main.py

import json  # to work with JSON
import threading  # for threading
import time  # for better HCI

import datasets  # to load the dataset
import faiss  # to create an index
import gradio  # for the interface
import numpy  # to work with vectors
import pandas  # to work with pandas
import sentence_transformers  # to load an embedding model
import spaces  # for GPU
import transformers  # to load an LLM

# Constants
GREETING = (
    "Howdy! I'm an AI agent that uses a [retrieval-augmented generation]("
    "https://en.wikipedia.org/wiki/Retrieval-augmented_generation) pipeline to answer questions about research by the "
    "[Design Research Collective](https://cmudrc.github.io/). And the best part is that I always cite my sources! What"
    " can I tell you about today?"
)
EXAMPLE_QUERIES = [
    "Tell me about new research at the intersection of additive manufacturing and machine learning",
    "What is a physics-informed neural network and what can it be used for?",
    "What can agent-based models do about climate change?",
]
EMBEDDING_MODEL_NAME = "allenai-specter"
LLM_MODEL_NAME = "Qwen/Qwen2-7B-Instruct"

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

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

# Create a FAISS index for fast similarity search
metric = faiss.METRIC_INNER_PRODUCT
vectors = numpy.stack(data["embedding"].tolist(), axis=0)
index = faiss.IndexFlatL2(len(data["embedding"][0]))
index.metric_type = metric
faiss.normalize_L2(vectors)
index.train(vectors)
index.add(vectors)

# Load the model for later use in embeddings
model = sentence_transformers.SentenceTransformer(EMBEDDING_MODEL_NAME)


def search(query: str, k: int) -> tuple[str, str]:
    """
    Searches the dataset for the top k most relevant papers to the query
    Args:
        query (str): The user's query
        k (int): The number of results to return
    Returns:
        tuple[str, str]: A tuple containing the search results and references
    """
    query = numpy.expand_dims(model.encode(query), axis=0)
    faiss.normalize_L2(query)
    D, I = index.search(query, k)
    top_five = data.loc[I[0]]

    search_results = (
        "You are an AI assistant who delights in helping people learn about research from the Design "
        "Research Collective. Here are several abstracts from really cool, and really relevant, "
        "papers:\n\n"
    )

    references = "\n\n## References\n\n"

    for i in range(k):
        search_results += top_five["bib_dict"].values[i]["abstract"] + "\n"
        references += (
            str(i + 1)
            + ". "
            + ", ".join(
                [
                    author.split(" ")[-1]
                    for author in top_five["bib_dict"]
                    .values[i]["author"]
                    .split(" and ")
                ]
            )
            + ". ("
            + str(int(top_five["bib_dict"].values[i]["pub_year"]))
            + "). ["
            + top_five["bib_dict"].values[i]["title"]
            + "]"
            + "(https://scholar.google.com/citations?view_op=view_citation&citation_for_view="
            + top_five["author_pub_id"].values[i]
            + ").\n"
        )

    search_results += (
        "\nUsing the information provided above, respond to this  query: "
    )

    return search_results, references


# Create an LLM pipeline that we can send queries to
tokenizer = transformers.AutoTokenizer.from_pretrained(LLM_MODEL_NAME)
streamer = transformers.TextIteratorStreamer(
    tokenizer, skip_prompt=True, skip_special_tokens=True
)
chatmodel = transformers.AutoModelForCausalLM.from_pretrained(
    LLM_MODEL_NAME, torch_dtype="auto", device_map="auto"
)


def preprocess(message: str) -> tuple[str, str]:
    """
    Applies a preprocessing step to the user's message before the LLM receives it
    Args:
        message (str): The user's message
    Returns:
        tuple[str, str]: A tuple containing the preprocessed message and a bypass variable
    """
    block_search_results, formatted_search_results = search(message, 5)
    return block_search_results + message, formatted_search_results


def postprocess(response: str, bypass_from_preprocessing: str) -> str:
    """
    Applies a postprocessing step to the LLM's response before the user receives it
    Args:
        response (str): The LLM's response
        bypass_from_preprocessing (str): The bypass variable from the preprocessing step
    Returns:
        str: The postprocessed response
    """
    return response + bypass_from_preprocessing


@spaces.GPU
def reply(message: str, history: list[str]) -> str:
    """
    This function is responsible for crafting a response
    Args:
        message (str): The user's message
        history (list[str]): The conversation history
    Returns:
        str: The AI's response
    """

    # Apply preprocessing
    message, bypass = preprocess(message)

    # This is some handling that is applied to the history variable to put it in a good format
    history_transformer_format = [
        {"role": role, "content": message_pair[idx]}
        for message_pair in history
        for idx, role in enumerate(["user", "assistant"])
        if message_pair[idx] is not None
    ] + [{"role": "user", "content": message}]

    # Stream a response from pipe
    text = tokenizer.apply_chat_template(
        history_transformer_format, tokenize=False, add_generation_prompt=True
    )
    model_inputs = tokenizer([text], return_tensors="pt").to("cuda:0")

    generate_kwargs = dict(model_inputs, streamer=streamer, max_new_tokens=512)
    t = threading.Thread(target=chatmodel.generate, kwargs=generate_kwargs)
    t.start()

    partial_message = ""
    for new_token in streamer:
        if new_token != "<":
            partial_message += new_token
            time.sleep(0.05)
            yield partial_message

    yield partial_message + bypass


# Create and run the gradio interface
gradio.ChatInterface(
    reply,
    examples=EXAMPLE_QUERIES,
    chatbot=gradio.Chatbot(
        show_label=False, show_copy_button=True, value=[[None, GREETING]]
    ),
    retry_btn=None,
    undo_btn=None,
    clear_btn=None,
    cache_examples=True,
    fill_height=True,
).launch(debug=True)