import os import re import secrets import string import yaml from datetime import datetime from zipfile import ZipFile import gradio as gr import nltk import pandas as pd from langchain.embeddings import OpenAIEmbeddings from langchain.chains import SimpleSequentialChain from langchain.chat_models import ChatOpenAI from nltk.tokenize import sent_tokenize from pandas import DataFrame import utils from chains import llm_chains # download NLTK dependencies nltk.download("punkt") nltk.download("stopwords") # load stop words const. from nltk.corpus import stopwords STOP_WORDS = stopwords.words("english") # load global spacy model # try: # SPACY_MODEL = spacy.load("en_core_web_sm") # except OSError: # print("[spacy] Downloading model: en_core_web_sm") # spacy.cli.download("en_core_web_sm") # SPACY_MODEL = spacy.load("en_core_web_sm") class Text2KG: """Text2KG class.""" def __init__(self, api_key: str, **kwargs): self.llm = ChatOpenAI(openai_api_key=api_key, **kwargs) self.embedding = OpenAIEmbeddings(openai_api_key=api_key) def init(self, steps: list[str]): """Initialize Text2KG pipeline from passed steps. Args: *steps (str): Steps to include in pipeline. Must be a top-level name present in the schema.yml file """ self.pipeline = SimpleSequentialChain( chains=[llm_chains[step](llm=self.llm) for step in steps], verbose=False ) def run(self, text: str) -> list[dict]: """Run Text2KG pipeline on passed text. Arg: text (str): The text input Returns: triplets (list): The list of extracted KG triplets """ triplets = self.pipeline.run(text) return triplets def clean(self, kg: DataFrame) -> DataFrame: """Text2KG post-processing.""" drop_list = [] for i, row in kg.iterrows(): # drop stopwords (e.g. pronouns) if (row.subject in STOP_WORDS) or (row.object in STOP_WORDS): drop_list.append(i) # drop broken triplets elif row.hasnans: drop_list.append(i) # lowercase nodes/edges, drop articles else: article_pattern = r'^(the|a|an) (.+)' be_pattern = r'^(are|is) (a )?(.+)' kg.at[i, "subject"] = re.sub(article_pattern, r'\2', row.subject.lower()) kg.at[i, "relation"] = re.sub(be_pattern, r'\3', row.relation.lower()) kg.at[i, "object"] = re.sub(article_pattern, r'\2', row.object.lower()) return kg.drop(drop_list) def normalize(self, kg: DataFrame, threshold: float=0.3) -> DataFrame: """Reduce dimensionality of Text2KG output by merging cosine-similar nodes/edges.""" ents = pd.concat([kg["subject"], kg["object"]]).unique() rels = kg["relation"].unique() ent_map = utils.condense_labels(ents, self.embedding.embed_documents, threshold=threshold) rel_map = utils.condense_labels(rels, self.embedding.embed_documents, threshold=threshold) kg_normal = pd.DataFrame() kg_normal["subject"] = kg["subject"].map(ent_map) kg_normal["relation"] = kg["relation"].map(rel_map) kg_normal["object"] = kg["object"].map(ent_map) return kg_normal def extract_knowledge_graph(api_key: str, batch_size: int, modules: list[str], text: str, progress=gr.Progress()): """Extract knowledge graph from text. Args: api_key (str): OpenAI API key batch_size (int): Number of sentences per forward pass modules (list): Additional modules to add before main extraction step text (str): Text from which Text2KG will extract knowledge graph from progress: Progress bar. The default is gradio's progress bar; for a command line progress bar, set `progress = tqdm` Returns: zip_path (str): Path to ZIP archive containing outputs knowledge_graph (DataFrame): The extracted knowledge graph """ # init if api_key == "": raise ValueError("API key is required") pipeline = Text2KG(api_key=api_key, temperature=0.3) # low temp. -> low randomness steps = [] for module in modules: m = module.lower().replace(' ', '_') steps.append(m) if (len(steps) == 0) or (steps[-1] != "triplet_extraction"): steps.append("triplet_extraction") pipeline.init(steps) # split text into batches sentences = sent_tokenize(text) batches = [" ".join(sentences[i:i+batch_size]) for i in range(0, len(sentences), batch_size)] # create KG knowledge_graph = [] for i, batch in progress.tqdm(list(enumerate(batches)), desc="Processing...", unit="batches"): output = pipeline.run(batch) [triplet.update({"sentence_id": i}) for triplet in output] knowledge_graph.extend(output) # convert to df, post-process data knowledge_graph = pd.DataFrame(knowledge_graph) knowledge_graph = pipeline.clean(knowledge_graph) # rearrange columns knowledge_graph = knowledge_graph[["sentence_id", "subject", "relation", "object"]] # metadata now = datetime.now() date = str(now.date()) metadata = { "_timestamp": now, "batch_size": batch_size, "modules": steps } # unique identifier for local saving uid = ''.join(secrets.choice(string.ascii_letters) for _ in range(6)) print(f"Run ID: {date}/{uid}") save_dir = os.path.join(".", "output", date, uid) os.makedirs(save_dir, exist_ok=True) # save metadata & data with open(os.path.join(save_dir, "metadata.yml"), 'w') as f: yaml.dump(metadata, f) batches_df = pd.DataFrame(enumerate(batches), columns=["sentence_id", "text"]) batches_df.to_csv(os.path.join(save_dir, "sentences.txt"), index=False) knowledge_graph.to_csv(os.path.join(save_dir, "kg.txt"), index=False) # create ZIP file zip_path = os.path.join(save_dir, "output.zip") with ZipFile(zip_path, 'w') as zipObj: zipObj.write(os.path.join(save_dir, "metadata.yml")) zipObj.write(os.path.join(save_dir, "sentences.txt")) zipObj.write(os.path.join(save_dir, "kg.txt")) return zip_path, knowledge_graph class App: def __init__(self): demo = gr.Interface( fn=extract_knowledge_graph, title="Text2KG", inputs=[ gr.Textbox(placeholder="API key...", label="OpenAI API Key", type="password"), gr.Slider(minimum=1, maximum=10, step=1, label="Sentence Batch Size"), gr.CheckboxGroup(choices=["Clause Deconstruction"], label="Optional Modules"), gr.Textbox(lines=2, placeholder="Text Here...", label="Input Text"), ], outputs=[ gr.File(label="Knowledge Graph"), gr.DataFrame(label="Preview", headers=["sentence_id", "subject", "relation", "object"], max_rows=10, overflow_row_behaviour="paginate") ], examples=[[None, 1, [], ("All cells share four common components: " "1) a plasma membrane, an outer covering that separates the " "cell's interior from its surrounding environment; 2) cytoplasm, " "consisting of a jelly-like cytosol within the cell in which " "there are other cellular components; 3) DNA, the cell's genetic " "material; and 4) ribosomes, which synthesize proteins. However, " "prokaryotes differ from eukaryotic cells in several ways. A " "prokaryote is a simple, mostly single-celled (unicellular) " "organism that lacks a nucleus, or any other membrane-bound " "organelle. We will shortly come to see that this is significantly " "different in eukaryotes. Prokaryotic DNA is in the cell's central " "part: the nucleoid.")]], allow_flagging="never", cache_examples=False ) demo.queue().launch(share=False) if __name__ == "__main__": App()