Concept not found if token order is slightly changed contrary to mentioned note in paper

[KimBenjaminTang]

Hello,

thank you for providing MedCat and also a Demo to try it out!

I found the paper very interesting and read that "MedCAT can ignore token order, but only for up-to two tokens".
This feature seems useful, but I somehow did not manage to test it in the available Demo.

As an example I used these two sentences:

We report on a patient who was under our inpatient care.

Diagnoses: Triple vessel coronary artery disease - slightly reduced syst. LVF

And it recognizes "Triple vessel coronary artery disease".

But when I try to change the token order, the concept is not matched anymore.

Swapped order with vessel and coronary

Swapped order with coronary and artery

I also tried this with the downloaded .zip file for the MedCat model specifically trained on SNOMED-CT and MIMIC III and the concept broke whenever the token order was changed by switching two tokens.

In the documentation for CAT.get_entities() I did not find an option to activate this behavior. Is it possible to turn it on or is it not available?

Thanks for your help!

[baixiac]

Hi, @KimBenjaminTang, I believe the "only for up-to two tokens" rule applies exclusively when the longest match consists of two tokens while your case has five. For instance, "Description: Intracerebral hemorrhage (very acute ..." vs "Description: Hemorrhage intracerebral (very acute...".

[KimBenjaminTang]

Hi @baixiac, thanks for your clarification! I understand now that I misunderstood how the phrase "only for up-to two tokens" was meant in the paper. I thought that it meant, that up to two tokens can be in a wrong order, not that the concept overall can only consist of two tokens and that then, in that case, the two tokens can have a mixed order.

This topic was discussed a bit more in the issue I opened on CogStack previously and is concluded from my side, since a workaround was suggested there and it poses a bit more of a complex conceptual issue, so I will close it on here.

[mart-r]

I will close it on here.

Closing on their behalf.