paper2slides.py

slide_datasource = {
    'introduction': ['abstract', 'Introduction'],
    'objective': ['abstract', 'Introduction'],
    'methodoloy': ['abstract', 'Introduction', 'Conclusion', 'Methods'],
    'results': ['abstract', 'Experiments', 'Conclusion'],
    'conclusion': ['abstract', 'Introduction', 'Conclusion'],
}

from pdf_helper import PDFPaper4LLMParser, dict_to_markdown_list
from sambaAPI import call_llama_chat, MODEL_ALIAS
from pdf_helper import markdown_to_slide_dicts
from pptx_utils import Dict2PPT, os
import json
import time
import string

SLIDE_SEP = '<slide_sep>'

def trim_string(s):
    return s.strip(string.whitespace + string.punctuation)

section_title_key_phrases = {
    'Introduction': ['introduction'],
    'Related Works': ['related work'],
    'Methods': ['method', 'approach'],
    'Experiments': ['experiment'],
    'Conclusion': ['conclusion'],
    'Acknowledgements': ['acknowledgement'],
    'References': ['references', ' references'], #
}

def find_string_index(string_list, target: str):
    """
    Returns the index of the target string in the list.
    If the target is not found, returns -1.

    Parameters:
    string_list (list): A list of strings
    target (str): The string to find in the list

    Returns:
    int: The index of the target string, or -1 if not found
    """
    try:
        return string_list.index(target)
    except ValueError:
        return -1


def get_section_category(section_name: str):
    """
    Scientist paper section name mapping
    """
    for key, phrases in section_title_key_phrases.items():
        for phrase in phrases:
            if phrase in section_name.lower():
                return key
    return 'Other'


class PaperReader(object):
    def __init__(self, page_chunks=False):
        self.paper_reader = PDFPaper4LLMParser(page_chunks=page_chunks)

    def pdf2text(self, paper_pdf_path: str):
        paper_content = self.paper_reader.run(pdf_path=paper_pdf_path, verbose=False)
        return paper_content
    
    def structurize(self, main_text_array: list):
        section_names = [_['title'] for _ in main_text_array]
        section_name_topics = [get_section_category(_) for _ in section_names]
        introduction_idx = find_string_index(section_name_topics, target='Introduction')
        refference_idx = find_string_index(section_name_topics, target='References')
        experiment_idx = find_string_index(section_name_topics, target='Experiments')
        conclusion_idx = find_string_index(section_name_topics, target='Conclusion')
        if refference_idx > 0:
            for idx in range(len(section_name_topics)):
                if idx < refference_idx:
                    if section_name_topics[idx] == 'Other':
                        section_name_topics[idx] = 'Methods'
                elif idx > refference_idx:
                    if not ('appendix' in section_name_topics[idx].lower()):
                        section_name_topics[idx] = 'Appendix: ' + section_name_topics[idx]
                else:
                    continue
            # print(section_name_topics)
            if experiment_idx > 0:
                for idx in range(experiment_idx +1, refference_idx):
                    if section_name_topics[idx] == 'Methods':
                        section_name_topics[idx] = 'Experiments'
        # print(section_name_topics)
        experiment_idx = find_string_index(section_name_topics, target='Experiments')
        method_idx = find_string_index(section_name_topics, target='Methods')
        relatedwork_idx = find_string_index(section_name_topics, target='Related Works')
        ack_idx = find_string_index(section_name_topics, target='Acknowledgements')
        
        paper_structure_dict = {
            'Introduction': [introduction_idx],
            'Related Works': [relatedwork_idx],
            'References': [refference_idx],
            'Conclusion': [conclusion_idx],
            'Acknowledgements': [ack_idx]
        }

