Enhance citation management and literature review guidelines

- Updated SKILL.md in citation management to include best practices for identifying seminal and high-impact papers, emphasizing citation count thresholds, venue quality tiers, and author reputation indicators.
- Expanded literature review SKILL.md to prioritize high-impact papers, detailing citation metrics, journal tiers, and author reputation assessment.
- Added comprehensive evaluation strategies for paper impact and quality in literature_search_strategies.md, including citation count significance and journal impact factor guidance.
- Improved research lookup scripts to prioritize results based on citation count, venue prestige, and author reputation, enhancing the quality of research outputs.
This commit is contained in:
Vinayak Agarwal
2026-01-05 13:01:10 -08:00
parent d243a12564
commit 3439a21f57
41 changed files with 11802 additions and 61 deletions

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# Scientific Schematics - Quick Reference
**How it works:** Describe your diagram → Nano Banana Pro generates it automatically
## Setup (One-Time)
```bash
# Get API key from https://openrouter.ai/keys
export OPENROUTER_API_KEY='sk-or-v1-your_key_here'
# Add to shell profile for persistence
echo 'export OPENROUTER_API_KEY="sk-or-v1-your_key"' >> ~/.bashrc # or ~/.zshrc
```
## Basic Usage
```bash
# Describe your diagram, Nano Banana Pro creates it
python scripts/generate_schematic.py "your diagram description" -o output.png
# That's it! Automatic:
# - Iterative refinement (3 rounds)
# - Quality review and improvement
# - Publication-ready output
```
## Common Examples
### CONSORT Flowchart
```bash
python scripts/generate_schematic.py \
"CONSORT flow: screened n=500, excluded n=150, randomized n=350" \
-o consort.png
```
### Neural Network
```bash
python scripts/generate_schematic.py \
"Transformer architecture with encoder and decoder stacks" \
-o transformer.png
```
### Biological Pathway
```bash
python scripts/generate_schematic.py \
"MAPK pathway: EGFR → RAS → RAF → MEK → ERK" \
-o mapk.png
```
### Circuit Diagram
```bash
python scripts/generate_schematic.py \
"Op-amp circuit with 1kΩ resistor and 10µF capacitor" \
-o circuit.png
```
## Command Options
| Option | Description | Example |
|--------|-------------|---------|
| `-o, --output` | Output file path | `-o figures/diagram.png` |
| `--iterations N` | Number of refinements (1-2) | `--iterations 2` |
| `-v, --verbose` | Show detailed output | `-v` |
| `--api-key KEY` | Provide API key | `--api-key sk-or-v1-...` |
## Prompt Tips
### ✓ Good Prompts (Specific)
- "CONSORT flowchart with screening (n=500), exclusion (n=150), randomization (n=350)"
- "Transformer architecture: encoder on left with 6 layers, decoder on right, cross-attention connections"
- "MAPK signaling: receptor → RAS → RAF → MEK → ERK → nucleus, label each phosphorylation"
### ✗ Avoid (Too Vague)
- "Make a flowchart"
- "Neural network"
- "Pathway diagram"
## Output Files
For input `diagram.png`, you get:
- `diagram_v1.png` - First iteration
- `diagram_v2.png` - Second iteration
- `diagram_v3.png` - Final iteration
- `diagram.png` - Copy of final
- `diagram_review_log.json` - Quality scores and critiques
## Review Log
```json
{
"iterations": [
{
"iteration": 1,
"score": 7.0,
"critique": "Good start. Font too small..."
},
{
"iteration": 2,
"score": 8.5,
"critique": "Much improved. Minor spacing issues..."
},
{
"iteration": 3,
"score": 9.5,
"critique": "Excellent. Publication ready."
