Implementing a Portable Clinical NLP System with a Common Data Model - a Lisp Perspective

This paper presents a Lisp architecture for a portable NLP system, termed LAPNLP, for processing clinical notes. LAPNLP integrates multiple standard, customized and in-house developed NLP tools. Our system facilitates portability across different institutions and data systems by incorporating an enriched Common Data Model (CDM) to standardize necessary data elements. It utilizes UMLS to perform domain adaptation when integrating generic domain NLP tools. It also features stand-off annotations that are specified by positional reference to the original document. We built an interval tree based search engine to efficiently query and retrieve the stand-off annotations by specifying positional requirements. We also developed a utility to convert an inline annotation format to stand-off annotations to enable the reuse of clinical text datasets with inline annotations. We experimented with our system on several NLP facilitated tasks including computational phenotyping for lymphoma patients and semantic relation extraction for clinical notes. These experiments showcased the broader applicability and utility of LAPNLP.Comment: 6 pages, accepted by IEEE BIBM 2018 as regular pape

Finding Academic Experts on a MultiSensor Approach using Shannon's Entropy

Expert finding is an information retrieval task concerned with the search for the most knowledgeable people, in some topic, with basis on documents describing peoples activities. The task involves taking a user query as input and returning a list of people sorted by their level of expertise regarding the user query. This paper introduces a novel approach for combining multiple estimators of expertise based on a multisensor data fusion framework together with the Dempster-Shafer theory of evidence and Shannon's entropy. More specifically, we defined three sensors which detect heterogeneous information derived from the textual contents, from the graph structure of the citation patterns for the community of experts, and from profile information about the academic experts. Given the evidences collected, each sensor may define different candidates as experts and consequently do not agree in a final ranking decision. To deal with these conflicts, we applied the Dempster-Shafer theory of evidence combined with Shannon's Entropy formula to fuse this information and come up with a more accurate and reliable final ranking list. Experiments made over two datasets of academic publications from the Computer Science domain attest for the adequacy of the proposed approach over the traditional state of the art approaches. We also made experiments against representative supervised state of the art algorithms. Results revealed that the proposed method achieved a similar performance when compared to these supervised techniques, confirming the capabilities of the proposed framework

Extraction of Keyphrases from Text: Evaluation of Four Algorithms

This report presents an empirical evaluation of four algorithms for automatically extracting keywords and keyphrases from documents. The four algorithms are compared using five different collections of documents. For each document, we have a target set of keyphrases, which were generated by hand. The target keyphrases were generated for human readers; they were not tailored for any of the four keyphrase extraction algorithms. Each of the algorithms was evaluated by the degree to which the algorithm’s keyphrases matched the manually generated keyphrases. The four algorithms were (1) the AutoSummarize feature in Microsoft’s Word 97, (2) an algorithm based on Eric Brill’s part-of-speech tagger, (3) the Summarize feature in Verity’s Search 97, and (4) NRC’s Extractor algorithm. For all five document collections, NRC’s Extractor yields the best match with the manually generated keyphrases

CBR and MBR techniques: review for an application in the emergencies domain

The purpose of this document is to provide an in-depth analysis of current reasoning engine practice and the integration strategies of Case Based Reasoning and Model Based Reasoning that will be used in the design and development of the RIMSAT system. RIMSAT (Remote Intelligent Management Support and Training) is a European Commission funded project designed to: a.. Provide an innovative, 'intelligent', knowledge based solution aimed at improving the quality of critical decisions b.. Enhance the competencies and responsiveness of individuals and organisations involved in highly complex, safety critical incidents - irrespective of their location. In other words, RIMSAT aims to design and implement a decision support system that using Case Base Reasoning as well as Model Base Reasoning technology is applied in the management of emergency situations. This document is part of a deliverable for RIMSAT project, and although it has been done in close contact with the requirements of the project, it provides an overview wide enough for providing a state of the art in integration strategies between CBR and MBR technologies.Postprint (published version