        ## Experiments and methodology
        method_idx_array = []
        if method_idx >=0:
            for idx in range(method_idx, len(section_name_topics)):
                if section_name_topics[idx] == 'Methods':
                    method_idx_array.append(idx)
                else:
                    break
        else:
            if introduction_idx >=0 and conclusion_idx >=0:
                for idx in range(introduction_idx+1, conclusion_idx):
                    if section_name_topics[idx] == 'Methods':
                        method_idx_array.append(idx)
                    else:
                        break

        
        exp_idx_array = []
        if experiment_idx >=0:
            for idx in range(experiment_idx, len(section_name_topics)):
                if section_name_topics[idx] == 'Experiments':
                    exp_idx_array.append(idx)
                else:
                    break
        else:
            if introduction_idx >=0 and conclusion_idx >=0:
                for idx in range(introduction_idx+1, conclusion_idx):
                    if section_name_topics[idx] == 'Experiments':
                        exp_idx_array.append(idx)
                    else:
                        break
        
        paper_structure_dict['Experiments'] = exp_idx_array
        paper_structure_dict['Methods'] = method_idx_array
        return section_name_topics, paper_structure_dict

    def run(self, paper_file_name: str):
        start_time = time.time()
        paper_content = self.pdf2text(paper_pdf_path=paper_file_name)
        section_name_topics, paper_structure_dict = self.structurize(main_text_array=paper_content['main_text'])
        paper_content['structure'] = paper_structure_dict
        paper_content['section_topic'] = section_name_topics
        print('Runtime for pdf2text = {:.4f} seconds.'.format(time.time() - start_time))
        return paper_content

### 1. General System Prompt
    
SCHOLAR_PROMPT = """
You are an assistant being skilled at critically reading and analyzing academic papers to extract key insights, trends, and findings.
"""

### 2. Paper Outline Generation from Abstract

ABSTRACT_SUMMARY_PROMPT = """
You are given the **title** and **abstract** of an academic paper. Please first identity the research topic, and then extract the following aspects in a minimal title draft (max 15 words) for PowerPoint presentation:
	
    1.	**Background**: Introduces the research context and importance.
	2.	**Research Problem**: Identifies the specific problem or knowledge gap.
	3.	**Objectives**: States the research goals or hypotheses.
	4.	**Methodology**: Summarizes the research design and key methods.
	5.	**Results**: Highlights the most significant findings.
	6.	**Conclusions**: Provides the main takeaways and their relation to the research question.

Reminder: Strictly output in JSON format **only**, using the keys: "Research topic", "Background", "Research problem", "Objectives", "Methodology", "Results" and "Conclusions".
"""

### 3. Evidence extraction from main paper text for "Background"
BACKGROUD_EVIDENCE_PROMPT = """
You are given the **title**, briefly description of **problem backgroud** and **introduction** of a research paper. From the introduction, extract an itemized list of **1 to 3 pieces of evidence** that support the problem background, each evidence should be described in a **minimal draft (min 10 words and max 25 words)** for PowerPoint presentation.

    Each piece of evidence must:
        1.	Be directly relevant to the problem background.
        2.	Be clear and concise.
        3.	Be unique, not repeating other evidence.

**Important**: Strictly output the itemized evidences ONLY.
"""


### 4. Evidence extraction from main paper text for "Research Problem"
RESEARCH_PROBLEM_PROMPT = """
You are given the **title**, briefly description of **research problem** and **introduction** of a research paper. Solely from the given introduction, extract the definition of the research problem for PowerPoint presentation, focusing on:
    
    1.	**Scope**: Define the problem’s boundaries as individual items;
	2.	**Challenges**: Identify key gaps or obstacles the research addresses as individual items;
    3.  **Assumptions**: State any assumptions guiding the research as individual items;
    4.  **Relevance*: Specify who benefits from solving the problem as individual items.

**Note**: Each item must be in one concise sentence. **Only** output "Scope", "Challenges", "Assumptions" and "Relevance".
"""


### 5. Evidence extraction from main paper text for "Objectives"

OBJECTIVE_PROMPT = """
You are given the **title**, **objectives** and **introduction** of a research paper. Solely from the given introduction, extract a list of **2 to 5 pieces of evidence** to support these objectives, each evidence should be described in a **minimal draft (min 10 words and max 20 words)** for PowerPoint presentation.

