aiagents4pharma 1.35.0__py3-none-any.whl → 1.37.0__py3-none-any.whl

{aiagents4pharma-1.35.0.dist-info → aiagents4pharma-1.37.0.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: aiagents4pharma
-Version: 1.35.0
+Version: 1.37.0
 Summary: AI Agents for drug discovery, drug development, and other pharmaceutical R&D.
 Classifier: Programming Language :: Python :: 3
 Classifier: License :: OSI Approved :: MIT License
@@ -62,6 +62,7 @@ Requires-Dist: umap-learn==0.5.7
 Requires-Dist: plotly-express==0.4.1
 Requires-Dist: seaborn==0.13.2
 Requires-Dist: scanpy==1.11.0
+Requires-Dist: openpyxl==3.1.5
 Dynamic: license-file
 
 [![Talk2BioModels](https://github.com/VirtualPatientEngine/AIAgents4Pharma/actions/workflows/tests_talk2biomodels.yml/badge.svg)](https://github.com/VirtualPatientEngine/AIAgents4Pharma/actions/workflows/tests_talk2biomodels.yml)
@@ -90,6 +91,17 @@ Our toolkit currently consists of the following agents:
 
 ![AIAgents4Pharma](docs/assets/AIAgents4Pharma.png)
 
+## News
+
+- T2B and T2KG accepted at the MLGenX workshop during ICLR #2025 in Singapore. [Read More](https://openreview.net/forum?id=av4QhBNeZo)
+
+<div align="center">
+  <strong>Watch the presentation:</strong><br><br>
+  <a href="https://www.youtube.com/watch?v=3cU_OxY4HiE">
+    <img src="https://img.youtube.com/vi/3cU_OxY4HiE/0.jpg" alt="Watch the presentation" width="480">
+  </a>
+</div>
+
 ## Getting Started
 
 ### Installation
@@ -250,15 +262,19 @@ If you are using docker on Windows, please follow these [Windows Setup Notes](#n
 ![Python Version from PEP 621 TOML](https://img.shields.io/python/required-version-toml?tomlFilePath=https%3A%2F%2Fraw.githubusercontent.com%2FVirtualPatientEngine%2FAIAgents4Pharma%2Frefs%2Fheads%2Fmain%2Fpyproject.toml)
 
 1. **Clone the repository:**
-   ```sh
-   git clone https://github.com/VirtualPatientEngine/AIAgents4Pharma
-   cd AIAgents4Pharma
-   ```
+
+```sh
+git clone https://github.com/VirtualPatientEngine/AIAgents4Pharma
+cd AIAgents4Pharma
+```
+
 2. **Install dependencies:**
 
-   ```python
-   pip install -r requirements.txt
-   ```
+We use Conda as our environment manager, Follow the official [Quickstart](https://www.anaconda.com/docs/getting-started/miniconda/install#quickstart-install-instructions) install instructions provided by anaconda/miniconda.
+
+```python
+conda create --name AIAgents4Pharma python=3.12 -y && conda activate AIAgents4Pharma && pip install --upgrade pip && pip install -r requirements.txt
+```
 
