vigil-ai 0.3.0

AI-powered workflow generation with foundation models (Claude, ESM, BioGPT, ChemBERTa, etc.)

vigil-ai

AI-powered workflow generation with foundation models for reproducible science

vigil-ai extends Vigil with AI capabilities, making scientific workflow creation accessible through natural language and specialized foundation models.

Features

• Natural language → Pipeline: Generate Snakemake workflows from plain English descriptions
• Foundation models: 10+ specialized models for biology, chemistry, materials science
• Domain-specific AI: Auto-select the best model for your scientific domain
• AI debugging: Get intelligent suggestions for fixing pipeline errors
• Workflow optimization: Analyze and optimize for speed, cost, or resource usage
• Task-based interface: Simple, high-level API for common workflows
• MCP integration: Works with Claude Desktop and AI assistants

Installation

Basic (Claude models only):

pip install vigil-ai

With science models (ESM-2, BioGPT, ChemBERTa, etc.):

pip install 'vigil-ai[science]'

Or install with Vigil:

pip install 'vigil[ai]'              # Basic
pip install 'vigil[ai,science]'      # With science models

Requirements

• Python 3.11+
• Vigil >= 0.2.1
• Anthropic API key (get one at https://console.anthropic.com/)

Setup

Set your Anthropic API key:

export ANTHROPIC_API_KEY='your-api-key-here'

Or add to your .env file:

ANTHROPIC_API_KEY=your-api-key-here

Usage

Generate Pipeline from Description

vigil ai create "Filter variants by quality >30, annotate with Ensembl, calculate Ti/Tv ratio"

Output:

✓ Pipeline created: app/code/pipelines/Snakefile

Next steps:
  1. Review the generated pipeline
  2. Create necessary step scripts
  3. vigil run --cores 4

Debug Pipeline Errors

vigil ai debug

# Or specify error log
vigil ai debug --error-log .snakemake/log/error.log

Output:

Analyzing error...

Root Cause:
The rule 'filter_variants' failed because the input file 'variants.csv' was not found.

Suggested Fix:
1. Check that your data exists: ls app/data/samples/
2. Verify file name matches exactly (case-sensitive)
3. If file is missing, download or create it
4. Run: vigil doctor to check project health

Prevention:
Add input validation before running pipeline.

Optimize Workflow

vigil ai optimize --focus speed

# Or optimize for cost
vigil ai optimize --focus cost

Output:

Optimization Suggestions:

Rule: filter_variants
Issue: Sequential processing
Suggestion: Add threads: 4 and use parallel processing
Impact: 4x faster with multi-core

Rule: annotate
Issue: Repeated API calls
Suggestion: Implement caching for Ensembl queries
Impact: 10x faster on reruns

Quick Start (Task-Based Interface)

The simplest way to use vigil-ai is through the task-based interface:

from vigil_ai.tasks import PipelineGenerator, ErrorDebugger, ModelSelector

# 1. Generate a pipeline for biology
bio_gen = PipelineGenerator(domain="biology")
pipeline = bio_gen.create("Filter variants >30, annotate, calculate Ti/Tv")
bio_gen.create_and_save(pipeline, "workflow.smk")

# 2. Debug errors when they occur
debugger = ErrorDebugger()
fix = debugger.analyze("FileNotFoundError: variants.csv not found")
print(fix)

# 3. Get model recommendations
selector = ModelSelector()
model, reason = selector.recommend("I need to analyze protein sequences")
print(reason)  # "Recommended biology model (ESM-2) for protein analysis"

Foundation Models

vigil-ai supports 10+ specialized foundation models across scientific domains:

Biology Models

• ESM-2 (650M, 3B, 15B) - Protein language models from Meta AI
• BioGPT - Biomedical text generation
• ProtGPT2 - Protein sequence generation

Chemistry Models

• ChemBERTa - Molecular property prediction
• MolFormer - Chemical structure analysis

Materials Science Models

• MatBERT - Materials property prediction

General Models

• Claude 3.5 Sonnet (default) - General-purpose, most capable
• Claude 3 Opus - Most powerful
• Galactica - Scientific knowledge and reasoning

