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

Text Mining of Patient Demographics and Diagnoses from Psychiatric Assessments

Automatic extraction of patient demographics and psychiatric diagnoses from clinical notes allows for the collection of patient data on a large scale. This data could be used for a variety of research purposes including outcomes studies or developing clinical trials. However, current research has not yet discussed the automatic extraction of demographics and psychiatric diagnoses in detail. The aim of this study is to apply text mining to extract patient demographics - age, gender, marital status, education level, and admission diagnoses from the psychiatric assessments at a mental health hospital and also assign codes to each category. Gender is coded as either Male or Female, marital status is coded as either Single, Married, Divorced, or Widowed, and education level can be coded starting with Some High School through Graduate Degree (PhD/JD/MD etc. Level). Classifications for diagnoses are based on the DSM-IV. For each category, a rule-based approach was developed utilizing keyword-based regular expressions as well as constituency trees and typed dependencies. We employ a two-step approach that first maximizes recall through the development of keyword-based patterns and if necessary, maximizes precision by using NLP-based rules to handle the problem of ambiguity. To develop and evaluate our method, we annotated a corpus of 200 assessments, using a portion of the corpus for developing the method and the rest as a test set. F-score was satisfactory for each category (Age: 0.997; Gender: 0.989; Primary Diagnosis: 0.983; Marital Status: 0.875; Education Level: 0.851) as was coding accuracy (Age: 1.0; Gender: 0.989; Primary Diagnosis: 0.922; Marital Status: 0.889; Education Level: 0.778). These results indicate that a rule-based approach could be considered for extracting these types of information in the psychiatric field. At the same time, the results showed a drop in performance from the development set to the test set, which is partly due to the need for more generality in the rules developed

Neural Techniques for German Dependency Parsing

Syntactic parsing is the task of analyzing the structure of a sentence based on some predefined formal assumption. It is a key component in many natural language processing (NLP) pipelines and is of great benefit for natural language understanding (NLU) tasks such as information retrieval or sentiment analysis. Despite achieving very high results with neural network techniques, most syntactic parsing research pays attention to only a few prominent languages (such as English or Chinese) or language-agnostic settings. Thus, we still lack studies that focus on just one language and design specific parsing strategies for that language with regards to its linguistic properties. In this thesis, we take German as the language of interest and develop more accurate methods for German dependency parsing by combining state-of-the-art neural network methods with techniques that address the specific challenges posed by the language-specific properties of German. Compared to English, German has richer morphology, semi-free word order, and case syncretism. It is the combination of those characteristics that makes parsing German an interesting and challenging task. Because syntactic parsing is a task that requires many levels of language understanding, we propose to study and improve the knowledge of parsing models at each level in order to improve syntactic parsing for German. These levels are: (sub)word level, syntactic level, semantic level, and sentence level. At the (sub)word level, we look into a surge in out-of-vocabulary words in German data caused by compounding. We propose a new type of embeddings for compounds that is a compositional model of the embeddings of individual components. Our experiments show that character-based embeddings are superior to word and compound embeddings in dependency parsing, and compound embeddings only outperform word embeddings when the part-of-speech (POS) information is unavailable. Thus, we conclude that it is the morpho-syntactic information of unknown compounds, not the semantic one, that is crucial for parsing German. At the syntax level, we investigate challenges for local grammatical function labeler that are caused by case syncretism. In detail, we augment the grammatical function labeling component in a neural dependency parser that labels each head-dependent pair independently with a new labeler that includes a decision history, using Long Short-Term Memory networks (LSTMs). All our proposed models significantly outperformed the baseline on three languages: English, German and Czech. However, the impact of the new models is not the same for all languages: the improvement for English is smaller than for the non-configurational languages (German and Czech). Our analysis suggests that the success of the history-based models is not due to better handling of long dependencies but that they are better in dealing with the uncertainty in head direction. We study the interaction of syntactic parsing with the semantic level via the problem of PP attachment disambiguation. Our motivation is to provide a realistic evaluation of the task where gold information is not available and compare the results of disambiguation systems against the output of a strong neural parser. To our best knowledge, this is the first time that PP attachment disambiguation is evaluated and compared against neural dependency parsing on predicted information. In addition, we present a novel approach for PP attachment disambiguation that uses biaffine attention and utilizes pre-trained contextualized word embeddings as semantic knowledge. Our end-to-end system outperformed the previous pipeline approach on German by a large margin simply by avoiding error propagation caused by predicted information. In the end, we show that parsing systems (with the same semantic knowledge) are in general superior to systems specialized for PP attachment disambiguation. Lastly, we improve dependency parsing at the sentence level using reranking techniques. So far, previous work on neural reranking has been evaluated on English and Chinese only, both languages with a configurational word order and poor morphology. We re-assess the potential of successful neural reranking models from the literature on English and on two morphologically rich(er) languages, German and Czech. In addition, we introduce a new variation of a discriminative reranker based on graph convolutional networks (GCNs). Our proposed reranker not only outperforms previous models on English but is the only model that is able to improve results over the baselines on German and Czech. Our analysis points out that the failure is due to the lower quality of the k-best lists, where the gold tree ratio and the diversity of the list play an important role

On the Use of Parsing for Named Entity Recognition

[Abstract] Parsing is a core natural language processing technique that can be used to obtain the structure underlying sentences in human languages. Named entity recognition (NER) is the task of identifying the entities that appear in a text. NER is a challenging natural language processing task that is essential to extract knowledge from texts in multiple domains, ranging from financial to medical. It is intuitive that the structure of a text can be helpful to determine whether or not a certain portion of it is an entity and if so, to establish its concrete limits. However, parsing has been a relatively little-used technique in NER systems, since most of them have chosen to consider shallow approaches to deal with text. In this work, we study the characteristics of NER, a task that is far from being solved despite its long history; we analyze the latest advances in parsing that make its use advisable in NER settings; we review the different approaches to NER that make use of syntactic information; and we propose a new way of using parsing in NER based on casting parsing itself as a sequence labeling task.Xunta de Galicia; ED431C 2020/11Xunta de Galicia; ED431G 2019/01This work has been funded by MINECO, AEI and FEDER of UE through the ANSWER-ASAP project (TIN2017-85160-C2-1-R); and by Xunta de Galicia through a Competitive Reference Group grant (ED431C 2020/11). CITIC, as Research Center of the Galician University System, is funded by the Consellería de Educación, Universidade e Formación Profesional of the Xunta de Galicia through the European Regional Development Fund (ERDF/FEDER) with 80%, the Galicia ERDF 2014-20 Operational Programme, and the remaining 20% from the Secretaría Xeral de Universidades (Ref. ED431G 2019/01). Carlos Gómez-Rodríguez has also received funding from the European Research Council (ERC), under the European Union’s Horizon 2020 research and innovation programme (FASTPARSE, Grant No. 714150)