aiagents4pharma 1.15.1__py3-none-any.whl → 1.16.0__py3-none-any.whl

aiagents4pharma/__init__.py

@@ -6,6 +6,6 @@ from . import (
     configs,
     talk2biomodels,
     talk2cells,
-    talk2competitors,
+    talk2scholars,
     talk2knowledgegraphs,
 )

aiagents4pharma/configs/config.yaml

@@ -1,4 +1,5 @@
 defaults:
   - _self_
   - talk2biomodels/agents/t2b_agent: default
-  - talk2biomodels/tools/ask_question: default
+  - talk2biomodels/tools/ask_question: default
+  - talk2biomodels/tools/get_annotation: default

aiagents4pharma/configs/talk2biomodels/tools/__init__.py

@@ -1,4 +1,5 @@
 '''
 Import all the modules in the package
 '''
-from . import ask_question
+from . import ask_question
+from . import get_annotation

aiagents4pharma/configs/talk2biomodels/tools/get_annotation/__init__.py

@@ -0,0 +1,3 @@
+'''
+Import all the modules in the package
+'''

aiagents4pharma/configs/talk2biomodels/tools/get_annotation/default.yaml

@@ -0,0 +1,6 @@
+_target_: talk2biomodels.tools.get_annotation.GetAnnotationTool
+prompt: >
+  Given the user question, extract the relevant species names.
+  If the user aks for a specific species, extract that species.
+  If none of the species match the user question, return None.
+  If the user asks for all species, return all species.

aiagents4pharma/talk2biomodels/tests/test_get_annotation.py

@@ -16,6 +16,7 @@ def make_graph_fixture():
     unique_id = random.randint(1000, 9999)
     graph = get_app(unique_id)
     config = {"configurable": {"thread_id": unique_id}}
+    graph.update_state(config, {"llm_model": "gpt-4o-mini"})
     return graph, config
 
 def test_no_model_provided(make_graph):
@@ -34,7 +35,7 @@ def test_no_model_provided(make_graph):
     # Assert that the state key model_id is empty.
     assert current_state.values["model_id"] == []
 
-def test_specific_species_provided(make_graph):
+def test_valid_species_provided(make_graph):
     '''
     Test the tool by providing a specific species name.
     We are testing a condition where the user asks for annotations
@@ -54,9 +55,15 @@ def test_specific_species_provided(make_graph):
     # The assert statement checks if IL6 is present in the returned annotations.
     assert dic_annotations_data[0]['data']["Species Name"][0] == "IL6"
 
+def test_invalid_species_provided(make_graph):
+    '''
+    Test the tool by providing an invalid species name.
+    We are testing a condition where the user asks for annotations
+    of an invalid species in a specific model.
+    '''
     # Test with an invalid species name
     app, config = make_graph
-    prompt = "Extract annotations of species NADH in model 537."
+    prompt = "Extract annotations of only species NADH in model 537."
     app.invoke(
         {"messages": [HumanMessage(content=prompt)]},
         config=config
@@ -73,15 +80,20 @@ def test_specific_species_provided(make_graph):
         if isinstance(msg, ToolMessage) and msg.name == "get_annotation":
             #If a ToolMessage exists and artifact is None (meaning no valid annotation was found)
             #and the rejected species (NADH) is mentioned, the test passes.
-            if msg.artifact is None and 'NADH' in msg.content:
+            if msg.artifact is None and msg.status == "error":
                 #If artifact is None, it means no annotation was found
                 # (likely due to an invalid species).
-                #If artifact contains data, the tool successfully retrieved annotations.
                 test_condition = True
                 break
     # assert test_condition
-    assert test_condition, "Expected rejection message for NADH but did not find it."
+    assert test_condition
 
