flair.datasets.biomedical.CEMP

class flair.datasets.biomedical.CEMP(base_path=None, in_memory=True, sentence_splitter=None)View on GitHub

Bases: ColumnCorpus

Original CEMP corpus containing chemical annotations.

For further information see: https://biocreative.bioinformatics.udel.edu/tasks/biocreative-v/cemp-detailed-task-description/

__init__(base_path=None, in_memory=True, sentence_splitter=None)View on GitHub

Initialize the CEMP corpus.

Parameters:

• base_path (Union[str, Path, None]) – Path to the corpus on your machine

• in_memory (bool) – If True, keeps dataset in memory giving speedups in training.

• sentence_splitter (Optional[SentenceSplitter]) – Implementation of SentenceSplitter which segments documents into sentences and tokens (default SciSpacySentenceSplitter)

Methods

__init__([base_path, in_memory, ...])	Initialize the CEMP corpus.
add_label_noise(label_type, labels[, ...])	Generates uniform label noise distribution in the chosen dataset split.
download_dev_corpus(data_dir)
download_train_corpus(data_dir)
downsample([percentage, downsample_train, ...])	Randomly downsample the corpus to the given percentage (by removing data points).
filter_empty_sentences()	A method that filters all sentences consisting of 0 tokens.
filter_long_sentences(max_charlength)	A method that filters all sentences for which the plain text is longer than a specified number of characters.
get_all_sentences()	Returns all sentences (spanning all three splits) in the Corpus.
get_label_distribution()	Counts occurrences of each label in the corpus and returns them as a dictionary object.
make_label_dictionary(label_type[, ...])	Creates a dictionary of all labels assigned to the sentences in the corpus.
make_tag_dictionary(tag_type)	Create a tag dictionary of a given label type.
make_vocab_dictionary([max_tokens, min_freq])	Creates a Dictionary of all tokens contained in the corpus.
obtain_statistics([label_type, pretty_print])	Print statistics about the corpus, including the length of the sentences and the labels in the corpus.
parse_input_file(text_file, ann_file)

Attributes

dev	The dev split as a torch.utils.data.Dataset object.
test	The test split as a torch.utils.data.Dataset object.
train	The training split as a torch.utils.data.Dataset object.

classmethod download_train_corpus(data_dir)View on GitHub

Return type:

Path

classmethod download_dev_corpus(data_dir)View on GitHub

Return type:

Path

static parse_input_file(text_file, ann_file)View on GitHub

Return type:

InternalBioNerDataset