mkdocs.yml

site_name: AIAgents4Pharma

nav:
  - Home: index.md

  - Talk2AIAgents4Pharma:
      - Introduction: talk2aiagents4pharma/intro.md
      - Agents:
          - T2AA4P agent: talk2aiagents4pharma/agents/main_agent.md
      - States:
          - T2AA4P state: talk2aiagents4pharma/states/state_talk2aiagents4pharma.md

  - Talk2Biomodels:
      - Introduction: talk2biomodels/intro.md
      - FAQ: talk2biomodels/faq.md
      - Case Studies:
          - Precision medicine: talk2biomodels/cases/Case_1.md
          - Epidemiology: talk2biomodels/cases/Case_2.md
          - Emergent system properties: talk2biomodels/cases/Case_3.md
      - Tutorials:
          - Model Examples: ./notebooks/talk2biomodels/basico_tutorials/example_models.md
      - Benchmark:
          - Description: ./notebooks/talk2biomodels/benchmark/benchmark.md
      - Agents:
          - T2B agent: talk2biomodels/agents/t2b_agent.md
      - States:
          - T2B state: talk2biomodels/states/state_talk2biomodels.md
      - Models:
          - System Bio Model: talk2biomodels/models/sys_bio_model.md
          - Basico Model: talk2biomodels/models/basico_model.md
      - Tools:
          - Search models: talk2biomodels/tools/search_models.md
          - Model information: talk2biomodels/tools/get_modelinfo.md
          - Model annotation: talk2biomodels/tools/get_annotation.md
          - Simulate model: talk2biomodels/tools/simulate_model.md
          - Ask questions: talk2biomodels/tools/ask_question.md
          - Custom plots: talk2biomodels/tools/custom_plotter.md
          - Load biomodel: talk2biomodels/tools/load_biomodel.md
          - Save model: talk2biomodels/tools/save_model.md
          - Parameter scan: talk2biomodels/tools/parameter_scan.md
          - Steady state: talk2biomodels/tools/steady_state.md

  - Talk2Cells:
      - Introduction: talk2cells/intro.md
      - Tutorials:
          - cell2sentence: ./notebooks/talk2cells/tutorial_c2s.ipynb
          - Cell Annotation: ./notebooks/talk2cells/tutorial_cell_annotation.ipynb
          - Cell Discovery: ./notebooks/talk2cells/tutorial_cell_discovery.ipynb
          - UMAP Visualization: ./notebooks/talk2cells/tutorial_UMAP_visualization.ipynb
          - Cell Type Proportion: ./notebooks/talk2cells/tutorial_cell_type_proportion.ipynb
      - Agents:
          - Agent Introduction: talk2cells/agents/intro.md
          - SCP Agent: talk2cells/agents/scp_agent.md
      - States:
          - Talk2Cells: talk2cells/states/state_talk2cells.md
      - Tools:
          - Search studies: talk2cells/tools/search_studies.md
          - Display studies: talk2cells/tools/display_studies.md

