graph nlp

Discovering Related Clinical Concepts Using Large Amounts of Clinical Notes

Abstract

The ability to find highly related clinical concepts is essential for many applications such as for hypothesis generation, query expansion for medical literature search, search results filtering, ICD-10 code filtering and many other applications. While manually constructed medical terminologies such as SNOMED CT can surface certain related concepts, these terminologies are inadequate as they depend on expertise of several subject matter experts making the terminology curation process open to geographic and language bias. In addition, these terminologies also provide no quantifiable evidence on how related the concepts are. In this work, we explore an unsupervised graphical approach to mine related concepts by leveraging the volume within large amounts of clinical notes. Our evaluation shows that we are able to use a data driven approach to discovering highly related concepts for various search terms including medications, symptoms and diseases.

Mining Related Concepts

The Concept-Graph is used to mine related clinical terminology. For example if the query term is advair, related concepts can be singulair, combivent, inhaler, nebs, etc. The Concept-Graph is an undirected graph with each node representing a concept and the link between the nodes indicate a presence of relationship between two concepts. The results of this work was evaluated by experts in the medical field.

A similar graph data structure has been used for text summarization tasks.

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    Example Related Concepts

    Concepts related to chest pain

    concepts related to chest pain

    Concepts related to advair

    concepts related to advair

    Citation

  • Opinosis: A Graph Based Approach to Abstractive Summarization of Highly Redundant Opinions

    Abstract

    We present a novel graph-based summarization framework (Opinosis) that generates concise abstractive summaries of highly redundant opinions. Evaluation results on summarizing user reviews show that Opinosis summaries have better agreement with human summaries compared to the baseline extractive method. The summaries are readable, reasonably well-formed and are informative enough to convey the major opinions.

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    Opinosis External Discussions/Usage

    The Big Idea

    The Opinosis Summarization framework focuses on generating very short abstractive summaries from large amounts of text. These summaries can resemble micropinions or “micro-reviews” that you see on sites like twitter and four squares. The idea of the algorithm is to use a word graph data structure referred to as the Opinosis-Graph to represent the text to be summarized. Then, the resulting graph is repeatedly explored to find meaningful paths which in turn becomes candidate summary phrases. The Opinosis summarizer is considered a “shallow” abstractive summarizer as it uses the original text itself to generate summaries (this makes it shallow) but it can generate phrases that were previously not seen in the original text because of the way paths are explored (and this makes it abstractive rather than purely extractive). The summarization framework was evaluated on an opinion (user review) dataset. The approach itself is actually very general in that, it can be applied to any corpus containing high amounts of redundancies, for example, Twitter comments or user comments on blog/news articles.

    Here is another example of an Opinosis summary for a Car (Acura 2007) generated using the OpinRank Edmunds data set. :

    Additional Thoughts

    While most research projects in data mining and NLP focus on technical complexity, the focus of Opinosis was its practicality, in that it uses very shallow representation of text, relying mostly on redundancy to help generate summaries. This is not too much to ask given that we live in an era of big data, and we have ample user reviews on the Web to work with. Even though the Opinosis paper uses part-of-speech tags in its graph representation, you don’t have to use this at all and the algorithm will still work fine as long as you have sufficient volume of reviews and you make a few tweaks in finding sentence breaks.

    Related summarization works

    Other works using a similar graph data structure

    • Discovering Related Clinical Concepts – This paper focuses on using a concept graph similar to the Opinosis-Graph to mine clinical concepts that are highly related. For example, the drug advair is highly related to concepts like inhaler, puff, diskus, singulair, tiotropium, albuterol, combivent, spiriva. Such concepts are easily discovered using the Concept-Graph in this paper.
    • Multi-sentence compression: Finding shortest paths in word graphs
      Katja’s work was used to summarize news (google news) for both English and Spanish while Opinosis was evaluated on user reviews from various sources (English only). She studies the informativeness and grammaticality of sentences and in a similar way we evaluate these aspects by studying how close the Opinosis summaries are compared to the human composed summaries in terms of information overlap and readability (using a human assessor
    • Peilin Yang and Hui Fang – Contextual Suggestion – Another related work uses the Opinosis Algorithm to extract terms from reviews for the purpose of Contextual Suggestion. This was done as  part of the Contextual Suggestion TREC Task. It turns out that Yang and Fang had the highest rank and MRR scores in this track. Their paper can be found here: An Opinion-aware Approach to Contextual Suggestion. The details of the TREC run can be found here: Overview of the TREC 2013 Contextual Suggestion Track.

      Opinosis Presentation Slides


      Citation