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34ffd5b620f09d787deb594a055410486a7745d2 | ajlee21/snorkeling | playground/compound_disease/transfer_learning_experiment/data/label_functions/disease_gene_lf.py | [
"CC0-1.0",
"BSD-3-Clause"
] | Python | LF_DG_NO_CONCLUSION | <not_specific> | def LF_DG_NO_CONCLUSION(c):
"""
This label function fires a -1 if the number of negative label functinos is greater than the number
of positive label functions.
The main idea behind this label function is add support to sentences that could
mention a possible disease gene association.
"""
po... |
This label function fires a -1 if the number of negative label functinos is greater than the number
of positive label functions.
The main idea behind this label function is add support to sentences that could
mention a possible disease gene association.
| This label function fires a -1 if the number of negative label functinos is greater than the number
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The main idea behind this label function is add support to sentences that could
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positive_num = np.sum([LF_DG_ASSOCIATION(c), LF_DG_IS_BIOMARKER(c),LF_DG_NO_ASSOCIATION(c),
LF_DG_POSITIVE_DIRECTION(c), LF_DG_NEGATIVE_DIRECTION(c), LF_DG_DIAGNOSIS(c),
np.abs(LF_DG_WEAK_ASSOCIATION(c)), np.abs(LF_DG_NO_ASSOCIATION(c))])
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34ffd5b620f09d787deb594a055410486a7745d2 | ajlee21/snorkeling | playground/compound_disease/transfer_learning_experiment/data/label_functions/disease_gene_lf.py | [
"CC0-1.0",
"BSD-3-Clause"
] | Python | LF_DG_CONCLUSION | <not_specific> | def LF_DG_CONCLUSION(c):
"""
This label function fires a 1 if the number of positive label functions is greater than the number
of negative label functions.
The main idea behind this label function is add support to sentences that could
mention a possible disease gene association
"""
if LF_D... |
This label function fires a 1 if the number of positive label functions is greater than the number
of negative label functions.
The main idea behind this label function is add support to sentences that could
mention a possible disease gene association
| This label function fires a 1 if the number of positive label functions is greater than the number
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The main idea behind this label function is add support to sentences that could
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if LF_DG_NO_ASSOCIATION(c) or LF_DG_WEAK_ASSOCIATION(c):
return -1
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34ffd5b620f09d787deb594a055410486a7745d2 | ajlee21/snorkeling | playground/compound_disease/transfer_learning_experiment/data/label_functions/disease_gene_lf.py | [
"CC0-1.0",
"BSD-3-Clause"
] | Python | LF_DG_DISTANCE_LONG | <not_specific> | def LF_DG_DISTANCE_LONG(c):
"""
This LF is designed to make sure that the disease mention
and the gene mention aren't too far from each other.
"""
return -1 if len(list(get_between_tokens(c))) > 25 else 0 |
This LF is designed to make sure that the disease mention
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| This LF is designed to make sure that the disease mention
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} |
34ffd5b620f09d787deb594a055410486a7745d2 | ajlee21/snorkeling | playground/compound_disease/transfer_learning_experiment/data/label_functions/disease_gene_lf.py | [
"CC0-1.0",
"BSD-3-Clause"
] | Python | LF_DG_ALLOWED_DISTANCE | <not_specific> | def LF_DG_ALLOWED_DISTANCE(c):
"""
This LF is designed to make sure that the disease mention
and the gene mention are in an acceptable distance between
each other
"""
return 0 if any([
LF_DG_DISTANCE_LONG(c),
LF_DG_DISTANCE_SHORT(c)
]) else 1 if random.random() < 0.65 el... |
This LF is designed to make sure that the disease mention
and the gene mention are in an acceptable distance between
each other
| This LF is designed to make sure that the disease mention
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] | def LF_DG_ALLOWED_DISTANCE(c):
return 0 if any([
LF_DG_DISTANCE_LONG(c),
LF_DG_DISTANCE_SHORT(c)
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34ffd5b620f09d787deb594a055410486a7745d2 | ajlee21/snorkeling | playground/compound_disease/transfer_learning_experiment/data/label_functions/disease_gene_lf.py | [
"CC0-1.0",
"BSD-3-Clause"
] | Python | LF_DG_NO_VERB | <not_specific> | def LF_DG_NO_VERB(c):
"""
This label function is designed to fire if a given
sentence doesn't contain a verb. Helps cut out some of the titles
hidden in Pubtator abstracts
"""
if len([x for x in nltk.pos_tag(word_tokenize(c.get_parent().text)) if "VB" in x[1]]) == 0:
if "correlates with... |
This label function is designed to fire if a given
sentence doesn't contain a verb. Helps cut out some of the titles
hidden in Pubtator abstracts
| This label function is designed to fire if a given
sentence doesn't contain a verb. Helps cut out some of the titles
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] | def LF_DG_NO_VERB(c):
if len([x for x in nltk.pos_tag(word_tokenize(c.get_parent().text)) if "VB" in x[1]]) == 0:
if "correlates with" in c.get_parent().text:
return 0
return -1
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34ffd5b620f09d787deb594a055410486a7745d2 | ajlee21/snorkeling | playground/compound_disease/transfer_learning_experiment/data/label_functions/disease_gene_lf.py | [
"CC0-1.0",
"BSD-3-Clause"
] | Python | LF_DG_BICLUSTER_CASUAL_MUTATIONS | <not_specific> | def LF_DG_BICLUSTER_CASUAL_MUTATIONS(c):
"""
This label function uses the bicluster data located in the
A global network of biomedical relationships
"""
sen_pos = c.get_parent().position
pubmed_id = c.get_parent().document.name
query = bicluster_dep_df.query("pubmed_id==@pubmed_id&sentence_... |
This label function uses the bicluster data located in the
A global network of biomedical relationships
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] | def LF_DG_BICLUSTER_CASUAL_MUTATIONS(c):
sen_pos = c.get_parent().position
pubmed_id = c.get_parent().document.name
query = bicluster_dep_df.query("pubmed_id==@pubmed_id&sentence_num==@sen_pos")
if not(query.empty):
if query["U"].sum() > 0.0:
return 1
return 0 | [
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34ffd5b620f09d787deb594a055410486a7745d2 | ajlee21/snorkeling | playground/compound_disease/transfer_learning_experiment/data/label_functions/disease_gene_lf.py | [
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"BSD-3-Clause"
] | Python | LF_DG_BICLUSTER_MUTATIONS | <not_specific> | def LF_DG_BICLUSTER_MUTATIONS(c):
"""
This label function uses the bicluster data located in the
A global network of biomedical relationships
"""
sen_pos = c.get_parent().position
pubmed_id = c.get_parent().document.name
query = bicluster_dep_df.query("pubmed_id==@pubmed_id&sentence_num==@s... |
This label function uses the bicluster data located in the
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sen_pos = c.get_parent().position
pubmed_id = c.get_parent().document.name
query = bicluster_dep_df.query("pubmed_id==@pubmed_id&sentence_num==@sen_pos")
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34ffd5b620f09d787deb594a055410486a7745d2 | ajlee21/snorkeling | playground/compound_disease/transfer_learning_experiment/data/label_functions/disease_gene_lf.py | [
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] | Python | LF_DG_BICLUSTER_DRUG_TARGETS | <not_specific> | def LF_DG_BICLUSTER_DRUG_TARGETS(c):
"""
This label function uses the bicluster data located in the
A global network of biomedical relationships
"""
sen_pos = c.get_parent().position
pubmed_id = c.get_parent().document.name
query = bicluster_dep_df.query("pubmed_id==@pubmed_id&sentence_num=... |
This label function uses the bicluster data located in the
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sen_pos = c.get_parent().position
pubmed_id = c.get_parent().document.name
query = bicluster_dep_df.query("pubmed_id==@pubmed_id&sentence_num==@sen_pos")
if not(query.empty):
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34ffd5b620f09d787deb594a055410486a7745d2 | ajlee21/snorkeling | playground/compound_disease/transfer_learning_experiment/data/label_functions/disease_gene_lf.py | [
"CC0-1.0",
"BSD-3-Clause"
] | Python | LF_DG_BICLUSTER_PATHOGENESIS | <not_specific> | def LF_DG_BICLUSTER_PATHOGENESIS(c):
"""
This label function uses the bicluster data located in the
A global network of biomedical relationships
"""
sen_pos = c.get_parent().position
pubmed_id = c.get_parent().document.name
query = bicluster_dep_df.query("pubmed_id==@pubmed_id&sentence_num=... |
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] | def LF_DG_BICLUSTER_PATHOGENESIS(c):
sen_pos = c.get_parent().position
pubmed_id = c.get_parent().document.name
query = bicluster_dep_df.query("pubmed_id==@pubmed_id&sentence_num==@sen_pos")
if not(query.empty):
if query["J"].sum() > 0.0:
return 1
return 0 | [
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34ffd5b620f09d787deb594a055410486a7745d2 | ajlee21/snorkeling | playground/compound_disease/transfer_learning_experiment/data/label_functions/disease_gene_lf.py | [
"CC0-1.0",
"BSD-3-Clause"
] | Python | LF_DG_BICLUSTER_THERAPEUTIC | <not_specific> | def LF_DG_BICLUSTER_THERAPEUTIC(c):
"""
This label function uses the bicluster data located in the
A global network of biomedical relationships
"""
sen_pos = c.get_parent().position
pubmed_id = c.get_parent().document.name
query = bicluster_dep_df.query("pubmed_id==@pubmed_id&sentence_num==... |
This label function uses the bicluster data located in the
A global network of biomedical relationships
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] | def LF_DG_BICLUSTER_THERAPEUTIC(c):
sen_pos = c.get_parent().position
pubmed_id = c.get_parent().document.name
query = bicluster_dep_df.query("pubmed_id==@pubmed_id&sentence_num==@sen_pos")
if not(query.empty):
if query["Te"].sum() > 0.0:
return 1
return 0 | [
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34ffd5b620f09d787deb594a055410486a7745d2 | ajlee21/snorkeling | playground/compound_disease/transfer_learning_experiment/data/label_functions/disease_gene_lf.py | [
"CC0-1.0",
"BSD-3-Clause"
] | Python | LF_DG_BICLUSTER_POLYMORPHISMS | <not_specific> | def LF_DG_BICLUSTER_POLYMORPHISMS(c):
"""
This label function uses the bicluster data located in the
A global network of biomedical relationships
"""
sen_pos = c.get_parent().position
pubmed_id = c.get_parent().document.name