  - Talk2KnowledgeGraphs:
      - Introduction: talk2knowledgegraphs/intro.md
      - Deployment:
          - Custom Data: talk2knowledgegraphs/deployment/custom_data.md
          - Deployment: talk2knowledgegraphs/deployment/deployment.md
      - FAQ: talk2knowledgegraphs/faq.md
      - Tutorials:
          - PrimeKG: ./notebooks/talk2knowledgegraphs/tutorial_primekg_loader.ipynb
          - StarkQA-PrimeKG: ./notebooks/talk2knowledgegraphs/tutorial_starkqa_primekg_loader.ipynb
          - BioBridge-PrimeKG: ./notebooks/talk2knowledgegraphs/tutorial_biobridge_primekg_loader.ipynb
          - PrimeKG Subgraph Extraction: ./notebooks/talk2knowledgegraphs/tutorial_primekg_subgraph.ipynb
          - BioBridge-PrimeKG Multimodal: ./notebooks/talk2knowledgegraphs/tutorial_biobridge_multimodal.ipynb
          - BioBridge-PrimeKG (IBD) Multimodal: ./notebooks/talk2knowledgegraphs/tutorial_biobridge_ibd_multimodal.ipynb
          - Textual Embeddings (all-minilm): ./notebooks/talk2knowledgegraphs/tutorial_starkqa_primekg_textual_embeddings_all_minilm.ipynb
          - Textual Embeddings (nomic-embed-text): ./notebooks/talk2knowledgegraphs/tutorial_starkqa_primekg_textual_embeddings_nomic_embed_text.ipynb
          - Textual Enrichments: ./notebooks/talk2knowledgegraphs/tutorial_starkqa_primekg_textual_enrichments.ipynb
          - Drug Enrichments/Embeddings (SMILES/molmim): ./notebooks/talk2knowledgegraphs/tutorial_primekg_smiles_enrich_embed.ipynb
          - PrimeKG enrichments/embeddings: ./notebooks/talk2knowledgegraphs/tutorial_primekg_enrichment.ipynb
          - Protein Embeddings: ./notebooks/talk2knowledgegraphs/tutorial_biobridge_primekg_protein_embeddings.ipynb
          - Embedding Alignment: ./notebooks/talk2knowledgegraphs/tutorial_multimodal_embeddings_alignment.ipynb
          - Evaluation (VSS): ./notebooks/talk2knowledgegraphs/tutorial_starkqa_primekg_evaluation_vss.ipynb
          - Talk2KG Agentic Tools: ./notebooks/talk2knowledgegraphs/tutorial_talk2kg_agentic_tools.ipynb
          - PyG2DataFrame: ./notebooks/talk2knowledgegraphs/tutorial_pyg2dataframe.ipynb
          - UniProt ID Mapping: ./notebooks/talk2knowledgegraphs/tutorial_uniprot_mapping.ipynb
      - Milvus Vector DB Setup:
          - BioBridge-PrimeKG (IBD) Multimodal Data Prep.: ./notebooks/talk2knowledgegraphs/tutorial_biobridge_ibd_multimodal.ipynb
          - BioBridge-PrimeKG (IBD) Multimodal Data Dump: ./notebooks/talk2knowledgegraphs/tutorial_primekg_milvus_ibd_primekg_dump.ipynb
          - BioBridge-PrimeKG Multimodal Data Prep.: ./notebooks/talk2knowledgegraphs/tutorial_biobridge_multimodal.ipynb
          - BioBridge-PrimeKG Multimodal Data Dump: ./notebooks/talk2knowledgegraphs/tutorial_primekg_milvus_data_dump.ipynb
      - Datasets:
          - Dataset: talk2knowledgegraphs/datasets/dataset.md
          - PrimeKG: talk2knowledgegraphs/datasets/primekg.md
          - StarkQA-PrimeKG: talk2knowledgegraphs/datasets/starkqa_primekg.md
          - BioBridge-PrimeKG: talk2knowledgegraphs/datasets/biobridge_primekg.md
      - Utils:
          - Database:
              - MilvusConnectionManager: talk2knowledgegraphs/utils/database/milvus_connection_manager.md
          - Embeddings:
              - Embeddings: talk2knowledgegraphs/utils/embeddings/embeddings.md
              - EmbeddingWithSentenceTransformer: talk2knowledgegraphs/utils/embeddings/sentence_transformer.md
              - EmbeddingWithHuggingFace: talk2knowledgegraphs/utils/embeddings/huggingface.md
              - EmbeddingWithOllama: talk2knowledgegraphs/utils/embeddings/ollama.md
              - EmbeddingWithMOLMIM: talk2knowledgegraphs/utils/embeddings/nim_molmim.md
          - Enrichments:
              - Enrichments: talk2knowledgegraphs/utils/enrichments/enrichments.md
              - EnrichmentWithOllama: talk2knowledgegraphs/utils/enrichments/ollama.md
              - EnrichmentWithPubChem: talk2knowledgegraphs/utils/enrichments/pubchem_strings.md
              - EnrichmentWithUniProt: talk2knowledgegraphs/utils/enrichments/uniprot_proteins.md
              - EnrichmentWithReactome: talk2knowledgegraphs/utils/enrichments/reactome_pathways.md
              - EnrichmentWithOLS: talk2knowledgegraphs/utils/enrichments/ols_terms.md
          - Extractions:
              - PCST: talk2knowledgegraphs/utils/extractions/pcst.md
              - PCST (Multimodal): talk2knowledgegraphs/utils/extractions/multimodal_pcst.md
              - PCST (Milvus Multimodal): talk2knowledgegraphs/utils/extractions/milvus_multimodal_pcst.md
      - Agents:
          - Talk2KG Agent: talk2knowledgegraphs/agents/t2kg_agent.md
      - States:
          - Talk2KG State: talk2knowledgegraphs/states/state_talk2knowledgegraphs.md
      - Tools:
          - Subgraph Extraction: talk2knowledgegraphs/tools/subgraph_extraction.md
          - Subgraph Extraction (Multimodal): talk2knowledgegraphs/tools/multimodal_subgraph_extraction.md
          - Subgraph Extraction (Milvus Multimodal): talk2knowledgegraphs/tools/milvus_multimodal_subgraph_extraction.md
          - Subgraph Summarization: talk2knowledgegraphs/tools/subgraph_summarization.md
          - GraphRAG Reasoning: talk2knowledgegraphs/tools/graphrag_reasoning.md
          - Load Arguments: talk2knowledgegraphs/tools/load_arguments.md

