aiagents4pharma 1.17.1__py3-none-any.whl → 1.19.0__py3-none-any.whl

aiagents4pharma/talk2knowledgegraphs/utils/extractions/__init__.py

@@ -0,0 +1,4 @@
+'''
+This file is used to import all the models in the package.
+'''
+from . import pcst

aiagents4pharma/talk2knowledgegraphs/utils/extractions/pcst.py

@@ -0,0 +1,225 @@
+"""
+Exctraction of subgraph using Prize-Collecting Steiner Tree (PCST) algorithm.
+"""
+
+from typing import Tuple, NamedTuple
+import numpy as np
+import torch
+import pcst_fast
+from torch_geometric.data.data import Data
+
+class PCSTPruning(NamedTuple):
+    """
+    Prize-Collecting Steiner Tree (PCST) pruning algorithm implementation inspired by G-Retriever
+    (He et al., 'G-Retriever: Retrieval-Augmented Generation for Textual Graph Understanding and
+    Question Answering', NeurIPS 2024) paper.
+    https://arxiv.org/abs/2402.07630
+    https://github.com/XiaoxinHe/G-Retriever/blob/main/src/dataset/utils/retrieval.py
+
+    Args:
+        topk: The number of top nodes to consider.
+        topk_e: The number of top edges to consider.
+        cost_e: The cost of the edges.
+        c_const: The constant value for the cost of the edges computation.
+        root: The root node of the subgraph, -1 for unrooted.
+        num_clusters: The number of clusters.
+        pruning: The pruning strategy to use.
+        verbosity_level: The verbosity level.
+    """
+    topk: int = 3
+    topk_e: int = 3
+    cost_e: float = 0.5
+    c_const: float = 0.01
+    root: int = -1
+    num_clusters: int = 1
+    pruning: str = "gw"
+    verbosity_level: int = 0
+
+    def compute_prizes(self, graph: Data, query_emb: torch.Tensor) -> np.ndarray:
+        """
+        Compute the node prizes based on the cosine similarity between the query and nodes,
+        as well as the edge prizes based on the cosine similarity between the query and edges.
+        Note that the node and edge embeddings shall use the same embedding model and dimensions
+        with the query.
+
+        Args:
+            graph: The knowledge graph in PyTorch Geometric Data format.
+            query_emb: The query embedding in PyTorch Tensor format.
+
+        Returns:
+            The prizes of the nodes and edges.
+        """
+        # Compute prizes for nodes
+        n_prizes = torch.nn.CosineSimilarity(dim=-1)(query_emb, graph.x)
+        topk = min(self.topk, graph.num_nodes)
+        _, topk_n_indices = torch.topk(n_prizes, topk, largest=True)
+        n_prizes = torch.zeros_like(n_prizes)
+        n_prizes[topk_n_indices] = torch.arange(topk, 0, -1).float()
+
+        # Compute prizes for edges
+        # e_prizes = torch.nn.CosineSimilarity(dim=-1)(query_emb, graph.edge_attr)
+        # topk_e = min(self.topk_e, e_prizes.unique().size(0))
+        # topk_e_values, _ = torch.topk(e_prizes.unique(), topk_e, largest=True)
+        # e_prizes[e_prizes < topk_e_values[-1]] = 0.0
+        # last_topk_e_value = topk_e
+        # for k in range(topk_e):
+        #     indices = e_prizes == topk_e_values[k]
+        #     value = min((topk_e - k) / sum(indices), last_topk_e_value)
+        #     e_prizes[indices] = value
+        #     last_topk_e_value = value * (1 - self.c_const)
+
+        # Optimized version of the above code
+        e_prizes = torch.nn.CosineSimilarity(dim=-1)(query_emb, graph.edge_attr)
+        unique_prizes, inverse_indices = e_prizes.unique(return_inverse=True)
+        topk_e = min(self.topk_e, unique_prizes.size(0))
+        topk_e_values, _ = torch.topk(unique_prizes, topk_e, largest=True)
+        e_prizes[e_prizes < topk_e_values[-1]] = 0.0
+        last_topk_e_value = topk_e
+        for k in range(topk_e):
+            indices = inverse_indices == (
+                unique_prizes == topk_e_values[k]
+            ).nonzero(as_tuple=True)[0]
+            value = min((topk_e - k) / indices.sum().item(), last_topk_e_value)
+            e_prizes[indices] = value
+            last_topk_e_value = value * (1 - self.c_const)
+
+        return {"nodes": n_prizes, "edges": e_prizes}
+
+    def compute_subgraph_costs(
+        self, graph: Data, prizes: dict
+    ) -> Tuple[np.ndarray, np.ndarray, np.ndarray]:
+        """
+        Compute the costs in constructing the subgraph proposed by G-Retriever paper.
