aiagents4pharma 1.17.0__py3-none-any.whl → 1.18.0__py3-none-any.whl

aiagents4pharma/__init__.py

@@ -3,7 +3,6 @@ This file is used to import aiagents4pharma modules.
 """
 
 from . import (
-    configs,
     talk2biomodels,
     talk2cells,
     talk2scholars,

aiagents4pharma/talk2biomodels/__init__.py

@@ -6,3 +6,4 @@ from . import tools
 from . import agents
 from . import states
 from . import api
+from . import configs

aiagents4pharma/talk2biomodels/agents/t2b_agent.py

@@ -8,6 +8,7 @@ import logging
 from typing import Annotated
 import hydra
 from langchain_openai import ChatOpenAI
+from langchain_core.language_models.chat_models import BaseChatModel
 from langgraph.checkpoint.memory import MemorySaver
 from langgraph.graph import START, StateGraph
 from langgraph.prebuilt import create_react_agent, ToolNode, InjectedState
@@ -26,7 +27,8 @@ from ..states.state_talk2biomodels import Talk2Biomodels
 logging.basicConfig(level=logging.INFO)
 logger = logging.getLogger(__name__)
 
-def get_app(uniq_id, llm_model='gpt-4o-mini'):
+def get_app(uniq_id,
+            llm_model: BaseChatModel = ChatOpenAI(model='gpt-4o-mini', temperature=0)):
     '''
     This function returns the langraph app.
     '''
@@ -51,18 +53,16 @@ def get_app(uniq_id, llm_model='gpt-4o-mini'):
                     QueryArticle()
                 ])
 
-    # Define the model
-    llm = ChatOpenAI(model=llm_model, temperature=0)
     # Load hydra configuration
     logger.log(logging.INFO, "Load Hydra configuration for Talk2BioModels agent.")
-    with hydra.initialize(version_base=None, config_path="../../configs"):
+    with hydra.initialize(version_base=None, config_path="../configs"):
         cfg = hydra.compose(config_name='config',
-                            overrides=['talk2biomodels/agents/t2b_agent=default'])
-        cfg = cfg.talk2biomodels.agents.t2b_agent
+                            overrides=['agents/t2b_agent=default'])
+        cfg = cfg.agents.t2b_agent
     logger.log(logging.INFO, "state_modifier: %s", cfg.state_modifier)
     # Create the agent
     model = create_react_agent(
-                llm,
+                llm_model,
                 tools=tools,
                 state_schema=Talk2Biomodels,
                 state_modifier=cfg.state_modifier,

aiagents4pharma/{configs/talk2biomodels → talk2biomodels/configs}/agents/t2b_agent/default.yaml

@@ -1,4 +1,4 @@
-_target_: talk2biomodels.agents.t2b_agent.get_app
+_target_: agents.t2b_agent.get_app
 state_modifier: >
   You are Talk2BioModels agent.
   If the user asks for the uploaded model, 

aiagents4pharma/{configs/talk2biomodels → talk2biomodels/configs}/tools/ask_question/default.yaml

@@ -1,4 +1,4 @@
-_target_: talk2biomodels.tools.ask_question.AskQuestionTool
+_target_: tools.ask_question.AskQuestionTool
 steady_state_prompt: >
   Following are header columns of the data:
   `species_name`: Name of the species,
@@ -10,22 +10,14 @@ steady_state_prompt: >
 
   Here are some instructions to help you answer questions:
 
-  1. Before you answer any question, follow the plan and solve
-  technique. Start by understanding the question, then plan your
-  approach to solve the question, and finally solve the question
-  by following the plan. Always give a brief explanation of your
-  answer to the user.
+  1. If the user wants to know the time taken by the model to reach
+  steady state, you should look at the `steady_state_transition_time`
+  column of the data for the model species.
+  
+  2. The highest value in the column `steady_state_transition_time`
+  is the time taken by the model to reach steady state.
 
