aiagents4pharma 1.42.0__py3-none-any.whl → 1.44.0__py3-none-any.whl

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Files changed (47) hide show
  1. aiagents4pharma/talk2knowledgegraphs/configs/tools/multimodal_subgraph_extraction/default.yaml +17 -2
  2. aiagents4pharma/talk2knowledgegraphs/tests/test_tools_milvus_multimodal_subgraph_extraction.py +618 -413
  3. aiagents4pharma/talk2knowledgegraphs/tests/test_utils_extractions_milvus_multimodal_pcst.py +362 -25
  4. aiagents4pharma/talk2knowledgegraphs/tools/milvus_multimodal_subgraph_extraction.py +146 -109
  5. aiagents4pharma/talk2knowledgegraphs/utils/extractions/milvus_multimodal_pcst.py +240 -83
  6. aiagents4pharma/talk2scholars/agents/paper_download_agent.py +7 -4
  7. aiagents4pharma/talk2scholars/configs/agents/talk2scholars/main_agent/default.yaml +49 -95
  8. aiagents4pharma/talk2scholars/configs/agents/talk2scholars/paper_download_agent/default.yaml +15 -1
  9. aiagents4pharma/talk2scholars/configs/agents/talk2scholars/pdf_agent/default.yaml +16 -2
  10. aiagents4pharma/talk2scholars/configs/agents/talk2scholars/s2_agent/default.yaml +40 -5
  11. aiagents4pharma/talk2scholars/configs/agents/talk2scholars/zotero_agent/default.yaml +15 -5
  12. aiagents4pharma/talk2scholars/configs/config.yaml +1 -3
  13. aiagents4pharma/talk2scholars/configs/tools/paper_download/default.yaml +124 -0
  14. aiagents4pharma/talk2scholars/tests/test_arxiv_downloader.py +478 -0
  15. aiagents4pharma/talk2scholars/tests/test_base_paper_downloader.py +620 -0
  16. aiagents4pharma/talk2scholars/tests/test_biorxiv_downloader.py +697 -0
  17. aiagents4pharma/talk2scholars/tests/test_medrxiv_downloader.py +534 -0
  18. aiagents4pharma/talk2scholars/tests/test_paper_download_agent.py +22 -12
  19. aiagents4pharma/talk2scholars/tests/test_paper_downloader.py +545 -0
  20. aiagents4pharma/talk2scholars/tests/test_pubmed_downloader.py +1067 -0
  21. aiagents4pharma/talk2scholars/tools/paper_download/__init__.py +2 -4
  22. aiagents4pharma/talk2scholars/tools/paper_download/paper_downloader.py +457 -0
  23. aiagents4pharma/talk2scholars/tools/paper_download/utils/__init__.py +20 -0
  24. aiagents4pharma/talk2scholars/tools/paper_download/utils/arxiv_downloader.py +209 -0
  25. aiagents4pharma/talk2scholars/tools/paper_download/utils/base_paper_downloader.py +343 -0
  26. aiagents4pharma/talk2scholars/tools/paper_download/utils/biorxiv_downloader.py +321 -0
  27. aiagents4pharma/talk2scholars/tools/paper_download/utils/medrxiv_downloader.py +198 -0
  28. aiagents4pharma/talk2scholars/tools/paper_download/utils/pubmed_downloader.py +337 -0
  29. aiagents4pharma/talk2scholars/tools/s2/query_dataframe.py +97 -45
  30. aiagents4pharma/talk2scholars/tools/s2/retrieve_semantic_scholar_paper_id.py +47 -29
  31. {aiagents4pharma-1.42.0.dist-info → aiagents4pharma-1.44.0.dist-info}/METADATA +3 -1
  32. {aiagents4pharma-1.42.0.dist-info → aiagents4pharma-1.44.0.dist-info}/RECORD +36 -33
  33. aiagents4pharma/talk2scholars/configs/tools/download_arxiv_paper/default.yaml +0 -4
  34. aiagents4pharma/talk2scholars/configs/tools/download_biorxiv_paper/__init__.py +0 -3
  35. aiagents4pharma/talk2scholars/configs/tools/download_biorxiv_paper/default.yaml +0 -2
  36. aiagents4pharma/talk2scholars/configs/tools/download_medrxiv_paper/__init__.py +0 -3
  37. aiagents4pharma/talk2scholars/configs/tools/download_medrxiv_paper/default.yaml +0 -2
  38. aiagents4pharma/talk2scholars/tests/test_paper_download_biorxiv.py +0 -151
  39. aiagents4pharma/talk2scholars/tests/test_paper_download_medrxiv.py +0 -151
  40. aiagents4pharma/talk2scholars/tests/test_paper_download_tools.py +0 -249
  41. aiagents4pharma/talk2scholars/tools/paper_download/download_arxiv_input.py +0 -177
  42. aiagents4pharma/talk2scholars/tools/paper_download/download_biorxiv_input.py +0 -114
  43. aiagents4pharma/talk2scholars/tools/paper_download/download_medrxiv_input.py +0 -114
  44. /aiagents4pharma/talk2scholars/configs/tools/{download_arxiv_paper → paper_download}/__init__.py +0 -0
  45. {aiagents4pharma-1.42.0.dist-info → aiagents4pharma-1.44.0.dist-info}/WHEEL +0 -0
  46. {aiagents4pharma-1.42.0.dist-info → aiagents4pharma-1.44.0.dist-info}/licenses/LICENSE +0 -0
  47. {aiagents4pharma-1.42.0.dist-info → aiagents4pharma-1.44.0.dist-info}/top_level.txt +0 -0
aiagents4pharma/talk2knowledgegraphs/configs/tools/multimodal_subgraph_extraction/default.yaml CHANGED
@@ -3,6 +3,8 @@ 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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+
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+ # PCST Algorithm Parameters
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  topk: 15
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  topk_e: 15
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  cost_e: 0.5
@@ -11,7 +13,20 @@ 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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+
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+ # Hardware-Specific Vector Processing
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+ vector_processing:
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+ # Enable dynamic metric type selection based on hardware
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+ dynamic_metrics: true
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+
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+ # Milvus Database Configuration
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+ milvus_db:
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+ # Database and collection names
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+ database_name: "t2kg_primekg"
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+
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+ # Cache settings for edge index
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+ cache_edge_index_path: "${oc.env:CACHE_EDGE_INDEX_PATH,aiagents4pharma/talk2knowledgegraphs/tests/files/t2kg_primekg_edge_index.pkl}"
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+
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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"
@@ -34,4 +49,4 @@ biobridge:
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  - "cellular_component"
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  - "biological_process"
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  - "drug"
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- - "disease"
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+ - "disease"