[FEATURE REQUEST] Use medaCy with spaCy pipeline

[baumanab]

This is more of a question/clarification about existing functionality. I would like to use use a medaCy in the way that one would typically use spaCy, in terms of pipeline components. That is, create a doc and use the doc attributes (ents, annotations, etc). Is there a way to load something like a clinical note and use it like you would in a spaCy pipeline? Is there a way to extend the spaCy pipeline with medaCy models so that annotations can be visualized with displaCy, or some approximation of these things. I read the docs and looked at the code base, but it wasn't clear to me whether this was currently possible or not. Any help and/or clarification would be appreciated. I'm currently trying out medaCy to extract drug doseage information from clinical notes. The ner is doing a great job of extraction, being able to use this model in the way one would use models in spaCy would be very helpful for our proof of concept stage.

[AndriyMulyar]

Hi,

Unfortunately there is no way currently of integrating a medacy model in spaCy as medaCy does not use it's deep learning framework thinc. We have spaCy as a dependency to facilitate tokenization and keeping track of tags on documents in an efficient manner. We delegate the actual machine learning to custom utilization of a conditional random field.

[baumanab]

that makes sense, thank you for clarifying.

On Mon, May 13, 2019 at 1:23 PM Andriy Mulyar notifications@github.com wrote:

Hi,

Unfortunately there is no way currently of integrating a medacy model in spaCy as medaCy does not use it's deep learning framework thinc. We have spaCy as a dependency to facilitate tokenization and keeping track of tags on documents in an efficient manner. We delegate the actual machine learning to custom utilization of a conditional random field.

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