+def test_invalid_and_valid_species_provided(make_graph):
+    '''
+    Test the tool by providing an invalid species name and a valid species name.
+    We are testing a condition where the user asks for annotations
+    of an invalid species and a valid species in a specific model.
+    '''
     # Test with an invalid species name and a valid species name
     app, config = make_graph
     prompt = "Extract annotations of species NADH, NAD, and IL7 in model 64."
@@ -90,21 +102,24 @@ def test_specific_species_provided(make_graph):
         config=config
     )
     current_state = app.get_state(config)
-    # dic_annotations_data = current_state.values["dic_annotations_data"]
+    dic_annotations_data = current_state.values["dic_annotations_data"]
+    # List of species that are expected to be found in the annotations
+    extracted_species = []
+    for idx in dic_annotations_data[0]['data']["Species Name"]:
+        extracted_species.append(dic_annotations_data[0]['data']["Species Name"][idx])
     reversed_messages = current_state.values["messages"][::-1]
     # Loop through the reversed messages until a
     # ToolMessage is found.
-    artifact_was_none = False
+    tool_status_success = False
     for msg in reversed_messages:
         # Assert that the one of the messages is a ToolMessage
         # and its artifact is None.
         if isinstance(msg, ToolMessage) and msg.name == "get_annotation":
-            # print (msg.artifact, msg.content)
-
-            if msg.artifact is True and 'IL7' in msg.content:
-                artifact_was_none = True
+            if msg.artifact is True and msg.status == "success":
+                tool_status_success = True
                 break
-    assert artifact_was_none
+    assert tool_status_success
+    assert set(extracted_species) == set(["NADH", "NAD"])
 
 def test_all_species_annotations(make_graph):
     '''
@@ -146,7 +161,7 @@ def test_all_species_annotations(make_graph):
                 # Expect a successful extraction (artifact is True) and that the content
                 # matches what is returned by prepare_content_msg for species.
                 # And that the first or second description of the LacI protein is missing.
-                if (msg.artifact is True and msg.content == prepare_content_msg([],[])
+                if (msg.artifact is True and msg.content == prepare_content_msg([])
                     and msg.status=="success" and (first_descp_laci_protein == '-' or
                                                     second_descp_laci_protein == '-')):
                     test_condition = True
@@ -164,7 +179,7 @@ def test_all_species_annotations(make_graph):
                 # Expect a successful extraction (artifact is True) and that the content
                 # matches for for missing description ['ORI'].
                 if (msg.artifact is True and
-                msg.content == prepare_content_msg([],['ORI'])
+                msg.content == prepare_content_msg(['ORI'])
                 and msg.status == "success"):
                     test_condition = True
                     break

aiagents4pharma/talk2biomodels/tests/test_getmodelinfo.py

@@ -2,7 +2,7 @@
 Test cases for Talk2Biomodels get_modelinfo tool.
 '''
 
-from langchain_core.messages import HumanMessage
+from langchain_core.messages import HumanMessage, ToolMessage
 from ..agents.t2b_agent import get_app
 
 def test_get_modelinfo_tool():
@@ -24,3 +24,34 @@ def test_get_modelinfo_tool():
     assistant_msg = response["messages"][-1].content
     # Check if the assistant message is a string
     assert isinstance(assistant_msg, str)
+
+def test_model_with_no_species():
+    '''
+    Test the get_modelinfo tool with a model that does not
+    return any species.
+
+    This should raise a tool error.
+    '''
+    unique_id = 12345
+    app = get_app(unique_id)
+    config = {"configurable": {"thread_id": unique_id}}
+    prompt = "Extract all species from model 20"
+    # Test the tool get_modelinfo
+    app.invoke(
+                {"messages": [HumanMessage(content=prompt)]},
+                config=config
+            )
+    current_state = app.get_state(config)
+    reversed_messages = current_state.values["messages"][::-1]
+    # Loop through the reversed messages until a
+    # ToolMessage is found.
+    test_condition = False
+    for msg in reversed_messages:
+        # Check if the message is a ToolMessage from the get_modelinfo tool
+        if isinstance(msg, ToolMessage) and msg.name == "get_modelinfo":
+            # Check if the message is an error message
+            if (msg.status == "error" and
+                "ValueError('Unable to extract species from the model.')" in msg.content):
+                test_condition = True
+                break
+    assert test_condition

aiagents4pharma/talk2biomodels/tests/test_integration.py

@@ -17,10 +17,9 @@ def test_integration():
     # ##########################################
     # ## Test simulate_model tool
     # ##########################################
-    prompt = '''Simulate the model 537 for 100 hours and intervals
-    100 with an initial concentration of `DoseQ2W`
-    set to 300 and `Dose` set to 0. Reset the concentration
-    of `Ab{serum}` to 100 every 25 hours.'''
+    prompt = '''Simulate the model 537 for 100 hours and time intervals
+    100 with an initial concentration of `DoseQ2W` set to 300 and `Dose`
+    set to 0. Reset the concentration of `Ab{serum}` to 100 every 25 hours.'''
     # Test the tool get_modelinfo
     response = app.invoke(
                         {"messages": [HumanMessage(content=prompt)]},