    Each piece of evidence must:
        1.	Be directly relevant to the objectives.
        2.	Be clear and concise.
        3.	Be unique, not repeating other evidence.
    
**Note**: Strictly output the itemized evidences ONLY.
"""

### 6. Evidence extraction from main paper text for "Conclusion"

CONCLUSION_PROMT = """
You are given the **title**, **birief conclusion**, and **full text conclusion** and **introduction** of a research paper. From the given conclusion and introduction, extract the **conclusion** for PowerPoint presentation, ensuring it includes:

	1.	**Summary of key results**: Highlight the main results.
	2.	**Implications**: Explain the significance or impact of these findings.
	3.	**Future directions**: Mention any suggestions for future research or applications.
	4.	**Final takeaway**: Provide the overall takeaway message of the study.

**Note**: Only output the conclusion. Limit each point in a minimal concise draft (at least 10 words).”
"""

### 7. Evidence extraction from main paper text for "Experimental results" (iterative)

RESULT_PROMPT_DICT = {
  "system_instruction": """Given the title, the main results of an experimental study, and a paragraph from a research paper, your task is to extract and summarize evidence from the paragraph that supports the 'main results'.

   Follow these steps for each paragraph:
        1.	**Detect Evidence**: Check if the paragraph contains:
            1) Any evidence supporting the main results, or
            2) Experimental study information, including:
                - **Dataset**: Details on datasets, preprocessing, or train/test splits.
                - **Model Description**: Information of baselines, hyperparameters, and training.
                - **Evaluation Metrics**: Relevant metrics like accuracy, F1 score, and their justification.
                - **Comparative Analysis**: Comparisons with baselines, ablation studies, statistical significance.
                - **Runtime & Scalability**: Computational complexity and scalability.
        2.	**Response**: Choose 'YES' or 'NO':
            - If 'YES', extract and summarize the evidence or experimental details in 200 words. Ensure the summary is:
                - Clear and concise
                - Well-formatted for easy reading
                - Focused on key points: dataset, model Description, evaluation metrics, comparative analysis and runtime & scalability.
            - If 'NO', just respond with 'NO EVIDENCE'.
  """,

  "iterative_prompt": """Summarize the experimental details or evidence supporting the 'main results' in 200 words from the following paragraph (with title and content) if experiment-related information is detected. Follow these instructions:

	1.	List 2 to 4 itemized points.
	2.	Each point must specify the type ('Evidence' or 'Experimental Setup') and provide a minimal draft sentence of content (max 15 words).

**Note**: Only provide the itemized summary.
  """,

  "final_prompt": """Using the **title**, the **main results** of an experimental study, and a list of experiment summaries from the research paper, follow these steps to summarize the results:

	1.	**Evidence Summary**: prive a numbered, itemized summary of **2-3** key points. Keep each point brief and focused (only 1 sentence).

	2.	**Experimental Summary**: Based all 'Experimental Setup' points and provide a concise summary covering the following aspects:
        1) **Datasets**: List only the names of all datasets or benchmarks used.
        2) **Baselines**: List only the names of all models/algorithms used.
        3) **Metrics**: List only the evaluation metrics used for model performance, such as accuracy, F1-score, recall, precision, AUC, etc.
        4) **Results**: Summarize key comparisons and ablation results, focusing on the most important details.

  **Note**: Only output the “Evidence Summary” and “Experimental Summary”
     """
}

## Methodology extraction

METHOD_PROMPT_DICT = {
    "system_instruction": """Given the **title**, the **method overview**, and a paragraph of a research paper. You task is identify and extract text being relevant to 'method overview' from the given paragraph for PowerPoint presentation.