+
+        Args:
+            graph: The knowledge graph in PyTorch Geometric Data format.
+            prizes: The prizes of the nodes and the edges.
+
+        Returns:
+            edges: The edges of the subgraph, consisting of edges and number of edges without
+                virtual edges.
+            prizes: The prizes of the subgraph.
+            costs: The costs of the subgraph.
+        """
+        # Logic to reduce the cost of the edges such that at least one edge is selected
+        updated_cost_e = min(
+            self.cost_e,
+            prizes["edges"].max().item() * (1 - self.c_const / 2),
+        )
+
+        # Initialize variables
+        edges = []
+        costs = []
+        virtual = {
+            "n_prizes": [],
+            "edges": [],
+            "costs": [],
+        }
+        mapping = {"nodes": {}, "edges": {}}
+
+        # Compute the costs, edges, and virtual variables based on the prizes
+        for i, (src, dst) in enumerate(graph.edge_index.T.numpy()):
+            prize_e = prizes["edges"][i]
+            if prize_e <= updated_cost_e:
+                mapping["edges"][len(edges)] = i
+                edges.append((src, dst))
+                costs.append(updated_cost_e - prize_e)
+            else:
+                virtual_node_id = graph.num_nodes + len(virtual["n_prizes"])
+                mapping["nodes"][virtual_node_id] = i
+                virtual["edges"].append((src, virtual_node_id))
+                virtual["edges"].append((virtual_node_id, dst))
+                virtual["costs"].append(0)
+                virtual["costs"].append(0)
+                virtual["n_prizes"].append(prize_e - updated_cost_e)
+        prizes = np.concatenate([prizes["nodes"], np.array(virtual["n_prizes"])])
+        edges_dict = {}
+        edges_dict["edges"] = edges
+        edges_dict["num_prior_edges"] = len(edges)
+        # Final computation of the costs and edges based on the virtual costs and virtual edges
+        if len(virtual["costs"]) > 0:
+            costs = np.array(costs + virtual["costs"])
+            edges = np.array(edges + virtual["edges"])
+            edges_dict["edges"] = edges
+
+        return edges_dict, prizes, costs, mapping
+
+    def get_subgraph_nodes_edges(
+        self, graph: Data, vertices: np.ndarray, edges_dict: dict, mapping: dict,
+    ) -> dict:
+        """
+        Get the selected nodes and edges of the subgraph based on the vertices and edges computed
+        by the PCST algorithm.
+
+        Args:
+            graph: The knowledge graph in PyTorch Geometric Data format.
+            vertices: The vertices of the subgraph computed by the PCST algorithm.
+            edges_dict: The dictionary of edges of the subgraph computed by the PCST algorithm,
+                and the number of prior edges (without virtual edges).
+            mapping: The mapping dictionary of the nodes and edges.
+            num_prior_edges: The number of edges before adding virtual edges.
+
+        Returns:
+            The selected nodes and edges of the extracted subgraph.
+        """
+        # Get edges information
+        edges = edges_dict["edges"]
+        num_prior_edges = edges_dict["num_prior_edges"]
+        # Retrieve the selected nodes and edges based on the given vertices and edges
+        subgraph_nodes = vertices[vertices < graph.num_nodes]
+        subgraph_edges = [mapping["edges"][e] for e in edges if e < num_prior_edges]
+        virtual_vertices = vertices[vertices >= graph.num_nodes]
+        if len(virtual_vertices) > 0:
+            virtual_vertices = vertices[vertices >= graph.num_nodes]
+            virtual_edges = [mapping["nodes"][i] for i in virtual_vertices]
+            subgraph_edges = np.array(subgraph_edges + virtual_edges)
+        edge_index = graph.edge_index[:, subgraph_edges]
+        subgraph_nodes = np.unique(
+            np.concatenate(
+                [subgraph_nodes, edge_index[0].numpy(), edge_index[1].numpy()]
+            )
+        )
+
+        return {"nodes": subgraph_nodes, "edges": subgraph_edges}
+
+    def extract_subgraph(self, graph: Data, query_emb: torch.Tensor) -> dict:
+        """
+        Perform the Prize-Collecting Steiner Tree (PCST) algorithm to extract the subgraph.