-  2. If the user wants to know the time taken by the model to reach
-  steady state, you should look at the steady_state_transition_time
-  column of the data for the model species. The highest value in
-  this column is the time taken by the model to reach steady state.
-
-  3. To get accurate results, trim the data to the relevant columns
-  before performing any calculations. This will help you avoid
-  errors in your calculations, and ignore irrelevant data.
-
-  4. Please use the units provided below to answer the questions.
+  3. Please use the units provided below to answer the questions.
 simulation_prompt: >
   Following is the information about the data frame:
   1. First column is the time column, and the rest of the columns

aiagents4pharma/{configs/talk2biomodels → talk2biomodels/configs}/tools/get_annotation/default.yaml

@@ -1,4 +1,4 @@
-_target_: talk2biomodels.tools.get_annotation.GetAnnotationTool
+_target_: 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.

aiagents4pharma/talk2biomodels/states/state_talk2biomodels.py

@@ -7,6 +7,8 @@ This is the state file for the Talk2BioModels agent.
 from typing import Annotated
 import operator
 from langgraph.prebuilt.chat_agent_executor import AgentState
+from langchain_core.language_models import BaseChatModel
+from langchain_core.embeddings import Embeddings
 
 def add_data(data1: dict, data2: dict) -> dict:
     """
@@ -26,7 +28,8 @@ class Talk2Biomodels(AgentState):
     """
     The state for the Talk2BioModels agent.
     """
-    llm_model: str
+    llm_model: BaseChatModel
+    text_embedding_model: Embeddings
     pdf_file_name: str
     # A StateGraph may receive a concurrent updates
     # which is not supported by the StateGraph. Hence,

aiagents4pharma/talk2biomodels/tests/test_ask_question.py

@@ -3,6 +3,7 @@ Test cases for Talk2Biomodels.
 '''
 
 from langchain_core.messages import HumanMessage, ToolMessage
+from langchain_openai import ChatOpenAI
 from ..agents.t2b_agent import get_app
 
 def test_ask_question_tool():
@@ -10,7 +11,7 @@ def test_ask_question_tool():
     Test the ask_question tool without the simulation results.
     '''
     unique_id = 12345
-    app = get_app(unique_id, llm_model='gpt-4o-mini')
+    app = get_app(unique_id)
     config = {"configurable": {"thread_id": unique_id}}
 
     ##########################################
@@ -20,7 +21,8 @@ def test_ask_question_tool():
     # case, the tool should return an error
     ##########################################
     # Update state
-    app.update_state(config, {"llm_model": "gpt-4o-mini"})
+    app.update_state(config,
+            {"llm_model": ChatOpenAI(model='gpt-4o-mini', temperature=0)})
     # Define the prompt
     prompt = "Call the ask_question tool to answer the "
     prompt += "question: What is the concentration of CRP "

aiagents4pharma/talk2biomodels/tests/test_get_annotation.py

@@ -5,6 +5,7 @@ Test cases for Talk2Biomodels get_annotation tool.
 import random
 import pytest
 from langchain_core.messages import HumanMessage, ToolMessage
+from langchain_openai import ChatOpenAI
 from ..agents.t2b_agent import get_app
 from ..tools.get_annotation import prepare_content_msg
 
@@ -16,7 +17,9 @@ 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"})
+    graph.update_state(config, {"llm_model": ChatOpenAI(model='gpt-4o-mini',
+                                    temperature=0)
+                                })
     return graph, config
 
 def test_no_model_provided(make_graph):
@@ -85,7 +88,6 @@ def test_invalid_species_provided(make_graph):
                 # (likely due to an invalid species).
                 test_condition = True
                 break
-    # assert test_condition
     assert test_condition
 
 def test_invalid_and_valid_species_provided(make_graph):

aiagents4pharma/talk2biomodels/tests/test_integration.py

@@ -4,8 +4,11 @@ Test cases for Talk2Biomodels.
 