query = bicluster_dep_df.query("pubmed_id==@pubmed_id&sentence_num... |
This label function uses the bicluster data located in the
A global network of biomedical relationships
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] | def LF_DG_BICLUSTER_POLYMORPHISMS(c):
sen_pos = c.get_parent().position
pubmed_id = c.get_parent().document.name
query = bicluster_dep_df.query("pubmed_id==@pubmed_id&sentence_num==@sen_pos")
if not(query.empty):
if query["Y"].sum() > 0.0:
return 1
return 0 | [
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34ffd5b620f09d787deb594a055410486a7745d2 | ajlee21/snorkeling | playground/compound_disease/transfer_learning_experiment/data/label_functions/disease_gene_lf.py | [
"CC0-1.0",
"BSD-3-Clause"
] | Python | LF_DG_BICLUSTER_PROGRESSION | <not_specific> | def LF_DG_BICLUSTER_PROGRESSION(c):
"""
This label function uses the bicluster data located in the
A global network of biomedical relationships
"""
sen_pos = c.get_parent().position
pubmed_id = c.get_parent().document.name
query = bicluster_dep_df.query("pubmed_id==@pubmed_id&sentence_num==... |
This label function uses the bicluster data located in the
A global network of biomedical relationships
| This label function uses the bicluster data located in the
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"biomedical",
"relationships"
] | def LF_DG_BICLUSTER_PROGRESSION(c):
sen_pos = c.get_parent().position
pubmed_id = c.get_parent().document.name
query = bicluster_dep_df.query("pubmed_id==@pubmed_id&sentence_num==@sen_pos")
if not(query.empty):
if query["G"].sum() > 0.0:
return 1
return 0 | [
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34ffd5b620f09d787deb594a055410486a7745d2 | ajlee21/snorkeling | playground/compound_disease/transfer_learning_experiment/data/label_functions/disease_gene_lf.py | [
"CC0-1.0",
"BSD-3-Clause"
] | Python | LF_DG_BICLUSTER_BIOMARKERS | <not_specific> | def LF_DG_BICLUSTER_BIOMARKERS(c):
"""
This label function uses the bicluster data located in the
A global network of biomedical relationships
"""
sen_pos = c.get_parent().position
pubmed_id = c.get_parent().document.name
query = bicluster_dep_df.query("pubmed_id==@pubmed_id&sentence_num==@... |
This label function uses the bicluster data located in the
A global network of biomedical relationships
| This label function uses the bicluster data located in the
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"biomedical",
"relationships"
] | def LF_DG_BICLUSTER_BIOMARKERS(c):
sen_pos = c.get_parent().position
pubmed_id = c.get_parent().document.name
query = bicluster_dep_df.query("pubmed_id==@pubmed_id&sentence_num==@sen_pos")
if not(query.empty):
if query["Md"].sum() > 0.0:
return 1
return 0 | [
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34ffd5b620f09d787deb594a055410486a7745d2 | ajlee21/snorkeling | playground/compound_disease/transfer_learning_experiment/data/label_functions/disease_gene_lf.py | [
"CC0-1.0",
"BSD-3-Clause"
] | Python | LF_DG_BICLUSTER_OVEREXPRESSION | <not_specific> | def LF_DG_BICLUSTER_OVEREXPRESSION(c):
"""
This label function uses the bicluster data located in the
A global network of biomedical relationships
"""
sen_pos = c.get_parent().position
pubmed_id = c.get_parent().document.name
query = bicluster_dep_df.query("pubmed_id==@pubmed_id&sentence_nu... |
This label function uses the bicluster data located in the
A global network of biomedical relationships
| This label function uses the bicluster data located in the
A global network of biomedical relationships | [
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"biomedical",
"relationships"
] | def LF_DG_BICLUSTER_OVEREXPRESSION(c):
sen_pos = c.get_parent().position
pubmed_id = c.get_parent().document.name
query = bicluster_dep_df.query("pubmed_id==@pubmed_id&sentence_num==@sen_pos")
if not(query.empty):
if query["X"].sum() > 0.0:
return 1
return 0 | [
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34ffd5b620f09d787deb594a055410486a7745d2 | ajlee21/snorkeling | playground/compound_disease/transfer_learning_experiment/data/label_functions/disease_gene_lf.py | [
"CC0-1.0",
"BSD-3-Clause"
] | Python | LF_DG_BICLUSTER_REGULATION | <not_specific> | def LF_DG_BICLUSTER_REGULATION(c):
"""
This label function uses the bicluster data located in the
A global network of biomedical relationships
"""
sen_pos = c.get_parent().position
pubmed_id = c.get_parent().document.name
query = bicluster_dep_df.query("pubmed_id==@pubmed_id&sentence_num==@... |
This label function uses the bicluster data located in the
A global network of biomedical relationships
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] | def LF_DG_BICLUSTER_REGULATION(c):
sen_pos = c.get_parent().position
pubmed_id = c.get_parent().document.name
query = bicluster_dep_df.query("pubmed_id==@pubmed_id&sentence_num==@sen_pos")
if not(query.empty):
if query["L"].sum() > 0.0:
return 1
return 0 | [
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8bd14d5184d76c121d56e0234cc1e3799c63685f | ajlee21/snorkeling | create_database/database_insertion.py | [
"CC0-1.0",
"BSD-3-Clause"
] | Python | offsets_to_token | <not_specific> | def offsets_to_token(left, right, offset_array, lemmas, punc=set(punctuation)):
"""Calculate the offset from tag to token
Ripped off from the snorkel custom tagger.
Designed to get the offset where a given token is found so it can receive a custom entity tag.
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Keyword argument... | Calculate the offset from tag to token
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Designed to get the offset where a given token is found so it can receive a custom entity tag.
(i.e. Gene or Chemical)
Keyword arguments
left - the start of the tag
right - the end of the tag
offset_array - arr... | Calculate the offset from tag to token
Ripped off from the snorkel custom tagger.
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8bd14d5184d76c121d56e0234cc1e3799c63685f | ajlee21/snorkeling | create_database/database_insertion.py | [
"CC0-1.0",
"BSD-3-Clause"
] | Python | tag | <not_specific> | def tag(self, parts):
"""Tag each Sentence
Keyword arguments:
self -- the class object
parts -- standford's corenlp object which consists of nlp properties
Returns:
An updated parts object containing specified custom tags.
"""
pubmed_id, _, _, sent_start,... | Tag each Sentence
Keyword arguments:
self -- the class object
parts -- standford's corenlp object which consists of nlp properties
Returns:
An updated parts object containing specified custom tags.
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Keyword arguments:
self -- the class object
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] | def tag(self, parts):
pubmed_id, _, _, sent_start, sent_end = parts['stable_id'].split(':')
sent_start, sent_end = int(sent_start), int(sent_end)
try:
for index, tag in self.annt_df.get_group(int(pubmed_id)).iterrows():
if not (sent_start <= int(tag['offset']) <= sent... | [
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8bd14d5184d76c121d56e0234cc1e3799c63685f | ajlee21/snorkeling | create_database/database_insertion.py | [
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8bd14d5184d76c121d56e0234cc1e3799c63685f | ajlee21/snorkeling | create_database/database_insertion.py | [
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Keyword Arguments:
fpath - the absolute path of the file.
"""
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7f1be78607f6994d08587d0d3906da18f5c37acb | ajlee21/snorkeling | playground/epilepsy/scripts/2.epilepsy-labeler.py | [
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"""
If variation keyword in close proximity then label as positive
"""
if len(variation_words.intersection(get_left_tokens(c[1]))) > 0:
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if len(variation_words.intersection(get_right_tokens(c[1]))) > 0:
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if len(variation_words.intersection(get_right_tokens(c[1]))) > 0:
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7f1be78607f6994d08587d0d3906da18f5c37acb | ajlee21/snorkeling | playground/epilepsy/scripts/2.epilepsy-labeler.py | [
"CC0-1.0",
"BSD-3-Clause"
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"""
If mentions model organism then c[1] should be a gene
"""
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return 0 |
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if len(model_organisms.intersection(get_left_tokens(c[1]))) > 0:
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7f1be78607f6994d08587d0d3906da18f5c37acb | ajlee21/snorkeling | playground/epilepsy/scripts/2.epilepsy-labeler.py | [
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"""
If the causual keywords are between disease and gene then should be positive predictor
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if len(cause_words.intersection(get_between_tokens(c))) > 0:
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If the causual keywords are between disease and gene then should be positive predictor
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7f1be78607f6994d08587d0d3906da18f5c37acb | ajlee21/snorkeling | playground/epilepsy/scripts/2.epilepsy-labeler.py | [
"CC0-1.0",
"BSD-3-Clause"
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"""
If it mentions serum or intervention before or after gene then negative
"""
if len(neg_words.intersection(get_left_tokens(c[1],window=3))) > 0:
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return 0 |
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7f1be78607f6994d08587d0d3906da18f5c37acb | ajlee21/snorkeling | playground/epilepsy/scripts/2.epilepsy-labeler.py | [
"CC0-1.0",
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"""
If candidate has gene word near it
"""
if "gene" in get_left_tokens(c[1]) or "gene" in get_right_tokens(c[1]):
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7f1be78607f6994d08587d0d3906da18f5c37acb | ajlee21/snorkeling | playground/epilepsy/scripts/2.epilepsy-labeler.py | [
"CC0-1.0",
"BSD-3-Clause"
] | Python | LF_unrelated_disease | <not_specific> | def LF_unrelated_disease(c):
"""
If the disease is completely unrelated remove
"""
if c[0].get_span() in unrelated_diseases:
return -1
return 0 |
If the disease is completely unrelated remove
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7f1be78607f6994d08587d0d3906da18f5c37acb | ajlee21/snorkeling | playground/epilepsy/scripts/2.epilepsy-labeler.py | [
"CC0-1.0",
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If there is a GENE with a -related tag next to it, then it might be important.
