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Sorry for the delayed reply on this. The NER loss calculation is here, it's pretty basic but optimized for whole-entity matching rather than best-effort token overlap.

Loss for the Transformer is just the backpropagated loss from other components in the pipeline, in your case the NER. In your case you should just be able to ignore it. You can see the source here.

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Answer selected by polm
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training Training and updating models feat / ner Feature: Named Entity Recognizer feat / transformer Feature: Transformer
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