Adaptive Graph of Thoughts MCP Server

# Configuration Reference - **app/** - `app.name`: `Adaptive Graph of Thoughts` - `app.version`: `0.1.0` - `app.host`: `0.0.0.0` - `app.port`: `8000` - `app.mcp_transport_type`: `http` - `app.mcp_stdio_enabled`: `True` - `app.mcp_http_enabled`: `True` - `app.log_level`: `INFO` - **asr_got/** - **asr_got.default_parameters/** - `asr_got.default_parameters.initial_confidence`: `[0.9, 0.9, 0.9, 0.9]` - `asr_got.default_parameters.initial_layer`: `root_layer` - `asr_got.default_parameters.default_decomposition_dimensions`: `[{'label': 'Scope and Delimitations', 'description': 'Clearly define the boundaries and specific focus of the research question.'}, {'label': 'Core Objectives', 'description': 'Identify the primary goals and desired outcomes of the analysis.'}, {'label': 'Methodological Approach', 'description': 'Outline the research methods and analytical techniques to be employed.'}, {'label': 'Data Requirements and Availability', 'description': 'Specify the types of data needed and assess their accessibility and quality.'}, {'label': 'Key Assumptions', 'description': 'List any underlying assumptions made at the outset of the investigation.'}, {'label': 'Potential Challenges and Limitations', 'description': 'Anticipate obstacles, constraints, or limitations that might affect the research.'}, {'label': 'Expected Impact and Applications', 'description': 'Consider the potential significance of the findings and their practical use cases.'}, {'label': 'Ethical Considerations', 'description': 'Address any ethical implications related to the research topic or methodology.'}, {'label': 'Identification of Knowledge Gaps', 'description': 'Pinpoint areas of uncertainty or missing information relevant to the query.'}, {'label': 'Assessment of Potential Biases', 'description': 'Identify possible cognitive, methodological, or data-related biases.'}]` - `asr_got.default_parameters.dimension_confidence`: `[0.8, 0.8, 0.8, 0.8]` - **asr_got.default_parameters.hypotheses_per_dimension/** - `asr_got.default_parameters.hypotheses_per_dimension.min`: `2` - `asr_got.default_parameters.hypotheses_per_dimension.max`: `4` - `asr_got.default_parameters.hypothesis_confidence`: `[0.5, 0.5, 0.5, 0.5]` - `asr_got.default_parameters.default_disciplinary_tags`: `['general_science', 'interdisciplinary_studies']` - `asr_got.default_parameters.default_plan_types`: `['literature_review', 'data_analysis', 'simulation', 'expert_consultation']` - `asr_got.default_parameters.evidence_max_iterations`: `5` - `asr_got.default_parameters.pruning_confidence_threshold`: `0.2` - `asr_got.default_parameters.pruning_impact_threshold`: `0.3` - `asr_got.default_parameters.merging_semantic_overlap_threshold`: `0.8` - `asr_got.default_parameters.subgraph_min_confidence_threshold`: `0.6` - `asr_got.default_parameters.subgraph_min_impact_threshold`: `0.5` - `asr_got.pipeline_stages`: `[{'name': 'Initialization', 'module_path': 'adaptive_graph_of_thoughts.domain.stages.stage_1_initialization.InitializationStage', 'enabled': True}, {'name': 'Decomposition', 'module_path': 'adaptive_graph_of_thoughts.domain.stages.stage_2_decomposition.DecompositionStage', 'enabled': True}, {'name': 'Hypothesis Generation', 'module_path': 'adaptive_graph_of_thoughts.domain.stages.stage_3_hypothesis.HypothesisStage', 'enabled': True}, {'name': 'Evidence Integration', 'module_path': 'adaptive_graph_of_thoughts.domain.stages.stage_4_evidence.EvidenceStage', 'enabled': True}, {'name': 'Pruning and Merging', 'module_path': 