}
],
"final_score": 9.5
}
```
## Python API
```python
from scripts.generate_schematic_ai import ScientificSchematicGenerator
# Initialize
gen = ScientificSchematicGenerator(api_key="your_key")
# Generate
results = gen.generate_iterative(
user_prompt="diagram description",
output_path="output.png",
iterations=2
)
# Check quality
print(f"Score: {results['final_score']}/10")
```
## Troubleshooting
### API Key Not Found
```bash
# Check if set
echo $OPENROUTER_API_KEY
# Set it
export OPENROUTER_API_KEY='your_key'
```
### Import Error
```bash
# Install requests
pip install requests
```
### Low Quality Score
- Make prompt more specific
- Include layout details (left-to-right, top-to-bottom)
- Specify label requirements
- Increase iterations: `--iterations 2`
## Testing
```bash
# Verify installation
python test_ai_generation.py
# Should show: "6/6 tests passed"
```
## Cost
Typical cost per diagram (max 2 iterations):
- Simple (1 iteration): $0.05-0.15
- Complex (2 iterations): $0.10-0.30
## How Nano Banana Pro Works
**Simply describe your diagram in natural language:**
- ✓ No coding required
- ✓ No templates needed
- ✓ No manual drawing
- ✓ Automatic quality review
- ✓ Publication-ready output
- ✓ Works for any diagram type
**Just describe what you want, and it's generated automatically.**
## Getting Help
```bash
# Show help
python scripts/generate_schematic.py --help
# Verbose mode for debugging
python scripts/generate_schematic.py "diagram" -o out.png -v
```
## Quick Start Checklist
- [ ] Set `OPENROUTER_API_KEY` environment variable
- [ ] Run `python test_ai_generation.py` (should pass 6/6)
- [ ] Try: `python scripts/generate_schematic.py "test diagram" -o test.png`
- [ ] Review output files (test_v1.png, v2, v3, review_log.json)
- [ ] Read SKILL.md for detailed documentation
- [ ] Check README.md for examples
## Resources
- Full documentation: `SKILL.md`
- Detailed guide: `README.md`
- Implementation details: `IMPLEMENTATION_SUMMARY.md`
- Example script: `example_usage.sh`
- Get API key: https://openrouter.ai/keys

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# Scientific Schematics - Nano Banana Pro
**Generate any scientific diagram by describing it in natural language.**
Nano Banana Pro creates publication-quality diagrams automatically - no coding, no templates, no manual drawing required.
## Quick Start
### Generate Any Diagram
```bash
# Set your OpenRouter API key
export OPENROUTER_API_KEY='your_api_key_here'
# Generate any scientific diagram
python scripts/generate_schematic.py "CONSORT participant flow diagram" -o figures/consort.png
# Neural network architecture
python scripts/generate_schematic.py "Transformer encoder-decoder architecture" -o figures/transformer.png
# Biological pathway
python scripts/generate_schematic.py "MAPK signaling pathway" -o figures/pathway.png
```
### What You Get
- **Up to two iterations** (v1, v2) with progressive refinement
- **Automatic quality review** after each iteration
- **Detailed review log** with scores and critiques (JSON format)
- **Publication-ready images** following scientific standards
## Features
### Iterative Refinement Process
1. **Generation 1**: Create initial diagram from your description
2. **Review 1**: AI evaluates clarity, labels, accuracy, accessibility
3. **Generation 2**: Improve based on critique
4. **Review 2**: Second evaluation with specific feedback
5. **Generation 3**: Final polished version
### Automatic Quality Standards
All diagrams automatically follow:
- Clean white/light background
- High contrast for readability
- Clear labels (minimum 10pt font)
- Professional typography
- Colorblind-friendly colors
- Proper spacing between elements
- Scale bars, legends, axes where appropriate
## Installation
### For AI Generation
```bash
# Get OpenRouter API key
# Visit: https://openrouter.ai/keys
# Set environment variable
export OPENROUTER_API_KEY='sk-or-v1-...'
