Advanced Topics
Here are a few reasons you may wish to modify the Java code or the Drools rules
- alter which sections of your documents are annotated (processed)
See the SectionRemover Java class
Read about Section Headings - add to the list of body locations that should not be allowed to be the site of a Primary Tumor for the melanoma domain
See ExcludeFromPT within mela_metastasis.drl - add to the list of body locations that you consider close enough to be counted as a match by the evaluation tool
You can use DeepPhe-Viz to see the results of the system.
If you have a set of expected results for some set of documents, and you you create files in a specific format required by the included evaluation tool (PhenotypeEval), you can evaluate the results programmatically. Read about the PhenotypeEval tool in Evaluating system results.
If you make changes to the system configuration, if you customize the system code, or if you change the formatting of the files you input to the system, you could use a text file comparison (diff) tool to see how your changes affect the system output. You could use also the PhenotypeEval tool to compare the output of two different runs of the system. Again, see Evaluating system results.
The pipeline was developed using separate training and development sets from 8 corpora. The corpora included notes from 4 sites and 3 cancer types. There was also variation in note types and counts per patient in the corpora. Results of system evaluations are pending publication.
- Visit the DeepPhe-Viz project.
- Visit the Pages section of the sidebar on this page to see all the base DeepPhe system documentation.