    Follow these steps:
    1. **Method Information Detection**: Check if the paragraph contains:
       1) Any mention of the **method overview** or
       2) Specific method details, such as:
           - **Problem Definition**: The task, input, and expected output.
           - **Model Architecture**: Structure, key components, and learning type.
           - **Algorithm**: Steps of the method.
           - **Training Process**: Training data, optimization method, and loss function.
    2. **Response**: Choose 'YES' or 'NO':
        - If 'YES', summarize the method details in a minimal draft with max 20 words, ensuring it is:
            - Clear and concise
            - Well-formatted for readability
            - Focused on key points.
        - If 'NO', simply respond with 'NO Information'.
    """,
    "iterative_prompt": """Summarize the method description in 200 words from the following paragraph (with title and content) if method-related information is found. Follow these steps:
        
        1. List **2 to 4** method steps in numbered format..
        2. Ensure each step is related to the **method overview**.
        3. Keep each step clear and concise (only minimal draft with max 15 words).
    
    **Note**: Only output the itemized method steps.
    """,

    "final_prompt": """Using **title**, **method overview**, and a list of itemized method step summary from a research paper, follow these instructions to summarize the method description::
        
        1. Provide a numbered list of **3-6 method steps** detailing the **method overview**.
        2. Keep each step clear and concise (only 1 sentence).
    
    **Note**: Only output the itemized method steps.
    """
}

SLIDES_REVISION_PROMPT = """You are an expert research assistant. Revise the following research paper slides to enhance clarity and readability while preserving the original markdown structure. Keep all first-level markdown headers unchanged. Sections are separated by '{}'. Follow these guidelines:

	1.	Simplify language and make content more concise, especially in the outline.
	2.	Preserve the logical flow and overall structure.
	3.	Make key points and conclusions clear and easy to follow.
	4.	Use bullet points where appropriate for better clarity.
	5.	Minimize jargon to ensure accessibility for a broad academic audience.

""".format(SLIDE_SEP)

def make_api_call(model, messages, max_tokens, temperature):
    try:
        response = call_llama_chat(messages=messages, model=model, temperature=temperature, max_tokens=max_tokens)
        return response
    except Exception as e:
         return f"Failed to generate final answer. Error: {str(e)}", {}

def convert_to_dict(input_string: str):
    # Split the string by the delimiter (e.g., semicolon)
    lines = input_string.strip().split('\n')
    # Initialize an empty dictionary
    result_dict = {}
    # Iterate over each line
    for line in lines:
        # Split each line into key and value by the delimiter (e.g., colon)
        if ':' in line:
            key, value = line.split(':', 1)  # Split only on the first occurrence
            # Strip any whitespace and store in the dictionary
            result_dict[key.strip()] = value.strip()
    return result_dict


class Paper2Slides(object):
    def __init__(self, paper_contents: dict, model: str, max_tokens = 512, temprature=0.1):
        self.paper_contents = paper_contents
        if not self.valid_paper_checking():
            print('Not a valid paper structure, cannot generate slides')
            exit(1)
        self.model = MODEL_ALIAS[model]
        self.is_rate_limitation = ('405B' in self.model) or ('70B' in self.model)
        self.temprature = temprature
        self.max_failure_attempt_each_step = 3
        if '405B' in self.model:
            self.sleep_time = 0.25
        else:
            self.sleep_time = 0.25
        self.max_tokens = max_tokens
        print('{} model is used for slides generation!\nRate limitation = {}'.format(self.model, self.is_rate_limitation))
        self.revise_model = MODEL_ALIAS['llama3_70b']
    
    def valid_paper_checking(self):
        try:
            assert 'abstract' in self.paper_contents, 'No abstract is detected'
            assert 'title' in self.paper_contents, 'No title is detected'
            paper_structure = self.paper_contents['structure']
            introduction_idx_array = paper_structure['Introduction']
            conclusion_idx_array = paper_structure['Conclusion']
            assert introduction_idx_array[0] >=0, 'No introduction is detected'
            assert conclusion_idx_array[0] >=0, 'No conclusion is detected'
        except AssertionError as e:
            print(f"AssertionError: {e}")
            return False
        return True

