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

Distribution-Based Categorization of Classifier Transfer Learning

Transfer Learning (TL) aims to transfer knowledge acquired in one problem, the source problem, onto another problem, the target problem, dispensing with the bottom-up construction of the target model. Due to its relevance, TL has gained significant interest in the Machine Learning community since it paves the way to devise intelligent learning models that can easily be tailored to many different applications. As it is natural in a fast evolving area, a wide variety of TL methods, settings and nomenclature have been proposed so far. However, a wide range of works have been reporting different names for the same concepts. This concept and terminology mixture contribute however to obscure the TL field, hindering its proper consideration. In this paper we present a review of the literature on the majority of classification TL methods, and also a distribution-based categorization of TL with a common nomenclature suitable to classification problems. Under this perspective three main TL categories are presented, discussed and illustrated with examples