1. Shock Group NER Progress
Laura Christiansen

2. Overview System needs to identify NE in shock abstracts
Metamap is an untrainable option and sometimes wrong
Find an alternative to Metamap for NER
Modified version of ABNER
Use Metamap initially

3. Data Prep
Metamap-processed abstracts with IOB notation used to train model
Needs minor modification
Distribution of 5 named entities calculated across entire corpus
Modified k-means algorithm used to create n folds for stratified cross-validation
Each fold roughly the same size
Each fold has roughly the same distribution as the corpus

4. Stratified Cross Validation
Using folds selected in data prep:
Train ABNER model based on Metamap IOB output
Use model to identify NE in test set(s)
Compute confusion matrix results
Output selected test cases for manual review

5. Results Program currently running on smaller dataset
Testing program and reading through output
Minor problems with the larger dataset need to be addressed
Will run full dataset of 281 abstracts later in the week