Phil GoochSchool of Arts and HumanitiesDepartment of Digital Humanities

Tools for discourse analysis and visualisation of clinical narrativesExtracting event chains from psychotherapy narratives

Overview

• Current state of play of natural language processing (NLP) in the clinical domain

• Narrative medicine: reflective patient and clinician stories vs traditional clinical

notes

• Cognitive analytic therapy and the use of narrative

• Narrative event chains

• Discourse analysis and visualisation of narrative

• Development and application of a framework for extraction and visualisation of

event chains from clinical narratives

• Results and discussion

Unstructured text to structured data

http://www.marywood.edu/web/content-editors/tutorials/structures/

Unstructured text to structured data

http://www.45cat.com/record/am792

Unstructured text to structured data

Clinical natural language processing

• Current state of the art: hybrid approaches that combine rules, machine learning,

and external knowledge resources (e.g. UMLS, WordNet) and ontologies to identify

and classify:

• Current vs historical problems

• Current vs historical medications and procedures

• Family history

• Experiencer (patient vs other), negation, possibility

• Coreference and anaphora resolution

• Most recently, temporal concept and relation discovery (Sun et al, JAMIA 2013)

• Focus however has been on corpora of traditional clinical narratives: discharge

summaries, progress notes, lab reports

• Medical model of patient as a set of problems to be solved; NLP for decision support

to identify these problems and the best treatment for them (e.g. Wagholikar et al,

JAMIA 2012)

Narrative medicine

• Patient-described medical history is more than a set of problems

• Reframing: events and situations that have meaning for the patient

• Rich material that helps the clinician better understand the patient experience, build

empathy and trust (Charon 2001)

• Reflective practice and professional development

• Narrative as a temporal flow of unfolding events from the viewpoint of different

protagonists with different roles (Greenhalgh & Hurwitz, BMJ 1999)

Visualisation of a schizophrenia narrative

Cometstarmoon (2005) http://www.flickr.com/photos/45499571@N00/3402234312

Cognitive analytic therapy (CAT) (Ryle 2002)• A model of psychotherapy that makes use of narrative as a ‘key tool of understanding

and therapeutic change’ (Jefferis 2001)• Life as a narrative form

• Goal is to reformulate the patient’s story in terms of the event sequences and reciprocal roles that lead to and maintain maladaptive personal relations

• Reformulation letter aims to retell the patient story in a way that makes it accessible to therapeutic change

http://www.catsandwomenwilldo.com/archives/tag/cats

CAT procedural sequences and reciprocal roles

Potter 2002, http://www.acat.me.uk/reformulation.php?issue_id=20&article_id=197

CAT reciprocal role procedures

Ahmadi 2011, http://www.acat.me.uk/reformulation.php?issue_id=1&article_id=25

Research goals

• How to apply NLP to narrative medicine, in particular CAT narratives?• Can existing tools for working with ‘traditional’ clinical narratives be usefully applied

to these richer, patient and clinician narratives?• Can we identify the flow of events in a narrative, and their associated protagonists

and roles?• Structured data for summarisation and visualisation

• Narrative event chains: partially ordered (just ‘before’ and ‘after’) events related by a common protagonist (Chambers & Jurafsky 2008)

• Machine learning of narrative schema from Gigaword newswire corpus (C & J 2010):

Events Roles

A write B A = author

A edit B B = book

A publish B

C distribute B C = company

C sell B

Narrative event chains

• Three steps

• Identifying events (narrative event induction)

• Temporal ordering of events

• Event pruning into discrete chains for each protagonist (coreference resolution)

• Problem

• Require large corpora of clinical narratives for application of Chambers &

Jurafsky’s unsupervised learning approach

• C & J’s code not publicly available?

• Anyway, we are interested in in-depth processing and visualisation of individual

narratives, rather than learning general schema from a large corpus

• Possible solution

• Extend existing modular framework for processing clinical discharge summaries

Pipeline structure

• GATE framework (visual editor, modular, plug-and-play architecture, no

programming skills required for end users)

• Standard NLP modules (Tokenization, Sentence splitting, POS tagging, Noun-phrase

chunking) plus

• Temporal relation identification (for event ordering)

• Predicate phrase chunking (verb events)

• Clinical concept identification (disease, symptom, procedure, medication)

• Clinical abbreviation expansion

• Domain knowledge integration (UMLS, WordNet)

• Protagonist-based coreference resolution (Gooch & Roudsari 2012)

Example: ‘Sam’ narrative (Ryle & Kerr 2002)

Shows coreferring Person entities (e.g. ‘Sam’, ‘who’ and ‘his’), temporal concepts (TIMEX3, Age), clinical concepts, verb group phrases (VG) and unclassified entities (Thing)

Narrative event chains: timeline visualisation

Wellcome Timeline[1] visualisation generated from annotated output of NLP pipeline

[1] https://github.com/wellcomelibrary/timeline

… vs traditional visualisation

Application to CAT: diagrammatic reformulation

• As noted on Slide 10, part of CAT process involves therapist writing a letter to the

patient that reformulates the patient’s story according to the CAT model

• The letter is then expressed in visual form, in collaboration with the patient

• Diagrammatic reformulation is often difficult for CAT trainees (Jenaway 2011)

• Can NLP help?