    def step(self, messages):
        result = self.run(messages=messages)
        if 'Failed' in result:
            time.sleep(self.sleep_time)
        if self.is_rate_limitation:
            print('sleep {} seconds'.format(self.sleep_time))
            time.sleep(self.sleep_time)
        return result
    
    def run(self, messages):
        for attempt in range(self.max_failure_attempt_each_step):
            try:
                response = make_api_call(messages=messages, model=self.model, max_tokens=self.max_tokens, temperature=self.temprature)
                return response
            except Exception as e:
                if attempt == self.max_failure_attempt_each_step - 1:
                    return "Failed to generate step after {} attempts. $ERROR$: {}".format(self.max_failure_attempt_each_step, str(e))
                else:
                    return "Failed to generate step. $ERROR$: {}".format(str(e))
                time.sleep(2)  # Wait for 1 second before retrying
        return 'Failed to generate reasoning step.'
        
    
    def abstract_summary(self):
        """
        Extract the outline for the slides from abstract
        """
        assert len(self.paper_contents['title']) > 0 and len(self.paper_contents['abstract']) > 512
        prompt = "**title**: {}\n\n**abstract**: {}".format(self.paper_contents['title'], self.paper_contents['abstract'])
        messages = [
            {"role": "system", "content": SCHOLAR_PROMPT},
            {"role": "system", "content": ABSTRACT_SUMMARY_PROMPT},
            {"role": "user", "content": prompt},
            {"role": "assistant", "content": "I will extract the evidences following my instructions."}
        ]
        abstract_summary = self.step(messages=messages)
        try:
            abstract_summary_dict = json.loads(abstract_summary)
        except Exception as e:
            abstract_summary_dict = convert_to_dict(input_string=abstract_summary)
        
        trim_abstract_summary_dict = {}
        for k, v in abstract_summary_dict.items():
            trim_abstract_summary_dict[trim_string(k)] = v
        return trim_abstract_summary_dict

    def support_background(self, background: str, introduction: str):
        """
        Extract support evidences for background from introduction
        """
        prompt = "**title**: {}\n\n**promblem background**: {}\n\n**introduction**: {}".format(self.paper_contents['title'], background, introduction)
        messages = [
            {"role": "system", "content": SCHOLAR_PROMPT},
            {"role": "system", "content": BACKGROUD_EVIDENCE_PROMPT},
            {"role": "user", "content": prompt},
            {"role": "assistant", "content": "I will extract the evidences following my instructions."}
        ]
        evidences = self.step(messages=messages)
        # print('Background evidences = {}'.format(evidences))
        step_num = 1
        return evidences, step_num

    def support_research_problem(self, research_problem: str, introduction: str):
        """
        Extract support evidences for research problem from introduction
        """
        prompt = "**title**: {}\n\n**research problem**: {}\n\n**introduction**: {}".format(self.paper_contents['title'], research_problem, introduction)
        messages = [
            {"role": "system", "content": SCHOLAR_PROMPT},
            {"role": "system", "content": RESEARCH_PROBLEM_PROMPT},
            {"role": "user", "content": prompt},
            {"role": "assistant", "content": "I will extract the evidences following my instructions."}
        ]
        evidences = self.step(messages=messages)
        step_num = 1
        return evidences, step_num
    
    def support_objectives(self, objectives: str, introduction: str):
        """
        Extract support evidences for objectives from introduction
        """
        prompt = "**title**: {}\n\n**objectives**: {}\n\n**introduction**: {}".format(self.paper_contents['title'], objectives, introduction)
        messages = [
            {"role": "system", "content": SCHOLAR_PROMPT},
            {"role": "system", "content": OBJECTIVE_PROMPT},
            {"role": "user", "content": prompt},
            {"role": "assistant", "content": "I will extract the evidences following my instructions."}
        ]
        evidences = self.step(messages=messages)
        step_num = 1
        return evidences, step_num