 import pandas as pd
 from langchain_core.messages import HumanMessage, ToolMessage
+from langchain_openai import ChatOpenAI
 from ..agents.t2b_agent import get_app
 
+LLM_MODEL = ChatOpenAI(model='gpt-4o-mini', temperature=0)
+
 def test_integration():
     '''
     Test the integration of the tools.
@@ -13,7 +16,7 @@ def test_integration():
     unique_id = 1234567
     app = get_app(unique_id)
     config = {"configurable": {"thread_id": unique_id}}
-    app.update_state(config, {"llm_model": "gpt-4o-mini"})
+    app.update_state(config, {"llm_model": LLM_MODEL})
     # ##########################################
     # ## Test simulate_model tool
     # ##########################################
@@ -34,7 +37,7 @@ def test_integration():
     # results are available
     ##########################################
     # Update state
-    app.update_state(config, {"llm_model": "gpt-4o-mini"})
+    app.update_state(config, {"llm_model": LLM_MODEL})
     prompt = """What is the concentration of CRP in serum after 100 hours?
     Round off the value to 2 decimal places."""
     # Test the tool get_modelinfo
@@ -49,12 +52,15 @@ def test_integration():
 
     ##########################################
     # Test custom_plotter tool when the
-    # simulation results are available
+    # simulation results are available but
+    # the species is not available
     ##########################################
-    prompt = "Plot only CRP related species."
-
+    prompt = """Call the custom_plotter tool to make a plot
+        showing only species `TP53` and `Pyruvate`. Let me
+        know if these species were not found. Do not
+        invoke any other tool."""
     # Update state
-    app.update_state(config, {"llm_model": "gpt-4o-mini"}
+    app.update_state(config, {"llm_model": LLM_MODEL}
                     )
     # Test the tool get_modelinfo
     response = app.invoke(
@@ -66,11 +72,8 @@ def test_integration():
     # Get the messages from the current state
     # and reverse the order
     reversed_messages = current_state.values["messages"][::-1]
-    # Loop through the reversed messages
-    # until a ToolMessage is found.
-    expected_header = ['Time', 'CRP{serum}', 'CRPExtracellular']
-    expected_header += ['CRP Suppression (%)', 'CRP (% of baseline)']
-    expected_header += ['CRP{liver}']
+    # Loop through the reversed messages until a
+    # ToolMessage is found.
     predicted_artifact = []
     for msg in reversed_messages:
         if isinstance(msg, ToolMessage):
@@ -80,24 +83,17 @@ def test_integration():
             if msg.name == "custom_plotter":
                 predicted_artifact = msg.artifact
                 break
-    # Convert the artifact into a pandas dataframe
-    # for easy comparison
-    df = pd.DataFrame(predicted_artifact)
-    # Extract the headers from the dataframe
-    predicted_header = df.columns.tolist()
-    # Check if the header is in the expected_header
-    # assert expected_header in predicted_artifact
-    assert set(expected_header).issubset(set(predicted_header))
+    # Check if the the predicted artifact is `None`
+    assert predicted_artifact is None
+
     ##########################################
     # Test custom_plotter tool when the
-    # simulation results are available but
-    # the species is not available
+    # simulation results are available
     ##########################################
-    prompt = """Make a custom plot showing the
-        concentration of the species `TP53` over
-        time. Do not show any other species."""
+    prompt = "Plot only CRP related species."
+
     # Update state
-    app.update_state(config, {"llm_model": "gpt-4o-mini"}
+    app.update_state(config, {"llm_model": LLM_MODEL}
                     )
     # Test the tool get_modelinfo
     response = app.invoke(
@@ -105,13 +101,15 @@ def test_integration():
                         config=config
                     )
     assistant_msg = response["messages"][-1].content
-    # print (response["messages"])
     current_state = app.get_state(config)
     # Get the messages from the current state
     # and reverse the order
     reversed_messages = current_state.values["messages"][::-1]
-    # Loop through the reversed messages until a
-    # ToolMessage is found.
+    # Loop through the reversed messages
+    # until a ToolMessage is found.
+    expected_header = ['Time', 'CRP{serum}', 'CRPExtracellular']
+    expected_header += ['CRP Suppression (%)', 'CRP (% of baseline)']
+    expected_header += ['CRP{liver}']
     predicted_artifact = []
     for msg in reversed_messages:
         if isinstance(msg, ToolMessage):
@@ -121,5 +119,11 @@ def test_integration():
             if msg.name == "custom_plotter":
                 predicted_artifact = msg.artifact
                 break
-    # Check if the the predicted artifact is `None`
-    assert predicted_artifact is None
+    # Convert the artifact into a pandas dataframe
+    # for easy comparison
+    df = pd.DataFrame(predicted_artifact)
+    # Extract the headers from the dataframe
+    predicted_header = df.columns.tolist()
+    # Check if the header is in the expected_header
+    # assert expected_header in predicted_artifact
+    assert set(expected_header).issubset(set(predicted_header))

