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Hypogenic

Overview

Hypogenic provides automated hypothesis generation and testing using large language models to accelerate scientific discovery. The framework supports three approaches: HypoGeniC (data-driven hypothesis generation), HypoRefine (synergistic literature and data integration), and Union methods (mechanistic combination of literature and data-driven hypotheses).

Quick Start

Get started with Hypogenic in minutes:

# Install the package
uv pip install hypogenic

# Clone example datasets
git clone https://github.com/ChicagoHAI/HypoGeniC-datasets.git ./data

# Run basic hypothesis generation
hypogenic_generation --config ./data/your_task/config.yaml --method hypogenic --num_hypotheses 20

# Run inference on generated hypotheses
hypogenic_inference --config ./data/your_task/config.yaml --hypotheses output/hypotheses.json

Or use Python API:

from hypogenic import BaseTask

# Create task with your configuration
task = BaseTask(config_path="./data/your_task/config.yaml")

# Generate hypotheses
task.generate_hypotheses(method="hypogenic", num_hypotheses=20)

# Run inference
results = task.inference(hypothesis_bank="./output/hypotheses.json")

When to Use This Skill

Use this skill when working on:

• Generating scientific hypotheses from observational datasets
• Testing multiple competing hypotheses systematically
• Combining literature insights with empirical patterns
• Accelerating research discovery through automated hypothesis ideation
• Domains requiring hypothesis-driven analysis: deception detection, AI-generated content identification, mental health indicators, predictive modeling, or other empirical research

Key Features

Automated Hypothesis Generation

• Generate 10-20+ testable hypotheses from data in minutes
• Iterative refinement based on validation performance
• Support for both API-based (OpenAI, Anthropic) and local LLMs

Literature Integration

• Extract insights from research papers via PDF processing
• Combine theoretical foundations with empirical patterns
• Systematic literature-to-hypothesis pipeline with GROBID

Performance Optimization

• Redis caching reduces API costs for repeated experiments
• Parallel processing for large-scale hypothesis testing
• Adaptive refinement focuses on challenging examples

Flexible Configuration

• Template-based prompt engineering with variable injection
• Custom label extraction for domain-specific tasks
• Modular architecture for easy extension

Proven Results

• 8.97% improvement over few-shot baselines
• 15.75% improvement over literature-only approaches
• 80-84% hypothesis diversity (non-redundant insights)
• Human evaluators report significant decision-making improvements

Core Capabilities

1. HypoGeniC: Data-Driven Hypothesis Generation

Generate hypotheses solely from observational data through iterative refinement.

Process:

1. Initialize with a small data subset to generate candidate hypotheses
2. Iteratively refine hypotheses based on performance
3. Replace poorly-performing hypotheses with new ones from challenging examples

Best for: Exploratory research without existing literature, pattern discovery in novel datasets

2. HypoRefine: Literature and Data Integration

Synergistically combine existing literature with empirical data through an agentic framework.

Process:

1. Extract insights from relevant research papers (typically 10 papers)
2. Generate theory-grounded hypotheses from literature
3. Generate data-driven hypotheses from observational patterns
4. Refine both hypothesis banks through iterative improvement

Best for: Research with established theoretical foundations, validating or extending existing theories

3. Union Methods

Mechanistically combine literature-only hypotheses with framework outputs.

Variants:

• Literature ∪ HypoGeniC: Combines literature hypotheses with data-driven generation
• Literature ∪ HypoRefine: Combines literature hypotheses with integrated approach

Best for: Comprehensive hypothesis coverage, eliminating redundancy while maintaining diverse perspectives

Installation

Install via pip:

uv pip install hypogenic

Optional dependencies:

• Redis server (port 6832): Enables caching of LLM responses to significantly reduce API costs during iterative hypothesis generation
• s2orc-doc2json: Required for processing literature PDFs in HypoRefine workflows
• GROBID: Required for PDF preprocessing (see Literature Processing section)

