Mojo Academic Research Workflow System

A comprehensive research workflow assistance system designed to support academic researchers in organizing, validating, and preparing research for publication while maintaining strict ethical standards and human oversight.

Overview

This system provides tools to assist researchers like Oates R. in managing their cognitive science research on topics such as mind-wandering, recursive cognition, and attention dynamics. The system emphasizes:

• Human-Centered Design: All critical decisions require explicit human approval
• Ethical Compliance: Comprehensive checks for IRB approval, consent, and data privacy
• Quality Assurance: Multi-stage peer review and validation processes
• Reproducibility: Support for open science practices and transparent methodologies

Dependencies

Some components of this repository rely on PyTorch. If PyTorch is not installed—such as on macOS systems without GPU support—the unit tests that require it will be skipped automatically. Installing PyTorch is recommended to access full functionality.

Key Features

1. Research Identification & Organization

• Pattern-based recognition of research contributions
• Thematic clustering of related papers
• Automatic metadata extraction
• Author signature verification

2. Manuscript Development

• Structured abstract generation
• Journal-specific formatting
• Co-author management
• Theoretical framework integration

3. Validation & Review System

• Comprehensive peer review management
• Statistical validation checks
• Reproducibility assessment
• Quality metrics evaluation

4. Ethical Safeguards

• Mandatory IRB compliance checking
• Multi-stakeholder consent verification
• Institutional approval workflows
• Comprehensive audit trails

5. Human Oversight Requirements

• No autonomous publication capability
• Explicit approval required at all stages
• Timeout protections with automatic holds
• Appeal processes for disputed decisions

System Architecture

Core Components

1. academic_research_workflow.mojo

   • Main workflow orchestration
   • Paper management and tracking
   • Approval workflow implementation
   • Ethics compliance verification

2. pattern_matcher.mojo

   • Research signature recognition
   • Pattern-based content analysis
   • Author contribution identification
   • Metadata extraction

3. validation_system.mojo

   • Peer review management
   • Statistical validation
   • Reproducibility checking
   • Quality assessment

4. research_config.mojo

   • Domain-specific configurations
   • Ethical guidelines
   • Journal requirements
   • Workflow safeguards

Usage Example

# Initialize the research workflow system
workflow = create_oates_research_system()

# Process a research paper
research_data = {
    "title": "Fractal Dynamics in Mind-Wandering Episodes",
    "background": "Mind-wandering exhibits recursive patterns",
    "methods": "fMRI analysis with fractal dimension calculations",
    "results": "Discovered scale-invariant attention fluctuations",
    "conclusions": "Attention operates as a fractal system",
    "framework": "recursive cognition",
    "co_authors": "Smith, J., Johnson, K."
}

# Generate manuscript outline (requires human review)
manuscript = workflow.generate_manuscript_outline(research_data, "Cognitive Science")

# Create ethics compliance record
paper_id = str(hash(manuscript.title))
ethics = workflow.create_ethics_compliance_record(paper_id)

# Initiate human approval workflow
approvers = ["primary_author", "co_author_1", "co_author_2", 
             "department_chair", "ethics_board"]
approval_workflow = workflow.initiate_approval_workflow(paper_id, approvers, 14)

# Check publication readiness
readiness = workflow.check_publication_readiness(paper_id)

Ethical Guidelines

Mandatory Requirements

1. IRB Approval: All research involving human participants must have institutional review board approval
2. Informed Consent: Explicit consent required from all participants
3. Data Privacy: GDPR compliance and anonymization protocols
4. Author Consent: All authors must explicitly approve submission
5. Institutional Approval: Required from affiliated institutions

Human Oversight Checkpoints

1. Initial manuscript review
2. Ethics compliance verification
3. Peer review assignments
4. Final publication decision
5. Post-publication monitoring

Research Domains Supported

Cognitive Neuroscience

• Mind-wandering and spontaneous thought
• Attention regulation and dynamics
• Default mode network function
• Consciousness and awareness

Computational Cognition

• Recursive processing models
• Fractal dynamics in cognition
• Hierarchical Bayesian approaches
• Complex systems analysis

Methodological Approaches

• fMRI and EEG neuroimaging
• Behavioral experiments
• Computational modeling
• Meta-analysis techniques