"""
for adj in gene_adj:
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If there is a GENE with a -related tag next to it, then it might be important.
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7f1be78607f6994d08587d0d3906da18f5c37acb | ajlee21/snorkeling | playground/epilepsy/scripts/2.epilepsy-labeler.py | [
"CC0-1.0",
"BSD-3-Clause"
] | Python | LF_disease_context | <not_specific> | def LF_disease_context(c):
"""
If mentions cases of or patients with -> disease
"""
tokens = "".join(get_left_tokens(c[1],window=3))
for context in disease_context:
if context in tokens:
return -1
return 0 |
If mentions cases of or patients with -> disease
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tokens = "".join(get_left_tokens(c[1],window=3))
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7f1be78607f6994d08587d0d3906da18f5c37acb | ajlee21/snorkeling | playground/epilepsy/scripts/2.epilepsy-labeler.py | [
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] | Python | LF_is_gene | <not_specific> | def LF_is_gene(c):
"""
If the name is a gene
"""
if c[1].get_span() in set(gene_list["gene_name"]) or c[1].get_span() in set(gene_list["gene_symbol"]):
return 0
return -1 |
If the name is a gene
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if c[1].get_span() in set(gene_list["gene_name"]) or c[1].get_span() in set(gene_list["gene_symbol"]):
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b948b6ddb6bec4c6c36614a2966cb603ff448827 | ajlee21/snorkeling | modules/utils/notebook_utils/label_matrix_helper.py | [
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] | Python | label_candidates_db | <not_specific> | def label_candidates_db(labeler, cids_query, label_functions, apply_existing=False):
"""
This function is designed to label candidates and place the annotations inside a database.
Will be rarely used since snorkel metal doesn't use a database for annotations.
Important to keep if I were to go back towar... |
This function is designed to label candidates and place the annotations inside a database.
Will be rarely used since snorkel metal doesn't use a database for annotations.
Important to keep if I were to go back towards snorkel's original database version
labeler - the labeler object
cids_query - th... | This function is designed to label candidates and place the annotations inside a database.
Will be rarely used since snorkel metal doesn't use a database for annotations.
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b948b6ddb6bec4c6c36614a2966cb603ff448827 | ajlee21/snorkeling | modules/utils/notebook_utils/label_matrix_helper.py | [
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"""
This function is called when each thread is created.
lfs - the label functions to annotate candidates
multitask - a boolean that tells the function to label candidates in a multitask format
"""
while not(candidate_queue.empty()):
... |
This function is called when each thread is created.
lfs - the label functions to annotate candidates
multitask - a boolean that tells the function to label candidates in a multitask format
| This function is called when each thread is created.
lfs - the label functions to annotate candidates
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472a8b430c450c27fafa8a5f4e35174f7ae7eff7 | ajlee21/snorkeling | modules/utils/notebook_utils/dataframe_helper.py | [
"CC0-1.0",
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"""
This function is designed to create a dataframe that will hold
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L_data - the sparse matrix generated fromt eh label functions
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L_data - the sparse matrix generated fromt eh label functions
models - the list of generative models
lfs_columns - a listing of column indexes that correspond to desired label fucntions... | This function is designed to create a dataframe that will hold
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the sparse matrix generated fromt eh label functions
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472a8b430c450c27fafa8a5f4e35174f7ae7eff7 | ajlee21/snorkeling | modules/utils/notebook_utils/dataframe_helper.py | [
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"""
This function is desgined get the predicted marginals from the sklearn models
models - list of sklearn models that marginals will be generated from
test_data - the dev set data used to generate testing marginals
return a dataframe containing mar... |
This function is desgined get the predicted marginals from the sklearn models
models - list of sklearn models that marginals will be generated from
test_data - the dev set data used to generate testing marginals
return a dataframe containing marginal probabilities for each sklearn model
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472a8b430c450c27fafa8a5f4e35174f7ae7eff7 | ajlee21/snorkeling | modules/utils/notebook_utils/dataframe_helper.py | [
"CC0-1.0",
"BSD-3-Clause"
] | Python | tag_sentence | <not_specific> | def tag_sentence(x, class_table):
"""
This function tags the mentions of each candidate sentence.
x - dataframe with candidate sentences
class_table - the table for each candidate
"""
candidates=(
session
.query(class_table)
.filter(class_table.id.in_(x.candidate_id.astyp... |
This function tags the mentions of each candidate sentence.
x - dataframe with candidate sentences
class_table - the table for each candidate
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x - dataframe with candidate sentences
class_table - the table for each candidate | [
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472a8b430c450c27fafa8a5f4e35174f7ae7eff7 | ajlee21/snorkeling | modules/utils/notebook_utils/dataframe_helper.py | [
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] | Python | make_sentence_df | <not_specific> | def make_sentence_df(candidates):
"""
This function creats a dataframe for all candidates (sentences that contain at least two mentions)
located in our database.
candidates - a list of candidate objects passed in from sqlalchemy
return a Dataframe that contains each candidate sentence and th... |
This function creats a dataframe for all candidates (sentences that contain at least two mentions)
located in our database.
candidates - a list of candidate objects passed in from sqlalchemy
return a Dataframe that contains each candidate sentence and the corresponding candidate entities
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472a8b430c450c27fafa8a5f4e35174f7ae7eff7 | ajlee21/snorkeling | modules/utils/notebook_utils/dataframe_helper.py | [
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"BSD-3-Clause"
] | Python | write_candidates_to_excel | <not_specific> | def write_candidates_to_excel(candidate_df, spreadsheet_name):
"""
This function is designed to save the candidates to an excel
spreadsheet. This is needed for manual curation of candidate
sentences
candidate_df - the dataframe that holds all the candidates
spreadsheet_name - the name of t... |
This function is designed to save the candidates to an excel
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candidate_df - the dataframe that holds all the candidates
spreadsheet_name - the name of the excel spreadsheet
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472a8b430c450c27fafa8a5f4e35174f7ae7eff7 | ajlee21/snorkeling | modules/utils/notebook_utils/dataframe_helper.py | [
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"""
This function reads in the candidates excel files to preform analyses.
dataframe - the path of the dataframe to load
"""
data_df = pd.read_excel(filename)
data_df = data_df.query("{}.notnull()".format(curated_field))
return data_df... |
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dataframe - the path of the dataframe to load
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dataframe - the path of the dataframe to load | [
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9661a0a1ecee4f24de1e2517a4112f61e5d604f5 | ajlee21/snorkeling | playground/disease_gene/generative_model_experiments/data_210/label_functions/disease_gene_lf.py | [
"CC0-1.0",
"BSD-3-Clause"
] | Python | LF_DG_NEGATIVE_DIRECTION | <not_specific> | def LF_DG_NEGATIVE_DIRECTION(c):
"""
This label function is designed to search for words that indicate
a sort of negative response or imply an downregulates association
"""
return 1 if any([rule_regex_search_btw_AB(c, r'.*'+ltp(negative_direction)+r'.*', 1), rule_regex_search_btw_BA(c, r'.*'+ltp(neg... |
This label function is designed to search for words that indicate
a sort of negative response or imply an downregulates association
| This label function is designed to search for words that indicate
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9661a0a1ecee4f24de1e2517a4112f61e5d604f5 | ajlee21/snorkeling | playground/disease_gene/generative_model_experiments/data_210/label_functions/disease_gene_lf.py | [
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"BSD-3-Clause"
] | Python | LF_DaG_NO_CONCLUSION | <not_specific> | def LF_DaG_NO_CONCLUSION(c):
"""
This label function fires a -1 if the number of negative label functinos is greater than the number
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The main idea behind this label function is add support to sentences that could
mention a possible disease gene association.
"""
p... |
This label function fires a -1 if the number of negative label functinos is greater than the number
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The main idea behind this label function is add support to sentences that could
mention a possible disease gene association.
| This label function fires a -1 if the number of negative label functinos is greater than the number
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positive_num = np.sum([LF_DG_ASSOCIATION(c), LF_DG_IS_BIOMARKER(c),LF_DG_NO_ASSOCIATION(c),
LF_DG_POSITIVE_DIRECTION(c), LF_DG_NEGATIVE_DIRECTION(c), LF_DG_DIAGNOSIS(c),
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9661a0a1ecee4f24de1e2517a4112f61e5d604f5 | ajlee21/snorkeling | playground/disease_gene/generative_model_experiments/data_210/label_functions/disease_gene_lf.py | [
"CC0-1.0",
"BSD-3-Clause"
] | Python | LF_DaG_CONCLUSION | <not_specific> | def LF_DaG_CONCLUSION(c):
"""
This label function fires a 1 if the number of positive label functions is greater than the number
of negative label functions.
The main idea behind this label function is add support to sentences that could
mention a possible disease gene association
"""
if LF_... |
This label function fires a 1 if the number of positive label functions is greater than the number
of negative label functions.
The main idea behind this label function is add support to sentences that could
mention a possible disease gene association
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9661a0a1ecee4f24de1e2517a4112f61e5d604f5 | ajlee21/snorkeling | playground/disease_gene/generative_model_experiments/data_210/label_functions/disease_gene_lf.py | [
"CC0-1.0",
"BSD-3-Clause"
] | Python | LF_DuG_NO_CONCLUSION | <not_specific> | def LF_DuG_NO_CONCLUSION(c):
"""
This label function fires a -1 if the number of negative label functinos is greater than the number
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The main idea behind this label function is add support to sentences that could
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"""
p... |
This label function fires a -1 if the number of negative label functinos is greater than the number
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The main idea behind this label function is add support to sentences that could
mention a possible disease gene association.
