aiagents4pharma 1.40.1__py3-none-any.whl → 1.42.0__py3-none-any.whl

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Files changed (53) hide show
  1. aiagents4pharma/talk2knowledgegraphs/configs/app/frontend/default.yaml +1 -1
  2. aiagents4pharma/talk2knowledgegraphs/configs/tools/multimodal_subgraph_extraction/default.yaml +37 -0
  3. aiagents4pharma/talk2knowledgegraphs/configs/utils/enrichments/ols_terms/default.yaml +3 -0
  4. aiagents4pharma/talk2knowledgegraphs/configs/utils/enrichments/reactome_pathways/default.yaml +3 -0
  5. aiagents4pharma/talk2knowledgegraphs/configs/utils/enrichments/uniprot_proteins/default.yaml +6 -0
  6. aiagents4pharma/talk2knowledgegraphs/configs/utils/pubchem_utils/default.yaml +5 -0
  7. aiagents4pharma/talk2knowledgegraphs/milvus_data_dump.py +752 -350
  8. aiagents4pharma/talk2scholars/configs/agents/talk2scholars/s2_agent/default.yaml +4 -0
  9. aiagents4pharma/talk2scholars/configs/tools/question_and_answer/default.yaml +44 -4
  10. aiagents4pharma/talk2scholars/tests/test_nvidia_nim_reranker.py +127 -0
  11. aiagents4pharma/talk2scholars/tests/test_pdf_answer_formatter.py +66 -0
  12. aiagents4pharma/talk2scholars/tests/test_pdf_batch_processor.py +101 -0
  13. aiagents4pharma/talk2scholars/tests/test_pdf_collection_manager.py +150 -0
  14. aiagents4pharma/talk2scholars/tests/test_pdf_document_processor.py +69 -0
  15. aiagents4pharma/talk2scholars/tests/test_pdf_generate_answer.py +75 -0
  16. aiagents4pharma/talk2scholars/tests/test_pdf_gpu_detection.py +140 -0
  17. aiagents4pharma/talk2scholars/tests/test_pdf_paper_loader.py +116 -0
  18. aiagents4pharma/talk2scholars/tests/test_pdf_rag_pipeline.py +98 -0
  19. aiagents4pharma/talk2scholars/tests/test_pdf_retrieve_chunks.py +197 -0
  20. aiagents4pharma/talk2scholars/tests/test_pdf_singleton_manager.py +156 -0
  21. aiagents4pharma/talk2scholars/tests/test_pdf_vector_normalization.py +121 -0
  22. aiagents4pharma/talk2scholars/tests/test_pdf_vector_store.py +434 -0
  23. aiagents4pharma/talk2scholars/tests/test_question_and_answer_tool.py +89 -509
  24. aiagents4pharma/talk2scholars/tests/test_tool_helper_utils.py +34 -89
  25. aiagents4pharma/talk2scholars/tools/paper_download/download_biorxiv_input.py +8 -6
  26. aiagents4pharma/talk2scholars/tools/paper_download/download_medrxiv_input.py +6 -4
  27. aiagents4pharma/talk2scholars/tools/pdf/question_and_answer.py +74 -40
  28. aiagents4pharma/talk2scholars/tools/pdf/utils/__init__.py +26 -1
  29. aiagents4pharma/talk2scholars/tools/pdf/utils/answer_formatter.py +62 -0
  30. aiagents4pharma/talk2scholars/tools/pdf/utils/batch_processor.py +200 -0
  31. aiagents4pharma/talk2scholars/tools/pdf/utils/collection_manager.py +172 -0
  32. aiagents4pharma/talk2scholars/tools/pdf/utils/document_processor.py +76 -0
  33. aiagents4pharma/talk2scholars/tools/pdf/utils/generate_answer.py +14 -14
  34. aiagents4pharma/talk2scholars/tools/pdf/utils/get_vectorstore.py +63 -0
  35. aiagents4pharma/talk2scholars/tools/pdf/utils/gpu_detection.py +154 -0
  36. aiagents4pharma/talk2scholars/tools/pdf/utils/nvidia_nim_reranker.py +60 -40
  37. aiagents4pharma/talk2scholars/tools/pdf/utils/paper_loader.py +123 -0
  38. aiagents4pharma/talk2scholars/tools/pdf/utils/rag_pipeline.py +122 -0
  39. aiagents4pharma/talk2scholars/tools/pdf/utils/retrieve_chunks.py +162 -40
  40. aiagents4pharma/talk2scholars/tools/pdf/utils/singleton_manager.py +140 -0
  41. aiagents4pharma/talk2scholars/tools/pdf/utils/tool_helper.py +40 -78
  42. aiagents4pharma/talk2scholars/tools/pdf/utils/vector_normalization.py +159 -0
  43. aiagents4pharma/talk2scholars/tools/pdf/utils/vector_store.py +277 -96
  44. aiagents4pharma/talk2scholars/tools/s2/multi_paper_rec.py +12 -9
  45. aiagents4pharma/talk2scholars/tools/s2/query_dataframe.py +0 -1
  46. aiagents4pharma/talk2scholars/tools/s2/retrieve_semantic_scholar_paper_id.py +9 -8
  47. aiagents4pharma/talk2scholars/tools/s2/single_paper_rec.py +5 -5
  48. {aiagents4pharma-1.40.1.dist-info → aiagents4pharma-1.42.0.dist-info}/METADATA +52 -126
  49. {aiagents4pharma-1.40.1.dist-info → aiagents4pharma-1.42.0.dist-info}/RECORD +52 -25
  50. aiagents4pharma/talk2scholars/tests/test_nvidia_nim_reranker_utils.py +0 -28
  51. {aiagents4pharma-1.40.1.dist-info → aiagents4pharma-1.42.0.dist-info}/WHEEL +0 -0
  52. {aiagents4pharma-1.40.1.dist-info → aiagents4pharma-1.42.0.dist-info}/licenses/LICENSE +0 -0
  53. {aiagents4pharma-1.40.1.dist-info → aiagents4pharma-1.42.0.dist-info}/top_level.txt +0 -0
aiagents4pharma/talk2knowledgegraphs/configs/app/frontend/default.yaml CHANGED
@@ -60,4 +60,4 @@ milvus_db:
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  collection_nodes_drug: "t2kg_primekg_nodes_drug"
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  collection_nodes_disease: "t2kg_primekg_nodes_disease"
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  query_batch_size: 1000000
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- cache_edge_index_path: "aiagents4pharma/talk2knowledgegraphs/tests/files/t2kg_primekg_edge_index.pkl"
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+ cache_edge_index_path: "${oc.env:CACHE_EDGE_INDEX_PATH,aiagents4pharma/talk2knowledgegraphs/tests/files/t2kg_primekg_edge_index.pkl}"