+
+        Args:
+            graph: The knowledge graph in PyTorch Geometric Data format.
+            query_emb: The query embedding.
+
+        Returns:
+            The selected nodes and edges of the subgraph.
+        """
+        # Assert the topk and topk_e values for subgraph retrieval
+        assert self.topk > 0, "topk must be greater than or equal to 0"
+        assert self.topk_e > 0, "topk_e must be greater than or equal to 0"
+
+        # Retrieve the top-k nodes and edges based on the query embedding
+        prizes = self.compute_prizes(graph, query_emb)
+
+        # Compute costs in constructing the subgraph
+        edges_dict, prizes, costs, mapping = self.compute_subgraph_costs(
+            graph, prizes
+        )
+
+        # Retrieve the subgraph using the PCST algorithm
+        result_vertices, result_edges = pcst_fast.pcst_fast(
+            edges_dict["edges"],
+            prizes,
+            costs,
+            self.root,
+            self.num_clusters,
+            self.pruning,
+            self.verbosity_level,
+        )
+
+        subgraph = self.get_subgraph_nodes_edges(
+            graph,
+            result_vertices,
+            {"edges": result_edges, "num_prior_edges": edges_dict["num_prior_edges"]},
+            mapping)
+
+        return subgraph

{aiagents4pharma-1.17.1.dist-info → aiagents4pharma-1.19.0.dist-info}/METADATA

@@ -1,7 +1,7 @@
 Metadata-Version: 2.2
 Name: aiagents4pharma
-Version: 1.17.1
-Summary: AI Agents for drug discovery, drug development, and other pharmaceutical R&D
+Version: 1.19.0
+Summary: AI Agents for drug discovery, drug development, and other pharmaceutical R&D.
 Classifier: Programming Language :: Python :: 3
 Classifier: License :: OSI Approved :: MIT License
 Classifier: Operating System :: OS Independent
@@ -12,6 +12,7 @@ Requires-Dist: copasi_basico==0.78
 Requires-Dist: coverage==7.6.4
 Requires-Dist: einops==0.8.0
 Requires-Dist: gdown==5.2.0
+Requires-Dist: gravis==0.1.0
 Requires-Dist: huggingface_hub==0.26.5
 Requires-Dist: hydra-core==1.3.2
 Requires-Dist: joblib==1.4.2
@@ -19,6 +20,7 @@ Requires-Dist: langchain==0.3.7
 Requires-Dist: langchain-community==0.3.5
 Requires-Dist: langchain-core==0.3.31
 Requires-Dist: langchain-experimental==0.3.3
+Requires-Dist: langchain-nvidia-ai-endpoints==0.3.9
 Requires-Dist: langchain-openai==0.2.5
 Requires-Dist: langchain_ollama==0.2.2
 Requires-Dist: langgraph==0.2.66
@@ -26,6 +28,7 @@ Requires-Dist: matplotlib==3.9.2
 Requires-Dist: openai==1.59.4
 Requires-Dist: ollama==0.4.6
 Requires-Dist: pandas==2.2.3
+Requires-Dist: pcst_fast==1.0.10
 Requires-Dist: plotly==5.24.1
 Requires-Dist: pydantic==2.9.2
 Requires-Dist: pylint==3.3.1
@@ -93,10 +96,16 @@ Check out the tutorials on each agent for detailed instrcutions.
    ```bash
    pip install .
    ```
-3. **Initialize OPENAI_API_KEY**
+3. **Initialize OPENAI_API_KEY and NVIDIA_API_KEY**
    ```bash
    export OPENAI_API_KEY=....
    ```
+   ```bash
+   export NVIDIA_API_KEY=....