  - Talk2Scholars:
      - Introduction: talk2scholars/intro.md
      - Tutorials: ./notebooks/talk2scholars/tutorial.ipynb
      - Agents:
          - Main Agent: talk2scholars/agents/main_agent.md
          - S2 Agent: talk2scholars/agents/s2_agent.md
          - Paper Download Agent: talk2scholars/agents/paper_download_agent.md
          - Zotero Agent: talk2scholars/agents/zotero_agent.md
          - PDF Agent: talk2scholars/agents/pdf_agent.md
      - States:
          - Talk2Scholars state: talk2scholars/states/state_talk2scholars.md
      - Tools:
          - Search Papers: talk2scholars/tools/search.md
          - Single Paper Recommendation: talk2scholars/tools/single_paper_rec.md
          - Multi Paper Recommendation: talk2scholars/tools/multi_paper_rec.md
          - Display Dataframe: talk2scholars/tools/display_dataframe.md
          - Query Dataframe: talk2scholars/tools/query_dataframe.md
          - Retrieve Semantic Scholar ID: talk2scholars/tools/retrieve_semantic_scholar_paper_id.md
          - Paper Downloader: talk2scholars/tools/paper_downloader.md
          - Question and answer: talk2scholars/tools/question_and_answer.md
          - Zotero Read: talk2scholars/tools/zotero_read.md
          - Zotero Write: talk2scholars/tools/zotero_write.md
          - Zotero Review: talk2scholars/tools/zotero_review.md
      - Utils:
          S2 Agent:
            - Search Helper: talk2scholars/utils/search_helper.md
            - Single Paper Recommendation Helper: talk2scholars/utils/single_helper.md
            - Multi Paper Recommendation Helper: talk2scholars/utils/multi_helper.md
          PDF Agent:
            - Vector Store: talk2scholars/utils/vector_store.md
            - Singleton Manager: talk2scholars/utils/singleton_manager.md
            - GPU Detection: talk2scholars/utils/gpu_detection.md
            - Collection Manager: talk2scholars/utils/collection_manager.md
            - Get Vector Store: talk2scholars/utils/get_vectorstore.md
            - Document Processor: talk2scholars/utils/document_processor.md
            - Paper Loader: talk2scholars/utils/paper_loader.md
            - Batch Processor: talk2scholars/utils/batch_processor.md
            - RAG Pipeline: talk2scholars/utils/rag_pipeline.md
            - Vector Normalization: talk2scholars/utils/vector_normalization.md
            - Retrieve Chunks: talk2scholars/utils/retrieve_chunks.md
            - Nvidia NIM Reranker: talk2scholars/utils/nvidia_nim_reranker.md
            - Generate Answer: talk2scholars/utils/generate_answer.md
            - Answer Formatter: talk2scholars/utils/answer_formatter.md
            - Tool Helper: talk2scholars/utils/tool_helper.md
          Paper Download Agent:
            - Base Paper Downloader: talk2scholars/utils/base_paper_downloader.md
            - Arxiv Downloader: talk2scholars/utils/arxiv_downloader.md
            - Biorxiv Downloader: talk2scholars/utils/biorxiv_downloader.md
            - Medrxiv Downloader: talk2scholars/utils/medrxiv_downloader.md
            - Pubmed Downloader: talk2scholars/utils/pubmed_downloader.md
          Zotero Agent:
            - Zotero Write Helper: talk2scholars/utils/write_helper.md
            - Zotero Read Helper: talk2scholars/utils/read_helper.md
            - Zotero Review Helper: talk2scholars/utils/review_helper.md
            - Zotero Path: talk2scholars/utils/zotero_path.md
            - Zotero PDF Downloader: talk2scholars/utils/zotero_pdf_downloader.md

  # Developer Documentation Section
  - Documentation:
      - Developer Guides:
          - Setup Guide: developer/README.md
          - Testing & Linting: developer/TESTING_LINTING.md
          - GitHub Workflows: developer/WORKFLOWS.md
          - Streamlit Security: developer/STREAMLIT_SECURITY.md
          - SonarCloud Setup: developer/SONARCLOUD_SETUP.md
          - Azure Deployment: developer/AZURE_DEPLOYMENT.md
      - Operations:
          - Operations Overview: ops/Documentation_intro.md
          - Code Operations: ops/CodeOps.md
          - Dev Operations: ops/DevOps.md
      - Project Guidelines:
          - Contributing Guide: CONTRIBUTING.md

repo_url: https://github.com/VirtualPatientEngine/AIAgents4Pharma
repo_name: VPE/AIAgents4Pharma

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