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9661a0a1ecee4f24de1e2517a4112f61e5d604f5 | ajlee21/snorkeling | playground/disease_gene/generative_model_experiments/data_210/label_functions/disease_gene_lf.py | [
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"BSD-3-Clause"
] | Python | LF_DdG_NO_CONCLUSION | <not_specific> | def LF_DdG_NO_CONCLUSION(c):
"""
This label function fires a -1 if the number of negative label functinos is greater than the number
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The main idea behind this label function is add support to sentences that could
mention a possible disease gene association.
"""
p... |
This label function fires a -1 if the number of negative label functinos is greater than the number
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The main idea behind this label function is add support to sentences that could
mention a possible disease gene association.
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13165b1ff01e6a231e6aab2b39e34461dc912c0b | ajlee21/snorkeling | playground/compound_disease/transfer_learning_experiment/data/label_functions/compound_disease_lf.py | [
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"BSD-3-Clause"
] | Python | LF_HETNET_CD_ABSENT | <not_specific> | def LF_HETNET_CD_ABSENT(c):
"""
This label function fires -1 if the given Disease Gene pair does not appear
in the databases above.
"""
return 0 if any([
LF_HETNET_PHARMACOTHERAPYDB(c)
]) else -1 |
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13165b1ff01e6a231e6aab2b39e34461dc912c0b | ajlee21/snorkeling | playground/compound_disease/transfer_learning_experiment/data/label_functions/compound_disease_lf.py | [
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] | Python | LF_CD_CHECK_DISEASE_TAG | <not_specific> | def LF_CD_CHECK_DISEASE_TAG(c):
"""
This label function is used for labeling each passed candidate as either pos or neg.
Keyword Args:
c- the candidate object to be passed in.
"""
sen = c[1].get_parent()
disease_name = re.sub("\) ?", "", c[1].get_span())
disease_name = re.sub(r"(\w)-(\w)... |
This label function is used for labeling each passed candidate as either pos or neg.
Keyword Args:
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disease_name = re.sub("\) ?", "", c[1].get_span())
disease_name = re.sub(r"(\w)-(\w)", r"\g<1> \g<2>", disease_name)
disease_name = " ".join([word for word in word_tokenize(disease_name) if word not in set(stop_word_list)])
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13165b1ff01e6a231e6aab2b39e34461dc912c0b | ajlee21/snorkeling | playground/compound_disease/transfer_learning_experiment/data/label_functions/compound_disease_lf.py | [
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"BSD-3-Clause"
] | Python | LF_CD_WEAKLY_TREATS | <not_specific> | def LF_CD_WEAKLY_TREATS(c):
"""
This label function is designed to look for phrases
that imply a compound binding to a gene/protein
"""
if re.search(ltp(weak_treatment_indications), get_text_between(c), flags=re.I):
return 1
elif re.search(ltp(weak_treatment_indications), " ".join(get_le... |
This label function is designed to look for phrases
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] | def LF_CD_WEAKLY_TREATS(c):
if re.search(ltp(weak_treatment_indications), get_text_between(c), flags=re.I):
return 1
elif re.search(ltp(weak_treatment_indications), " ".join(get_left_tokens(c[0], window=5)), flags=re.I):
return 1
elif re.search(ltp(weak_treatment_indications), " ".join(get_r... | [
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],
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} |
13165b1ff01e6a231e6aab2b39e34461dc912c0b | ajlee21/snorkeling | playground/compound_disease/transfer_learning_experiment/data/label_functions/compound_disease_lf.py | [
"CC0-1.0",
"BSD-3-Clause"
] | Python | LF_CD_PALLIATES | <not_specific> | def LF_CD_PALLIATES(c):
"""
This label function is designed to look for phrases
that could imply a compound binding to a gene/protein
"""
if re.search(ltp(palliates_indication), get_text_between(c), flags=re.I):
return 1
elif re.search(ltp(palliates_indication), " ".join(get_left_tokens(... |
This label function is designed to look for phrases
that could imply a compound binding to a gene/protein
| This label function is designed to look for phrases
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"/",
"protein"
] | def LF_CD_PALLIATES(c):
if re.search(ltp(palliates_indication), get_text_between(c), flags=re.I):
return 1
elif re.search(ltp(palliates_indication), " ".join(get_left_tokens(c[0], window=5)), flags=re.I):
return 1
elif re.search(ltp(palliates_indication), " ".join(get_right_tokens(c[0], wind... | [
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13165b1ff01e6a231e6aab2b39e34461dc912c0b | ajlee21/snorkeling | playground/compound_disease/transfer_learning_experiment/data/label_functions/compound_disease_lf.py | [
"CC0-1.0",
"BSD-3-Clause"
] | Python | LF_CD_COMPOUND_INDICATION | <not_specific> | def LF_CD_COMPOUND_INDICATION(c):
"""
This label function is designed to look for phrases
that implies a compound increaseing activity of a gene/protein
"""
if re.search(ltp(compound_indications), get_text_between(c), flags=re.I):
return 1
elif re.search(ltp(compound_indications), " ".jo... |
This label function is designed to look for phrases
that implies a compound increaseing activity of a gene/protein
| This label function is designed to look for phrases
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"increaseing",
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"/",
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] | def LF_CD_COMPOUND_INDICATION(c):
if re.search(ltp(compound_indications), get_text_between(c), flags=re.I):
return 1
elif re.search(ltp(compound_indications), " ".join(get_left_tokens(c[0], window=5)), flags=re.I):
return 1
elif re.search(ltp(compound_indications), " ".join(get_right_tokens(... | [
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} |
13165b1ff01e6a231e6aab2b39e34461dc912c0b | ajlee21/snorkeling | playground/compound_disease/transfer_learning_experiment/data/label_functions/compound_disease_lf.py | [
"CC0-1.0",
"BSD-3-Clause"
] | Python | LF_CD_IN_SERIES | <not_specific> | def LF_CD_IN_SERIES(c):
"""
This label function is designed to look for a mention being caught
in a series of other genes or compounds
"""
if len(re.findall(r',', get_tagged_text(c))) >= 2:
if re.search(', and', get_tagged_text(c)):
return -1
if re.search(r"\(a\)|\(b\)|\(c\)"... |
This label function is designed to look for a mention being caught
in a series of other genes or compounds
| This label function is designed to look for a mention being caught
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] | def LF_CD_IN_SERIES(c):
if len(re.findall(r',', get_tagged_text(c))) >= 2:
if re.search(', and', get_tagged_text(c)):
return -1
if re.search(r"\(a\)|\(b\)|\(c\)", get_tagged_text(c)):
return -1
return 0 | [
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13165b1ff01e6a231e6aab2b39e34461dc912c0b | ajlee21/snorkeling | playground/compound_disease/transfer_learning_experiment/data/label_functions/compound_disease_lf.py | [
"CC0-1.0",
"BSD-3-Clause"
] | Python | LF_CD_METHOD_DESC | <not_specific> | def LF_CD_METHOD_DESC(c):
"""
This label function is designed to look for phrases
that imply a sentence is description an experimental design
"""
if re.search(ltp(method_indication), get_tagged_text(c), flags=re.I):
return -1
else:
return 0 |
This label function is designed to look for phrases
that imply a sentence is description an experimental design
| This label function is designed to look for phrases
that imply a sentence is description an experimental design | [
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] | def LF_CD_METHOD_DESC(c):
if re.search(ltp(method_indication), get_tagged_text(c), flags=re.I):
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else:
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13165b1ff01e6a231e6aab2b39e34461dc912c0b | ajlee21/snorkeling | playground/compound_disease/transfer_learning_experiment/data/label_functions/compound_disease_lf.py | [
"CC0-1.0",
"BSD-3-Clause"
] | Python | LF_CD_NO_CONCLUSION | <not_specific> | def LF_CD_NO_CONCLUSION(c):
"""
This label function fires a -1 if the number of negative label functinos is greater than the number
of positive label functions.
The main idea behind this label function is add support to sentences that could
mention a possible disease gene association.
"""
po... |
This label function fires a -1 if the number of negative label functinos is greater than the number
of positive label functions.
The main idea behind this label function is add support to sentences that could
mention a possible disease gene association.
| This label function fires a -1 if the number of negative label functinos is greater than the number
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positive_num = np.sum([
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LF_CD_CHECK_DEPRESSION_USAGE(c),
LF_CD_WEAKLY_TREATS(c),
LF_CD_PALLIATES(c),
LF_CD_COMPOUND_INDICATION(c),
LF_CD_TRIAL(c)])
negative_num = np.abs(np.sum([LF_CD_METHOD_DESC(c), LF_CD_IN_SERIES(c)]... | [
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} |
13165b1ff01e6a231e6aab2b39e34461dc912c0b | ajlee21/snorkeling | playground/compound_disease/transfer_learning_experiment/data/label_functions/compound_disease_lf.py | [
"CC0-1.0",
"BSD-3-Clause"
] | Python | LF_CD_CONCLUSION | <not_specific> | def LF_CD_CONCLUSION(c):
"""
This label function fires a 1 if the number of positive label functions is greater than the number
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The main idea behind this label function is add support to sentences that could
mention a possible disease gene association
"""
if not ... |
This label function fires a 1 if the number of positive label functions is greater than the number
of negative label functions.
The main idea behind this label function is add support to sentences that could
mention a possible disease gene association
| This label function fires a 1 if the number of positive label functions is greater than the number
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13165b1ff01e6a231e6aab2b39e34461dc912c0b | ajlee21/snorkeling | playground/compound_disease/transfer_learning_experiment/data/label_functions/compound_disease_lf.py | [
"CC0-1.0",
"BSD-3-Clause"
] | Python | LF_CD_DISTANCE_SHORT | <not_specific> | def LF_CD_DISTANCE_SHORT(c):
"""
This LF is designed to make sure that the compound mention
and the gene mention aren't right next to each other.