+   ```
+_You can create a free account at NVIDIA and apply for their
+free credits [here](https://build.nvidia.com/explore/discover)._
+
 4. **[Optional] Initialize LANGSMITH_API_KEY**
    ```bash
    export LANGCHAIN_TRACING_V2=true

{aiagents4pharma-1.17.1.dist-info → aiagents4pharma-1.19.0.dist-info}/RECORD

@@ -1,7 +1,7 @@
 aiagents4pharma/__init__.py,sha256=Ua9fqYW5gV1SZ0nOyOMd4T3wTlBui1-mrlJzFUQLFgY,161
 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=CXlqDRqG_cxb1TUEL6960s2ActFiXblYPraagDDGQpo,3416
+aiagents4pharma/talk2biomodels/agents/t2b_agent.py,sha256=bbktkTinp5VHHmAZEs1yMPN3Bu7rnyxRq2Cb7xVe8Gw,3477
 aiagents4pharma/talk2biomodels/api/__init__.py,sha256=_GmDQqDLYpsUPUeE1nBNlT5AI9oTXIcqgOfNfvmonqA,123
 aiagents4pharma/talk2biomodels/api/kegg.py,sha256=QzYDAfJ16E7tbHGxP8ZNWRizMkMRS_HJuucueXEC1Gg,2943
 aiagents4pharma/talk2biomodels/api/ols.py,sha256=qq0Qy-gJDxanQW-HfCChDsTQsY1M41ua8hMlTnfuzrA,2202
@@ -12,37 +12,37 @@ aiagents4pharma/talk2biomodels/configs/agents/t2b_agent/__init__.py,sha256=-fAOR
 aiagents4pharma/talk2biomodels/configs/agents/t2b_agent/default.yaml,sha256=pSViMKwKyMQDm8LzbfIaGdxph73iHYaXMiv5YOuxM7k,536
 aiagents4pharma/talk2biomodels/configs/tools/__init__.py,sha256=B08KWjj7bpizuTETGnnngrEVK4nzdWGREdoCCSw1Sm4,102
 aiagents4pharma/talk2biomodels/configs/tools/ask_question/__init__.py,sha256=-fAORvyFmG2iSvFOFDixmt9OTQRR58y89uhhu2EgbA8,46
-aiagents4pharma/talk2biomodels/configs/tools/ask_question/default.yaml,sha256=pMjs-peecRl8xtIucbEM1Z8Mm_8KGZj0JBrKKD3cMxU,1732
+aiagents4pharma/talk2biomodels/configs/tools/ask_question/default.yaml,sha256=7k49GkLbPy4v7w5-zfwkgBUPaH6R1IrRPCXvUiUiCKE,1300
 aiagents4pharma/talk2biomodels/configs/tools/get_annotation/__init__.py,sha256=-fAORvyFmG2iSvFOFDixmt9OTQRR58y89uhhu2EgbA8,46
 aiagents4pharma/talk2biomodels/configs/tools/get_annotation/default.yaml,sha256=o5kqLJ5QGJsLMUhAqotudIMhxxNfPUVcDVH1tdRIutU,304
 aiagents4pharma/talk2biomodels/models/__init__.py,sha256=5fTHHm3PVloYPNKXbgNlcPgv3-u28ZquxGydFYDfhJA,122
 aiagents4pharma/talk2biomodels/models/basico_model.py,sha256=PH25FTOuUjsmw_UUxoRb-4kptOYpicEn4GqS0phS3nk,4807
 aiagents4pharma/talk2biomodels/models/sys_bio_model.py,sha256=JeoiGQAvQABHnG0wKR2XBmmxqQdtgO6kxaLDUTUmr1s,2001
 aiagents4pharma/talk2biomodels/states/__init__.py,sha256=YLg1-N0D9qyRRLRqwqfLCLAqZYDtMVZTfI8Y0b_4tbA,139
-aiagents4pharma/talk2biomodels/states/state_talk2biomodels.py,sha256=d_tDh93ip36hlUpMh-KOkYfBZ2SQwZlaY8p-1ZWKPhY,1355
+aiagents4pharma/talk2biomodels/states/state_talk2biomodels.py,sha256=S1UtXvocWR8Y9OVUp6pIDFnmaCcjbwmUbW8u79TuGcg,1508
 aiagents4pharma/talk2biomodels/tests/__init__.py,sha256=Jbw5tJxSrjGoaK5IX3pJWDCNzhrVQ10lkYq2oQ_KQD8,45
