The avatar for @ndobb
Nic Dobbins
Biomedical Software Engineer @uwrit, @uwbhi, @uw-bionlp. Creator of the Leaf clinical data explorer app. PhD from the University of Washington.
Published
Edited
Apr 23, 2021
5 stars
2
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relations.view(5);
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toksByLabel.view(5);
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tokLabelCounts.view(5);
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jsonEntities = FileAttachment("clinical_trials_annotation_entities.json").json()
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jsonRelations = FileAttachment("clinical_trials_annotation_relations@5.json").json()
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tokFreqsJs = {
const freqs = {};
for (let i = 0; i < jsonEntities.length; i++) {
const toks = jsonEntities[i].span.toLowerCase().split(" ");
for (let j = 0; j < toks.length; j++) {
const tok = toks[j];
if (tok in freqs) freqs[tok] += 1;
else freqs[tok] = 1;
}
}
return Object.entries(freqs);
}
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tokFreqs = aq.from(tokFreqsJs);
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toksByLabelPivot = tokFreqs
.join(entities.unroll('tokens'), ['0', 'tokens'])
.filter(d => op.length(d.tokens) > 3)
.groupby('tokens', 'type')
.count()
.groupby('tokens')
.pivot('type', { value: d => op.sum(d.count) });
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toksByLabel = tokFreqs
.join(entities.unroll('tokens'), ['0', 'tokens'])
.filter(d => op.length(d.tokens) > 3)
.groupby('tokens', 'type','metatype')
.count();
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