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Duplicate from ADRXtractor/ADR_Xtractor
Browse filesCo-authored-by: Abhishek bisht <abhibisht89@users.noreply.huggingface.co>
- .gitattributes +27 -0
- README.md +38 -0
- app.py +46 -0
- requirements.txt +3 -0
.gitattributes
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README.md
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---
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title: ADR_Xtractor
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emoji: 🌍
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colorFrom: red
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colorTo: blue
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sdk: gradio
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app_file: app.py
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pinned: false
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duplicated_from: ADRXtractor/ADR_Xtractor
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---
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# Configuration
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`title`: _string_
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Display title for the Space
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`emoji`: _string_
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Space emoji (emoji-only character allowed)
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`colorFrom`: _string_
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Color for Thumbnail gradient (red, yellow, green, blue, indigo, purple, pink, gray)
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`colorTo`: _string_
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Color for Thumbnail gradient (red, yellow, green, blue, indigo, purple, pink, gray)
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`sdk`: _string_
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Can be either `gradio` or `streamlit`
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`sdk_version` : _string_
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Only applicable for `streamlit` SDK.
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See [doc](https://hf.co/docs/hub/spaces) for more info on supported versions.
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`app_file`: _string_
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Path to your main application file (which contains either `gradio` or `streamlit` Python code).
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Path is relative to the root of the repository.
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`pinned`: _boolean_
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Whether the Space stays on top of your list.
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app.py
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import gradio as gr
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from spacy import displacy
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from transformers import AutoTokenizer, AutoModelForTokenClassification,pipeline
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tokenizer = AutoTokenizer.from_pretrained("abhibisht89/spanbert-large-cased-finetuned-ade_corpus_v2")
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model = AutoModelForTokenClassification.from_pretrained("abhibisht89/spanbert-large-cased-finetuned-ade_corpus_v2").to('cpu')
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adr_ner_model = pipeline(task="ner", model=model, tokenizer=tokenizer,grouped_entities=True)
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def get_adr_from_text(sentence):
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tokens = adr_ner_model(sentence)
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entities = []
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for token in tokens:
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label = token["entity_group"]
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if label != "O":
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token["label"] = label
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entities.append(token)
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params = [{"text": sentence,
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"ents": entities,
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"title": None}]
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html = displacy.render(params, style="ent", manual=True, options={
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"colors": {
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"DRUG": "#f08080",
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"ADR": "#9bddff",
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},
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})
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return html
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exp=["Abortion, miscarriage or uterine hemorrhage associated with misoprostol (Cytotec), a labor-inducing drug.",
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"Addiction to many sedatives and analgesics, such as diazepam, morphine, etc.",
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"Birth defects associated with thalidomide",
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"Bleeding of the intestine associated with aspirin therapy",
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"Cardiovascular disease associated with COX-2 inhibitors (i.e. Vioxx)",
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"Deafness and kidney failure associated with gentamicin (an antibiotic)",
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"Having fever after taking paracetamol"]
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desc="An adverse drug reaction (ADR) can be defined as an appreciably harmful or unpleasant reaction resulting from an intervention related to the use of a medicinal product.\
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The goal of this project is to extracts the adverse drug reaction from unstructured text with the Drug."
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inp=gr.inputs.Textbox(lines=5, placeholder=None, default="", label="text to extract adverse drug reaction and drug mention")
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out=gr.outputs.HTML(label=None)
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iface = gr.Interface(fn=get_adr_from_text, inputs=inp, outputs=out,examples=exp,article=desc,title="Adverse Drug Reaction Xtractor",theme="huggingface",layout='horizontal')
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iface.launch()
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requirements.txt
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spacy==3.0.2
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torch==1.5.0
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transformers==4.12.5
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