (one of eight everyday actions). We gather and analyze a large set of 640 human perceptions over 96 videos in 3 different supervoxel scales. Furthermore, we conduct machine recognition experiments on a feature defined on supervoxel segmentation, called supervoxel shape context, which is inspired by the higher order processes in human perception. Our ultimate findings suggest that a significant amount of semantics have been well retained in the video supervoxel segmentation and can be used for further video analysis.Comment: This article is in review at the International Journal of Semantic Computin