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

On the Effect of Semantically Enriched Context Models on Software Modularization

Many of the existing approaches for program comprehension rely on the linguistic information found in source code, such as identifier names and comments. Semantic clustering is one such technique for modularization of the system that relies on the informal semantics of the program, encoded in the vocabulary used in the source code. Treating the source code as a collection of tokens loses the semantic information embedded within the identifiers. We try to overcome this problem by introducing context models for source code identifiers to obtain a semantic kernel, which can be used for both deriving the topics that run through the system as well as their clustering. In the first model, we abstract an identifier to its type representation and build on this notion of context to construct contextual vector representation of the source code. The second notion of context is defined based on the flow of data between identifiers to represent a module as a dependency graph where the nodes correspond to identifiers and the edges represent the data dependencies between pairs of identifiers. We have applied our approach to 10 medium-sized open source Java projects, and show that by introducing contexts for identifiers, the quality of the modularization of the software systems is improved. Both of the context models give results that are superior to the plain vector representation of documents. In some cases, the authoritativeness of decompositions is improved by 67%. Furthermore, a more detailed evaluation of our approach on JEdit, an open source editor, demonstrates that inferred topics through performing topic analysis on the contextual representations are more meaningful compared to the plain representation of the documents. The proposed approach in introducing a context model for source code identifiers paves the way for building tools that support developers in program comprehension tasks such as application and domain concept location, software modularization and topic analysis

Mostly-Unsupervised Statistical Segmentation of Japanese Kanji Sequences

Given the lack of word delimiters in written Japanese, word segmentation is generally considered a crucial first step in processing Japanese texts. Typical Japanese segmentation algorithms rely either on a lexicon and syntactic analysis or on pre-segmented data; but these are labor-intensive, and the lexico-syntactic techniques are vulnerable to the unknown word problem. In contrast, we introduce a novel, more robust statistical method utilizing unsegmented training data. Despite its simplicity, the algorithm yields performance on long kanji sequences comparable to and sometimes surpassing that of state-of-the-art morphological analyzers over a variety of error metrics. The algorithm also outperforms another mostly-unsupervised statistical algorithm previously proposed for Chinese. Additionally, we present a two-level annotation scheme for Japanese to incorporate multiple segmentation granularities, and introduce two novel evaluation metrics, both based on the notion of a compatible bracket, that can account for multiple granularities simultaneously.Comment: 22 pages. To appear in Natural Language Engineerin

Spoken content retrieval: A survey of techniques and technologies

Speech media, that is, digital audio and video containing spoken content, has blossomed in recent years. Large collections are accruing on the Internet as well as in private and enterprise settings. This growth has motivated extensive research on techniques and technologies that facilitate reliable indexing and retrieval. Spoken content retrieval (SCR) requires the combination of audio and speech processing technologies with methods from information retrieval (IR). SCR research initially investigated planned speech structured in document-like units, but has subsequently shifted focus to more informal spoken content produced spontaneously, outside of the studio and in conversational settings. This survey provides an overview of the field of SCR encompassing component technologies, the relationship of SCR to text IR and automatic speech recognition and user interaction issues. It is aimed at researchers with backgrounds in speech technology or IR who are seeking deeper insight on how these fields are integrated to support research and development, thus addressing the core challenges of SCR

“Peri Nomou” System: Automated Codification and Interrelation of Legal Elements Based on Text Mining

One of the most promising developments comes with the use of innovative technologies and thus with the availability of novel services. The combination of text mining with legal elements may contribute to the development of many innovative legal information systems. Moreover, in the case of public admin-istrations and governments, the distribution, availability, and access towards legal information are es-sential and urgent. On the other hand, legal data and law texts are a potential open Government data category in order for innovation to be achieved, regarding the development of new, better, and more cost-effective services for citizens. Those data need to be available 24/7 basis and compliant towards a standard. Yet, there exist some severe issues at the moment regarding this access. This, in turn, makes the use of automated crawling and analysis more than difficult. This paper describes the “Peri Nomou” (about law) system: an innovative legal information system for Greek laws utilising text mining tech-niques to indexing legal documents, identifying correlations and dividing legal documents into their articles. The first version of the system has been evaluated by legal experts and the second version is developed based on the previous evaluation and presented in this paper. The results from the evaluation indicate the significance of the “Peri Nomou” system for the legal experts and allow us to promote the Peri Nomou system to other user groups, such as business, public administration

Open Information Extraction: A Review of Baseline Techniques, Approaches, and Applications

With the abundant amount of available online and offline text data, there arises a crucial need to extract the relation between phrases and summarize the main content of each document in a few words. For this purpose, there have been many studies recently in Open Information Extraction (OIE). OIE improves upon relation extraction techniques by analyzing relations across different domains and avoids requiring hand-labeling pre-specified relations in sentences. This paper surveys recent approaches of OIE and its applications on Knowledge Graph (KG), text summarization, and Question Answering (QA). Moreover, the paper describes OIE basis methods in relation extraction. It briefly discusses the main approaches and the pros and cons of each method. Finally, it gives an overview about challenges, open issues, and future work opportunities for OIE, relation extraction, and OIE applications.Comment: 15 pages, 9 figure