 3. **Initialize API Keys**
 

{aiagents4pharma-1.35.0.dist-info → aiagents4pharma-1.37.0.dist-info}/RECORD

@@ -9,7 +9,7 @@ aiagents4pharma/talk2aiagents4pharma/configs/agents/main_agent/default.yaml,sha2
 aiagents4pharma/talk2aiagents4pharma/states/__init__.py,sha256=3wSvCpM29oqvVjhbhabm7FNm9Zt0rHO5tEn63YW6doc,108
 aiagents4pharma/talk2aiagents4pharma/states/state_talk2aiagents4pharma.py,sha256=NxujEBDKubvpV9UG7ERTDRB6psr0XnObCNHyztLAhgo,485
 aiagents4pharma/talk2aiagents4pharma/tests/__init__.py,sha256=Jbw5tJxSrjGoaK5IX3pJWDCNzhrVQ10lkYq2oQ_KQD8,45
-aiagents4pharma/talk2aiagents4pharma/tests/test_main_agent.py,sha256=ndHQT4ycWy-uKRAND7JmX_SuNg4g9hJw4UCW0CbKSp0,4165
+aiagents4pharma/talk2aiagents4pharma/tests/test_main_agent.py,sha256=_zUm8i8vrBbcDgpwExa1sVGr1A9FgZFuwoLS395RnhU,4418
 aiagents4pharma/talk2biomodels/__init__.py,sha256=1cq1HX2xoi_a0nDPuXYoSTrnL26OHQBW3zXNwwwjFO0,181
 aiagents4pharma/talk2biomodels/agents/__init__.py,sha256=sn5-fREjMdEvb-OUan3iOqrgYGjplNx3J8hYOaW0Po8,128
 aiagents4pharma/talk2biomodels/agents/t2b_agent.py,sha256=g0DIW5P-dtJoVyG4weFdDgTrJPL_Dx1MMbTWextJDZ4,3455
@@ -73,17 +73,18 @@ aiagents4pharma/talk2cells/tools/scp_agent/display_studies.py,sha256=6q59gh_NQai
 aiagents4pharma/talk2cells/tools/scp_agent/search_studies.py,sha256=MLe-twtFnOu-P8P9diYq7jvHBHbWFRRCZLcfpUzqPMg,2806
 aiagents4pharma/talk2knowledgegraphs/__init__.py,sha256=Z0Eo7LTiKk0STsr8VI7wkCLq7PHrK1vYlH4I1hSNLiA,165
 aiagents4pharma/talk2knowledgegraphs/agents/__init__.py,sha256=iOAzuy_8A03tQDFtSBhC9dldUo62z5gfxcVtXAdLOJs,92
-aiagents4pharma/talk2knowledgegraphs/agents/t2kg_agent.py,sha256=IcXSZ2qQA1m-gS-o0Pj_g1oar8uPdhsbaovloUFka3Q,3058
+aiagents4pharma/talk2knowledgegraphs/agents/t2kg_agent.py,sha256=w4wSSQ9gw_fzpcHZ2Bnqok17YDkFeQ3d72JenvQm6Oc,3089
 aiagents4pharma/talk2knowledgegraphs/configs/__init__.py,sha256=4_DVdpahaJ55yPl0aZotlFA_MYWLFF2cubWyKtBVI_Q,126
-aiagents4pharma/talk2knowledgegraphs/configs/config.yaml,sha256=X91262b-wkygiH4HrEr0bIzHxHDuDWwuxLQAmdUe-E4,367
+aiagents4pharma/talk2knowledgegraphs/configs/config.yaml,sha256=-AJXKnR2z5ig0SK_3vLL9JFjNRri7q7blHYFWxoTDl0,417
 aiagents4pharma/talk2knowledgegraphs/configs/agents/t2kg_agent/__init__.py,sha256=-fAORvyFmG2iSvFOFDixmt9OTQRR58y89uhhu2EgbA8,46
 aiagents4pharma/talk2knowledgegraphs/configs/agents/t2kg_agent/default.yaml,sha256=ENCGROwYFpR6g4QD518h73sshdn3vPVpotBMk1QJcpU,4830
 aiagents4pharma/talk2knowledgegraphs/configs/app/__init__.py,sha256=fKfc3FR7g5KjY9b6jzrU6cwKTVVpkoVZQS3dvUowu34,69
 aiagents4pharma/talk2knowledgegraphs/configs/app/frontend/__init__.py,sha256=-fAORvyFmG2iSvFOFDixmt9OTQRR58y89uhhu2EgbA8,46
-aiagents4pharma/talk2knowledgegraphs/configs/app/frontend/default.yaml,sha256=4azC4cH-_-zt-bRVgNjkFM24mjNke6Rgn9pNl7XWrPQ,912