"""
return -1 if len(list(get_between_tokens(c))) <= 2 else 0 |
This LF is designed to make sure that the compound mention
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| This LF is designed to make sure that the compound mention
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} |
13165b1ff01e6a231e6aab2b39e34461dc912c0b | ajlee21/snorkeling | playground/compound_disease/transfer_learning_experiment/data/label_functions/compound_disease_lf.py | [
"CC0-1.0",
"BSD-3-Clause"
] | Python | LF_CD_DISTANCE_LONG | <not_specific> | def LF_CD_DISTANCE_LONG(c):
"""
This LF is designed to make sure that the compound mention
and the gene mention aren't too far from each other.
"""
return -1 if len(list(get_between_tokens(c))) > 25 else 0 |
This LF is designed to make sure that the compound mention
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| This LF is designed to make sure that the compound mention
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} |
13165b1ff01e6a231e6aab2b39e34461dc912c0b | ajlee21/snorkeling | playground/compound_disease/transfer_learning_experiment/data/label_functions/compound_disease_lf.py | [
"CC0-1.0",
"BSD-3-Clause"
] | Python | LF_CD_ALLOWED_DISTANCE | <not_specific> | def LF_CD_ALLOWED_DISTANCE(c):
"""
This LF is designed to make sure that the compound mention
and the gene mention are in an acceptable distance between
each other
"""
return 0 if any([
LF_CD_DISTANCE_LONG(c),
LF_CD_DISTANCE_SHORT(c)
]) else 1 if random.random() < 0.65 e... |
This LF is designed to make sure that the compound mention
and the gene mention are in an acceptable distance between
each other
| This LF is designed to make sure that the compound mention
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] | def LF_CD_ALLOWED_DISTANCE(c):
return 0 if any([
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LF_CD_DISTANCE_SHORT(c)
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} |
13165b1ff01e6a231e6aab2b39e34461dc912c0b | ajlee21/snorkeling | playground/compound_disease/transfer_learning_experiment/data/label_functions/compound_disease_lf.py | [
"CC0-1.0",
"BSD-3-Clause"
] | Python | LF_CD_NO_VERB | <not_specific> | def LF_CD_NO_VERB(c):
"""
This label function is designed to fire if a given
sentence doesn't contain a verb. Helps cut out some of the titles
hidden in Pubtator abstracts
"""
if len([x for x in nltk.pos_tag(word_tokenize(c.get_parent().text)) if "VB" in x[1]]) == 0:
if "correlates with... |
This label function is designed to fire if a given
sentence doesn't contain a verb. Helps cut out some of the titles
hidden in Pubtator abstracts
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] | def LF_CD_NO_VERB(c):
if len([x for x in nltk.pos_tag(word_tokenize(c.get_parent().text)) if "VB" in x[1]]) == 0:
if "correlates with" in c.get_parent().text:
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return -1
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13165b1ff01e6a231e6aab2b39e34461dc912c0b | ajlee21/snorkeling | playground/compound_disease/transfer_learning_experiment/data/label_functions/compound_disease_lf.py | [
"CC0-1.0",
"BSD-3-Clause"
] | Python | LF_CD_PARENTHETICAL_DESC | <not_specific> | def LF_CD_PARENTHETICAL_DESC(c):
"""
This label function looks for mentions that are in paranthesis.
Some of the gene mentions are abbreviations rather than names of a gene.
"""
if ")" in c[1].get_span() and "(" in list(get_left_tokens(c[1], window=1)):
if LF_CD_DISTANCE_SHORT(c):
... |
This label function looks for mentions that are in paranthesis.
Some of the gene mentions are abbreviations rather than names of a gene.
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] | def LF_CD_PARENTHETICAL_DESC(c):
if ")" in c[1].get_span() and "(" in list(get_left_tokens(c[1], window=1)):
if LF_CD_DISTANCE_SHORT(c):
return -1
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13165b1ff01e6a231e6aab2b39e34461dc912c0b | ajlee21/snorkeling | playground/compound_disease/transfer_learning_experiment/data/label_functions/compound_disease_lf.py | [
"CC0-1.0",
"BSD-3-Clause"
] | Python | LF_CD_BICLUSTER_TREATMENT | <not_specific> | def LF_CD_BICLUSTER_TREATMENT(c):
"""
This label function uses the bicluster data located in the
A global network of biomedical relationships
"""
sen_pos = c.get_parent().position
pubmed_id = c.get_parent().document.name
query = bicluster_dep_df.query("pubmed_id==@pubmed_id&sentence_num==@s... |
This label function uses the bicluster data located in the
A global network of biomedical relationships
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] | def LF_CD_BICLUSTER_TREATMENT(c):
sen_pos = c.get_parent().position
pubmed_id = c.get_parent().document.name
query = bicluster_dep_df.query("pubmed_id==@pubmed_id&sentence_num==@sen_pos")
if not(query.empty):
if query["T"].sum() > 0.0:
return 1
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13165b1ff01e6a231e6aab2b39e34461dc912c0b | ajlee21/snorkeling | playground/compound_disease/transfer_learning_experiment/data/label_functions/compound_disease_lf.py | [
"CC0-1.0",
"BSD-3-Clause"
] | Python | LF_CD_BICLUSTER_INHIBITS | <not_specific> | def LF_CD_BICLUSTER_INHIBITS(c):
"""
This label function uses the bicluster data located in the
A global network of biomedical relationships
"""
sen_pos = c.get_parent().position
pubmed_id = c.get_parent().document.name
query = bicluster_dep_df.query("pubmed_id==@pubmed_id&sentence_num==@se... |
This label function uses the bicluster data located in the
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] | def LF_CD_BICLUSTER_INHIBITS(c):
sen_pos = c.get_parent().position
pubmed_id = c.get_parent().document.name
query = bicluster_dep_df.query("pubmed_id==@pubmed_id&sentence_num==@sen_pos")
if not(query.empty):
if query["C"].sum() > 0.0:
return 1
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13165b1ff01e6a231e6aab2b39e34461dc912c0b | ajlee21/snorkeling | playground/compound_disease/transfer_learning_experiment/data/label_functions/compound_disease_lf.py | [
"CC0-1.0",
"BSD-3-Clause"
] | Python | LF_CD_BICLUSTER_SIDE_EFFECT | <not_specific> | def LF_CD_BICLUSTER_SIDE_EFFECT(c):
"""
This label function uses the bicluster data located in the
A global network of biomedical relationships
"""
sen_pos = c.get_parent().position
pubmed_id = c.get_parent().document.name
query = bicluster_dep_df.query("pubmed_id==@pubmed_id&sentence_num==... |
This label function uses the bicluster data located in the
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] | def LF_CD_BICLUSTER_SIDE_EFFECT(c):
sen_pos = c.get_parent().position
pubmed_id = c.get_parent().document.name
query = bicluster_dep_df.query("pubmed_id==@pubmed_id&sentence_num==@sen_pos")
if not(query.empty):
if query["Sa"].sum() > 0.0:
return 1
return 0 | [
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13165b1ff01e6a231e6aab2b39e34461dc912c0b | ajlee21/snorkeling | playground/compound_disease/transfer_learning_experiment/data/label_functions/compound_disease_lf.py | [
"CC0-1.0",
"BSD-3-Clause"
] | Python | LF_CD_BICLUSTER_PREVENTS | <not_specific> | def LF_CD_BICLUSTER_PREVENTS(c):
"""
This label function uses the bicluster data located in the
A global network of biomedical relationships
"""
sen_pos = c.get_parent().position
pubmed_id = c.get_parent().document.name
query = bicluster_dep_df.query("pubmed_id==@pubmed_id&sentence_num==@se... |
This label function uses the bicluster data located in the
A global network of biomedical relationships
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] | def LF_CD_BICLUSTER_PREVENTS(c):
sen_pos = c.get_parent().position
pubmed_id = c.get_parent().document.name
query = bicluster_dep_df.query("pubmed_id==@pubmed_id&sentence_num==@sen_pos")
if not(query.empty):
if query["Pr"].sum() > 0.0:
return 1
return 0 | [
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13165b1ff01e6a231e6aab2b39e34461dc912c0b | ajlee21/snorkeling | playground/compound_disease/transfer_learning_experiment/data/label_functions/compound_disease_lf.py | [
"CC0-1.0",
"BSD-3-Clause"
] | Python | LF_CD_BICLUSTER_ALLEVIATES | <not_specific> | def LF_CD_BICLUSTER_ALLEVIATES(c):
"""
This label function uses the bicluster data located in the
A global network of biomedical relationships
"""
sen_pos = c.get_parent().position
pubmed_id = c.get_parent().document.name
query = bicluster_dep_df.query("pubmed_id==@pubmed_id&sentence_num==@... |
This label function uses the bicluster data located in the
A global network of biomedical relationships
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] | def LF_CD_BICLUSTER_ALLEVIATES(c):
sen_pos = c.get_parent().position
pubmed_id = c.get_parent().document.name
query = bicluster_dep_df.query("pubmed_id==@pubmed_id&sentence_num==@sen_pos")
if not(query.empty):
if query["Pa"].sum() > 0.0:
return 1
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13165b1ff01e6a231e6aab2b39e34461dc912c0b | ajlee21/snorkeling | playground/compound_disease/transfer_learning_experiment/data/label_functions/compound_disease_lf.py | [
"CC0-1.0",
"BSD-3-Clause"
] | Python | LF_CD_BICLUSTER_DISEASE_ROLE | <not_specific> | def LF_CD_BICLUSTER_DISEASE_ROLE(c):
"""
This label function uses the bicluster data located in the
A global network of biomedical relationships
"""
sen_pos = c.get_parent().position
pubmed_id = c.get_parent().document.name
query = bicluster_dep_df.query("pubmed_id==@pubmed_id&sentence_num=... |
This label function uses the bicluster data located in the
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] | def LF_CD_BICLUSTER_DISEASE_ROLE(c):
sen_pos = c.get_parent().position
pubmed_id = c.get_parent().document.name
query = bicluster_dep_df.query("pubmed_id==@pubmed_id&sentence_num==@sen_pos")
if not(query.empty):
if query["J"].sum() > 0.0:
return 1
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13165b1ff01e6a231e6aab2b39e34461dc912c0b | ajlee21/snorkeling | playground/compound_disease/transfer_learning_experiment/data/label_functions/compound_disease_lf.py | [
