Information extraction from medical records1
Information extraction from medical
records
Tomáš Houfek
Information extraction from medical records2
Overview
̶ General approaches to information extraction
̶ IE of medical records
̶ What tools are used for IE in medical records
̶ IE of Czech medical records
̶ Problems of information extraction in medical records
̶ How to approach IE of Czech medical records
̶ Examples
Information extraction of medical records3
General approaches
̶ Pre-processing
̶ Part of Speech tagging
̶ Name entity recognition
̶ Syntactic analysis
̶ Semantic analysis
̶ ML
̶ Regex
Information extraction from medical records4
IE in medical records
̶ Results of 67 studies on IE of medical records
̶ Majority in US, on US medical records (61%)
̶ Majority used for detecting cases in medical records (87%)
̶ Only minority used on hospital EMR (13%)
Information extraction from medical records5
Tools used for medical records
̶ Majority used rule-bases NLP algorithms (67%)
̶ Keyword search (24%)
̶ Only 9% of ML, Bayesian or hybrid approaches
̶ A lot of reoccurring IE systems MedLEE (9 studies), cTAKES (5
studies), HITEx (4 studies)
Information extraction from medical records6
Algorithm accuracy
Information extraction from medical records7
IE of Czech medical records
̶ No cTAKES or any other already existing tools
̶ For every task a specific solution
̶ Little to none research
Information extraction from medical records8
Problem of Czech medical records
̶ Text of Czech medical records is not typical Czech text
̶ Lingvistic analysis cannot be used successfully
̶ Partial solution: Třífázová metoda předběžného zpracování (3PP)
̶ Tokenization
̶ Normalization
̶ Semantic annotation
Extrakce informací z lékařských textů, Ing. Karel Zvára PhD.
Information extraction from medical records9
Example of Czech medical record
Information extraction from medical records10
IE of Czech medical records
̶ Available data
̶ 122 patients
̶ 17 216 records
̶ Types of records – (16)
̶ Subtypes of records - (192)
Information extraction from medical records11
What data I want to extract
̶ Diagnosis date
̶ Diagnosis (MNK-10)
̶ Diagnosis determined by what?
̶ Morphology
̶ Laterality
̶ Treatment in time
̶ Operations
̶ Chemo
̶ TNM classification
̶ pTNM classification
̶ Lokalization of metastasis
̶ Clinical stage
̶ Progression of disease
̶ State of tumour in time
̶ Stadium
̶ Size
̶ Recurrence
Information extraction from medical records12
Example of tagged records
Information extraction from medical records13
Example of record tagged
Information extraction from medical records14
Sources
̶ Extrakce informací z lékařských textů, Ing. Karel Zvára PhD.
̶ http://hdl.handle.net/20.500.11956/94214
̶ Extracting information from the text of electronic medical records to improve case detection: a
systematic review
̶ https://pubmed.ncbi.nlm.nih.gov/26911811/
̶ Data Mining from Free-Text Health Records: State of the Art, New Polish Corpus
̶ https://nlp.fi.muni.cz/raslan/2020/paper5.pdf