Bump flair from 0.13.1 to 0.14.0

[dependabot]

Bumps flair from 0.13.1 to 0.14.0.

Release notes

Sourced from flair's releases.

Release 0.14.0

This release adds major new support for biomedical text analytics! It adds improved biomedical NER and a state-of-the-art model for biomedical entity linking. Other new features include (1) support for parameter-efficient fine-tuning and (2) various new datasets, bug fixes and enhancements! We also removed a few dependencies, so Flair should install faster and take up less space!

Biomedical NER and Entity Linking

With Flair 0.14.0, you can now detect and normalize biomedical entities in text.

For example, to analyze the sentence "We correlate genetic variants in IFNAR2 and POLG with long-COVID syndrome", use this code snippet:

from flair.models import EntityMentionLinker
from flair.nn import Classifier
from flair.data import Sentence
A sentence from biomedical literature
sentence = Sentence("We correlate genetic variants in IFNAR2 and POLG with long-COVID syndrome.")
Tag named entities in the text
ner_tagger = Classifier.load("hunflair2")
ner_tagger.predict(sentence)
Normalize disease names
disease_linker = EntityMentionLinker.load("gene-linker")
disease_linker.predict(sentence)
Normalize gene names
gene_linker = EntityMentionLinker.load("disease-linker")
gene_linker.predict(sentence)
Iterate over predicted entities and print
for label in sentence.get_labels():
print(label)

This should print out:

Span[5:6]: "IFNAR2" → Gene (1.0)
Span[5:6]: "IFNAR2" → 3455/name=IFNAR2 
Span[7:8]: "POLG" → Gene (1.0)
Span[7:8]: "POLG" → 5428/name=POLG
Span[9:11]: "long-COVID syndrome" → Disease (1.0)
Span[9:11]: "long-COVID syndrome" → MESH:D000094024/name=Post-Acute COVID-19 Syndrome

The printout shows that:

• "IFNAR2" is a gene. Further, it is recognized as gene 3455 ("interferon alpha and beta receptor subunit 2") in the NCBI database.

... (truncated)

Commits

• e17ab12 Merge pull request #3507 from flairNLP/release-0.14.0
• c81596c Add pointer to hunflair2 tutorial
• d6fedc8 Remove unused import
• 0b7acdd Small modifications to tutorials for release
• b7c08e2 Exclude FutureWarning on GradScaler and handle torch.load
• 7112273 Try excluding FutureWarning on GradScaler from pytest
• 141b4fe Mypy fix
• f376f5d Take historic German models from HF Hub
• ee4f3c6 Make mypy happy
• 750d9dc Change default bioner model to hunflair2
• Additional commits viewable in compare view

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