    def support_conclusion(self, conclusion: str, introduction: str, conclusion_text: str, step_wise=True):
        """
        Expand conclusion based on full-text conclusion and introducton. 
        If step_wise = True:
            1. Summarize introduction while focusing on conclusion part
            2. Extract conclusion points from introduction summary and full-context conclusion.
        """
        step_num = 0
        prompt = "**title**: {}\n\n**introduction**: {}".format(self.paper_contents['title'], introduction)
        if step_wise:
            messages = [
                {"role": "system", "content": SCHOLAR_PROMPT},
                {"role": "system", "content": "Given a **tititle** and **introduction** of a research paper, summarize and extract conclusion related information in about 200 words."},
                {"role": "user", "content": prompt},
                {"role": "assistant", "content": "I will extract the conclusion following my instructions."}
            ]
            instruction_conclusion_summary = self.step(messages=messages)
            step_num = step_num + 1
        else:
            instruction_conclusion_summary = introduction

        prompt = "**title**: {}\n\n**brief conclusion**: {}\n\n**conclusion**: \n\n{}**introduction**: {}".format(self.paper_contents['title'], conclusion, conclusion_text, instruction_conclusion_summary)
        messages = [
            {"role": "system", "content": SCHOLAR_PROMPT},
            {"role": "system", "content": CONCLUSION_PROMT},
            {"role": "user", "content": prompt},
            {"role": "assistant", "content": "I will extract the conclusions following my instructions."}
        ]
        evidences = self.step(messages=messages)
        step_num = step_num + 1
        return evidences, step_num
    
    def support_experiment_results(self, main_results: str, paragraph_list: list):
        step_num = 0
        prompt = "**title**: {}\n\n**main results**: {}\n\n".format(self.paper_contents['title'], main_results)
        iterative_sys_prompt = RESULT_PROMPT_DICT['iterative_prompt']
        messages = [
            {"role": "system", "content": SCHOLAR_PROMPT},
            {"role": "system", "content": RESULT_PROMPT_DICT['system_instruction']},
            {"role": "user", "content": prompt},
            {"role": "system", "content": iterative_sys_prompt},
        ]

        follow_instruction = {"role": "assistant", "content": "I will extract the experimental information following my instructions."}

        paragraph_summary_array = []
        for para_idx in range(len(paragraph_list)):
            para_input_prompt = "Paragraph title: {}\n\nContent: {}\n\n".format(paragraph_list[para_idx]['title'], paragraph_list[para_idx]['content'])
            user_input = {'role': 'user', 'content': para_input_prompt}
            messages.append(user_input)
            messages.append(follow_instruction)
            para_summary = self.step(messages=messages)
            step_num = step_num + 1
            paragraph_summary_array.append(para_summary)
            messages.pop()
            messages.pop()

        ## Experimental result summary

        prompt = "**title**: {}\n\n**main results**: {}\n\n".format(self.paper_contents['title'], main_results)
        summary_prompt = '\n'.join(['**summary** {}:\n\n{}'.format(idx+1, summary) for idx, summary in enumerate(paragraph_summary_array)])
        input_prompt = prompt + summary_prompt

        messages = [
            {"role": "system", "content": SCHOLAR_PROMPT},
            {"role": "system", "content": RESULT_PROMPT_DICT['final_prompt']},
            {"role": "user", "content": input_prompt},
            {"role": "assistant", "content": "I will summarize the experimental results following my instructions."},
        ]

        result_summary = self.step(messages=messages)
        step_num = step_num + 1
        return result_summary, step_num

    def experiment_paragraph_extraction(self,):
        intro_idx = self.paper_contents['structure']['Introduction'][0]
        conclusion_idx = self.paper_contents['structure']['Conclusion'][0]
        experiment_idx_array = self.paper_contents['structure']['Experiments']
        if len(experiment_idx_array) == 0:
            experiment_idx_array = [_ for _ in range(intro_idx+1, conclusion_idx)]
        assert len(experiment_idx_array) > 0 and max(experiment_idx_array) < len(self.paper_contents['main_text'])
        experiment_idx_array = [intro_idx] + experiment_idx_array
        paragraphs = [self.paper_contents['main_text'][_] for _ in experiment_idx_array]
        return paragraphs
    