# Or add to .env file
echo "OPENROUTER_API_KEY=sk-or-v1-..." >> .env
# Install Python dependencies (if not already installed)
pip install requests
```
## Usage Examples
### Example 1: CONSORT Flowchart
```bash
python scripts/generate_schematic.py \
"CONSORT participant flow diagram for RCT. \
Assessed for eligibility (n=500). \
Excluded (n=150): age<18 (n=80), declined (n=50), other (n=20). \
Randomized (n=350) into Treatment (n=175) and Control (n=175). \
Lost to follow-up: 15 and 10 respectively. \
Final analysis: 160 and 165." \
-o figures/consort.png
```
**Output:**
- `figures/consort_v1.png` - Initial generation
- `figures/consort_v2.png` - After first review
- `figures/consort_v3.png` - Final version
- `figures/consort.png` - Copy of final version
- `figures/consort_review_log.json` - Detailed review log
### Example 2: Neural Network Architecture
```bash
python scripts/generate_schematic.py \
"Transformer architecture with encoder on left (input embedding, \
positional encoding, multi-head attention, feed-forward) and \
decoder on right (masked attention, cross-attention, feed-forward). \
Show cross-attention connection from encoder to decoder." \
-o figures/transformer.png \
--iterations 2
```
### Example 3: Biological Pathway
```bash
python scripts/generate_schematic.py \
"MAPK signaling pathway: EGFR receptor → RAS → RAF → MEK → ERK → nucleus. \
Label each step with phosphorylation. Use different colors for each kinase." \
-o figures/mapk.png
```
### Example 4: System Architecture
```bash
python scripts/generate_schematic.py \
"IoT system block diagram: sensors (bottom) → microcontroller → \
WiFi module and display (middle) → cloud server → mobile app (top). \
Label all connections with protocols." \
-o figures/iot_system.png
```
## Command-Line Options
```bash
python scripts/generate_schematic.py [OPTIONS] "description" -o output.png
Options:
--iterations N Number of AI refinement iterations (default: 2, max: 2)
--api-key KEY OpenRouter API key (or use env var)
-v, --verbose Verbose output
-h, --help Show help message
```
## Python API
```python
from scripts.generate_schematic_ai import ScientificSchematicGenerator
# Initialize
generator = ScientificSchematicGenerator(
api_key="your_key",
verbose=True
)
# Generate with iterative refinement
results = generator.generate_iterative(
user_prompt="CONSORT flowchart",
output_path="figures/consort.png",
iterations=2
)
# Access results
print(f"Final score: {results['final_score']}/10")
print(f"Final image: {results['final_image']}")
# Review iterations
for iteration in results['iterations']:
print(f"Iteration {iteration['iteration']}: {iteration['score']}/10")
print(f"Critique: {iteration['critique']}")
```
## Prompt Engineering Tips
### Be Specific About Layout
✓ "Flowchart with vertical flow, top to bottom"
✓ "Architecture diagram with encoder on left, decoder on right"
✗ "Make a diagram" (too vague)
### Include Quantitative Details
✓ "Neural network: input (784), hidden (128), output (10)"
✓ "Flowchart: n=500 screened, n=150 excluded, n=350 randomized"
✗ "Some numbers" (not specific)
### Specify Visual Style
✓ "Minimalist block diagram with clean lines"
✓ "Detailed biological pathway with protein structures"
✓ "Technical schematic with engineering notation"
### Request Specific Labels
✓ "Label all arrows with activation/inhibition"
✓ "Include layer dimensions in each box"
✓ "Show time progression with timestamps"
### Mention Color Requirements
✓ "Use colorblind-friendly colors"
✓ "Grayscale-compatible design"
✓ "Color-code by function: blue=input, green=processing, red=output"
## Review Log Format
Each generation produces a JSON review log:
```json
{
"user_prompt": "CONSORT participant flow diagram...",
"iterations": [
{
"iteration": 1,
"image_path": "figures/consort_v1.png",
"prompt": "Full generation prompt...",
"critique": "Score: 7/10. Issues: font too small...",
"score": 7.0,
"success": true
},
{
"iteration": 2,
"image_path": "figures/consort_v2.png",
"score": 8.5,
"critique": "Much improved. Remaining issues..."