+aiagents4pharma/talk2knowledgegraphs/configs/app/frontend/default.yaml,sha256=WJgd2ZU7_WQ1qlcTfkFlM8u23sH6eU2KgAm0E4kqqfs,941
 aiagents4pharma/talk2knowledgegraphs/configs/tools/__init__.py,sha256=C1yyRZW8hqWw46p_bh1vAJp2z9aVvn4HpKjKkjlWIqY,150
 aiagents4pharma/talk2knowledgegraphs/configs/tools/graphrag_reasoning/__init__.py,sha256=-fAORvyFmG2iSvFOFDixmt9OTQRR58y89uhhu2EgbA8,46
 aiagents4pharma/talk2knowledgegraphs/configs/tools/graphrag_reasoning/default.yaml,sha256=Ua99yECXiwp4ZCUDgsDskYbKzcJrv7roQuLj31Zky4c,1037
+aiagents4pharma/talk2knowledgegraphs/configs/tools/multimodal_subgraph_extraction/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 aiagents4pharma/talk2knowledgegraphs/configs/tools/subgraph_extraction/__init__.py,sha256=-fAORvyFmG2iSvFOFDixmt9OTQRR58y89uhhu2EgbA8,46
 aiagents4pharma/talk2knowledgegraphs/configs/tools/subgraph_extraction/default.yaml,sha256=U8HvMsYbaOwDwQPATj7EFvLtTy7XZEplE5WMoNjgYYc,1469
 aiagents4pharma/talk2knowledgegraphs/configs/tools/subgraph_summarization/__init__.py,sha256=-fAORvyFmG2iSvFOFDixmt9OTQRR58y89uhhu2EgbA8,46
@@ -94,32 +95,34 @@ aiagents4pharma/talk2knowledgegraphs/datasets/dataset.py,sha256=-LaPLse8BkALqwFe
 aiagents4pharma/talk2knowledgegraphs/datasets/primekg.py,sha256=KBMhCJ7yjMWqQJJctFYdpjYAlwv48Jl6i1dddXP4f08,7599
 aiagents4pharma/talk2knowledgegraphs/datasets/starkqa_primekg.py,sha256=Y-6-nORsnBJlU6rH0skyfr9S9J4PfTWK-af_p5UuknQ,7483
 aiagents4pharma/talk2knowledgegraphs/states/__init__.py,sha256=XaqorSvx634dWRRlXUdzlisHtYMyqgJ2q7TanzsKlhw,108
-aiagents4pharma/talk2knowledgegraphs/states/state_talk2knowledgegraphs.py,sha256=6HqGo-awqoyNJG0igm5so5A4Tq8RPkCsjPg8Go38csE,1066
+aiagents4pharma/talk2knowledgegraphs/states/state_talk2knowledgegraphs.py,sha256=y5bp6yObN-AQtTq-m8ml7UnZaeKYUiPV_yjskAzBJaI,1087
 aiagents4pharma/talk2knowledgegraphs/tests/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-aiagents4pharma/talk2knowledgegraphs/tests/test_agents_t2kg_agent.py,sha256=CCN6cyhEaiXSvIC-4y3ueDSzjDCBYDsmSmOor-DMeF4,3928
+aiagents4pharma/talk2knowledgegraphs/tests/test_agents_t2kg_agent.py,sha256=PPfHKnfqMbUOBKU7q4VbQvHQymX1M_zTYdysQgVxKCs,3851
 aiagents4pharma/talk2knowledgegraphs/tests/test_datasets_biobridge_primekg.py,sha256=crH0eFA3P8P6IYzi1UWNa4YvRVrtlBzoScf9NaE1lDk,9827
 aiagents4pharma/talk2knowledgegraphs/tests/test_datasets_dataset.py,sha256=NFUlsZvhfIrkF4YenWfahrLK93Xhm5UYEGG_uYN2LVM,566
 aiagents4pharma/talk2knowledgegraphs/tests/test_datasets_primekg.py,sha256=Pvu0r93CpnhjkfMxc-EiVLpAJ04FdW9iTamCnetu654,2272
 aiagents4pharma/talk2knowledgegraphs/tests/test_datasets_starkqa_primekg.py,sha256=TuIsqcN1Mww3DTqGk6ebgJBWzUWdMWEq2yRQuYSFqvA,4416