aiagents4pharma/talk2biomodels/tools/get_annotation.py

@@ -5,9 +5,10 @@ This module contains the `GetAnnotationTool` for fetching species annotations
 based on the provided model and species names.
 """
 import math
-from typing import List, Annotated, Type
+from typing import List, Annotated, Type, TypedDict, Union, Literal
 import logging
 from dataclasses import dataclass
+import hydra
 from pydantic import BaseModel, Field
 import basico
 import pandas as pd
@@ -16,6 +17,7 @@ from langgraph.prebuilt import InjectedState
 from langchain_core.tools.base import BaseTool
 from langchain_core.tools.base import InjectedToolCallId
 from langchain_core.messages import ToolMessage
+from langchain_openai import ChatOpenAI
 from .load_biomodel import ModelData, load_biomodel
 from ..api.uniprot import search_uniprot_labels
 from ..api.ols import search_ols_labels
@@ -27,16 +29,56 @@ logger = logging.getLogger(__name__)
 
 ols_ontology_abbreviations = {'pato', 'chebi', 'sbo', 'fma', 'pr','go'}
 
-def prepare_content_msg(species_not_found: List[str],
-                        species_without_description: List[str]):
+def extract_relevant_species_names(model_object, arg_data, state):
+    """
+    Extract relevant species names based on the user question.
+    """
+    # Load hydra configuration
+    with hydra.initialize(version_base=None, config_path="../../configs"):
+        cfg = hydra.compose(config_name='config',
+                            overrides=['talk2biomodels/tools/get_annotation=default'])
+        cfg = cfg.talk2biomodels.tools.get_annotation
+    logger.info("Loaded the following system prompt for the LLM"
+                " to get a structured output: %s", cfg.prompt)
+
+    # Extract all the species names from the model
+    df_species = basico.model_info.get_species(model=model_object.copasi_model)
+    if df_species is None:
+        raise ValueError("Unable to extract species from the model.")
+    # Get all the species names
+    all_species_names = df_species.index.tolist()
+
+    # Define a structured output for the LLM model
+    class CustomHeader(TypedDict):
+        """
+        A list of species based on user question.
+        """
+        relevant_species: Union[None, List[Literal[*all_species_names]]] = Field(
+                description="""List of species based on user question.
+                If no relevant species are found, it must be None.""")
+
+    # Create an instance of the LLM model
+    llm = ChatOpenAI(model=state['llm_model'], temperature=0)
+    # Get the structured output from the LLM model
+    llm_with_structured_output = llm.with_structured_output(CustomHeader)
+    # Define the question for the LLM model using the prompt
+    question = cfg.prompt
+    question += f'Here is the user question: {arg_data.user_question}'
+    # Invoke the LLM model with the user question
+    dic = llm_with_structured_output.invoke(question)
+    extracted_species = []
+    # Extract all the species names from the model
+    for species in dic['relevant_species']:
+        if species in all_species_names:
+            extracted_species.append(species)
+    logger.info("Extracted species: %s", extracted_species)
+    return extracted_species
+
+def prepare_content_msg(species_without_description: List[str]):
     """
     Prepare the content message.
     """
     content = 'Successfully extracted annotations for the species.'
-    if species_not_found:
-        content += f'''The following species do not exist, and
-                        hence their annotations were not extracted:
-                        {', '.join(species_not_found)}.'''
     if species_without_description:
         content += f'''The descriptions for the following species
                         were not found:
@@ -52,12 +94,7 @@ class ArgumentData:
                                     " the experiment based on human query"
                                     " and the context of the experiment."
                                     " This must be set before the experiment is run."]
-    list_species_names: List[str] = Field(
-        default=None,
-        description='''List of species names to fetch annotations for.
-                      If not provided, annotations for all
-                      species in the model will be fetched.'''
-    )
+    user_question: Annotated[str, "Description of the user question"]
 
 class GetAnnotationInput(BaseModel):
     """
@@ -90,31 +127,22 @@ class GetAnnotationTool(BaseTool):
         Run the tool.
         """
         logger.info("Running the GetAnnotationTool tool for species %s, %s",
-                    arg_data.list_species_names,
+                    arg_data.user_question,
                     arg_data.experiment_name)
 