},
{
"iteration": 3,
"image_path": "figures/consort_v3.png",
"score": 9.5,
"critique": "Excellent. Publication ready."
}
],
"final_image": "figures/consort_v3.png",
"final_score": 9.5,
"success": true
}
```
## Why Use Nano Banana Pro
**Simply describe what you want - Nano Banana Pro creates it:**
-**Fast**: Results in minutes
-**Easy**: Natural language descriptions (no coding)
-**Quality**: Automatic review and refinement
-**Universal**: Works for all diagram types
-**Publication-ready**: High-quality output immediately
**Just describe your diagram, and it's generated automatically.**
## Troubleshooting
### API Key Issues
```bash
# Check if key is set
echo $OPENROUTER_API_KEY
# Set temporarily
export OPENROUTER_API_KEY='your_key'
# Set permanently (add to ~/.bashrc or ~/.zshrc)
echo 'export OPENROUTER_API_KEY="your_key"' >> ~/.bashrc
```
### Import Errors
```bash
# Install requests library
pip install requests
# Or use the package manager
pip install -r requirements.txt
```
### Generation Fails
```bash
# Use verbose mode to see detailed errors
python scripts/generate_schematic.py "diagram" -o out.png -v
# Check API status
curl https://openrouter.ai/api/v1/models
```
### Low Quality Scores
If iterations consistently score below 7/10:
1. Make your prompt more specific
2. Include more details about layout and labels
3. Specify visual requirements explicitly
4. Increase iterations: `--iterations 2`
## Testing
Run verification tests:
```bash
python test_ai_generation.py
```
This tests:
- File structure
- Module imports
- Class initialization
- Error handling
- Prompt engineering
- Wrapper script
## Cost Considerations
OpenRouter pricing for models used:
- **Nano Banana Pro**: ~$2/M input tokens, ~$12/M output tokens
Typical costs per diagram:
- Simple diagram (1 iteration): ~$0.05-0.15
- Complex diagram (2 iterations): ~$0.10-0.30
## Examples Gallery
See the full SKILL.md for extensive examples including:
- CONSORT flowcharts
- Neural network architectures (Transformers, CNNs, RNNs)
- Biological pathways
- Circuit diagrams
- System architectures
- Block diagrams
## Support
For issues or questions:
1. Check SKILL.md for detailed documentation
2. Run test_ai_generation.py to verify setup
3. Use verbose mode (-v) to see detailed errors
4. Review the review_log.json for quality feedback
## License
Part of the scientific-writer package. See main repository for license information.

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#!/bin/bash
# Example usage of AI-powered scientific schematic generation
#
# Prerequisites:
# 1. Set OPENROUTER_API_KEY environment variable
# 2. Ensure Python 3.10+ is installed
# 3. Install requests: pip install requests
set -e
echo "=========================================="
echo "Scientific Schematics - AI Generation"
echo "Example Usage Demonstrations"
echo "=========================================="
echo ""
# Check for API key
if [ -z "$OPENROUTER_API_KEY" ]; then
echo "❌ Error: OPENROUTER_API_KEY environment variable not set"
echo ""
echo "Get an API key at: https://openrouter.ai/keys"
echo "Then set it with: export OPENROUTER_API_KEY='your_key'"
exit 1
fi
echo "✓ OPENROUTER_API_KEY is set"
echo ""
# Create output directory
mkdir -p figures
echo "✓ Created figures/ directory"
echo ""
# Example 1: Simple flowchart
echo "Example 1: CONSORT Flowchart"
echo "----------------------------"
python scripts/generate_schematic.py \
"CONSORT participant flow diagram. Assessed for eligibility (n=500). Excluded (n=150) with reasons: age<18 (n=80), declined (n=50), other (n=20). Randomized (n=350) into Treatment (n=175) and Control (n=175). Lost to follow-up: 15 and 10. Final analysis: 160 and 165." \
-o figures/consort_example.png \
--iterations 2
echo ""
echo "✓ Generated: figures/consort_example.png"