aiagents4pharma/talk2knowledgegraphs/configs/tools/multimodal_subgraph_extraction/default.yaml ADDED
@@ -0,0 +1,37 @@
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+ _target_: talk2knowledgegraphs.tools.multimodal_subgraph_extraction
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+ ollama_embeddings:
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+ - "nomic-embed-text"
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+ temperature: 0.1
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+ streaming: False
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+ topk: 15
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+ topk_e: 15
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+ cost_e: 0.5
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+ c_const: 0.01
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+ root: -1
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+ num_clusters: 1
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+ pruning: "gw"
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+ verbosity_level: 0
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+ search_metric_type: "IP" # Inner Product
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+ node_id_column: "node_id"
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+ node_attr_column: "node_attr"
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+ edge_src_column: "edge_src"
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+ edge_attr_column: "edge_attr"
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+ edge_dst_column: "edge_dst"
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+ node_colors_dict:
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+ "gene/protein": "#6a79f7"
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+ "molecular_function": "#82cafc"
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+ "cellular_component": "#3f9b0b"
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+ "biological_process": "#c5c9c7"
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+ "drug": "#c4a661"
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+ "disease": "#80013f"
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+
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+ biobridge:
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+ # source: "aiagents4pharma/talk2knowledgegraphs/tests/files/ibd_biobridge_multimodal/"
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+ source: "/mnt/blockstorage/biobridge_multimodal/"
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+ node_type:
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+ - "gene/protein"
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+ - "molecular_function"
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+ - "cellular_component"
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+ - "biological_process"
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+ - "drug"
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+ - "disease"
aiagents4pharma/talk2knowledgegraphs/configs/utils/enrichments/ols_terms/default.yaml ADDED
@@ -0,0 +1,3 @@
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+ _target_: talk2knowledgegraphs.utils.ols_terms
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+ base_url: https://www.ebi.ac.uk/ols4/api/terms/
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+ timeout: 10
aiagents4pharma/talk2knowledgegraphs/configs/utils/enrichments/reactome_pathways/default.yaml ADDED
@@ -0,0 +1,3 @@
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+ _target_: talk2knowledgegraphs.utils.reactome_pathways
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+ base_url: https://reactome.org/ContentService/data/query/
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+ timeout: 10
aiagents4pharma/talk2knowledgegraphs/configs/utils/enrichments/uniprot_proteins/default.yaml ADDED
@@ -0,0 +1,6 @@
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+ _target_: talk2knowledgegraphs.utils.enrichments.uniprot_proteins
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+ uniprot_url: https://www.ebi.ac.uk/proteins/api/proteins
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+ reviewed: true
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+ isoform: 0
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+ organism: Homo sapiens
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+ timeout: 10
aiagents4pharma/talk2knowledgegraphs/configs/utils/pubchem_utils/default.yaml ADDED
@@ -0,0 +1,5 @@
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+ _target_: talk2knowledgegraphs.utils.pubchem_utils
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+ pubchem_cid_base_url: https://pubchem.ncbi.nlm.nih.gov/rest/pug/substance/sourceid/
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+ pubchem_cid_description_url: https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/cid/
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+ pubchem_casrn2cid_url: https://pubchem.ncbi.nlm.nih.gov/rest/pug/substance/xref/RN/
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+ pubchem_cid2smiles_url: https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/cid/