Clone example datasets:

# For HypoGeniC examples
git clone https://github.com/ChicagoHAI/HypoGeniC-datasets.git ./data

# For HypoRefine/Union examples
git clone https://github.com/ChicagoHAI/Hypothesis-agent-datasets.git ./data

Dataset Format

Datasets must follow HuggingFace datasets format with specific naming conventions:

Required files:

• <TASK>_train.json: Training data
• <TASK>_val.json: Validation data
• <TASK>_test.json: Test data

Required keys in JSON:

• text_features_1 through text_features_n: Lists of strings containing feature values
• label: List of strings containing ground truth labels

Example (headline click prediction):

{
  "headline_1": [
    "What Up, Comet? You Just Got *PROBED*",
    "Scientists Made a Breakthrough in Quantum Computing"
  ],
  "headline_2": [
    "Scientists Everywhere Were Holding Their Breath Today. Here's Why.",
    "New Quantum Computer Achieves Milestone"
  ],
  "label": [
    "Headline 2 has more clicks than Headline 1",
    "Headline 1 has more clicks than Headline 2"
  ]
}

Important notes:

• All lists must have the same length
• Label format must match your extract_label() function output format
• Feature keys can be customized to match your domain (e.g., review_text, post_content, etc.)

Configuration

Each task requires a config.yaml file specifying:

Required elements:

• Dataset paths (train/val/test)
• Prompt templates for:

- Observations generation - Batched hypothesis generation - Hypothesis inference - Relevance checking - Adaptive methods (for HypoRefine)

Template capabilities:

• Dataset placeholders for dynamic variable injection (e.g., ${text_features_1}, ${num_hypotheses})
• Custom label extraction functions for domain-specific parsing
• Role-based prompt structure (system, user, assistant roles)

Configuration structure:

task_name: your_task_name

train_data_path: ./your_task_train.json
val_data_path: ./your_task_val.json
test_data_path: ./your_task_test.json

prompt_templates:
  # Extra keys for reusable prompt components
  observations: |
    Feature 1: ${text_features_1}
    Feature 2: ${text_features_2}
    Observation: ${label}
  
  # Required templates
  batched_generation:
    system: "Your system prompt here"
    user: "Your user prompt with ${num_hypotheses} placeholder"
  
  inference:
    system: "Your inference system prompt"
    user: "Your inference user prompt"
  
  # Optional templates for advanced features
  few_shot_baseline: {...}
  is_relevant: {...}
  adaptive_inference: {...}
  adaptive_selection: {...}

Refer to references/config_template.yaml for a complete example configuration.

Literature Processing (HypoRefine/Union Methods)

To use literature-based hypothesis generation, you must preprocess PDF papers:

Step 1: Setup GROBID (first time only)

bash ./modules/setup_grobid.sh

Step 2: Add PDF files Place research papers in literature/YOUR_TASK_NAME/raw/

Step 3: Process PDFs

# Start GROBID service
bash ./modules/run_grobid.sh

# Process PDFs for your task
cd examples
python pdf_preprocess.py --task_name YOUR_TASK_NAME

This converts PDFs to structured format for hypothesis extraction. Automated literature search will be supported in future releases.

CLI Usage

Hypothesis Generation

hypogenic_generation --help

Key parameters:

• Task configuration file path
• Model selection (API-based or local)
• Generation method (HypoGeniC, HypoRefine, or Union)
• Number of hypotheses to generate
• Output directory for hypothesis banks

Hypothesis Inference

hypogenic_inference --help

Key parameters:

• Task configuration file path
• Hypothesis bank file path
• Test dataset path
• Inference method (default or multi-hypothesis)
• Output file for results

Python API Usage

For programmatic control and custom workflows, use Hypogenic directly in your Python code:

Basic HypoGeniC Generation

from hypogenic import BaseTask

# Clone example datasets first
# git clone https://github.com/ChicagoHAI/HypoGeniC-datasets.git ./data

# Load your task with custom extract_label function
task = BaseTask(
    config_path="./data/your_task/config.yaml",
    extract_label=lambda text: extract_your_label(text)
)

# Generate hypotheses
task.generate_hypotheses(
    method="hypogenic",
    num_hypotheses=20,
    output_path="./output/hypotheses.json"
)

# Run inference
results = task.inference(
    hypothesis_bank="./output/hypotheses.json",
    test_data="./data/your_task/your_task_test.json"
)

HypoRefine/Union Methods

# For literature-integrated approaches
# git clone https://github.com/ChicagoHAI/Hypothesis-agent-datasets.git ./data

# Generate with HypoRefine
task.generate_hypotheses(
    method="hyporefine",
    num_hypotheses=15,
    literature_path="./literature/your_task/",
    output_path="./output/"
)
# This generates 3 hypothesis banks:
# - HypoRefine (integrated approach)
# - Literature-only hypotheses
# - Literature∪HypoRefine (union)

Multi-Hypothesis Inference

from examples.multi_hyp_inference import run_multi_hypothesis_inference

# Test multiple hypotheses simultaneously
results = run_multi_hypothesis_inference(
    config_path="./data/your_task/config.yaml",
    hypothesis_bank="./output/hypotheses.json",
    test_data="./data/your_task/your_task_test.json"
)

Custom Label Extraction

The extract_label() function is critical for parsing LLM outputs. Implement it based on your task:

def extract_label(llm_output: str) -> str:
    """Extract predicted label from LLM inference text.
    
    Default behavior: searches for 'final answer:\s+(.*)' pattern.
    Customize for your domain-specific output format.
    """
    import re
    match = re.search(r'final answer:\s+(.*)', llm_output, re.IGNORECASE)
    if match:
        return match.group(1).strip()
    return llm_output.strip()

Important: Extracted labels must match the format of label values in your dataset for correct accuracy calculation.

Workflow Examples

Example 1: Data-Driven Hypothesis Generation (HypoGeniC)

Scenario: Detecting AI-generated content without prior theoretical framework

Steps:

1. Prepare dataset with text samples and labels (human vs. AI-generated)
2. Create config.yaml with appropriate prompt templates
3. Run hypothesis generation:

   hypogenic_generation --config config.yaml --method hypogenic --num_hypotheses 20

1. Run inference on test set:

   hypogenic_inference --config config.yaml --hypotheses output/hypotheses.json --test_data data/test.json

1. Analyze results for patterns like formality, grammatical precision, and tone differences

Example 2: Literature-Informed Hypothesis Testing (HypoRefine)

Scenario: Deception detection in hotel reviews building on existing research

Steps:

1. Collect 10 relevant papers on linguistic deception cues
2. Prepare dataset with genuine and fraudulent reviews
3. Configure config.yaml with literature processing and data generation templates
4. Run HypoRefine:

   hypogenic_generation --config config.yaml --method hyporefine --papers papers/ --num_hypotheses 15

1. Test hypotheses examining pronoun frequency, detail specificity, and other linguistic patterns
2. Compare literature-based and data-driven hypothesis performance

Example 3: Comprehensive Hypothesis Coverage (Union Method)

Scenario: Mental stress detection maximizing hypothesis diversity

Steps:

1. Generate literature hypotheses from mental health research papers
2. Generate data-driven hypotheses from social media posts
3. Run Union method to combine and deduplicate:

   hypogenic_generation --config config.yaml --method union --literature_hypotheses lit_hyp.json

1. Inference captures both theoretical constructs (posting behavior changes) and data patterns (emotional language shifts)

Performance Optimization

Caching: Enable Redis caching to reduce API costs and computation time for repeated LLM calls

Parallel Processing: Leverage multiple workers for large-scale hypothesis generation and testing

Adaptive Refinement: Use challenging examples to iteratively improve hypothesis quality