echo " - Also created: consort_example_v1.png, v2.png, v3.png"
echo " - Review log: consort_example_review_log.json"
echo ""
# Example 2: Neural network (shorter for demo)
echo "Example 2: Simple Neural Network"
echo "--------------------------------"
python scripts/generate_schematic.py \
"Simple feedforward neural network diagram. Input layer with 4 nodes, hidden layer with 6 nodes, output layer with 2 nodes. Show all connections. Label layers clearly." \
-o figures/neural_net_example.png \
--iterations 2
echo ""
echo "✓ Generated: figures/neural_net_example.png"
echo ""
# Example 3: Biological pathway (minimal)
echo "Example 3: Signaling Pathway"
echo "---------------------------"
python scripts/generate_schematic.py \
"Simple signaling pathway: Receptor → Kinase A → Kinase B → Transcription Factor → Gene. Show arrows with 'activation' labels. Use different colors for each component." \
-o figures/pathway_example.png \
--iterations 2
echo ""
echo "✓ Generated: figures/pathway_example.png"
echo ""
echo "=========================================="
echo "All examples completed successfully!"
echo "=========================================="
echo ""
echo "Generated files in figures/:"
ls -lh figures/*example*.png 2>/dev/null || echo " (Files will appear after running with valid API key)"
echo ""
echo "Review the review_log.json files to see:"
echo " - Quality scores for each iteration"
echo " - Detailed critiques and suggestions"
echo " - Improvement progression"
echo ""
echo "Next steps:"
echo " 1. View the generated images"
echo " 2. Review the quality scores in *_review_log.json"
echo " 3. Try your own prompts!"
echo ""

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#!/usr/bin/env python3
"""
Test script to verify AI generation implementation.
This script performs dry-run tests without making actual API calls.
It verifies:
1. Script structure and imports
2. Class initialization
3. Method signatures
4. Error handling
5. Command-line interface
Usage:
python test_ai_generation.py
"""
import sys
import os
from pathlib import Path
# Add scripts directory to path
scripts_dir = Path(__file__).parent / "scripts"
sys.path.insert(0, str(scripts_dir))
def test_imports():
"""Test that all required modules can be imported."""
print("Testing imports...")
try:
from generate_schematic_ai import ScientificSchematicGenerator
print("✓ generate_schematic_ai imports successfully")
return True
except ImportError as e:
print(f"✗ Import failed: {e}")
return False
def test_class_structure():
"""Test class initialization and structure."""
print("\nTesting class structure...")
try:
from generate_schematic_ai import ScientificSchematicGenerator
# Test initialization with dummy key
generator = ScientificSchematicGenerator(api_key="test_key", verbose=False)
print("✓ Class initializes successfully")
# Check required methods exist
required_methods = [
'generate_image',
'review_image',
'improve_prompt',
'generate_iterative'
]
for method in required_methods:
if not hasattr(generator, method):
print(f"✗ Missing method: {method}")
return False
print(f"✓ Method exists: {method}")
# Check attributes
if not hasattr(generator, 'api_key'):
print("✗ Missing attribute: api_key")
return False
print("✓ Attribute exists: api_key")
if not hasattr(generator, 'image_model'):
print("✗ Missing attribute: image_model")
return False
print(f"✓ Image model: {generator.image_model}")
if not hasattr(generator, 'review_model'):
print("✗ Missing attribute: review_model")
return False
print(f"✓ Review model: {generator.review_model}")
return True
except Exception as e:
print(f"✗ Class structure test failed: {e}")
return False
def test_error_handling():
"""Test error handling for missing API key."""
print("\nTesting error handling...")
