flair-eml-biobert-bc2gn-gene

biobert-bc2gn-gene

Biomedical Entity Mention Linking for gene

Demo: How to use in Flair

Requires:

• Flair>=0.14.0 (pip install flair or pip install git+https://github.com/flairNLP/flair.git)

from flair.data import Sentence
from flair.models import Classifier, EntityMentionLinker

sentence = Sentence("Behavioral abnormalities in the Fmr1 KO2 Mouse Model of Fragile X Syndrome")

# load hunflair to detect the entity mentions we want to link.
tagger = Classifier.load("hunflair")
tagger.predict(sentence)

# load the linker and dictionary
linker = EntityMentionLinker.load("helpmefindaname/flair-eml-biobert-bc2gn-gene")
dictionary = linker.dictionary

# find then candidates for the mentions
linker.predict(sentence)

# print the results for each entity mention:
for span in sentence.get_spans(linker.entity_label_type):
    print(f"Span: {span.text}")
    for candidate_label in span.get_labels(linker.label_type):
        candidate = dictionary[candidate_label.value]
        print(f"Candidate: {candidate.concept_name}")

As an alternative to downloading the already precomputed model (much storage). You can also build the model and compute the embeddings for the dataset using:

linker = EntityMentionLinker.build("dmis-lab/biosyn-biobert-bc2gn", "gene", dictionary_name_or_path="ncbi-gene", hybrid_search=False, entity_type="gene-eml")

This will reduce the download requirements, at the cost of computation.

This EntityMentionLinker uses https://huggingface.co/dmis-lab/biosyn-biobert-bc2gn as embeddings for linking mentions to candidates.