"CC0-1.0",
"BSD-3-Clause"
] | Python | LF_CD_BICLUSTER_BIOMARKERS | <not_specific> | def LF_CD_BICLUSTER_BIOMARKERS(c):
"""
This label function uses the bicluster data located in the
A global network of biomedical relationships
"""
sen_pos = c.get_parent().position
pubmed_id = c.get_parent().document.name
query = bicluster_dep_df.query("pubmed_id==@pubmed_id&sentence_num==@... |
This label function uses the bicluster data located in the
A global network of biomedical relationships
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"network",
"of",
"biomedical",
"relationships"
] | def LF_CD_BICLUSTER_BIOMARKERS(c):
sen_pos = c.get_parent().position
pubmed_id = c.get_parent().document.name
query = bicluster_dep_df.query("pubmed_id==@pubmed_id&sentence_num==@sen_pos")
if not(query.empty):
if query["Mp"].sum() > 0.0:
return 1
return 0 | [
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632f68101e917b3144c8b44add82507d0cfe429f | ajlee21/snorkeling | compound_disease/compound_treats_disease/data/label_functions/compound_disease_lf.py | [
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"BSD-3-Clause"
] | Python | LF_CtD_WEAKLY_TREATS | <not_specific> | def LF_CtD_WEAKLY_TREATS(c):
"""
This label function is designed to look for phrases
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"""
if re.search(ltp(weak_treatment_indications), get_text_between(c), flags=re.I):
return 1
elif re.search(ltp(weak_treatment_indicatio... |
This label function is designed to look for phrases
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] | def LF_CtD_WEAKLY_TREATS(c):
if re.search(ltp(weak_treatment_indications), get_text_between(c), flags=re.I):
return 1
elif re.search(ltp(weak_treatment_indications), " ".join(get_left_tokens(c[0], window=5)), flags=re.I):
return 1
elif re.search(ltp(weak_treatment_indications), " ".join(get_... | [
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632f68101e917b3144c8b44add82507d0cfe429f | ajlee21/snorkeling | compound_disease/compound_treats_disease/data/label_functions/compound_disease_lf.py | [
"CC0-1.0",
"BSD-3-Clause"
] | Python | LF_CD_INCORRECT_COMPOUND | <not_specific> | def LF_CD_INCORRECT_COMPOUND(c):
"""
This label function is designed to capture phrases
that indicate the mentioned compound is a protein not a drug
"""
if re.search(ltp(incorrect_compound_indications), " ".join(get_left_tokens(c[0], window=5)), flags=re.I):
return -1
elif re.search(ltp(... |
This label function is designed to capture phrases
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] | def LF_CD_INCORRECT_COMPOUND(c):
if re.search(ltp(incorrect_compound_indications), " ".join(get_left_tokens(c[0], window=5)), flags=re.I):
return -1
elif re.search(ltp(incorrect_compound_indications), " ".join(get_right_tokens(c[0], window=5)), flags=re.I):
return -1
else:
return 0 | [
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632f68101e917b3144c8b44add82507d0cfe429f | ajlee21/snorkeling | compound_disease/compound_treats_disease/data/label_functions/compound_disease_lf.py | [
"CC0-1.0",
"BSD-3-Clause"
] | Python | LF_CpD_PALLIATES | <not_specific> | def LF_CpD_PALLIATES(c):
"""
This label function is designed to look for phrases
that could imply a compound binding to a gene/protein
"""
if re.search(ltp(palliates_indication), get_text_between(c), flags=re.I):
return 1
elif re.search(ltp(palliates_indication), " ".join(get_left_tokens... |
This label function is designed to look for phrases
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] | def LF_CpD_PALLIATES(c):
if re.search(ltp(palliates_indication), get_text_between(c), flags=re.I):
return 1
elif re.search(ltp(palliates_indication), " ".join(get_left_tokens(c[0], window=5)), flags=re.I):
return 1
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632f68101e917b3144c8b44add82507d0cfe429f | ajlee21/snorkeling | compound_disease/compound_treats_disease/data/label_functions/compound_disease_lf.py | [
"CC0-1.0",
"BSD-3-Clause"
] | Python | LF_CtD_COMPOUND_INDICATION | <not_specific> | def LF_CtD_COMPOUND_INDICATION(c):
"""
This label function is designed to look for phrases
that implies a compound increaseing activity of a gene/protein
"""
if re.search(ltp(compound_indications), get_text_between(c), flags=re.I):
return 1
elif re.search(ltp(compound_indications), " ".j... |
This label function is designed to look for phrases
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] | def LF_CtD_COMPOUND_INDICATION(c):
if re.search(ltp(compound_indications), get_text_between(c), flags=re.I):
return 1
elif re.search(ltp(compound_indications), " ".join(get_left_tokens(c[0], window=5)), flags=re.I):
return 1
elif re.search(ltp(compound_indications), " ".join(get_right_tokens... | [
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632f68101e917b3144c8b44add82507d0cfe429f | ajlee21/snorkeling | compound_disease/compound_treats_disease/data/label_functions/compound_disease_lf.py | [
"CC0-1.0",
"BSD-3-Clause"
] | Python | LF_CD_TITLE | <not_specific> | def LF_CD_TITLE(c):
"""
This label function is designed to look for phrases
that imply a sentence is the title
"""
if re.search(r'^(\[|\[ )?'+ltp(title_indication), get_tagged_text(c), flags=re.I):
return -1
elif re.search(ltp(title_indication)+r'$', get_tagged_text(c), flags=re.I):
... |
This label function is designed to look for phrases
that imply a sentence is the title
| This label function is designed to look for phrases
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] | def LF_CD_TITLE(c):
if re.search(r'^(\[|\[ )?'+ltp(title_indication), get_tagged_text(c), flags=re.I):
return -1
elif re.search(ltp(title_indication)+r'$', get_tagged_text(c), flags=re.I):
return -1
elif "(author's transl)" in get_tagged_text(c):
return -1
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632f68101e917b3144c8b44add82507d0cfe429f | ajlee21/snorkeling | compound_disease/compound_treats_disease/data/label_functions/compound_disease_lf.py | [
"CC0-1.0",
"BSD-3-Clause"
] | Python | LF_CtD_NO_CONCLUSION | <not_specific> | def LF_CtD_NO_CONCLUSION(c):
"""
This label function fires a -1 if the number of negative label functinos is greater than the number
of positive label functions.
The main idea behind this label function is add support to sentences that could
mention a possible disease gene association.
"""
p... |
This label function fires a -1 if the number of negative label functinos is greater than the number
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negative_num = np.abs(np.sum([LF_CD_METHOD_DESC(c), LF_CD_IN_SERIES(c)]))
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632f68101e917b3144c8b44add82507d0cfe429f | ajlee21/snorkeling | compound_disease/compound_treats_disease/data/label_functions/compound_disease_lf.py | [
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"""
This label function fires a 1 if the number of positive label functions is greater than the number
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The main idea behind this label function is add support to sentences that could
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632f68101e917b3144c8b44add82507d0cfe429f | ajlee21/snorkeling | compound_disease/compound_treats_disease/data/label_functions/compound_disease_lf.py | [
"CC0-1.0",
"BSD-3-Clause"
] | Python | LF_CD_ALLOWED_DISTANCE | <not_specific> | def LF_CD_ALLOWED_DISTANCE(c):
"""
This LF is designed to make sure that the compound mention
and the gene mention are in an acceptable distance between
each other
"""
return 0 if any([
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]) else 1 |
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632f68101e917b3144c8b44add82507d0cfe429f | ajlee21/snorkeling | compound_disease/compound_treats_disease/data/label_functions/compound_disease_lf.py | [
"CC0-1.0",
"BSD-3-Clause"
] | Python | LF_CD_BICLUSTER_TREATMENT | <not_specific> | def LF_CD_BICLUSTER_TREATMENT(c):
"""
This label function uses the bicluster data located in the
A global network of biomedical relationships
"""
sen_pos = c.get_parent().position
pubmed_id = int(c.get_parent().document.name)
if (pubmed_id, sen_pos) in treatment_base:
return 1
r... |
This label function uses the bicluster data located in the
A global network of biomedical relationships
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sen_pos = c.get_parent().position
pubmed_id = int(c.get_parent().document.name)
if (pubmed_id, sen_pos) in treatment_base:
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632f68101e917b3144c8b44add82507d0cfe429f | ajlee21/snorkeling | compound_disease/compound_treats_disease/data/label_functions/compound_disease_lf.py | [
"CC0-1.0",
"BSD-3-Clause"
] | Python | LF_CD_BICLUSTER_INHIBITS | <not_specific> | def LF_CD_BICLUSTER_INHIBITS(c):
"""
This label function uses the bicluster data located in the
A global network of biomedical relationships
"""
sen_pos = c.get_parent().position
pubmed_id = int(c.get_parent().document.name)
if (pubmed_id, sen_pos) in inhibits_base:
return 1
ret... |
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sen_pos = c.get_parent().position
pubmed_id = int(c.get_parent().document.name)
if (pubmed_id, sen_pos) in inhibits_base:
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632f68101e917b3144c8b44add82507d0cfe429f | ajlee21/snorkeling | compound_disease/compound_treats_disease/data/label_functions/compound_disease_lf.py | [
"CC0-1.0",
"BSD-3-Clause"
] | Python | LF_CD_BICLUSTER_SIDE_EFFECT | <not_specific> | def LF_CD_BICLUSTER_SIDE_EFFECT(c):
"""
This label function uses the bicluster data located in the
A global network of biomedical relationships
"""
sen_pos = c.get_parent().position
pubmed_id = int(c.get_parent().document.name)
if (pubmed_id, sen_pos) in side_effect_base:
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... |