 aiagents4pharma/talk2knowledgegraphs/tests/test_tools_graphrag_reasoning.py,sha256=aOKHTber2Cg3mjNjfIa6RZU7XdFj5C2ps1YEUXw76CI,10650
-aiagents4pharma/talk2knowledgegraphs/tests/test_tools_subgraph_extraction.py,sha256=zRi2j9Dm3VFywhhrPjVoJ7z_zJpAEM74MJRXapnhwVE,6246
+aiagents4pharma/talk2knowledgegraphs/tests/test_tools_multimodal_subgraph_extraction.py,sha256=Da-hXcu41_5Ge4DPlOoY6OqBwYnXPc58Q89wuywqVJM,5806
+aiagents4pharma/talk2knowledgegraphs/tests/test_tools_subgraph_extraction.py,sha256=C2HzmAG1XCeV1hwZzz3-9_2dm_84-i1BvTNWA1pqUwM,5393
 aiagents4pharma/talk2knowledgegraphs/tests/test_tools_subgraph_summarization.py,sha256=oBqfspXXOxH04OQuPb8BCW0liIQTGKXtaPNSrPpQtFc,7597
 aiagents4pharma/talk2knowledgegraphs/tests/test_utils_embeddings_embeddings.py,sha256=uYFoE_6zeU10_1mLLAHUr5c4S2XZMSc0Q_860o-KWEw,1517
 aiagents4pharma/talk2knowledgegraphs/tests/test_utils_embeddings_huggingface.py,sha256=hzX84pheZdEsTtikF2KtBFiH44_xPjYXxLA6p4Ax1CY,1623
 aiagents4pharma/talk2knowledgegraphs/tests/test_utils_embeddings_nim_molmim.py,sha256=LwtTZ-M7lHGxvRrGBXbyIT8AkA3T2OpeKqtNq3RK7Ik,2164
 aiagents4pharma/talk2knowledgegraphs/tests/test_utils_embeddings_ollama.py,sha256=jn-TrPwF0aR9kVoerwkbMZa3U6Hc6HjV6Zoau4qSH4g,1834
-aiagents4pharma/talk2knowledgegraphs/tests/test_utils_embeddings_sentencetransformer.py,sha256=Qxo6WeIDRy8aLh1tNKw0kSlzmUj3MtTak63oW2YwB24,1327
+aiagents4pharma/talk2knowledgegraphs/tests/test_utils_embeddings_sentencetransformer.py,sha256=Xkuf2UFGCXldj1zcsh6kqfQYLDf5i0B6KP3KcmNLSzQ,1452
 aiagents4pharma/talk2knowledgegraphs/tests/test_utils_enrichments_enrichments.py,sha256=N6HRr4lWHXY7bTHe2uXJe4D_EG9WqZPibZne6qLl9_k,1447
 aiagents4pharma/talk2knowledgegraphs/tests/test_utils_enrichments_ollama.py,sha256=JhY7axvVULLywDJ2ctA-gob5YPeaJYWsaMNjHT6L9CU,3021
-aiagents4pharma/talk2knowledgegraphs/tests/test_utils_enrichments_ols.py,sha256=woSm723ns9fHieu-QWFiniLlm5h22v1qzO4v6n20K5g,2413
+aiagents4pharma/talk2knowledgegraphs/tests/test_utils_enrichments_ols.py,sha256=5GTSkfKSDS5geR0YfilfnDyUsYli0hv7N8PiDwRvlIE,2370
 aiagents4pharma/talk2knowledgegraphs/tests/test_utils_enrichments_pubchem.py,sha256=0SgYvqdvxseUYTHx2KuSNI2hnmQ3VVVz0F-79_-P41o,1769
 aiagents4pharma/talk2knowledgegraphs/tests/test_utils_enrichments_reactome.py,sha256=r1D74mavsnSCm4xnWl0n0nM9PZqgm3doD2dulNrKNVQ,1754
 aiagents4pharma/talk2knowledgegraphs/tests/test_utils_enrichments_uniprot.py,sha256=G13Diw7cA5TGINUNO1CDnN4rM6KbepxRXNjuzY578DI,1611
 aiagents4pharma/talk2knowledgegraphs/tests/test_utils_kg_utils.py,sha256=pal76wi7WgQWUNk56BrzfFV8jKpbDaHHdbwtgx_gXLI,2410
 aiagents4pharma/talk2knowledgegraphs/tests/test_utils_pubchem_utils.py,sha256=K1Y6QM0MDP1IrAdcWkigl8R-O-i-lsL4NCyOrWewhdM,1246