aiagents4pharma/talk2biomodels/tests/test_query_article.py

@@ -5,6 +5,7 @@ Test cases for Talk2Biomodels query_article tool.
 from pydantic import BaseModel, Field
 from langchain_core.messages import HumanMessage, ToolMessage
 from langchain_openai import ChatOpenAI
+from langchain_nvidia_ai_endpoints import NVIDIAEmbeddings
 from ..agents.t2b_agent import get_app
 
 class Article(BaseModel):
@@ -21,8 +22,10 @@ def test_query_article_with_an_article():
     app = get_app(unique_id)
     config = {"configurable": {"thread_id": unique_id}}
     # Update state by providing the pdf file name
+    # and the text embedding model
     app.update_state(config,
-      {"pdf_file_name": "aiagents4pharma/talk2biomodels/tests/article_on_model_537.pdf"})
+      {"pdf_file_name": "aiagents4pharma/talk2biomodels/tests/article_on_model_537.pdf",
+       "text_embedding_model": NVIDIAEmbeddings(model='nvidia/llama-3.2-nv-embedqa-1b-v2')})
     prompt = "What is the title of the article?"
     # Test the tool query_article
     response = app.invoke(
@@ -55,6 +58,9 @@ def test_query_article_without_an_article():
     app = get_app(unique_id)
     config = {"configurable": {"thread_id": unique_id}}
     prompt = "What is the title of the uploaded article?"
+    # Update state by providing the text embedding model
+    app.update_state(config,
+      {"text_embedding_model": NVIDIAEmbeddings(model='nvidia/llama-3.2-nv-embedqa-1b-v2')})
     # Test the tool query_article
     app.invoke(
             {"messages": [HumanMessage(content=prompt)]},

aiagents4pharma/talk2biomodels/tests/test_search_models.py

@@ -3,6 +3,7 @@ Test cases for Talk2Biomodels search models tool.
 '''
 
 from langchain_core.messages import HumanMessage
+from langchain_nvidia_ai_endpoints import ChatNVIDIA
 from ..agents.t2b_agent import get_app
 
 def test_search_models_tool():
@@ -13,7 +14,8 @@ def test_search_models_tool():
     app = get_app(unique_id)
     config = {"configurable": {"thread_id": unique_id}}
     # Update state
-    app.update_state(config, {"llm_model": "gpt-4o-mini"})
+    app.update_state(config,
+            {"llm_model": ChatNVIDIA(model="meta/llama-3.3-70b-instruct")})
     prompt = "Search for models on Crohn's disease."
     # Test the tool get_modelinfo
     response = app.invoke(

aiagents4pharma/talk2biomodels/tests/test_steady_state.py

@@ -3,8 +3,11 @@ Test cases for Talk2Biomodels steady state tool.
 '''
 
 from langchain_core.messages import HumanMessage, ToolMessage
+from langchain_openai import ChatOpenAI
 from ..agents.t2b_agent import get_app
 