 aiagents4pharma/talk2biomodels/tests/test_api.py,sha256=7Kz2r5F5tjmn3F0LoM33oP-21W633936YHiyf5toGg0,1716
-aiagents4pharma/talk2biomodels/tests/test_ask_question.py,sha256=yRkKK9HLB1bGGWm_WwOckwaUmmRfRAD9z2NFFGLIGTY,1560
+aiagents4pharma/talk2biomodels/tests/test_ask_question.py,sha256=rdForKfj2zj2IXl6ntK9_I0AbgsCv8MXOZ2khBnaPms,1620
 aiagents4pharma/talk2biomodels/tests/test_basico_model.py,sha256=y82fpTJMPHwtXxlle1cGQ_2Bewwpxi0aJSVrVAYLhN0,2060
-aiagents4pharma/talk2biomodels/tests/test_get_annotation.py,sha256=GqS3kCxxTTMTJFjTnJhilrxT6jbNb7Yi0fbaKkadU4E,8159
+aiagents4pharma/talk2biomodels/tests/test_get_annotation.py,sha256=GbobfjtCAOV0HddM4pb2o3c49Q05fKIM0Ubnf8BRxHM,8273
 aiagents4pharma/talk2biomodels/tests/test_getmodelinfo.py,sha256=Y1sFhoMF4mbvlag7D-dEvv6ytjmAqzMLPvSvaVEI_Qk,2045
-aiagents4pharma/talk2biomodels/tests/test_integration.py,sha256=QHGOKrKyd0kBGy1tOMmkNSqN2Jc2oIXoUrAMpv-elBc,5058
+aiagents4pharma/talk2biomodels/tests/test_integration.py,sha256=XvQmnkIkAcgjmNwsW4FXiCwMMU7fpCpxfqhG2v2KyF4,5170
 aiagents4pharma/talk2biomodels/tests/test_param_scan.py,sha256=vRbnn4uVWFbfZbU4gVCjHi5WDCUrErut8ElzAPE5y84,2648
-aiagents4pharma/talk2biomodels/tests/test_query_article.py,sha256=HhFgU5HzCipecEYlfbpPxN-SCIPKep22gpXCutWXRb8,2820
-aiagents4pharma/talk2biomodels/tests/test_search_models.py,sha256=8ODFubLxWYD3I3KQWuUnJ2GZRzMjFpXInFBLxKxG_ME,929
+aiagents4pharma/talk2biomodels/tests/test_query_article.py,sha256=lArISS111mQUZmjLY82PkRVPSTcN2h8KNF4gpTTvwL0,3185
+aiagents4pharma/talk2biomodels/tests/test_search_models.py,sha256=ttOzN78b06ixYF_SbSyrhQSnmCgOMlSoeG9Q1FeRAis,1028
 aiagents4pharma/talk2biomodels/tests/test_simulate_model.py,sha256=GjLE1DZpcKUAFSmoHD86vkfK0b5LJPM8a4WYyraazig,1487
-aiagents4pharma/talk2biomodels/tests/test_steady_state.py,sha256=zt15KQoQku6jyzvpJXwINGTyhEnQl8wX81ueHlxnUCA,3467
+aiagents4pharma/talk2biomodels/tests/test_steady_state.py,sha256=2bzxj74vekazgLG7hiMALRiqP_4sVmue9cN4zCZ42T8,3556
 aiagents4pharma/talk2biomodels/tests/test_sys_bio_model.py,sha256=HSmBBViMi0jYf4gWX21IbppAfDzG0nr_S3KtKS9fZVQ,2165
 aiagents4pharma/talk2biomodels/tools/__init__.py,sha256=6H2HWv5Q4NZYEmw-Ti5KZnJlEqhaC2HXSDZa6kiSl-U,350
-aiagents4pharma/talk2biomodels/tools/ask_question.py,sha256=ASkqT6VHUWcMdkVAlqqfbwq7_EBVAXdtmlkMFy7-XxI,4698
-aiagents4pharma/talk2biomodels/tools/custom_plotter.py,sha256=HWwKTX3o4dk0GcRVTO2hPrFSu98mtJ4TKC_hbHXOe1c,4018
-aiagents4pharma/talk2biomodels/tools/get_annotation.py,sha256=Cea0vid_KX1xjI6ZqDygREAcM7sC7wZXNLTkAN8Nk3Y,13387
+aiagents4pharma/talk2biomodels/tools/ask_question.py,sha256=NZwKT7DHc4TW9e8LOkHaRG_nqUs_lEandvi89DTXilQ,4640