Security & Privacy

• Encrypted storage of sensitive data
• Role-based access control
• Comprehensive audit logging
• Secure communication channels
• Data retention policies

Limitations & Disclaimers

1. No Autonomous Publishing: This system cannot and will not publish research without explicit human approval
2. Advisory Role Only: All recommendations are advisory and require human judgment
3. Not a Replacement: Designed to assist, not replace, human academic processes
4. Compliance Required: Users must ensure compliance with their institutional policies

Personalization Notes

This system is designed to be adapted to specific research needs and institutional requirements. Here are some key areas you can modify:

1. Author Profile and Research Focus

• Update AuthorProfile: Modify the create_oates_research_system function in academic_research_workflow.mojo to define the AuthorProfile for your specific researcher, including their name, domains, signatures, frameworks, and institution.
• Customize Research Patterns: Edit the create_oates_signature function in pattern_matcher.mojo to refine the ResearchPattern list with keywords, types, weights, and context windows specific to the researcher's work and writing style. Adjust minimum_confidence and combination_rules as needed.

2. Validation and Review

• Modify Review Criteria: Update the _initialize_review_criteria function in validation_system.mojo to add, remove, or adjust review criteria and their weights to match disciplinary standards or specific project needs.
• Manage Reviewer Pool: Add or modify PeerReviewer entries in the validation_system.mojo to include relevant experts for assigning reviews. Enhance the assign_reviewers logic for more sophisticated matching or conflict detection.
• Refine Validation Checks: The validate_statistics and check_reproducibility functions in validation_system.mojo contain placeholder logic. Extend these functions to integrate with external tools, scripts, or manual verification steps for more rigorous validation.

3. Ethical and Workflow Configuration

• Adapt Ethical Guidelines: Modify the create_ethics_guidelines function in research_config.mojo to reflect specific institutional review board (IRB) requirements, data privacy regulations (e.g., GDPR, HIPAA), and consent protocols.
• Configure Journal Requirements: Update the create_journal_requirements function in research_config.mojo to add submission formats, peer review types, and ethical requirements for target journals.
• Adjust Workflow Safeguards: Review and modify the ResearchWorkflowConfig and create_workflow_safeguards in research_config.mojo. Adjust min_reviewers, approval_timeout_days, require_unanimous_approval, etc., to align with institutional policies, ensuring that critical human oversight is maintained.
• Customize Approval Workflows: Adapt the initiate_approval_workflow and record_approval_decision functions in academic_research_workflow.mojo to fit specific organizational structures and approval hierarchies.

4. Data Sources and Processing

• Integrate Content Streams: The identify_research_contributions function in academic_research_workflow.mojo takes a List[String] content_streams. Extend this to integrate with actual data sources like local file systems, online repositories (with appropriate access), or internal databases, ensuring privacy and security.
• Enhance Metadata Extraction: Improve the _extract_paper_metadata and extract_research_metadata functions to parse different file formats and extract more detailed information from research documents.

Remember to always maintain the core principle of mandatory human oversight for all publication-related decisions when personalizing the system.

Future Enhancements

• Integration with preprint servers (with human approval)
• Advanced collaboration features
• Multi-institutional workflow support
• Enhanced statistical analysis tools
• Expanded domain coverage

Command Line Interface

The repository includes a lightweight CLI wrapper to run the core Mojo modules. The script scripts/cli.py forwards commands to the mojo executable.

python scripts/cli.py <command> [-- <mojo args>]

Available commands:

• workflow – run academic_research_workflow.mojo
• match – run pattern_matcher.mojo
• validate – run validation_system.mojo
• config – run research_config.mojo
• example – run example_usage.mojo

Arguments after -- are passed directly to the Mojo script. Ensure the mojo binary is installed and reachable via PATH or set MOJO_BIN before running.

Contributing

This system is designed with extensibility in mind. Researchers can contribute:

• New domain configurations
• Additional validation criteria
• Enhanced pattern matching algorithms
• Improved quality metrics

License

This system is provided for academic research purposes. Users must comply with all applicable ethical guidelines and institutional policies.

Contact

For questions about ethical compliance, system capabilities, or research workflows, please consult with your institutional review board and research compliance office.

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Important Notice: This system prioritizes ethical research practices and human oversight. No research will be published without explicit approval from all required stakeholders.