Using and creating entity mention linker#

As of Flair 0.14 we ship the entity mention linker - the core framework behind the Hunflair BioNEN approach. You can read more at the Hunflair2 tutorials

Example 1: Printing Entity linking outputs to console#

To illustrate, let’s use the example the hunflair models on a biomedical sentence:

from flair.models import EntityMentionLinker
from flair.nn import Classifier
from flair.tokenization import SciSpacyTokenizer
from flair.data import Sentence

sentence = Sentence(
    "The mutation in the ABCD1 gene causes X-linked adrenoleukodystrophy, "
    "a neurodegenerative disease, which is exacerbated by exposure to high "
    "levels of mercury in dolphin populations.",
    use_tokenizer=SciSpacyTokenizer()
)

ner_tagger = Classifier.load("hunflair2")
ner_tagger.predict(sentence)

nen_tagger = EntityMentionLinker.load("disease-linker")
nen_tagger.predict(sentence)

for tag in sentence.get_labels():
    print(tag)

Note

Here we use the disease-linker-no-ab3p model, as it is the simplest model to run. You might get better results by using disease-linker instead, but that would require you to install pyab3p via pip install pyab3p.

Analogously to disease there are also linker for chemical, species and gene all work with the {entity_type}-linker or {entity_type}-linker-no-ab3p naming-schema

This should print:

Span[4:5]: "ABCD1" → Gene (0.9509)
Span[7:11]: "X-linked adrenoleukodystrophy" → Disease (0.9872)
Span[7:11]: "X-linked adrenoleukodystrophy" → MESH:D000326/name=Adrenoleukodystrophy (195.30780029296875)
Span[13:15]: "neurodegenerative disease" → Disease (0.8988)
Span[13:15]: "neurodegenerative disease" → MESH:D019636/name=Neurodegenerative Diseases (201.1804962158203)
Span[29:30]: "mercury" → Chemical (0.9484)
Span[31:32]: "dolphin" → Species (0.8071)

As we can see, the huflair-ner model resolved entities of several types, however for the disease linker, only those of type disease were relevant:

Example 2: Structured handling of predictions#

After the predictions, the flair sentence has multiple labels added to the sentence object.

  • Each NER prediction adds a span referenced by the label_type from the span tagger.

  • Each NEL prediction adds one or more labels (up to k) to the respective span. Those have the label_type from the entity mention linker.

  • The NEL labels are ordered by their score. Depending on the exact implementation, it is possible that the order is ascending or descending, however the first one is always the best.

Therefore, an example to extract the information to a dictionary that could be used for further processing is the following:

from flair.models import EntityMentionLinker
from flair.nn import Classifier
from flair.tokenization import SciSpacyTokenizer
from flair.data import Sentence

sentence = Sentence(
    "The mutation in the ABCD1 gene causes X-linked adrenoleukodystrophy, "
    "a neurodegenerative disease, which is exacerbated by exposure to high "
    "levels of mercury in dolphin populations.",
    use_tokenizer=SciSpacyTokenizer()
)

ner_tagger = Classifier.load("hunflair")
ner_tagger.predict(sentence)

nen_tagger = EntityMentionLinker.load("disease-linker-no-ab3p")

# top_k = 5 so that a span can have up to 5 labels assigned.
nen_tagger.predict(sentence, top_k=5)

result_mentions = []

for span in sentence.get_spans(ner_tagger.label_type):
    
    # basic information about the span that is tagged.
    span_data = {
        "start": span.start_position + sentence.start_position,
        "end": span.end_position + sentence.start_position,
        "text": span.text,
    }
    
    # add the ner label. We always have only one, so we can use `span.get_label(...)`
    span_data["ner_label"] = span.get_label(ner_tagger.label_type).value
    
    mentions_found = []
    
    # since `top_k` is larger than 1, we need to handle multiple nen labels. Therefore we use `span.get_labels(...)`
    for label in span.get_labels(nen_tagger.label_type):
        mentions_found.append({
            "id": label.value,
            "score": label.score,
        })
        
    # extract the most probable prediction if any prediction is found. 
    if mentions_found:
        span_data["nen_id"] = mentions_found[0]["id"]
    else:
        span_data["nen_id"] = None
        
    # add all found candidates with rating if you want to explore more than just the most probable prediction.
    span_data["mention_candidates"] = mentions_found
    
    result_mentions.append(span_data)

print(result_mentions)

Note

If you need more than the extracted ids, you can use nen_tagger.dictionary[span_data["nen_id"]] to look up the EntityCandidate which contains further information.

Next#

Congrats, you learned how to link biomedical entities with Flair!

Next, let’s discuss how to predict part-of-speech tags with Flair.