         # Prepare the model object
         sbml_file_path = state['sbml_file_path'][-1] if state['sbml_file_path'] else None
         model_object = load_biomodel(sys_bio_model, sbml_file_path=sbml_file_path)
 
-        # Extract all the species names from the model
-        df_species = basico.model_info.get_species(model=model_object.copasi_model)
+        # Extract relevant species names based on the user question
+        list_species_names = extract_relevant_species_names(model_object, arg_data, state)
 
-        if df_species is None:
-            # for example this may happen with model 20
-            raise ValueError("Unable to extract species from the model.")
-        # Fetch annotations for the species names
-        arg_data.list_species_names = arg_data.list_species_names or df_species.index.tolist()
+        # Check if the returned species names are empty
+        if not list_species_names:
+            raise ValueError("Model does not contain the requested species.")
 
         (annotations_df,
-         species_not_found,
-         species_without_description) = self._fetch_annotations(arg_data.list_species_names)
-
-        # Check if annotations are empty
-        # If empty, return a message
-        if annotations_df.empty:
-            logger.warning("The annotations dataframe is empty.")
-            return prepare_content_msg(species_not_found, species_without_description)
+         species_without_description) = self._fetch_annotations(list_species_names)
 
         # Process annotations
         annotations_df = self._process_annotations(annotations_df)
@@ -141,8 +169,7 @@ class GetAnnotationTool(BaseTool):
             update=dic_updated_state_for_model | {
                 "messages": [
                     ToolMessage(
-                        content=prepare_content_msg(species_not_found,
-                                                    species_without_description),
+                        content=prepare_content_msg(species_without_description),
                         artifact=True,
                         tool_call_id=tool_call_id
                     )
@@ -165,7 +192,6 @@ class GetAnnotationTool(BaseTool):
             tuple: A tuple containing the annotations dataframe, species not found list,
                    and description not found list.
         """
-        species_not_found = []
         description_not_found = []
         data = []
 
@@ -173,10 +199,6 @@ class GetAnnotationTool(BaseTool):
         for species in list_species_names:
             # Get the MIRIAM annotation for the species
             annotation = basico.get_miriam_annotation(name=species)
-            # If the annotation is not found, add the species to the list
-            if annotation is None:
-                species_not_found.append(species)
-                continue
 
             # Extract the descriptions from the annotation
             descriptions = annotation.get("descriptions", [])
@@ -197,7 +219,7 @@ class GetAnnotationTool(BaseTool):
         annotations_df = pd.DataFrame(data)
 
         # Return the annotations dataframe and the species not found list
-        return annotations_df, species_not_found, description_not_found
+        return annotations_df, description_not_found
 
     def _process_annotations(self, annotations_df: pd.DataFrame) -> pd.DataFrame:
         """

aiagents4pharma/talk2biomodels/tools/get_modelinfo.py

@@ -83,14 +83,33 @@ class GetModelInfoTool(BaseTool):
         # Extract species from the model
         if requested_model_info.species:
             df_species = basico.model_info.get_species(model=model_obj.copasi_model)
-            dic_results['Species'] = df_species['display_name'].tolist()
-            dic_results['Species'] = ','.join(dic_results['Species'])
+            if df_species is None:
+                raise ValueError("Unable to extract species from the model.")
+            # Convert index into a column
+            df_species.reset_index(inplace=True)
+            dic_results['Species'] = df_species[
+                                        ['name',
+                                         'compartment',
+                                         'type',
+                                         'unit',
+                                         'initial_concentration',
+                                         'display_name']]
+            # Convert this into a dictionary
+            dic_results['Species'] = dic_results['Species'].to_dict(orient='records')
 
         # Extract parameters from the model
         if requested_model_info.parameters:
             df_parameters = basico.model_info.get_parameters(model=model_obj.copasi_model)
-            dic_results['Parameters'] = df_parameters.index.tolist()
-            dic_results['Parameters'] = ','.join(dic_results['Parameters'])
+            # Convert index into a column
+            df_parameters.reset_index(inplace=True)
+            dic_results['Parameters'] = df_parameters[
+                                        ['name',
+                                         'type',
+                                         'unit',
+                                         'initial_value',
+                                         'display_name']]
+            # Convert this into a dictionary
+            dic_results['Parameters'] = dic_results['Parameters'].to_dict(orient='records')
 