+LLM_MODEL = ChatOpenAI(model='gpt-4o-mini', temperature=0)
+
 def test_steady_state_tool():
     '''
     Test the steady_state tool.
@@ -12,7 +15,7 @@ def test_steady_state_tool():
     unique_id = 123
     app = get_app(unique_id)
     config = {"configurable": {"thread_id": unique_id}}
-    app.update_state(config, {"llm_model": "gpt-4o-mini"})
+    app.update_state(config, {"llm_model": LLM_MODEL})
     #########################################################
     # In this case, we will test if the tool returns an error
     # when the model does not achieve a steady state. The tool
@@ -37,8 +40,8 @@ def test_steady_state_tool():
     #########################################################
     # In this case, we will test if the tool is indeed invoked
     # successfully
-    prompt = """Run a steady state analysis of model 64.
-    Set the initial concentration of `Pyruvate` to 0.2. The
+    prompt = """Bring model 64 to a steady state. Set the
+    initial concentration of `Pyruvate` to 0.2. The
     concentration of `NAD` resets to 100 every 2 time units."""
     # Invoke the agent
     app.invoke(

aiagents4pharma/talk2biomodels/tools/ask_question.py

@@ -12,7 +12,6 @@ import pandas as pd
 from pydantic import BaseModel, Field
 from langchain_core.tools.base import BaseTool
 from langchain_experimental.agents import create_pandas_dataframe_agent
-from langchain_openai import ChatOpenAI
 from langgraph.prebuilt import InjectedState
 
 # Initialize logger
@@ -66,10 +65,10 @@ class AskQuestionTool(BaseTool):
                    question_context,
                    experiment_name)
         # Load hydra configuration
-        with hydra.initialize(version_base=None, config_path="../../configs"):
+        with hydra.initialize(version_base=None, config_path="../configs"):
             cfg = hydra.compose(config_name='config',
-                                overrides=['talk2biomodels/tools/ask_question=default'])
-            cfg = cfg.talk2biomodels.tools.ask_question
+                                overrides=['tools/ask_question=default'])
+            cfg = cfg.tools.ask_question
         # Get the context of the question
         # and based on the context, get the data
         # and prompt content to ask the question
@@ -101,7 +100,7 @@ class AskQuestionTool(BaseTool):
         prompt_content += f"{basico.model_info.get_model_units()}\n\n"
         # Create a pandas dataframe agent
         df_agent = create_pandas_dataframe_agent(
-                        ChatOpenAI(model=state['llm_model']),
+                        state['llm_model'],
                         allow_dangerous_code=True,
                         agent_type='tool-calling',
                         df=df,
@@ -111,5 +110,6 @@ class AskQuestionTool(BaseTool):
                         verbose=True,
                         prefix=prompt_content)
         # Invoke the agent with the question
-        llm_result = df_agent.invoke(question)
+        llm_result = df_agent.invoke(question, stream_mode=None)
+        # print (llm_result)
         return llm_result["output"]

aiagents4pharma/talk2biomodels/tools/custom_plotter.py

@@ -5,10 +5,9 @@ Tool for plotting a custom figure.
 """
 
 import logging
-from typing import Type, List, TypedDict, Annotated, Tuple, Union, Literal
+from typing import Type, Annotated, List, Tuple, Union, Literal
 from pydantic import BaseModel, Field
 import pandas as pd
-from langchain_openai import ChatOpenAI
 from langchain_core.tools import BaseTool
 from langgraph.prebuilt import InjectedState
 