'adaptive_graph_of_thoughts.domain.stages.stage_5_pruning_merging.PruningMergingStage', 'enabled': True}, {'name': 'Subgraph Extraction', 'module_path': 'adaptive_graph_of_thoughts.domain.stages.stage_6_subgraph_extraction.SubgraphExtractionStage', 'enabled': True}, {'name': 'Composition', 'module_path': 'adaptive_graph_of_thoughts.domain.stages.stage_7_composition.CompositionStage', 'enabled': True}, {'name': 'Reflection', 'module_path': 'adaptive_graph_of_thoughts.domain.stages.stage_8_reflection.ReflectionStage', 'enabled': True}]` - **asr_got.layers/** - **asr_got.layers.root_layer/** - `asr_got.layers.root_layer.description`: `Core foundational layer for initial task understanding and decomposition.` - **asr_got.layers.evidence_layer/** - `asr_got.layers.evidence_layer.description`: `Layer primarily containing evidence nodes and their direct connections.` - **asr_got.layers.hypothesis_analysis_layer/** - `asr_got.layers.hypothesis_analysis_layer.description`: `Layer focused on hypothesis development, competition, and refinement.` - **asr_got.layers.integration_synthesis_layer/** - `asr_got.layers.integration_synthesis_layer.description`: `Layer for integrating diverse findings and synthesizing overall conclusions.` - **mcp_settings/** - `mcp_settings.protocol_version`: `2024-11-05` - `mcp_settings.server_version`: `0.1.0` - `mcp_settings.vendor_name`: `Adaptive Graph of Thoughts Development Team` - **google_scholar/** - `google_scholar.api_key`: `YOUR_GOOGLE_SCHOLAR_API_KEY_HERE` - `google_scholar.base_url`: `https://serpapi.com/search` - **pubmed/** - `pubmed.api_key`: `YOUR_PUBMED_API_KEY_HERE_IF_NEEDED` - `pubmed.base_url`: `https://eutils.ncbi.nlm.nih.gov/entrez/eutils/` - `pubmed.email`: `your_email@example.com` - **exa_search/** - `exa_search.api_key`: `YOUR_EXA_SEARCH_API_KEY_HERE` - `exa_search.base_url`: `https://api.exa.ai` - `knowledge_domains`: `[{'name': 'Skin Immunology', 'keywords': ['skin', 'immune', 'immunology', 'dermatitis', 'psoriasis'], 'description': 'Focuses on the immune responses and mechanisms within the skin.'}, {'name': 'Dermatology', 'keywords': ['dermatology', 'skin diseases', 'cutaneous'], 'description': 'Branch of medicine dealing with the skin, hair, nails, and their diseases.'}, {'name': 'Cutaneous Malignancies', 'keywords': ['skin cancer', 'melanoma', 'lymphoma', 'carcinoma'], 'description': 'Cancers arising from the skin.'}, {'name': 'CTCL (Cutaneous T-Cell Lymphoma)', 'keywords': ['ctcl', 'mycosis fungoides', 'sezary syndrome'], 'description': 'A rare type of non-Hodgkin lymphoma that affects the skin.'}, {'name': 'Genomics', 'keywords': ['genomics', 'gene expression', 'dna', 'rna', 'sequencing'], 'description': 'Study of genomes, their structure, function, evolution, and mapping.'}, {'name': 'Microbiome', 'keywords': ['microbiome', 'microbiota', 'bacteria', 'fungi', 'virome'], 'description': 'The community of microorganisms living together in a particular habitat, including the human body.'}, {'name': 'Molecular Biology', 'keywords': ['molecular biology', 'proteins', 'enzymes', 'pathways'], 'description': 'Branch of biology that seeks to understand the molecular basis of biological activity.'}, {'name': 'Machine Learning', 'keywords': ['machine learning', 'ai', 'neural networks', 'deep learning', 'prediction'], 'description': "Field of artificial intelligence that uses statistical techniques to give computer systems the ability to 'learn'."}, {'name': 'Biomedical LLMs', 'keywords': ['biomedical llm', 'medical ai', 'nlp in medicine'], 'description': 'Large language models specialized for biomedical applications.'}]`