Expected Outcomes

Research using hypogenic has demonstrated:

• 14.19% accuracy improvement in AI-content detection tasks
• 7.44% accuracy improvement in deception detection tasks
• 80-84% of hypothesis pairs offering distinct, non-redundant insights
• High helpfulness ratings from human evaluators across multiple research domains

Troubleshooting

Issue: Generated hypotheses are too generic Solution: Refine prompt templates in config.yaml to request more specific, testable hypotheses

Issue: Poor inference performance Solution: Ensure dataset has sufficient training examples, adjust hypothesis generation parameters, or increase number of hypotheses

Issue: Label extraction failures Solution: Implement custom extract_label() function for domain-specific output parsing

Issue: GROBID PDF processing fails Solution: Ensure GROBID service is running (bash ./modules/run_grobid.sh) and PDFs are valid research papers

Creating Custom Tasks

To add a new task or dataset to Hypogenic:

Step 1: Prepare Your Dataset

Create three JSON files following the required format:

• your_task_train.json
• your_task_val.json
• your_task_test.json

Each file must have keys for text features (text_features_1, etc.) and label.

Step 2: Create config.yaml

Define your task configuration with:

• Task name and dataset paths
• Prompt templates for observations, generation, inference
• Any extra keys for reusable prompt components
• Placeholder variables (e.g., ${text_features_1}, ${num_hypotheses})

Step 3: Implement extract_label Function

Create a custom label extraction function that parses LLM outputs for your domain:

from hypogenic import BaseTask

def extract_my_label(llm_output: str) -> str:
    """Custom label extraction for your task.
    
    Must return labels in same format as dataset 'label' field.
    """
    # Example: Extract from specific format
    if "Final prediction:" in llm_output:
        return llm_output.split("Final prediction:")[-1].strip()
    
    # Fallback to default pattern
    import re
    match = re.search(r'final answer:\s+(.*)', llm_output, re.IGNORECASE)
    return match.group(1).strip() if match else llm_output.strip()

# Use your custom task
task = BaseTask(
    config_path="./your_task/config.yaml",
    extract_label=extract_my_label
)

Step 4: (Optional) Process Literature

For HypoRefine/Union methods:

1. Create literature/your_task_name/raw/ directory
2. Add relevant research paper PDFs
3. Run GROBID preprocessing
4. Process with pdf_preprocess.py

Step 5: Generate and Test

Run hypothesis generation and inference using CLI or Python API:

# CLI approach
hypogenic_generation --config your_task/config.yaml --method hypogenic --num_hypotheses 20
hypogenic_inference --config your_task/config.yaml --hypotheses output/hypotheses.json

# Or use Python API (see Python API Usage section)

Repository Structure

Understanding the repository layout:

hypothesis-generation/
├── hypogenic/              # Core package code
├── hypogenic_cmd/          # CLI entry points
├── hypothesis_agent/       # HypoRefine agent framework
├── literature/            # Literature processing utilities
├── modules/               # GROBID and preprocessing modules
├── examples/              # Example scripts
│   ├── generation.py      # Basic HypoGeniC generation
│   ├── union_generation.py # HypoRefine/Union generation
│   ├── inference.py       # Single hypothesis inference
│   ├── multi_hyp_inference.py # Multiple hypothesis inference
│   └── pdf_preprocess.py  # Literature PDF processing
├── data/                  # Example datasets (clone separately)
├── tests/                 # Unit tests
└── IO_prompting/          # Prompt templates and experiments

Key directories:

• hypogenic/: Main package with BaseTask and generation logic
• examples/: Reference implementations for common workflows
• literature/: Tools for PDF processing and literature extraction
• modules/: External tool integrations (GROBID, etc.)

Related Publications

HypoBench (2025)

Liu, H., Huang, S., Hu, J., Zhou, Y., & Tan, C. (2025). HypoBench: Towards Systematic and Principled Benchmarking for Hypothesis Generation. arXiv preprint arXiv:2504.11524.