Using Domain-Specific Models

from vigil_ai import get_model, ModelDomain

# Automatically select best model for domain
bio_model = get_model(domain=ModelDomain.BIOLOGY)      # Returns ESM-2
chem_model = get_model(domain=ModelDomain.CHEMISTRY)   # Returns ChemBERTa
mat_model = get_model(domain=ModelDomain.MATERIALS)    # Returns MatBERT

# Use specific model by name
esm = get_model(name="esm-2-650m")
embedding = esm.embed("MKFLKFSLLTAVLLSVVFAFSSCGDDDDTGYLPPSQAIQDLL")

# Generate with domain-specific model
from vigil_ai import generate_pipeline
pipeline = generate_pipeline(
    "Analyze protein sequences and predict function",
    domain=ModelDomain.BIOLOGY  # Uses ESM-2
)

Python API (Low-Level)

For more control, use the low-level API:

from vigil_ai import generate_pipeline, ai_debug, ai_optimize

# Generate pipeline
pipeline = generate_pipeline(
    "Filter variants by quality >30, calculate Ti/Tv ratio",
    template="genomics-starter",
    model="claude-3-5-sonnet-20241022"  # Or specify domain
)
print(pipeline)

# Debug error
fix = ai_debug("FileNotFoundError: variants.csv not found")
print(fix)

# Optimize workflow
suggestions = ai_optimize(focus="speed")
print(suggestions)

Examples

Create Imaging Analysis Pipeline

vigil ai create "Segment cells from microscopy images, count cells per field, measure intensity"

Generates:

rule segment_cells:
    input: "data/images/{sample}.tif"
    output: "artifacts/masks/{sample}_mask.png"
    script: "../lib/steps/segment.py"

rule count_cells:
    input: "artifacts/masks/{sample}_mask.png"
    output: "artifacts/counts/{sample}_counts.json"
    script: "../lib/steps/count.py"

rule measure_intensity:
    input:
        image="data/images/{sample}.tif",
        mask="artifacts/masks/{sample}_mask.png"
    output: "artifacts/intensity/{sample}_intensity.csv"
    script: "../lib/steps/measure.py"

Interactive Mode

vigil ai chat

Starts interactive session:

> Create a pipeline to filter variants
✓ Pipeline generated

> Add a rule to calculate metrics
✓ Added metrics rule

> How can I make this faster?
Suggestions:
1. Add parallel processing
2. Cache intermediate results
...

Configuration

Create .vigil-ai.yaml in your project:

ai:
  model: claude-3-5-sonnet-20241022  # Claude model to use
  max_tokens: 4096                     # Max response length
  temperature: 0.7                     # Creativity (0-1)
  cache_responses: true                # Cache AI responses

Advanced Usage

Generate Step Script

from vigil_ai.generator import generate_step_script

script = generate_step_script(
    rule_name="filter_variants",
    description="Filter variants by quality score >30",
    inputs=["variants.csv"],
    outputs=["filtered.parquet"],
    language="python"
)

with open("app/code/lib/steps/filter.py", "w") as f:
    f.write(script)

Custom Prompts

from vigil_ai import generate_pipeline

pipeline = generate_pipeline(
    description="""
    Create a multi-sample variant calling pipeline:
    1. Align reads with BWA
    2. Mark duplicates with Picard
    3. Call variants with GATK
    4. Filter and annotate
    """,
    template="genomics-starter"
)

Architecture

vigil-ai is part of a three-layer architecture for reproducible science:

┌─────────────────────────────────────────────────────┐
│  Agents Layer: AI Assistants                        │
│  (Claude Desktop, custom agents)                    │
└─────────────────────────────────────────────────────┘
                        ▼
┌─────────────────────────────────────────────────────┐
│  Application Layer: vigil-ai (THIS PACKAGE)         │
│  - MCP Server Integration                           │
│  - Foundation Models (Claude, ESM, BioGPT, etc.)    │
│  - Task Interface (PipelineGenerator, etc.)         │
└─────────────────────────────────────────────────────┘
                        ▼
┌─────────────────────────────────────────────────────┐
│  Foundation Layer: Vigil Core                       │
│  - Snakemake pipelines                              │
│  - Artifact management                              │
│  - Receipt tracking                                 │
└─────────────────────────────────────────────────────┘