         # Extract compartments from the model
         if requested_model_info.compartments:

aiagents4pharma/{talk2competitors → talk2scholars}/agents/main_agent.py

@@ -1,7 +1,7 @@
 #!/usr/bin/env python3
 
 """
-Main agent for the talk2competitors app.
+Main agent for the talk2scholars app.
 """
 
 import logging
@@ -15,7 +15,7 @@ from langgraph.graph import END, START, StateGraph
 from langgraph.types import Command
 from ..agents import s2_agent
 from ..config.config import config
-from ..state.state_talk2competitors import Talk2Competitors
+from ..state.state_talk2scholars import Talk2Scholars
 
 logging.basicConfig(level=logging.INFO)
 logger = logging.getLogger(__name__)
@@ -34,12 +34,12 @@ def make_supervisor_node(llm: BaseChatModel) -> str:
     """
     # options = ["FINISH", "s2_agent"]
 
-    def supervisor_node(state: Talk2Competitors) -> Command[Literal["s2_agent", "__end__"]]:
+    def supervisor_node(state: Talk2Scholars) -> Command[Literal["s2_agent", "__end__"]]:
         """
         Supervisor node that routes to appropriate sub-agents.
 
         Args:
-            state (Talk2Competitors): The current state of the conversation.
+            state (Talk2Scholars): The current state of the conversation.
 
         Returns:
             Command[Literal["s2_agent", "__end__"]]: The command to execute next.
@@ -91,12 +91,12 @@ def get_app(thread_id: str, llm_model ='gpt-4o-mini') -> StateGraph:
     Returns:
         The compiled langraph app.
     """
-    def call_s2_agent(state: Talk2Competitors) -> Command[Literal["__end__"]]:
+    def call_s2_agent(state: Talk2Scholars) -> Command[Literal["__end__"]]:
         """
         Node for calling the S2 agent.
 
         Args:
-            state (Talk2Competitors): The current state of the conversation.
+            state (Talk2Scholars): The current state of the conversation.
 
         Returns:
             Command[Literal["__end__"]]: The command to execute next.
@@ -115,7 +115,7 @@ def get_app(thread_id: str, llm_model ='gpt-4o-mini') -> StateGraph:
             },
         )
     llm = ChatOpenAI(model=llm_model, temperature=0)
-    workflow = StateGraph(Talk2Competitors)
+    workflow = StateGraph(Talk2Scholars)
 
     supervisor = make_supervisor_node(llm)
     workflow.add_node("supervisor", supervisor)

aiagents4pharma/{talk2competitors → talk2scholars}/agents/s2_agent.py

@@ -11,7 +11,7 @@ from langgraph.graph import START, StateGraph
 from langgraph.prebuilt import create_react_agent
 from langgraph.checkpoint.memory import MemorySaver
 from ..config.config import config
-from ..state.state_talk2competitors import Talk2Competitors
+from ..state.state_talk2scholars import Talk2Scholars
 # from ..tools.s2 import s2_tools
 from ..tools.s2.search import search_tool
 from ..tools.s2.display_results import display_results
@@ -28,7 +28,7 @@ def get_app(uniq_id, llm_model='gpt-4o-mini'):
     '''
     This function returns the langraph app.
     '''
-    def agent_s2_node(state: Talk2Competitors):
+    def agent_s2_node(state: Talk2Scholars):
         '''
         This function calls the model.
         '''
@@ -47,13 +47,13 @@ def get_app(uniq_id, llm_model='gpt-4o-mini'):
     model = create_react_agent(
                             llm,
                             tools=tools,
-                            state_schema=Talk2Competitors,
+                            state_schema=Talk2Scholars,
                             state_modifier=config.S2_AGENT_PROMPT,
                             checkpointer=MemorySaver()
                         )
 
     # Define a new graph
-    workflow = StateGraph(Talk2Competitors)
+    workflow = StateGraph(Talk2Scholars)
 
     # Define the two nodes we will cycle between
     workflow.add_node("agent_s2", agent_s2_node)

aiagents4pharma/{talk2competitors → talk2scholars}/state/__init__.py

@@ -2,4 +2,4 @@
 This file is used to import all the modules in the package.
 '''
 