try:
from generate_schematic_ai import ScientificSchematicGenerator
# Clear environment variable
old_key = os.environ.get("OPENROUTER_API_KEY")
if old_key:
del os.environ["OPENROUTER_API_KEY"]
# Try to initialize without key
try:
generator = ScientificSchematicGenerator()
print("✗ Should have raised ValueError for missing API key")
return False
except ValueError as e:
if "OPENROUTER_API_KEY" in str(e):
print("✓ Correctly raises ValueError for missing API key")
else:
print(f"✗ Wrong error message: {e}")
return False
# Restore environment variable
if old_key:
os.environ["OPENROUTER_API_KEY"] = old_key
return True
except Exception as e:
print(f"✗ Error handling test failed: {e}")
return False
def test_wrapper_script():
"""Test wrapper script structure."""
print("\nTesting wrapper script...")
try:
import generate_schematic
print("✓ generate_schematic imports successfully")
# Check main functions exist
if not hasattr(generate_schematic, 'main'):
print("✗ Missing function: main")
return False
print("✓ Function exists: main")
return True
except Exception as e:
print(f"✗ Wrapper script test failed: {e}")
return False
def test_prompt_engineering():
"""Test prompt construction."""
print("\nTesting prompt engineering...")
try:
from generate_schematic_ai import ScientificSchematicGenerator
generator = ScientificSchematicGenerator(api_key="test_key", verbose=False)
# Test improve_prompt method
original = "Create a flowchart"
critique = "Add more spacing between boxes"
improved = generator.improve_prompt(original, critique, 2)
if not improved:
print("✗ improve_prompt returned empty string")
return False
if original not in improved:
print("✗ Improved prompt doesn't include original")
return False
if critique not in improved:
print("✗ Improved prompt doesn't include critique")
return False
if "ITERATION 2" not in improved:
print("✗ Improved prompt doesn't include iteration number")
return False
print("✓ Prompt engineering works correctly")
print(f" Original length: {len(original)} chars")
print(f" Improved length: {len(improved)} chars")
return True
except Exception as e:
print(f"✗ Prompt engineering test failed: {e}")
return False
def test_file_paths():
"""Test that all required files exist."""
print("\nTesting file structure...")
base_dir = Path(__file__).parent
required_files = [
"scripts/generate_schematic_ai.py",
"scripts/generate_schematic.py",
"SKILL.md",
"README.md"
]
all_exist = True
for file_path in required_files:
full_path = base_dir / file_path
if full_path.exists():
print(f"{file_path}")
else:
print(f"✗ Missing: {file_path}")
all_exist = False
return all_exist
def main():
"""Run all tests."""
print("="*60)
print("Scientific Schematics AI Generation - Verification Tests")
print("="*60)
tests = [
("File Structure", test_file_paths),
("Imports", test_imports),
("Class Structure", test_class_structure),
("Error Handling", test_error_handling),
("Wrapper Script", test_wrapper_script),
("Prompt Engineering", test_prompt_engineering),
]
results = []
for test_name, test_func in tests:
try:
result = test_func()
results.append((test_name, result))
except Exception as e:
print(f"\n✗ Test '{test_name}' crashed: {e}")
results.append((test_name, False))
# Summary
print("\n" + "="*60)
print("Test Summary")
print("="*60)
passed = sum(1 for _, result in results if result)
total = len(results)
for test_name, result in results:
status = "✓ PASS" if result else "✗ FAIL"
print(f"{status}: {test_name}")
print(f"\nTotal: {passed}/{total} tests passed")
if passed == total:
print("\n✓ All tests passed! Implementation verified.")
print("\nNext steps:")
print("1. Set OPENROUTER_API_KEY environment variable")
print("2. Test with actual API call:")
print(" python scripts/generate_schematic.py 'test diagram' -o test.png")
return 0
else:
print(f"\n{total - passed} test(s) failed. Please review errors above.")
return 1
if __name__ == "__main__":
sys.exit(main())