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:

          - ./notebooks/talk2biomodels/tutorial_load_model.ipynb

          - ./notebooks/talk2biomodels/example_models.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

          - 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

  - Talk2Cells:

      - Talk2Cells: talk2cells/intro.md

      - Tutorials:

          - 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:

          - 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

      - 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

          - 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

          - Drug Enrichments/Embeddings (SMILES/molmim): ./notebooks/talk2knowledgegraphs/tutorial_primekg_smiles_enrich_embed.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

      - 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:

          - 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

      - 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 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 results: talk2scholars/tools/display_results.md

          - Query results: talk2scholars/tools/query_results.md

          - Retrieve ID: talk2scholars/tools/retrieve_semantic_scholar_paper_id.md

          - Download Arxiv Input: talk2scholars/tools/download_arxiv_input.md

          - Arxiv Downloader: talk2scholars/tools/arxiv_downloader.md

          - Abstract Downloader: talk2scholars/tools/abstract_downloader.md          

          - Zotero Read: talk2scholars/tools/zotero_read.md

          - Question and answer: talk2scholars/tools/question_and_answer.md

  - Documentation:

      - Ops:

          - Introduction: ops/Documentation_intro.md

          - CodeOps: ops/CodeOps.md

          - DevOps: ops/DevOps.md

      - Contributing:

          - Contributing: CONTRIBUTING.md

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

repo_name: VPE/AIAgents4Pharma

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    - overview.md: notebooks/overview.md