-from . import state_talk2competitors
+from . import state_talk2scholars

aiagents4pharma/{talk2competitors/state/state_talk2competitors.py → talk2scholars/state/state_talk2scholars.py}

@@ -1,5 +1,5 @@
 """
-This is the state file for the talk2comp agent.
+This is the state file for the talk2scholars agent.
 """
 
 import logging
@@ -19,9 +19,9 @@ def replace_dict(existing: Dict[str, Any], new: Dict[str, Any]) -> Dict[str, Any
     return new
 
 
-class Talk2Competitors(AgentState):
+class Talk2Scholars(AgentState):
     """
-    The state for the talk2comp agent, inheriting from AgentState.
+    The state for the talk2scholars agent, inheriting from AgentState.
     """
 
     papers: Annotated[Dict[str, Any], replace_dict]  # Changed from List to Dict

aiagents4pharma/{talk2competitors → talk2scholars}/tests/test_langgraph.py

@@ -1,5 +1,5 @@
 """
-Unit and integration tests for Talk2Competitors system.
+Unit and integration tests for Talk2Scholars system.
 Each test focuses on a single, specific functionality.
 Tests are deterministic and independent of each other.
 """
@@ -10,7 +10,7 @@ import pytest
 from langchain_core.messages import AIMessage, HumanMessage
 
 from ..agents.main_agent import get_app, make_supervisor_node
-from ..state.state_talk2competitors import replace_dict
+from ..state.state_talk2scholars import replace_dict
 from ..tools.s2.display_results import display_results
 from ..tools.s2.multi_paper_rec import get_multi_paper_recommendations
 from ..tools.s2.search import search_tool

{aiagents4pharma-1.15.1.dist-info → aiagents4pharma-1.16.0.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.2
 Name: aiagents4pharma
-Version: 1.15.1
+Version: 1.16.0
 Summary: AI Agents for drug discovery, drug development, and other pharmaceutical R&D
 Classifier: Programming Language :: Python :: 3
 Classifier: License :: OSI Approved :: MIT License
@@ -50,11 +50,10 @@ Requires-Dist: streamlit-feedback
 [![Talk2BioModels](https://github.com/VirtualPatientEngine/AIAgents4Pharma/actions/workflows/tests_talk2biomodels.yml/badge.svg)](https://github.com/VirtualPatientEngine/AIAgents4Pharma/actions/workflows/tests_talk2biomodels.yml)
 [![Talk2Cells](https://github.com/VirtualPatientEngine/AIAgents4Pharma/actions/workflows/tests_talk2cells.yml/badge.svg)](https://github.com/VirtualPatientEngine/AIAgents4Pharma/actions/workflows/tests_talk2cells.yml)
 [![Talk2KnowledgeGraphs](https://github.com/VirtualPatientEngine/AIAgents4Pharma/actions/workflows/tests_talk2knowledgegraphs.yml/badge.svg)](https://github.com/VirtualPatientEngine/AIAgents4Pharma/actions/workflows/tests_talk2knowledgegraphs.yml)
-[![Talk2Competitors](https://github.com/VirtualPatientEngine/AIAgents4Pharma/actions/workflows/tests_talk2competitors.yml/badge.svg)](https://github.com/VirtualPatientEngine/AIAgents4Pharma/actions/workflows/tests_talk2competitors.yml)
+[![Talk2Scholars](https://github.com/VirtualPatientEngine/AIAgents4Pharma/actions/workflows/tests_talk2scholars.yml/badge.svg)](https://github.com/VirtualPatientEngine/AIAgents4Pharma/actions/workflows/tests_talk2scholars.yml)
 ![GitHub Release](https://img.shields.io/github/v/release/VirtualPatientEngine/AIAgents4Pharma)
 ![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)
 
-
 <h1 align="center" style="border-bottom: none;">🤖 AIAgents4Pharma</h1>
 
 Welcome to **AIAgents4Pharma** – an open-source project by [Team VPE](https://github.com/VirtualPatientEngine) that brings together AI-driven tools to help researchers and pharma interact seamlessly with complex biological data.
@@ -64,7 +63,7 @@ Our toolkit currently consists of three intelligent agents, each designed to sim
 - **Talk2BioModels**: Engage directly with mathematical models in systems biology.
 - **Talk2Cells** _(Work in progress)_: Query and analyze sequencing data with ease.
 - **Talk2KnowledgeGraphs** _(Work in progress)_: Access and explore complex biological knowledge graphs for insightful data connections.
-- **Talk2Competitors** _(Coming soon)_: Get recommendations for articles related to your choice. Download, query, and write/retrieve them to your reference manager (currently supporting Zotero).
+- **Talk2Scholars** _(Coming soon)_: Get recommendations for articles related to your choice. Download, query, and write/retrieve them to your reference manager (currently supporting Zotero).
 