@@ -71,30 +70,44 @@ class CustomPlotterTool(BaseTool):
         species_names = df.columns.tolist()
         # Exclude the time column
         species_names.remove('Time')
+        logging.log(logging.INFO, "Species names: %s", species_names)
         # In the following code, we extract the species
         # from the user question. We use Literal to restrict
         # the species names to the ones available in the
         # simulation results.
-        class CustomHeader(TypedDict):
+        class CustomHeader(BaseModel):
             """
             A list of species based on user question.
+
+            This is a Pydantic model that restricts the species
+            names to the ones available in the simulation results.
+            
+            If no species is relevant, set the attribute
+            `relevant_species` to None.
             """
             relevant_species: Union[None, List[Literal[*species_names]]] = Field(
-                    description="""List of species based on user question.
-                    If no relevant species are found, it will be None.""")
+                    description="This is a list of species based on the user question."
+                    "It is restricted to the species available in the simulation results."
+                    "If no species is relevant, set this attribute to None."
+                    "If the user asks for very specific species (for example, using the"
+                    "keyword `only` in the question), set this attribute to correspond "
+                    "to the species available in the simulation results, otherwise set it to None."
+                    )
         # Create an instance of the LLM model
-        llm = ChatOpenAI(model=state['llm_model'], temperature=0)
+        logging.log(logging.INFO, "LLM model: %s", state['llm_model'])
+        llm = state['llm_model']
         llm_with_structured_output = llm.with_structured_output(CustomHeader)
         results = llm_with_structured_output.invoke(question)
+        if results.relevant_species is None:
+            raise ValueError("No species found in the simulation results \
+                             that matches the user prompt.")
         extracted_species = []
         # Extract the species from the results
         # that are available in the simulation results
-        for species in results['relevant_species']:
+        for species in results.relevant_species:
             if species in species_names:
                 extracted_species.append(species)
-        logger.info("Extracted species: %s", extracted_species)
-        if len(extracted_species) == 0:
-            return "No species found in the simulation results that matches the user prompt.", None
+        logging.info("Extracted species: %s", extracted_species)
         # Include the time column
         extracted_species.insert(0, 'Time')
         return f"Custom plot {simulation_name}", df[extracted_species].to_dict(orient='records')

aiagents4pharma/talk2biomodels/tools/get_annotation.py

@@ -5,7 +5,7 @@ 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, TypedDict, Union, Literal
+from typing import List, Annotated, Type, Union, Literal
 import logging
 from dataclasses import dataclass
 import hydra
@@ -17,7 +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 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
@@ -34,10 +34,10 @@ 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"):
+    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
+                            overrides=['tools/get_annotation=default'])
+        cfg = cfg.tools.get_annotation
     logger.info("Loaded the following system prompt for the LLM"
                 " to get a structured output: %s", cfg.prompt)
 
@@ -49,7 +49,7 @@ def extract_relevant_species_names(model_object, arg_data, state):
     all_species_names = df_species.index.tolist()
 
     # Define a structured output for the LLM model
-    class CustomHeader(TypedDict):
+    class CustomHeader(BaseModel):
         """
         A list of species based on user question.
         """
@@ -58,17 +58,21 @@ def extract_relevant_species_names(model_object, arg_data, state):
                 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)
+    llm = state['llm_model']
     # 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)
+    results = llm_with_structured_output.invoke(question)
+    logging.info("Results from the LLM model: %s", results)
+    # Check if the returned species names are empty
+    if not results.relevant_species:
+        raise ValueError("Model does not contain the requested species.")
     extracted_species = []
     # Extract all the species names from the model
-    for species in dic['relevant_species']:
+    for species in results.relevant_species:
         if species in all_species_names:
             extracted_species.append(species)
     logger.info("Extracted species: %s", extracted_species)
@@ -136,10 +140,7 @@ class GetAnnotationTool(BaseTool):
 
         # Extract relevant species names based on the user question
         list_species_names = extract_relevant_species_names(model_object, arg_data, state)
-
-        # Check if the returned species names are empty
-        if not list_species_names:
-            raise ValueError("Model does not contain the requested species.")
+        print (list_species_names)
 