-aiagents4pharma/talk2knowledgegraphs/tools/__init__.py,sha256=zpD4h7EYtyq0QNOqLd6bkxrPlPb2XN64ceI9ncgESrA,171
+aiagents4pharma/talk2knowledgegraphs/tools/__init__.py,sha256=uleTEbhgvlYw4fOqV4NmoFvxGTon2Oim7jTQ5qPmYoU,216
 aiagents4pharma/talk2knowledgegraphs/tools/graphrag_reasoning.py,sha256=OEuOFncDRdb7TQEGq4rkT5On-jI-R7Nt8K5EBzaND8w,5338
 aiagents4pharma/talk2knowledgegraphs/tools/load_arguments.py,sha256=zhmsRp-8vjB5rRekqTA07d3yb-42HWqng9dDMkvK6hM,623
+aiagents4pharma/talk2knowledgegraphs/tools/multimodal_subgraph_extraction.py,sha256=Qjl8hXG8Gv5jQ4pBX8me0pGGakqRZmcDfTGgdEHD9pc,15394
 aiagents4pharma/talk2knowledgegraphs/tools/subgraph_extraction.py,sha256=te06QMFQfgJWrjaGrqpcOYeaV38jwm0KY_rXVSMHkeI,11468
 aiagents4pharma/talk2knowledgegraphs/tools/subgraph_summarization.py,sha256=mDSBOxopDfNhEJeU8fVI8b5lXTYrRzcc97aLbFgYSy4,4413
 aiagents4pharma/talk2knowledgegraphs/utils/__init__.py,sha256=cZqb3LZLmBnmyAtWFv2Z-4uJvQmx0M4zKsfiWrlM3Pk,195
@@ -138,7 +141,8 @@ aiagents4pharma/talk2knowledgegraphs/utils/enrichments/ols_terms.py,sha256=xSPP-
 aiagents4pharma/talk2knowledgegraphs/utils/enrichments/pubchem_strings.py,sha256=CQEGQ6Qsex2T91Vw7zTrclJBbSGGhxeWaVJb8tnURAQ,1691
 aiagents4pharma/talk2knowledgegraphs/utils/enrichments/reactome_pathways.py,sha256=I0cD0Fk2Uk27_4jEaIhpoGhoMh_RphY1VtkMnk4dkPg,2011
 aiagents4pharma/talk2knowledgegraphs/utils/enrichments/uniprot_proteins.py,sha256=z0Jb3tt8VzRjzqI9oVcUvRlPPg6BUdmslfKDIEFE_h8,3013
-aiagents4pharma/talk2knowledgegraphs/utils/extractions/__init__.py,sha256=7gwwtfzKhB8GuOBD47XRi0NprwEXkOzwNl5eeu-hDTI,86
+aiagents4pharma/talk2knowledgegraphs/utils/extractions/__init__.py,sha256=5bt3H6gGSAwN2K-IG7AHwG2lC4yQeMd2_jbhu2z5XKg,116
+aiagents4pharma/talk2knowledgegraphs/utils/extractions/multimodal_pcst.py,sha256=Irh5JXEhaLZ6Rxv3h5Anif_rGNItyLOGDWg1RACmoDA,12628
 aiagents4pharma/talk2knowledgegraphs/utils/extractions/pcst.py,sha256=m5p0yoJb7I19ua5yeQfXPf7c4r6S1XPwttsrM7Qoy94,9336
 aiagents4pharma/talk2scholars/__init__.py,sha256=NOZxTklAH1j1ggu97Ib8Xn9LCKudEWt-8dx8w7yxVD8,180
 aiagents4pharma/talk2scholars/agents/__init__.py,sha256=c_0Pk85bt-RfK5RMyALM3MXo3qXVMoYS7BOqM9wuFME,317
@@ -225,8 +229,8 @@ aiagents4pharma/talk2scholars/tools/zotero/utils/read_helper.py,sha256=lyrfpx8NH
 aiagents4pharma/talk2scholars/tools/zotero/utils/review_helper.py,sha256=IPD1V9yrBYaDnRe7sR6PrpwR82OBJbA2P_Tc6RbxAbM,2748
 aiagents4pharma/talk2scholars/tools/zotero/utils/write_helper.py,sha256=ALwLecy1QVebbsmXJiDj1GhGmyhq2R2tZlAyEl1vfhw,7410
 aiagents4pharma/talk2scholars/tools/zotero/utils/zotero_path.py,sha256=oIrfbOySgts50ksHKyjcWjRkPRIS88g3Lc0v9mBkU8w,6375
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