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

Natural language processing

Beginning with the basic issues of NLP, this chapter aims to chart the major research activities in this area since the last ARIST Chapter in 1996 (Haas, 1996), including: (i) natural language text processing systems - text summarization, information extraction, information retrieval, etc., including domain-specific applications; (ii) natural language interfaces; (iii) NLP in the context of www and digital libraries ; and (iv) evaluation of NLP systems

Analogy Mining for Specific Design Needs

Finding analogical inspirations in distant domains is a powerful way of solving problems. However, as the number of inspirations that could be matched and the dimensions on which that matching could occur grow, it becomes challenging for designers to find inspirations relevant to their needs. Furthermore, designers are often interested in exploring specific aspects of a product-- for example, one designer might be interested in improving the brewing capability of an outdoor coffee maker, while another might wish to optimize for portability. In this paper we introduce a novel system for targeting analogical search for specific needs. Specifically, we contribute a novel analogical search engine for expressing and abstracting specific design needs that returns more distant yet relevant inspirations than alternate approaches

Natural language interfaces to relational databases

Máster Universitario en Lógica, Computación e Inteligencia Artificia

Adaptive content mapping for internet navigation

The Internet as the biggest human library ever assembled keeps on growing. Although all kinds of information carriers (e.g. audio/video/hybrid file formats) are available, text based documents dominate. It is estimated that about 80% of all information worldwide stored electronically exists in (or can be converted into) text form. More and more, all kinds of documents are generated by means of a text processing system and are therefore available electronically. Nowadays, many printed journals are also published online and may even discontinue to appear in print form tomorrow. This development has many convincing advantages: the documents are both available faster (cf. prepress services) and cheaper, they can be searched more easily, the physical storage only needs a fraction of the space previously necessary and the medium will not age. For most people, fast and easy access is the most interesting feature of the new age; computer-aided search for specific documents or Web pages becomes the basic tool for information-oriented work. But this tool has problems. The current keyword based search machines available on the Internet are not really appropriate for such a task; either there are (way) too many documents matching the specified keywords are presented or none at all. The problem lies in the fact that it is often very difficult to choose appropriate terms describing the desired topic in the first place. This contribution discusses the current state-of-the-art techniques in content-based searching (along with common visualization/browsing approaches) and proposes a particular adaptive solution for intuitive Internet document navigation, which not only enables the user to provide full texts instead of manually selected keywords (if available), but also allows him/her to explore the whole database

Next generation software environments : principles, problems, and research directions

The past decade has seen a burgeoning of research and development in software environments. Conferences have been devoted to the topic of practical environments, journal papers produced, and commercial systems sold. Given all the activity, one might expect a great deal of consensus on issues, approaches, and techniques. This is not the case, however. Indeed, the term "environment" is still used in a variety of conflicting ways. Nevertheless substantial progress has been made and we are at least nearing consensus on many critical issues.The purpose of this paper is to characterize environments, describe several important principles that have emerged in the last decade or so, note current open problems, and describe some approaches to these problems, with particular emphasis on the activities of one large-scale research program, the Arcadia project. Consideration is also given to two related topics: empirical evaluation and technology transition. That is, how can environments and their constituents be evaluated, and how can new developments be moved effectively into the production sector

An infrastructure for building semantic web portals

In this paper, we present our KMi semantic web portal infrastructure, which supports two important tasks of semantic web portals, namely metadata extraction and data querying. Central to our infrastructure are three components: i) an automated metadata extraction tool, ASDI, which supports the extraction of high quality metadata from heterogeneous sources, ii) an ontology-driven question answering tool, AquaLog, which makes use of the domain specific ontology and the semantic metadata extracted by ASDI to answers questions in natural language format, and iii) a semantic search engine, which enhances traditional text-based searching by making use of the underlying ontologies and the extracted metadata. A semantic web portal application has been built, which illustrates the usage of this infrastructure