+aiagents4pharma/talk2biomodels/tools/custom_plotter.py,sha256=DsnQIKebchy6tgzLZnY7VLVesu3Es-OdqLfW61kIn3A,4762
+aiagents4pharma/talk2biomodels/tools/get_annotation.py,sha256=njxUmFuFwlzY3Doq-XlepGXJTMgnYfs88L4RkKSiptw,13438
 aiagents4pharma/talk2biomodels/tools/get_modelinfo.py,sha256=57dkXrBeRpyiaW3dYkoWIfr6zSsFHcWRhvUVNyLcvUs,6363
 aiagents4pharma/talk2biomodels/tools/load_arguments.py,sha256=bffNIlBDTCSFYiZprA73yi8Jbb8z3Oh2decVNh1UnZc,4162
 aiagents4pharma/talk2biomodels/tools/load_biomodel.py,sha256=pyVzLQoMnuJYEwsjeOlqcUrbU1F1Z-pNlgkhFaoKpy0,689
 aiagents4pharma/talk2biomodels/tools/parameter_scan.py,sha256=aNh94LgBgVXBIczuNkbSsOZ9j54YVEdZWmZbZr7Nk8k,12465
-aiagents4pharma/talk2biomodels/tools/query_article.py,sha256=1tpYiE69MYcqiNcRaBgNiYzkkNmuTnlxLuBL_FnRuBU,2058
-aiagents4pharma/talk2biomodels/tools/search_models.py,sha256=b2OK-Z4ilddbEaJPSQlnZ6sHX3UAWXr_Hq-knoSbbAE,2654
+aiagents4pharma/talk2biomodels/tools/query_article.py,sha256=6xfirRRMXN-wxqZxYYbKeEMXLMAHKl5IPShfpoOEBcc,2268
+aiagents4pharma/talk2biomodels/tools/search_models.py,sha256=LdvfCNeiO8fU6lszd7UUzk4NXP6ETuMsCRb2SpXcztw,2841
 aiagents4pharma/talk2biomodels/tools/simulate_model.py,sha256=qXs9lg9XgA7EaRiX3wBS8w_ug8tI-G3pzhcRg6dTRio,5060
 aiagents4pharma/talk2biomodels/tools/steady_state.py,sha256=j3ckuNlUtv7lT922MbN0JhT9H0JpWAdx2mLPwao6uu8,7123
 aiagents4pharma/talk2cells/__init__.py,sha256=zmOP5RAhabgKIQP-W4P4qKME2tG3fhAXM3MeO5_H8kE,120
@@ -55,31 +55,63 @@ aiagents4pharma/talk2cells/tools/__init__.py,sha256=38nK2a_lEFRjO3qD6Fo9a3983ZCY
 aiagents4pharma/talk2cells/tools/scp_agent/__init__.py,sha256=s7g0lyH1lMD9pcWHLPtwRJRvzmTh2II7DrxyLulpjmQ,163
 aiagents4pharma/talk2cells/tools/scp_agent/display_studies.py,sha256=6q59gh_NQaiOU2rn55A3sIIFKlXi4SK3iKgySvUDrtQ,600
 aiagents4pharma/talk2cells/tools/scp_agent/search_studies.py,sha256=MLe-twtFnOu-P8P9diYq7jvHBHbWFRRCZLcfpUzqPMg,2806
-aiagents4pharma/talk2knowledgegraphs/__init__.py,sha256=4smVQoSMM6rflVnNkABqlDAAlSn4bYsq7rMVWjRGvis,103
+aiagents4pharma/talk2knowledgegraphs/__init__.py,sha256=Z0Eo7LTiKk0STsr8VI7wkCLq7PHrK1vYlH4I1hSNLiA,165
+aiagents4pharma/talk2knowledgegraphs/agents/__init__.py,sha256=iOAzuy_8A03tQDFtSBhC9dldUo62z5gfxcVtXAdLOJs,92
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 aiagents4pharma/talk2knowledgegraphs/datasets/biobridge_primekg.py,sha256=QlzDXmXREoa9MA6-GwzqRjdzndQeGBAF11Td6NFk_9Y,23426
 aiagents4pharma/talk2knowledgegraphs/datasets/dataset.py,sha256=-LaPLse8BkALqwFetNK7wch2dt9Dz6QKGKZKBKM6bIk,409
 aiagents4pharma/talk2knowledgegraphs/datasets/primekg.py,sha256=KBMhCJ7yjMWqQJJctFYdpjYAlwv48Jl6i1dddXP4f08,7599