• Paper: https://arxiv.org/abs/2504.11524
• Description: Benchmarking framework for systematic evaluation of hypothesis generation methods

BibTeX:

@misc{liu2025hypobenchsystematicprincipledbenchmarking,
      title={HypoBench: Towards Systematic and Principled Benchmarking for Hypothesis Generation}, 
      author={Haokun Liu and Sicong Huang and Jingyu Hu and Yangqiaoyu Zhou and Chenhao Tan},
      year={2025},
      eprint={2504.11524},
      archivePrefix={arXiv},
      primaryClass={cs.AI},
      url={https://arxiv.org/abs/2504.11524}, 
}

Literature Meets Data (2024)

Liu, H., Zhou, Y., Li, M., Yuan, C., & Tan, C. (2024). Literature Meets Data: A Synergistic Approach to Hypothesis Generation. arXiv preprint arXiv:2410.17309.

• Paper: https://arxiv.org/abs/2410.17309
• Code: https://github.com/ChicagoHAI/hypothesis-generation
• Description: Introduces HypoRefine and demonstrates synergistic combination of literature-based and data-driven hypothesis generation

BibTeX:

@misc{liu2024literaturemeetsdatasynergistic,
      title={Literature Meets Data: A Synergistic Approach to Hypothesis Generation}, 
      author={Haokun Liu and Yangqiaoyu Zhou and Mingxuan Li and Chenfei Yuan and Chenhao Tan},
      year={2024},
      eprint={2410.17309},
      archivePrefix={arXiv},
      primaryClass={cs.AI},
      url={https://arxiv.org/abs/2410.17309}, 
}

Hypothesis Generation with Large Language Models (2024)

Zhou, Y., Liu, H., Srivastava, T., Mei, H., & Tan, C. (2024). Hypothesis Generation with Large Language Models. In Proceedings of EMNLP Workshop of NLP for Science.

• Paper: https://aclanthology.org/2024.nlp4science-1.10/
• Description: Original HypoGeniC framework for data-driven hypothesis generation

BibTeX:

@inproceedings{zhou2024hypothesisgenerationlargelanguage,
      title={Hypothesis Generation with Large Language Models}, 
      author={Yangqiaoyu Zhou and Haokun Liu and Tejes Srivastava and Hongyuan Mei and Chenhao Tan},
      booktitle = {Proceedings of EMNLP Workshop of NLP for Science},
      year={2024},
      url={https://aclanthology.org/2024.nlp4science-1.10/},
}

Additional Resources

Official Links

• GitHub Repository: https://github.com/ChicagoHAI/hypothesis-generation
• PyPI Package: https://pypi.org/project/hypogenic/
• License: MIT License
• Issues & Support: https://github.com/ChicagoHAI/hypothesis-generation/issues

Example Datasets

Clone these repositories for ready-to-use examples:

# HypoGeniC examples (data-driven only)
git clone https://github.com/ChicagoHAI/HypoGeniC-datasets.git ./data

# HypoRefine/Union examples (literature + data)
git clone https://github.com/ChicagoHAI/Hypothesis-agent-datasets.git ./data

Community & Contributions

• Contributors: 7+ active contributors
• Stars: 89+ on GitHub
• Topics: research-tool, interpretability, hypothesis-generation, scientific-discovery, llm-application

For contributions or questions, visit the GitHub repository and check the issues page.

Local Resources

references/

config_template.yaml - Complete example configuration file with all required prompt templates and parameters. This includes:

• Full YAML structure for task configuration
• Example prompt templates for all methods
• Placeholder variable documentation
• Role-based prompt examples

scripts/

Scripts directory is available for:

• Custom data preparation utilities
• Format conversion tools
• Analysis and evaluation scripts
• Integration with external tools

assets/

Assets directory is available for:

• Example datasets and templates
• Sample hypothesis banks
• Visualization outputs
• Documentation supplements