    def support_methodology(self, method_overview: str, paragraph_list: list):
        step_num = 0
        prompt = "**title**: {}\n\n**method overview**: {}\n\n".format(self.paper_contents['title'], method_overview)
        iterative_sys_prompt = METHOD_PROMPT_DICT['iterative_prompt']
        messages = [
            {"role": "system", "content": SCHOLAR_PROMPT},
            {"role": "system", "content": METHOD_PROMPT_DICT['system_instruction']},
            {"role": "user", "content": prompt},
            {"role": "system", "content": iterative_sys_prompt},
        ]

        follow_instruction = {"role": "assistant", "content": "I will extract the method information following my instructions."}

        method_summary_array = []
        for para_idx in range(len(paragraph_list)):
            para_input_prompt = "Paragraph title: {}\n\nContent: {}\n\n".format(paragraph_list[para_idx]['title'], paragraph_list[para_idx]['content'])
            user_input = {'role': 'user', 'content': para_input_prompt}
            messages.append(user_input)
            messages.append(follow_instruction)
            method_summary = self.step(messages=messages)
            step_num = step_num + 1
            method_summary_array.append(method_summary)
            messages.pop()
            messages.pop()

        ## Method summary
        prompt = "**title**: {}\n\n**method overview**: {}\n\n".format(self.paper_contents['title'], method_overview)
        method_summary_prompt = '\n'.join(['**method summary** {}:\n\n{}'.format(idx+1, summary) for idx, summary in enumerate(method_summary_array)])
        input_prompt = prompt + method_summary_prompt

        messages = [
            {"role": "system", "content": SCHOLAR_PROMPT},
            {"role": "system", "content": METHOD_PROMPT_DICT['final_prompt']},
            {"role": "user", "content": input_prompt},
            {"role": "assistant", "content": "I will generate a step-by-step method summary following my instructions."},
        ]
        method_summary = self.step(messages=messages)
        step_num = step_num + 1
        return method_summary, step_num
        
    def method_paragraph_extraction(self,):
        intro_idx = self.paper_contents['structure']['Introduction'][0]
        conclusion_idx = self.paper_contents['structure']['Conclusion'][0]
        method_idx_array = self.paper_contents['structure']['Methods']
        if len(method_idx_array) == 0:
            method_idx_array = [_ for _ in range(intro_idx+1, conclusion_idx)]
        assert len(method_idx_array) > 0 and max(method_idx_array) < len(self.paper_contents['main_text'])
        method_idx_array = [intro_idx] + method_idx_array
        paragraphs = [self.paper_contents['main_text'][_] for _ in method_idx_array]
        return paragraphs

    def generate_slides(self, verbose=False, revision=True):
        ## Step 1: Paper content extraction
        intro_idx = self.paper_contents['structure']['Introduction'][0]
        introduction = self.paper_contents['main_text'][intro_idx]['content']
        assert len(introduction) > 512, 'introduction = {}, content = {}'.format(introduction, self.paper_contents['main_text'])
        conclusion_idx = self.paper_contents['structure']['Conclusion'][0]
        conclusion = self.paper_contents['main_text'][conclusion_idx]['content']
        assert len(conclusion) > 128, 'conclusion = {}, content = {}'.format(introduction, self.paper_contents['main_text'])
        method_paragraphs = self.method_paragraph_extraction()
        experiment_paragraphs = self.experiment_paragraph_extraction()

        start_time = time.time()
        ## Step 2: slides structure extraction from abstract
        model_call_number = 0
        print('Slides structure generation')
        slides = {'Title': self.paper_contents['title']}
        outline_dict = self.abstract_summary()
        model_call_number += 1
        slides['Outline'] = outline_dict