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 aiagents4pharma/talk2knowledgegraphs/tests/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
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 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
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 aiagents4pharma/talk2knowledgegraphs/tests/test_utils_embeddings_embeddings.py,sha256=uYFoE_6zeU10_1mLLAHUr5c4S2XZMSc0Q_860o-KWEw,1517
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 aiagents4pharma/talk2knowledgegraphs/tests/test_utils_embeddings_sentencetransformer.py,sha256=Qxo6WeIDRy8aLh1tNKw0kSlzmUj3MtTak63oW2YwB24,1327
 aiagents4pharma/talk2knowledgegraphs/tests/test_utils_enrichments_enrichments.py,sha256=N6HRr4lWHXY7bTHe2uXJe4D_EG9WqZPibZne6qLl9_k,1447
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 aiagents4pharma/talk2knowledgegraphs/utils/kg_utils.py,sha256=6vQnPkeOWae_8jePjhma3sJuMTngy0I0tqzdFt6OqKg,2507
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 aiagents4pharma/talk2knowledgegraphs/utils/embeddings/embeddings.py,sha256=1nGznrAj-xT0xuSMBGz2dOujJ7M_IwSR84njxtxsy9A,2523
 aiagents4pharma/talk2knowledgegraphs/utils/embeddings/huggingface.py,sha256=2vi_elf6EgzfagFAO5QnL3a_aXZyN7B1EBziu44MTfM,3806
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 aiagents4pharma/talk2knowledgegraphs/utils/embeddings/sentence_transformer.py,sha256=36iKlisOpMtGR5xfTAlSHXWvPqVC_Jbezod8kbBBMVg,2136
 aiagents4pharma/talk2knowledgegraphs/utils/enrichments/__init__.py,sha256=tW426knki2DBIHcWyF_K04iMMdbpIn_e_TpPmTgz2dI,113
 aiagents4pharma/talk2knowledgegraphs/utils/enrichments/enrichments.py,sha256=Bx8x6zzk5614ApWB90N_iv4_Y_Uq0-KwUeBwYSdQMU4,924
 aiagents4pharma/talk2knowledgegraphs/utils/enrichments/ollama.py,sha256=8eoxR-VHo0G7ReQIwje7xEhE-SJlHdef7_wJRpnvFIc,4116
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 aiagents4pharma/talk2scholars/__init__.py,sha256=gphERyVKZHvOnMQsml7TIHlaIshHJ75R1J3FKExkfuY,120
 aiagents4pharma/talk2scholars/agents/__init__.py,sha256=ykszlVGxz3egLHZAttlNoTPxIrnQJZYva_ssR8fwIFk,117
 aiagents4pharma/talk2scholars/agents/main_agent.py,sha256=etPQUCjHtD-in-kD7Wg_UD6jRtCHj-mj41y03PYbAQM,4616
@@ -112,8 +144,8 @@ aiagents4pharma/talk2scholars/tools/s2/display_results.py,sha256=B8JJGohi1Eyx8C3
 aiagents4pharma/talk2scholars/tools/s2/multi_paper_rec.py,sha256=0Y3q8TkF_Phng9L7g1kk9Fhyit9UNitWurp03H0GZv8,4455
 aiagents4pharma/talk2scholars/tools/s2/search.py,sha256=CcgFN7YuuQ9Vl1DJcldnnvPrswABKjNxeauK1rABps8,4176
 aiagents4pharma/talk2scholars/tools/s2/single_paper_rec.py,sha256=irS-igdG8BZbVb0Z4VlIjzsyBlUfREd0v0_RlUM-0_U,4994
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