MCP Integration

vigil-ai extends the Vigil MCP server with 5 AI-powered verbs:

• ai_generate_pipeline - Generate Snakemake workflow from description
• ai_debug_error - Analyze and fix pipeline errors
• ai_optimize_workflow - Suggest performance optimizations
• ai_list_models - List available foundation models
• ai_get_model_info - Get model metadata and capabilities

Use with Claude Desktop:

{
  "mcpServers": {
    "vigil": {
      "command": "vigil",
      "args": ["mcp"]
    }
  }
}

Then ask Claude: "Generate a pipeline to filter variants and calculate metrics"

All Supported Models

General-Purpose (API-based)

• claude-3-5-sonnet-20241022 (default, recommended)
• claude-3-opus-20240229 (most powerful)
• claude-3-sonnet-20240229 (balanced)
• claude-3-haiku-20240307 (fastest, cheapest)

Biology (requires [science] install)

• esm-2-650m - Meta AI protein model, 650M params
• esm-2-3b - Meta AI protein model, 3B params (GPU recommended)
• esm-2-15b - Meta AI protein model, 15B params (GPU required)
• biogpt - Microsoft biomedical text model
• protgpt2 - Protein sequence generation

Chemistry (requires [science] install)

• chemberta-v2 - DeepChem molecular property model
• molformer - Molecular structure analysis

Materials Science (requires [science] install)

• matbert - Materials property prediction

Cost Estimates

Claude models (API-based):

• Pipeline generation: ~$0.02-0.05 per request
• Debugging: ~$0.01-0.03 per request
• Optimization: ~$0.03-0.07 per request

Science models (local inference):

• Free to use (runs on your hardware)
• Requires GPU for optimal performance (ESM-2, BioGPT)
• CPU inference possible but slower

Cost optimization tips:

• Enable response caching: cache_responses: true in .vigil-ai.yaml
• Use smaller models for simpler tasks (claude-3-haiku vs claude-3-opus)
• Use local science models when applicable (no API costs)

Example Gallery

See the examples/ directory for complete examples:

• task_based_workflow.py - Complete workflow using task interface
• domain_specific_models.py - Using biology/chemistry/materials models
• basic_pipeline_generation.py - Low-level API examples
• with_caching_and_config.py - Configuration and caching

Run any example:

python examples/task_based_workflow.py

Limitations

General:

• Claude models require internet connection and API key
• Generated pipelines need review before use in production
• AI suggestions should be validated by domain experts
• Not a replacement for scientific expertise

Science models:

• Require pip install vigil-ai[science] and additional dependencies
• Large models (ESM-2 15B) require significant GPU memory (40GB+)
• Local inference slower than API-based models
• May require domain-specific preprocessing

Development

# Clone repo
git clone https://github.com/Science-Abundance/vigil
cd vigil/packages/vigil-core-ai

# Install in dev mode with all dependencies
pip install -e '.[dev,science]'

# Run tests
pytest

# Run tests with science models (requires GPU)
pytest -m science

# Lint
ruff check .

# Type check
mypy src/

# Run examples
python examples/task_based_workflow.py
python examples/domain_specific_models.py

Contributing

Contributions welcome! See CONTRIBUTING.md

License

Apache-2.0

Support

• GitHub Issues: https://github.com/Science-Abundance/vigil/issues
• Documentation: https://github.com/Science-Abundance/vigil
• Discord: [coming soon]

Acknowledgments

Built with:

• Anthropic Claude - General-purpose AI capabilities
• Vigil - Reproducible science platform
• HuggingFace Transformers - Foundation model infrastructure

Foundation models:

• ESM-2 - Meta AI (paper)
• BioGPT - Microsoft Research (paper)
• ChemBERTa - DeepChem (paper)
• MatBERT - Materials Project (paper)
• Galactica - Meta AI (paper)