Report on the EHCR (Deliverable 26.2)

This deliverable is the second for Workpackage 26. The first, submitted after Month 12, summarised the areas of research that the partners had identified as being relevant to the semantic indexing of the EHR. This second one reports progress on the key threads of work identified by the partners during the project to contribute towards semantically interoperable and processable EHRs. This report provides a set of short summaries on key topics that have emerged as important, and to which the partners are able to make strong contributions. Some of these are also being extended via two new EU Framework 6 proposals that include WP26 partners: this is also a measure of the success of this Network of Excellence

Hypotheses Generation as Supervised Link Discovery with Automated Class Labeling on Large-scale Biomedical Concept Networks

Computational approaches to generate hypotheses from biomedical literature have been studied intensively in recent years. Nevertheless, it still remains a challenge to automatically discover novel, cross-silo biomedical hypotheses from large-scale literature repositories. In order to address this challenge, we first model a biomedical literature repository as a comprehensive network of biomedical concepts and formulate hypotheses generation as a process of link discovery on the concept network. We extract the relevant information from the biomedical literature corpus and generate a concept network and concept-author map on a cluster using Map-Reduce framework. We extract a set of heterogeneous features such as random walk based features, neighborhood features and common author features. The potential number of links to consider for the possibility of link discovery is large in our concept network and to address the scalability problem, the features from a concept network are extracted using a cluster with Map-Reduce framework. We further model link discovery as a classification problem carried out on a training data set automatically extracted from two network snapshots taken in two consecutive time duration. A set of heterogeneous features, which cover both topological and semantic features derived from the concept network, have been studied with respect to their impacts on the accuracy of the proposed supervised link discovery process. A case study of hypotheses generation based on the proposed method has been presented in the paper

Ontology-assisted database integration to support natural language processing and biomedical data-mining

Successful biomedical data mining and information extraction require a complete picture of biological phenomena such as genes, biological processes, and diseases; as these exist on different levels of granularity. To realize this goal, several freely available heterogeneous databases as well as proprietary structured datasets have to be integrated into a single global customizable scheme. We will present a tool to integrate different biological data sources by mapping them to a proprietary biomedical ontology that has been developed for the purposes of making computers understand medical natural language

An Ontology-Based Method for Semantic Integration of Business Components

Building new business information systems from reusable components is today an approach widely adopted and used. Using this approach in analysis and design phases presents a great interest and requires the use of a particular class of components called Business Components (BC). Business Components are today developed by several manufacturers and are available in many repositories. However, reusing and integrating them in a new Information System requires detection and resolution of semantic conflicts. Moreover, most of integration and semantic conflict resolution systems rely on ontology alignment methods based on domain ontology. This work is positioned at the intersection of two research areas: Integration of reusable Business Components and alignment of ontologies for semantic conflict resolution. Our contribution concerns both the proposal of a BC integration solution based on ontologies alignment and a method for enriching the domain ontology used as a support for alignment.Comment: IEEE New Technologies of Distributed Systems (NOTERE), 2011 11th Annual International Conference; ISSN: 2162-1896 Print ISBN: 978-1-4577-0729-2 INSPEC Accession Number: 12122775 201

Medical Knowledge-enriched Textual Entailment Framework

One of the cardinal tasks in achieving robust medical question answering systems is textual entailment. The existing approaches make use of an ensemble of pre-trained language models or data augmentation, often to clock higher numbers on the validation metrics. However, two major shortcomings impede higher success in identifying entailment: (1) understanding the focus/intent of the question and (2) ability to utilize the real-world background knowledge to capture the context beyond the sentence. In this paper, we present a novel Medical Knowledge-Enriched Textual Entailment framework that allows the model to acquire a semantic and global representation of the input medical text with the help of a relevant domain-specific knowledge graph. We evaluate our framework on the benchmark MEDIQA-RQE dataset and manifest that the use of knowledge enriched dual-encoding mechanism help in achieving an absolute improvement of 8.27% over SOTA language models. We have made the source code available here