app.py

import json
from collections import defaultdict

import matplotlib.pyplot as plt
import gradio as gr
import pandas as pd
from transformers import pipeline, AutoTokenizer, AutoModelForTokenClassification

tokenizer = AutoTokenizer.from_pretrained("d4data/biomedical-ner-all")
model = AutoModelForTokenClassification.from_pretrained("d4data/biomedical-ner-all")

plt.switch_backend("Agg")

EXAMPLE_MAP = {}
with open("examples.json", "r") as f:
    example_json = json.load(f)
    EXAMPLE_MAP = {x["text"]: x["label"] for x in example_json}

pipe = pipeline("ner", model=model, tokenizer=tokenizer, aggregation_strategy="simple")


def group_by_entity(raw):
    out = defaultdict(int)
    for ent in raw:
        out[ent["entity_group"]] += 1
    # out["total"] = sum(out.values())
    return out


def plot_to_figure(grouped):
    fig = plt.figure()
    plt.bar(x=list(grouped.keys()), height=list(grouped.values()))
    plt.margins(0.2)
    plt.subplots_adjust(bottom=0.4)
    plt.xticks(rotation=90)
    return fig


def ner(text):
    raw = pipe(text)
    ner_content = {
        "text": text,
        "entities": [
            {
                "entity": x["entity_group"],
                "word": x["word"],
                "score": x["score"],
                "start": x["start"],
                "end": x["end"],
            }
            for x in raw
        ],
    }
    grouped = group_by_entity(raw)
    figure = plot_to_figure(grouped)
    label = EXAMPLE_MAP.get(text, "Unknown")

    meta = {
        "entity_counts": grouped,
        "entities": len(set(grouped.keys())),
        "counts": sum(grouped.values()),
    }

    return (ner_content, meta, label, figure)


interface = gr.Interface(
    ner,
    inputs=gr.Textbox(label="Note text", value=""),
    outputs=[
        gr.HighlightedText(label="NER", combine_adjacent=True),
        gr.JSON(label="Entity Counts"),
        gr.Label(label="Rating"),
        gr.Plot(label="Bar"),
    ],
    examples=list(EXAMPLE_MAP.keys()),
    allow_flagging="never",
)

interface.launch()