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sen_pos = c.get_parent().position
pubmed_id = int(c.get_parent().document.name)
if (pubmed_id, sen_pos) in side_effect_base:
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632f68101e917b3144c8b44add82507d0cfe429f | ajlee21/snorkeling | compound_disease/compound_treats_disease/data/label_functions/compound_disease_lf.py | [
"CC0-1.0",
"BSD-3-Clause"
] | Python | LF_CD_BICLUSTER_PREVENTS | <not_specific> | def LF_CD_BICLUSTER_PREVENTS(c):
"""
This label function uses the bicluster data located in the
A global network of biomedical relationships
"""
sen_pos = c.get_parent().position
pubmed_id = int(c.get_parent().document.name)
if (pubmed_id, sen_pos) in prevents_base:
return 1
ret... |
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] | def LF_CD_BICLUSTER_PREVENTS(c):
sen_pos = c.get_parent().position
pubmed_id = int(c.get_parent().document.name)
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632f68101e917b3144c8b44add82507d0cfe429f | ajlee21/snorkeling | compound_disease/compound_treats_disease/data/label_functions/compound_disease_lf.py | [
"CC0-1.0",
"BSD-3-Clause"
] | Python | LF_CD_BICLUSTER_ALLEVIATES | <not_specific> | def LF_CD_BICLUSTER_ALLEVIATES(c):
"""
This label function uses the bicluster data located in the
A global network of biomedical relationships
"""
sen_pos = c.get_parent().position
pubmed_id = int(c.get_parent().document.name)
if (pubmed_id, sen_pos) in alleviates_base:
return 1
... |
This label function uses the bicluster data located in the
A global network of biomedical relationships
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] | def LF_CD_BICLUSTER_ALLEVIATES(c):
sen_pos = c.get_parent().position
pubmed_id = int(c.get_parent().document.name)
if (pubmed_id, sen_pos) in alleviates_base:
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632f68101e917b3144c8b44add82507d0cfe429f | ajlee21/snorkeling | compound_disease/compound_treats_disease/data/label_functions/compound_disease_lf.py | [
"CC0-1.0",
"BSD-3-Clause"
] | Python | LF_CD_BICLUSTER_DISEASE_ROLE | <not_specific> | def LF_CD_BICLUSTER_DISEASE_ROLE(c):
"""
This label function uses the bicluster data located in the
A global network of biomedical relationships
"""
sen_pos = c.get_parent().position
pubmed_id = int(c.get_parent().document.name)
if (pubmed_id, sen_pos) in disease_role_base:
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] | def LF_CD_BICLUSTER_DISEASE_ROLE(c):
sen_pos = c.get_parent().position
pubmed_id = int(c.get_parent().document.name)
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632f68101e917b3144c8b44add82507d0cfe429f | ajlee21/snorkeling | compound_disease/compound_treats_disease/data/label_functions/compound_disease_lf.py | [
"CC0-1.0",
"BSD-3-Clause"
] | Python | LF_CD_BICLUSTER_BIOMARKERS | <not_specific> | def LF_CD_BICLUSTER_BIOMARKERS(c):
"""
This label function uses the bicluster data located in the
A global network of biomedical relationships
"""
sen_pos = c.get_parent().position
pubmed_id = int(c.get_parent().document.name)
if (pubmed_id, sen_pos) in biomarkers_base:
return 1
... |
This label function uses the bicluster data located in the
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] | def LF_CD_BICLUSTER_BIOMARKERS(c):
sen_pos = c.get_parent().position
pubmed_id = int(c.get_parent().document.name)
if (pubmed_id, sen_pos) in biomarkers_base:
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498b6146498b27a03a9b99a273680b7852cf674f | ajlee21/snorkeling | modules/utils/notebook_utils/doc2vec_helper.py | [
"CC0-1.0",
"BSD-3-Clause"
] | Python | write_sentences_to_file | <not_specific> | def write_sentences_to_file(candidate_obj_dict, sentences_file_dict):
"""
This function is designed to get candiadte objects from the postgres database
candidate_obj_dict - a dictionary containing candidates objects
sentences_file_dict - a dictionary containing directories to write each file to.
""... |
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candidate_obj_dict - a dictionary containing candidates objects
sentences_file_dict - a dictionary containing directories to write each file to.
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498b6146498b27a03a9b99a273680b7852cf674f | ajlee21/snorkeling | modules/utils/notebook_utils/doc2vec_helper.py | [
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training_file - a file path that contains training sentences used for embeddings
word_file - a file path that tells doc2v... |
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ae2086908c37946bf640a0565011053391bf202e | ajlee21/snorkeling | playground/compound_disease/transfer_learning_experiment/data/label_functions/compound_gene_lf.py | [
"CC0-1.0",
"BSD-3-Clause"
] | Python | LF_HETNET_DRUGBANK | <not_specific> | def LF_HETNET_DRUGBANK(c):
"""
This label function returns 1 if the given Disease Gene pair is
located in the Drugbank database
"""
return 1 if (c.Gene_cid, c.Compound_cid, "DrugBank") in knowledge_base else 0 |
This label function returns 1 if the given Disease Gene pair is
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ae2086908c37946bf640a0565011053391bf202e | ajlee21/snorkeling | playground/compound_disease/transfer_learning_experiment/data/label_functions/compound_gene_lf.py | [
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] | Python | LF_HETNET_DRUGCENTRAL | <not_specific> | def LF_HETNET_DRUGCENTRAL(c):
"""
This label function returns 1 if the given Disease Gene pair is
located in the Drugcentral database
"""
return 1 if (c.Gene_cid, c.Compound_cid, "DrugCentral") in knowledge_base else 0 |
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ae2086908c37946bf640a0565011053391bf202e | ajlee21/snorkeling | playground/compound_disease/transfer_learning_experiment/data/label_functions/compound_gene_lf.py | [
"CC0-1.0",
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] | Python | LF_HETNET_ChEMBL | <not_specific> | def LF_HETNET_ChEMBL(c):
"""
This label function returns 1 if the given Disease Gene pair is
located in the ChEMBL database
"""
return 1 if (c.Gene_cid, c.Compound_cid, "ChEMBL") in knowledge_base else 0 |
This label function returns 1 if the given Disease Gene pair is
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ae2086908c37946bf640a0565011053391bf202e | ajlee21/snorkeling | playground/compound_disease/transfer_learning_experiment/data/label_functions/compound_gene_lf.py | [
"CC0-1.0",
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] | Python | LF_HETNET_BINDINGDB | <not_specific> | def LF_HETNET_BINDINGDB(c):
"""
This label function returns 1 if the given Disease Gene pair is
located in the BindingDB database
"""
return 1 if (c.Gene_cid, c.Compound_cid, "BindingDB") in knowledge_base else 0 |
This label function returns 1 if the given Disease Gene pair is
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ae2086908c37946bf640a0565011053391bf202e | ajlee21/snorkeling | playground/compound_disease/transfer_learning_experiment/data/label_functions/compound_gene_lf.py | [
"CC0-1.0",
"BSD-3-Clause"
] | Python | LF_HETNET_PDSP_KI | <not_specific> | def LF_HETNET_PDSP_KI(c):
"""
This label function returns 1 if the given Disease Gene pair is
located in the PDSP_KI database
"""
return 1 if (c.Gene_cid, c.Compound_cid, "PDSP Ki") in knowledge_base else 0 |
This label function returns 1 if the given Disease Gene pair is
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ae2086908c37946bf640a0565011053391bf202e | ajlee21/snorkeling | playground/compound_disease/transfer_learning_experiment/data/label_functions/compound_gene_lf.py | [
"CC0-1.0",
"BSD-3-Clause"
] | Python | LF_HETNET_US_PATENT | <not_specific> | def LF_HETNET_US_PATENT(c):
"""
This label function returns 1 if the given Disease Gene pair is
located in the US PATENT database
"""
return 1 if (c.Gene_cid, c.Compound_cid, "US Patent") in knowledge_base else 0 |
This label function returns 1 if the given Disease Gene pair is
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ae2086908c37946bf640a0565011053391bf202e | ajlee21/snorkeling | playground/compound_disease/transfer_learning_experiment/data/label_functions/compound_gene_lf.py | [
"CC0-1.0",
"BSD-3-Clause"
] | Python | LF_HETNET_PUBCHEM | <not_specific> | def LF_HETNET_PUBCHEM(c):
"""
This label function returns 1 if the given Disease Gene pair is
located in the PUBCHEM database
"""
return 1 if (c.Gene_cid, c.Compound_cid, "PubChem") in knowledge_base else 0 |
This label function returns 1 if the given Disease Gene pair is
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ae2086908c37946bf640a0565011053391bf202e | ajlee21/snorkeling | playground/compound_disease/transfer_learning_experiment/data/label_functions/compound_gene_lf.py | [
"CC0-1.0",
"BSD-3-Clause"
] | Python | LF_HETNET_CG_ABSENT | <not_specific> | def LF_HETNET_CG_ABSENT(c):
"""
This label function fires -1 if the given Disease Gene pair does not appear
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"""
return 0 if any([
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LF_HETNET_P... |
This label function fires -1 if the given Disease Gene pair does not appear
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ae2086908c37946bf640a0565011053391bf202e | ajlee21/snorkeling | playground/compound_disease/transfer_learning_experiment/data/label_functions/compound_gene_lf.py | [
"CC0-1.0",
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] | Python | LF_CG_CHECK_GENE_TAG | <not_specific> | def LF_CG_CHECK_GENE_TAG(c):
"""
This label function is used for labeling each passed candidate as either pos or neg.
Keyword Args:
c- the candidate object to be passed in.
"""
sen = c[1].get_parent()
gene_name = re.sub("\)", "", c[1].get_span().lower())
gene_id = sen.entity_cids[c[1].ge... |
This label function is used for labeling each passed candidate as either pos or neg.
