Sunday, August 17, 2014

Natural Language Processing (NLP) for Clinical Decision Support: A Practical Approach

A significant portion of the electronic documentation of clinical care is captured in the form of unstructured narrative text like psychotherapy and progress notes. Despite the big push to adopt structured data entry (as required by the Meaningful Use incentive program for example), many clinicians still like to document care using free narrative text. The advantage of using narrative text as opposed to coded entries is that narrative text can tell the story of the patient and the care provided particularly in complex cases. My opinion is that free narrative text should be used to complement coded entries when necessary to capture relevant information.

Furthermore, medical knowledge is expanding very rapidly. For example, PubMed has more than 24 millions citations for biomedical literature from MEDLINE, life science journals, and online books. It is impossible for the human brain to keep up with that amount of knowledge. These unstructured sources of knowledge contain the scientific evidence that is required for effective clinical decision making in what is referred to as Evidence-Based Medicine (EBM).

In this blog, I discuss two practical applications of Natural Language Processing (NLP). The first is the use of NLP tools and techniques to automatically extract clinical concepts and other insight from clinical notes for the purpose of providing treatment recommendations in Clinical Decision Support (CDS) systems. The second is the use of text analytics techniques like clustering and summarization for Clinical Question Answering (CQA).

The emphasis of this post is on a practical approach using freely available and mature open source tools as opposed to an academic or theoretical approach. For a theoretical treatment of the subject, please refer to the book Speech and Language Processing by Daniel Jurafsky and James Martin.

Clinical NLP with Apache cTAKES

Based on the Apache Unstructured Information Management Architecture (UIMA) framework and the Apache OpenNLP natural language processing toolkit, Apache cTAKES provides a modular architecture utilizing both rule-based and machine learning techniques for information extraction from clinical notes. cTAKES can extract named entities (clinical concepts) from clinical notes in plain text or HL7 CDA format and map these entities to various dictionaries including the following Unified Medical Language System (UMLS) semantic types: diseases/disorders, signs/symptoms, anatomical sites, procedures, and medications.

cTAKES includes the following key components which can be assembled to create processing pipelines:

  • Sentence boundary detector based on the OpenNLP Maximum Entropy (ME) sentence detector.
  • Tokenizor
  • Normalizer using the National Library of Medicine's Lexical Variant Generation (LVG) tool
  • Part-of-speech (POS) tagger
  • Shallow parser
  • Named Entity Recognition (NER) annotator using dictionary look-up to UMLS concepts and semantic types. The Drug NER can extract drug entities and their attributes such as dosage, strength, route, etc.
  • Assertion module which determines the subject of the statement (e.g., is the subject of the statement the patient or a parent of the patient) and whether a named entity or event is negated (e.g., does the presence of the word "depression" in the text implies that the patient has depression).
Apache cTAKES 3.2 has added YTEX, a set of extensions developed at Yale University which provide integration with MetaMap, semantic similarity, export to Machine Learning packages like Weka and R, and feature engineering.

The following diagram from the Apache cTAKES Wiki provides an overview of these components and their dependencies (click to enlarge):

Massively Parallel Clinical Text Analytics in the Cloud with GATECloud

The General Architecture for Text Engineering (GATE) is a mature, comprehensive, and open source text analytics platform. GATE is a family of tools which includes:

  • GATE Developer: an integrated development environment (IDE) for language processing components with a comprehensive set of available plugins called CREOLE (Collection of REusable Objects for Language Engineering). 
  • GATE Embedded: an object library for embedding services developed with GATE Developer into third-party applications.
  • GATE Teamware: a collaborative semantic annotation environment based on a workflow engine for creating manually annotated corpora for applying machine learning algorithms. 
  • GATE Mímir: the "Multi-paradigm Information Management Index and Repository" which supports a multi-paradigm approach to index and search over text, ontologies, and semantic metadata.
  • GATE Cloud: a massively parallel clinical text analytics platform (Platform as a Service or PaaS) built on the Amazon AWS Cloud.
What makes GATE particularly attractive is the recent addition of PaaS which can boost the productivity of people involved in large scale text analytics tasks.


Clustering, Classification, Text Summarization, and Clinical Question Answering (CQA)


An unsupervised machine learning approach called Clustering can be used to classify large volumes of medical literature into groups (clusters) based on some similarity measure (such as the Euclidean distance). Clustering can be applied at the document, search result, and word/topic levels. Carrot2 and Apache Mahout are open source projects that provide several methods for document clustering. For example, the Latent Dirichlet Allocation learning algorithm in Apache Mahout automatically clusters words into topics and documents into mixtures of topics. Other clustering algorithms in Apache Mahout include: Canopy, Mean-Shift, Spectral, K-Means and Fuzzy K-Means. Apache Mahout is part of the Hadoop ecosystem and can therefore scale to very large volumes of unstructured text.

Document classification essentially consists in assigning predefined set of labels to documents. This can be achieved through supervised machine learning algorithms. Apache Mahout implements the Naive Bayes classifier.

Text summarization techniques can be used to present succinct and clinically relevant evidence to clinicians at the point of care. MEAD ( is an open source project that implements multiple summarization algorithms. In the biomedical domain, SemRep is a program that extracts semantic predications (subject-relation-object triples) from biomedical free text. Subject and object arguments of each predication are concepts from the UMLS Metathesaurus and the relation is from the UMLS Semantic Network (e.g., TREATS, Co-OCCURS_WITH). The SemRep summarization provides a short summary of these concepts and their semantic relations.

AskHermes (Help clinicians to Extract and aRrticulate Multimedia information for answering clinical quEstionS) is a project that attempts to implement these techniques in the clinical domain. It allows clinicians to enter questions in natural language and uses the following unstructured information sources: MEDLINE abstracts, PubMed Central full-text articles, eMedicine documents, clinical guidelines, and Wikipedia articles.

The processing pipeline in AskHermes includes the following: Question Analysis, Related Questions Extraction, Information Retrieval, Summarization and Answer Presentation. AskHermes performs question classification using MMTx (MetaMap Technology Transfer) to map keywords to UMLS concepts and semantic types. Classification is achieved through supervised machine learning algorithms such as Support Vector Machine (SVM) and conditional random fields (CFRs). Summarization and answer presentation are based on clustering techniques. AskHermes is powered by open source components including: JBoss Seam, Weka, Mallet , Carrot2 , Lucene/Solr, and WordNet (a lexical database for the English language).

1 comment:

TechNeilogy said...

Good article.

The primary obstacle to cTAKES at this point is that it remains somewhat difficult to adopt and implement. Effectively making use of it requires a Java programmer with some UIMA familiarity. The current Eclipse tooling is good, but preliminary.

It would be nice to have a simpler, perhaps graphical tool for building and integrating UIMA modules. Something a Java or Scala programmer could learn in a day or two. A simple Scala internal DSL would also be handy. (Saying this makes me feel lazy because I should probably write the tools rather than complain, lol.)

Also important will be the development of “meta” standards to help developers create UIMA modules specific to use in cTAKES (and other OpenNLP UIMA efforts). These standards could then be exposed as DSLs, JAR libraries, and configuration files to simply development and testing of modules.

I really like cTAKES, OpenNLP, and UIMA, and I wish them a bright future. I've been working in the field of unstructured medical text processing for a long time, and the UIMA-based efforts of the last few years have me excited and hopeful.