        print('Slides generation...')
        background = outline_dict.get('Background', '')
        slides['Background'], b_steps = self.support_background(background=background, introduction=introduction)
        model_call_number += b_steps

        research_problem = outline_dict.get('Research problem', '')
        slides['Research problem'], r_steps = self.support_research_problem(research_problem=research_problem, introduction=introduction)
        model_call_number += r_steps
        
        objectives = outline_dict.get('Objectives', '')
        slides['Objectives'], o_steps = self.support_objectives(objectives=objectives, introduction=introduction)
        model_call_number += o_steps

        brief_conclusion = outline_dict.get('Conclusions', '')
        slides['Conclusions'], c_steps = self.support_conclusion(conclusion=brief_conclusion, introduction=introduction, conclusion_text=conclusion, step_wise=True)
        model_call_number += c_steps

        results = outline_dict.get('Results', '')
        result_summary, res_steps = self.support_experiment_results(main_results=results, paragraph_list=experiment_paragraphs)
        slides['Results'] = result_summary
        model_call_number += res_steps

        methodology = outline_dict.get('Methodology', '')
        method_summary, m_steps = self.support_methodology(method_overview=methodology, paragraph_list=method_paragraphs)
        model_call_number += m_steps
        slides['Methodology'] = method_summary
        runtime = time.time() - start_time
        print('Slide generation takes {:.4f} seconds with {} function calls'.format(runtime, model_call_number))
        if verbose:
            slides_content = self.slides2markdown_v2(slides=slides)
            if revision:
                slides_content = self.slides_revision(slide_content=slides_content)
                slides_array = markdown_to_slide_dicts(full_markdown=slides_content)
                revised_slides = {k: v for d in slides_array for k, v in d.items()}
                if verbose:
                    print('Json format:\n{}'.format(json.dumps(revised_slides, indent=4)))
                    print('\n' * 3)
                    print('paper keywords:\n{}'.format(self.paper_contents.keys()))
                return revised_slides
            if verbose:
                print('Generated slides:\n{}'.format(slides_content))
                print('Json format:\n{}'.format(json.dumps(slides, indent=4)))
        return slides
    
    def slides_revision(self, slide_content: str):
        messages = [
            {"role": "system", "content": SLIDES_REVISION_PROMPT},
            {"role": "user", "content": slide_content},
            {"role": "assistant", "content": "I will revise the representation slides following my instructions."}
        ]
        print('Slides final revision')
        revised_slides = make_api_call(model=self.revise_model, messages=messages, max_tokens=2048, temperature=self.temprature)
        return revised_slides

    def slides2markdown(self, slides: dict):
        slides_content = ''
        slides_content += '**Title**\n{}\n\n'.format(slides['Title'])
        slides_content += '{}\n'.format(SLIDE_SEP)
        slides_content += '**Outline**\n\n'
        outline_dict = slides['Outline']
        for sect_name, sect_content in outline_dict.items():
            slides_content += '{}\n--\t\t{}\n\n'.format(sect_name, sect_content)
        slides_content += '{}\n'.format(SLIDE_SEP)
        for sect_name in outline_dict.keys():
            if sect_name in slides:
                slides_content += '**{}**\n\n'.format(sect_name)
                slides_content += '{}\n\n'.format(slides[sect_name])
                slides_content += '{}\n'.format(SLIDE_SEP)
        return slides_content
    
    def slides2markdown_v2(self, slides: dict, indent=0):
        slides_content = dict_to_markdown_list(d=slides, indent=indent)
        return slides_content

    def save_to_slides(self, slides: dict, logo_path='logo.png', file_name='slides.pptx'):
        authors = self.paper_contents.get('author', None)
        if isinstance(authors, list):
            authors = authors[0]
        else:
            authors = None
        # print('authors', authors)
        dict2ppt = Dict2PPT(logo_path=logo_path)
        dict2ppt.build_slides(slide_dict=slides, authors=authors)
        dict2ppt.save(file_name=file_name)
        full_path = os.path.abspath(file_name)
        return full_path