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gene_entry_df = gene_desc.query("GeneID == @gene_id")
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ae2086908c37946bf640a0565011053391bf202e | ajlee21/snorkeling | playground/compound_disease/transfer_learning_experiment/data/label_functions/compound_gene_lf.py | [
"CC0-1.0",
"BSD-3-Clause"
] | Python | LF_CG_BINDING | <not_specific> | def LF_CG_BINDING(c):
"""
This label function is designed to look for phrases
that imply a compound binding to a gene/protein
"""
if re.search(ltp(binding_indication), get_text_between(c), flags=re.I):
return 1
elif re.search(ltp(binding_indication), " ".join(get_left_tokens(c[0], window... |
This label function is designed to look for phrases
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| This label function is designed to look for phrases
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if re.search(ltp(binding_indication), get_text_between(c), flags=re.I):
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elif re.search(ltp(binding_indication), " ".join(get_left_tokens(c[0], window=5)), flags=re.I):
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elif re.search(ltp(binding_indication), " ".join(get_right_tokens(c[0], window=5)), ... | [
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ae2086908c37946bf640a0565011053391bf202e | ajlee21/snorkeling | playground/compound_disease/transfer_learning_experiment/data/label_functions/compound_gene_lf.py | [
"CC0-1.0",
"BSD-3-Clause"
] | Python | LF_CG_WEAK_BINDING | <not_specific> | def LF_CG_WEAK_BINDING(c):
"""
This label function is designed to look for phrases
that could imply a compound binding to a gene/protein
"""
if re.search(ltp(weak_binding_indications), get_text_between(c), flags=re.I):
return 1
else:
return 0 |
This label function is designed to look for phrases
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if re.search(ltp(weak_binding_indications), get_text_between(c), flags=re.I):
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ae2086908c37946bf640a0565011053391bf202e | ajlee21/snorkeling | playground/compound_disease/transfer_learning_experiment/data/label_functions/compound_gene_lf.py | [
"CC0-1.0",
"BSD-3-Clause"
] | Python | LF_CG_UPREGULATES | <not_specific> | def LF_CG_UPREGULATES(c):
"""
This label function is designed to look for phrases
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"""
if re.search(ltp(upregulates), get_text_between(c), flags=re.I):
return 1
elif upregulates.intersection(get_left_tokens(c[1], window=2)):
... |
This label function is designed to look for phrases
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] | def LF_CG_UPREGULATES(c):
if re.search(ltp(upregulates), get_text_between(c), flags=re.I):
return 1
elif upregulates.intersection(get_left_tokens(c[1], window=2)):
return 1
else:
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ae2086908c37946bf640a0565011053391bf202e | ajlee21/snorkeling | playground/compound_disease/transfer_learning_experiment/data/label_functions/compound_gene_lf.py | [
"CC0-1.0",
"BSD-3-Clause"
] | Python | LF_CG_DOWNREGULATES | <not_specific> | def LF_CG_DOWNREGULATES(c):
"""
This label function is designed to look for phrases
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"""
if re.search(ltp(downregulates), get_text_between(c), flags=re.I):
return 1
elif downregulates.intersection(get_right_tokens(c[1... |
This label function is designed to look for phrases
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] | def LF_CG_DOWNREGULATES(c):
if re.search(ltp(downregulates), get_text_between(c), flags=re.I):
return 1
elif downregulates.intersection(get_right_tokens(c[1], window=2)):
return 1
else:
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ae2086908c37946bf640a0565011053391bf202e | ajlee21/snorkeling | playground/compound_disease/transfer_learning_experiment/data/label_functions/compound_gene_lf.py | [
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] | Python | LF_CG_GENE_RECEIVERS | <not_specific> | def LF_CG_GENE_RECEIVERS(c):
"""
This label function is designed to look for phrases
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"""
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return 1
elif re.search(ltp(gene_receivers), c[1].get_span(), flags=re.I):
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ae2086908c37946bf640a0565011053391bf202e | ajlee21/snorkeling | playground/compound_disease/transfer_learning_experiment/data/label_functions/compound_gene_lf.py | [
"CC0-1.0",
"BSD-3-Clause"
] | Python | LF_CG_ASE_SUFFIX | <not_specific> | def LF_CG_ASE_SUFFIX(c):
"""
This label function is designed to look parts of the gene tags
that implies a sort of "ase" or enzyme
"""
if re.search(r"ase\b", c[1].get_span(), flags=re.I):
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else:
return 0 |
This label function is designed to look parts of the gene tags
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| This label function is designed to look parts of the gene tags
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ae2086908c37946bf640a0565011053391bf202e | ajlee21/snorkeling | playground/compound_disease/transfer_learning_experiment/data/label_functions/compound_gene_lf.py | [
"CC0-1.0",
"BSD-3-Clause"
] | Python | LF_CG_IN_SERIES | <not_specific> | def LF_CG_IN_SERIES(c):
"""
This label function is designed to look for a mention being caught
in a series of other genes or compounds
"""
if len(re.findall(r',', get_tagged_text(c))) >= 2:
if re.search(', and', get_tagged_text(c)):
return -1
return 0 |
This label function is designed to look for a mention being caught
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| This label function is designed to look for a mention being caught
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if len(re.findall(r',', get_tagged_text(c))) >= 2:
if re.search(', and', get_tagged_text(c)):
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ae2086908c37946bf640a0565011053391bf202e | ajlee21/snorkeling | playground/compound_disease/transfer_learning_experiment/data/label_functions/compound_gene_lf.py | [
"CC0-1.0",
"BSD-3-Clause"
] | Python | LF_CG_ANTIBODY | <not_specific> | def LF_CG_ANTIBODY(c):
"""
This label function is designed to look for phrase
antibody.
"""
if "antibody" in c[1].get_span() or re.search("antibody", " ".join(get_right_tokens(c[1], window=3))):
return 1
elif "antibodies" in c[1].get_span() or re.search("antibodies", " ".join(get_right_t... |
This label function is designed to look for phrase
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| This label function is designed to look for phrase
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] | def LF_CG_ANTIBODY(c):
if "antibody" in c[1].get_span() or re.search("antibody", " ".join(get_right_tokens(c[1], window=3))):
return 1
elif "antibodies" in c[1].get_span() or re.search("antibodies", " ".join(get_right_tokens(c[1], window=3))):
return 1
else:
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ae2086908c37946bf640a0565011053391bf202e | ajlee21/snorkeling | playground/compound_disease/transfer_learning_experiment/data/label_functions/compound_gene_lf.py | [
"CC0-1.0",
"BSD-3-Clause"
] | Python | LF_CG_METHOD_DESC | <not_specific> | def LF_CG_METHOD_DESC(c):
"""
This label function is designed to look for phrases
that imply a sentence is description an experimental design
"""
if re.search(ltp(method_indication), get_tagged_text(c), flags=re.I):
return -1
else:
return 0 |
This label function is designed to look for phrases
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| This label function is designed to look for phrases
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] | def LF_CG_METHOD_DESC(c):
if re.search(ltp(method_indication), get_tagged_text(c), flags=re.I):
return -1
else:
return 0 | [
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ae2086908c37946bf640a0565011053391bf202e | ajlee21/snorkeling | playground/compound_disease/transfer_learning_experiment/data/label_functions/compound_gene_lf.py | [
"CC0-1.0",
"BSD-3-Clause"
] | Python | LF_CG_NO_CONCLUSION | <not_specific> | def LF_CG_NO_CONCLUSION(c):
"""
This label function fires a -1 if the number of negative label functinos is greater than the number
of positive label functions.
The main idea behind this label function is add support to sentences that could
mention a possible disease gene association.
"""
po... |
This label function fires a -1 if the number of negative label functinos is greater than the number
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The main idea behind this label function is add support to sentences that could
mention a possible disease gene association.
| This label function fires a -1 if the number of negative label functinos is greater than the number
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The main idea behind this label function is add support to sentences that could
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positive_num = np.sum([LF_CG_BINDING(c), LF_CG_WEAK_BINDING(c),
LF_CG_GENE_RECEIVERS(c), LF_CG_ANTIBODY(c),
LF_CG_UPREGULATES(c), LF_CG_DOWNREGULATES(c)])
negative_num = np.abs(np.sum(LF_CG_METHOD_DESC(c)))
if positive_num - negative_num >= 1:
return 0
... | [
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] | [
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} |
ae2086908c37946bf640a0565011053391bf202e | ajlee21/snorkeling | playground/compound_disease/transfer_learning_experiment/data/label_functions/compound_gene_lf.py | [
"CC0-1.0",
"BSD-3-Clause"
] | Python | LF_CG_CONCLUSION | <not_specific> | def LF_CG_CONCLUSION(c):
"""
This label function fires a 1 if the number of positive label functions is greater than the number
of negative label functions.
The main idea behind this label function is add support to sentences that could
mention a possible disease gene association
"""
if not ... |
This label function fires a 1 if the number of positive label functions is greater than the number
of negative label functions.
The main idea behind this label function is add support to sentences that could
mention a possible disease gene association
| This label function fires a 1 if the number of positive label functions is greater than the number
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The main idea behind this label function is add support to sentences that could
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if not LF_CG_NO_CONCLUSION(c):
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} |
ae2086908c37946bf640a0565011053391bf202e | ajlee21/snorkeling | playground/compound_disease/transfer_learning_experiment/data/label_functions/compound_gene_lf.py | [
"CC0-1.0",
"BSD-3-Clause"
] | Python | LF_CG_DISTANCE_SHORT | <not_specific> | def LF_CG_DISTANCE_SHORT(c):
"""
This LF is designed to make sure that the compound mention
and the gene mention aren't right next to each other.
"""
return -1 if len(list(get_between_tokens(c))) <= 2 else 0 |
This LF is designed to make sure that the compound mention
and the gene mention aren't right next to each other.
| This LF is designed to make sure that the compound mention
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] | def LF_CG_DISTANCE_SHORT(c):
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],
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} |
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