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mkdocs.yml
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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
extra_css:
- VPE.png
theme:
name: material
logo: assets/VPE.png
palette:
- accent: black
primary: white
scheme: default
toggle:
icon: material/toggle-switch-off-outline
name: Switch to dark mode
- accent: black
primary: white
scheme: slate
toggle:
icon: material/toggle-switch
name: Switch to light mode
features:
- navigation.top
- navigation.tabs
- navigation.instant
- navigation.expand
- search.suggest
- search.highlight
- content.code.copy
- navigation.scrollable
plugins:
- search:
lang:
- en
- de
- mkdocstrings:
handlers:
python:
options:
filters: None
- mkdocs-jupyter:
include_source: True
- tags
- include-markdown
markdown_extensions:
- pymdownx.highlight
# anchor_linenums: true
# line_spans: __span
# pygments_lang_class: true
- pymdownx.superfences
extra:
notebooks:
- overview.md: notebooks/overview.md