main.py

import json  # For stringifying a dict
import random # For selecting a search hint

import gradio  # GUI framework
import datasets  # Used to load publication dataset

import numpy  # For a few simple matrix operations
import pandas  # Needed for operating on dataset
import sentence_transformers  # Needed for query embedding
import faiss  # Needed for fast similarity search

# Load the dataset and convert to pandas
full_data = datasets.load_dataset("ccm/publications")["train"].to_pandas()

# Define the base URL for Google Scholar
SCHOLAR_URL = "https://scholar.google.com"

# Filter out any publications without an abstract
filter = [
    '"abstract": null' in json.dumps(bibdict)
    for bibdict in full_data["bib_dict"].values
]
data = full_data[~pandas.Series(filter)]
data.reset_index(inplace=True)

# Create a FAISS index for fast similarity search
indices = []
metrics = [faiss.METRIC_INNER_PRODUCT ,faiss.METRIC_L2]
normalization = [True, False]
vectors = numpy.stack(data["embedding"].tolist(), axis=0)
for  metric in metrics:
    for normal in normalization:
        index = faiss.IndexFlatL2(len(data["embedding"][0]))
        index.metric_type = metric
        if normal:
            faiss.normalize_L2(vectors)
        index.train(vectors)
        index.add(vectors)
        indices.append(index)

# Load the model for later use in embeddings
model = sentence_transformers.SentenceTransformer("allenai-specter")

# Define the search function
def search(query: str, k: int, n: int):
    query = numpy.expand_dims(model.encode(query), axis=0)
    faiss.normalize_L2(query)
    D, I = indices[n].search(query, k)
    top_five = data.loc[I[0]]
    search_results = ""

    for i in range(k):
        search_results += "### " + top_five["bib_dict"].values[i]["title"] + "\n\n"
        search_results += str(int(100*D[0][i])) + "% relevant  "
        if top_five["author_pub_id"].values[i] is not None:
            search_results += "/  [Full Text](https://scholar.google.com/citations?view_op=view_citation&citation_for_view=" + top_five["author_pub_id"].values[i] + ")  "
        if top_five["citedby_url"].values[i] is not None:
            search_results += (
                "/  [Cited By](" + SCHOLAR_URL + top_five["citedby_url"].values[i] + ")  "
            )
        if top_five["url_related_articles"].values[i] is not None:
            search_results += (
                "/  [Related Articles]("
                + SCHOLAR_URL
                + top_five["url_related_articles"].values[i]
                + ")  "
            )
        search_results += "\n\n```bibtex\n"
        search_results += (
            json.dumps(top_five["bibtex"].values[i], indent=4)
            .replace("\\n", "\n")
            .replace("\\t", "\t")
            .strip('"')
        )
        search_results += "```\n"
    return search_results


with gradio.Blocks() as demo:
    with gradio.Group():
        query = gradio.Textbox(
            placeholder = random.choice([
                "design for additive manufacturing",
                "best practices for agent based modeling",
                "arctic environmental science",
                "analysis of student teamwork"
            ]), 
            show_label=False, 
            lines=1, 
            max_lines=1
        )
        with gradio.Accordion("Settings", open=False):
            k = gradio.Number(10.0, label="Number of results", precision=0)
            k = gradio.Radio([True, False], label="Normalized")
    results = gradio.Markdown()
    query.change(fn=search, inputs=[query, k, n], outputs=results)
    k.change(fn=search, inputs=[query, k, n], outputs=results)
    n.change(fn=search, inputs=[query, k, n], outputs=results)

demo.launch(debug=True)