 ---
 
@@ -87,7 +86,9 @@ Our toolkit currently consists of three intelligent agents, each designed to sim
 
 **Talk2KnowledgeGraphs** is an agent designed to enable interaction with biological knowledge graphs (KGs). KGs integrate vast amounts of structured biological data into a format that highlights relationships between entities, such as proteins, genes, and diseases.
 
-### 4. Talk2Competitors _(Coming soon)_
+### 4. Talk2Scholars _(Work in Progress)_
+
+Talk2Scholars is an AI-powered hierarchical agent system designed to revolutionize academic paper search and analysis. Through intelligent conversation, users can discover, analyze, and receive recommendations for academic papers using state-of-the-art natural language processing.
 
 ## Getting Started
 
@@ -198,7 +199,7 @@ Check out our [CONTRIBUTING.md](CONTRIBUTING.md) for more information.
 - **User Interface**: Interactive web UI for all agents.
 - **Talk2Cells**: Integration of sequencing data analysis tools.
 - **Talk2KnowledgeGraphs**: Interface for biological knowledge graph interaction.
-- **Talk2Competitors**: Interface for exploring articles
+- **Talk2Scholars**: Interface for exploring articles
 
 We’re excited to bring AIAgents4Pharma to the bioinformatics and pharmaceutical research community. Together, let’s make data-driven biological research more accessible and insightful.
 