• Exploratory processing of the ‘Bobby’ and ‘Beatrice’ reformulation letters from Ryle

(2002)

‘Bobby’ reformulation

‘Bobby’ reformulation: XML event chains

<actors> <actor> <name>Bobby</name> <events> <event>childhood either feeling especially loved and treasured or being a nuisance and ignored</event> <event>were cared for if ill otherwise ignored by your older brothers and sisters</event> <event>tried to please them … always felt scared</event> <event>neglect … ignore your needs … or seek comfort through drink or smoking dope</event> <event>are usually neglectful of your body … .have not seen a doctor … asthma … other ailments</event> <event>tend to cling anxiously and alienate others … Elizabeth your partner leaving you</event> <event>to drink smoke dope … ignore problems which then build up</event> <event>receive care if 'special’ … strive to create special claims … feel you must suffer to deserve it … become agitated drink smoke dope</event> <event>the limited options of your childhood … they seem to have given you some intimacy relief</event> <event>this difficult time you are no longer in a relationship with a woman who will rescue you</event> <event>have said you have been impressed with my help … the honeymoon phase … one your relationships</event> <event>neediness</event> </events> </actor> <actor> <name>Steve Potter</name> <events> <event>suspect it will be hard to imagine short our relationship is 16 sessions … how you will cope with tolerating the disappointment</event> <event>cannot meet your current pattern of neediness</event> </events> </actor> <actor> <name>your [Bobby] older brothers and sisters</name> <events> <event>always felt scared</event> </events> </actor> </actors>

‘Bobby’: simplified diagrammatic reformulation

loved and treasured or being a nuisance and ignored

neglectful of your body

seek comfort through drink or smoking dope

asthma and other ailments

cling anxiously and alienate others

strive to create special claims

need to be rescued

neediness

Linear narrative chains vs reciprocal role procedures identified in Ryle & Kerr (2002):

Source: Fig. 2.1 in Ryle & Kerr (2002)

‘Beatrice’ reformulation: XML event chains

<actor> <name>Beatrice</name> <events> <event>father's desertion</event> <event>remember mother’s unaffectionate figure ... you felt she was concerned with appearances not your feelings</event> <event>set off ended up making a success of work making two or three good woman friends</event> <event>felt securely loved</event> <event>learned to expect little from others ... it was safer to manage on your own</event> <event>trying to please others ... the hope getting acceptance only to be used by them which makes you hate yourself</event> <event>have experienced abandoned uncared feelings which I feel you had learned to put aside in your early life</event> <event>the belief that you be emotionally involved and doomed to be abandoned</event> <event>deserved the difficulties of your childhood ... the brief rebellion at school may be the source of your irrational guilt</event> <event>were not to be happy so you sabotage things that do go well</event> <event>need to please me to be accepted- you may feel angry with yourself</event> <event>will certainly be abandoned at the end of our 12 further weeks</event> <event>this may make you reluctant to be involved it will also protect you feeling overwhelmed by dependency</event> </events> </actor> <actor> <name>Kate Freshwater</name> <events> <event>feel that you learned to expect little from others it was safer to manage on your own</event> <event>believe that working next three months will give you support for you to revise the damaging ways you have relied on up to now</event> </events> </actor> <actor> <name>your [Beatrice] mother</name> <events><event>was concerned with appearances ... not your feelings</event></events> </actor> <actor> <name>Richard</name> <events><event>was the first person whom you experienced the depth of your need for affection</event> <event>leaving was a terrible blow ... you have experienced abandoned uncared feelings … had learned to put aside in your early life</event> </events> </actor>

‘Beatrice’: simplified diagrammatic reformulation

Father’s desertion, mother unaffectionate

making a success of work

felt securely loved

learned to expect little from others

trying to please others only to be used by them

experienced abandoned feelings

doomed to be abandoned

rebellion at school

source of irrational guilt

sabotage things that do go well

will certainly be abandoned at the end of 12 further weeks [of therapy]

reluctant to be involved

protect you feeling overwhelmed by dependency

‘Beatrice’: reformulation from Ryle & Kerr (2002)

Source: Fig 6.2 in Ryle & Kerr (2002)

Conclusion

• Protagonists and their associated events can be explored, extracted and visualised

using an NLP framework originally developed for processing discharge summaries

• Configurable, component based architecture utilising generalised linguistic patterns

makes this possible

• But the linear diagrams generated lack sophistication

• Grouping events according to protagonist loses the interaction between events and

multiple actors

• ‘leaving was a terrible blow’ event associated with Richard’s event chain, but this is

more relevant to Beatrice

• Much more work to be done. E.g. combine machine learning with the linguistic

patterns used in this pipeline.

• Pipeline components available at https://github.com/philgooch

THANK YOUPhil GoochResearch DeveloperDepartment of Digital HumanitiesKing’s College London

philip.gooch@kcl.ac.uk