{aiagents4pharma-1.15.1.dist-info → aiagents4pharma-1.16.0.dist-info}/RECORD

@@ -1,13 +1,15 @@
-aiagents4pharma/__init__.py,sha256=5muWWIg89VHPybfxonO_5xOMJPasKNsGdQRhozDaEmk,177
+aiagents4pharma/__init__.py,sha256=nFCe1As_SuRkmhcdZVsU0aYjYccHxk1DbduLpy8XulY,174
 aiagents4pharma/configs/__init__.py,sha256=hNkSrXw1Ix1HhkGn_aaidr2coBYySfM0Hm_pMeRcX7k,76
-aiagents4pharma/configs/config.yaml,sha256=4t7obD0gOSfqnDDZZBB53ZC7zsmk7QDcM7T_1Hf1wIQ,112
+aiagents4pharma/configs/config.yaml,sha256=e0w2GOBVWcoPDtX-z4S6yKbv2rja5PfGRBhmTPVIXNU,161
 aiagents4pharma/configs/talk2biomodels/__init__.py,sha256=safyFKhkd5Wlirl9dMZIHWDLTpY2oLw9wjIM7ZtLIHk,88
 aiagents4pharma/configs/talk2biomodels/agents/__init__.py,sha256=_ZoG8snICK2bidWtc2KOGs738LWg9_r66V9mOMnEb-E,71
 aiagents4pharma/configs/talk2biomodels/agents/t2b_agent/__init__.py,sha256=-fAORvyFmG2iSvFOFDixmt9OTQRR58y89uhhu2EgbA8,46
 aiagents4pharma/configs/talk2biomodels/agents/t2b_agent/default.yaml,sha256=eLrJIezoPJ6_DvrSYsi3eALl03o0hJhntej3ESoeKKg,551
-aiagents4pharma/configs/talk2biomodels/tools/__init__.py,sha256=WxK7h5n39l-NSMvjLZyxDqzwWlVA6mQ69gzsbJ17vEk,72
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 aiagents4pharma/configs/talk2biomodels/tools/ask_question/__init__.py,sha256=-fAORvyFmG2iSvFOFDixmt9OTQRR58y89uhhu2EgbA8,46
 aiagents4pharma/configs/talk2biomodels/tools/ask_question/default.yaml,sha256=yy-Sq1u4dBlTFi_UeoWYoHkWRDWueJWVNK_rcUCC5bw,1747
+aiagents4pharma/configs/talk2biomodels/tools/get_annotation/__init__.py,sha256=-fAORvyFmG2iSvFOFDixmt9OTQRR58y89uhhu2EgbA8,46
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 aiagents4pharma/talk2biomodels/__init__.py,sha256=2ICwVh1u07SZv31Jd2DKHobauOxWNWY29_Gqq3kOnNQ,159
 aiagents4pharma/talk2biomodels/agents/__init__.py,sha256=sn5-fREjMdEvb-OUan3iOqrgYGjplNx3J8hYOaW0Po8,128
 aiagents4pharma/talk2biomodels/agents/t2b_agent.py,sha256=5h4n7dF13KuT5f9vzfK7EQTu_b0a0hB7ScLFlTKaNko,3449
@@ -24,9 +26,9 @@ aiagents4pharma/talk2biomodels/tests/__init__.py,sha256=Jbw5tJxSrjGoaK5IX3pJWDCN
 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_basico_model.py,sha256=y82fpTJMPHwtXxlle1cGQ_2Bewwpxi0aJSVrVAYLhN0,2060
-aiagents4pharma/talk2biomodels/tests/test_get_annotation.py,sha256=mKOacH28OB6xpFPygAlhBUQS93gnI5j-jAfSGu6uQMI,7465
-aiagents4pharma/talk2biomodels/tests/test_getmodelinfo.py,sha256=6kChSc_MCnzXlDao_R8pKdhIELlg3MZrUa7hg8piJ4E,883
-aiagents4pharma/talk2biomodels/tests/test_integration.py,sha256=ZsBXWSFLIcdzrO8obLJx8Ib2f9AAW3BI7H9Eqjdc5to,5057
+aiagents4pharma/talk2biomodels/tests/test_get_annotation.py,sha256=GqS3kCxxTTMTJFjTnJhilrxT6jbNb7Yi0fbaKkadU4E,8159
+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_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
@@ -36,8 +38,8 @@ aiagents4pharma/talk2biomodels/tests/test_sys_bio_model.py,sha256=HSmBBViMi0jYf4
 aiagents4pharma/talk2biomodels/tools/__init__.py,sha256=6H2HWv5Q4NZYEmw-Ti5KZnJlEqhaC2HXSDZa6kiSl-U,350
 aiagents4pharma/talk2biomodels/tools/ask_question.py,sha256=hWXg7o0sTMDWH1ZnxtashTALvXpvNoaomfcniEhw-Bw,4684
 aiagents4pharma/talk2biomodels/tools/custom_plotter.py,sha256=HWwKTX3o4dk0GcRVTO2hPrFSu98mtJ4TKC_hbHXOe1c,4018
-aiagents4pharma/talk2biomodels/tools/get_annotation.py,sha256=jCGkidvafuk1YzAH9GFwaVUF35maXTjg6XqBg_zLk44,12475
-aiagents4pharma/talk2biomodels/tools/get_modelinfo.py,sha256=qA-4FOI-O728Nmn7s8JJ8HKwxvA9MZbst7NkPKTAMV4,5391
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 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
@@ -55,22 +57,6 @@ 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/talk2competitors/__init__.py,sha256=haaikzND3c0Euqq86ndA4fl9q42aOop5rYG_8Zh1D-o,119
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-aiagents4pharma/talk2competitors/state/state_talk2competitors.py,sha256=GUl1ZfM77XsjIEu-3xy4dtvaiMTA1pXf6i1ozVcX5Gg,993
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 aiagents4pharma/talk2knowledgegraphs/__init__.py,sha256=4smVQoSMM6rflVnNkABqlDAAlSn4bYsq7rMVWjRGvis,103
 aiagents4pharma/talk2knowledgegraphs/datasets/__init__.py,sha256=L3gPuHskSegmtXskVrLIYr7FXe_ibKgJ2GGr1_Wok6k,173
 aiagents4pharma/talk2knowledgegraphs/datasets/biobridge_primekg.py,sha256=QlzDXmXREoa9MA6-GwzqRjdzndQeGBAF11Td6NFk_9Y,23426
@@ -96,8 +82,24 @@ aiagents4pharma/talk2knowledgegraphs/utils/embeddings/sentence_transformer.py,sh
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