         (annotations_df,
          species_without_description) = self._fetch_annotations(list_species_names)

aiagents4pharma/talk2biomodels/tools/query_article.py

@@ -9,7 +9,6 @@ from typing import Type, Annotated
 from pydantic import BaseModel, Field
 from langchain_core.tools import BaseTool
 from langchain_core.vectorstores import InMemoryVectorStore
-from langchain_openai.embeddings import OpenAIEmbeddings
 from langchain_community.document_loaders import PyPDFLoader
 from langgraph.prebuilt import InjectedState
 
@@ -51,8 +50,13 @@ class QueryArticle(BaseTool):
         pages = []
         for page in loader.lazy_load():
             pages.append(page)
+        # Set up text embedding model
+        text_embedding_model = state['text_embedding_model']
+        logging.info("Loaded text embedding model %s", text_embedding_model)
         # Create a vector store from the pages
-        vector_store = InMemoryVectorStore.from_documents(pages, OpenAIEmbeddings())
+        vector_store = InMemoryVectorStore.from_documents(
+                                            pages,
+                                            text_embedding_model)
         # Search the article with the question
         docs = vector_store.similarity_search(question)
         # Return the content of the pages

aiagents4pharma/talk2biomodels/tools/search_models.py

@@ -5,14 +5,18 @@ Tool for searching models based on search query.
 """
 
 from typing import Type, Annotated
+import logging
 from pydantic import BaseModel, Field
 from basico import biomodels
 from langchain_core.tools import BaseTool
 from langchain_core.output_parsers import StrOutputParser
 from langchain_core.prompts import ChatPromptTemplate
-from langchain_openai import ChatOpenAI
 from langgraph.prebuilt import InjectedState
 
+# Initialize logger
+logging.basicConfig(level=logging.INFO)
+logger = logging.getLogger(__name__)
+
 class SearchModelsInput(BaseModel):
     """
     Input schema for the search models tool.
@@ -29,7 +33,7 @@ class SearchModelsTool(BaseTool):
     name: str = "search_models"
     description: str = "Search models in the BioMmodels database based on keywords."
     args_schema: Type[BaseModel] = SearchModelsInput
-    return_direct: bool = True
+    return_direct: bool = False
 
     def _run(self,
              query: str,
@@ -43,8 +47,10 @@ class SearchModelsTool(BaseTool):
         Returns:
             dict: The answer to the question in the form of a dictionary.
         """
+        logger.log(logging.INFO, "Searching models with the query and model: %s, %s",
+                   query, state['llm_model'])
         search_results = biomodels.search_for_model(query)
-        llm = ChatOpenAI(model=state['llm_model'])
+        llm = state['llm_model']
         # Check if run_manager's metadata has the key 'prompt_content'
         prompt_content = f'''
                         Convert the input into a table.

aiagents4pharma-1.18.0.dist-info/METADATA

@@ -0,0 +1,157 @@
+Metadata-Version: 2.2
+Name: aiagents4pharma
+Version: 1.18.0
+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
+Requires-Python: >=3.12
+Description-Content-Type: text/markdown
+License-File: LICENSE
+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: huggingface_hub==0.26.5
+Requires-Dist: hydra-core==1.3.2
+Requires-Dist: joblib==1.4.2
+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
+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: plotly==5.24.1
+Requires-Dist: pydantic==2.9.2
+Requires-Dist: pylint==3.3.1
+Requires-Dist: pypdf==5.2.0
+Requires-Dist: pytest==8.3.3
+Requires-Dist: pytest-asyncio==0.25.2
+Requires-Dist: streamlit==1.39.0
+Requires-Dist: sentence_transformers==3.3.1
+Requires-Dist: tabulate==0.9.0
+Requires-Dist: torch==2.2.2
+Requires-Dist: torch_geometric==2.6.1
+Requires-Dist: tqdm==4.66.6
+Requires-Dist: transformers==4.48.0
+Requires-Dist: mkdocs==1.6.1
+Requires-Dist: mkdocs-jupyter==0.25.1
+Requires-Dist: mkdocs-material==9.5.47
+Requires-Dist: mkdocstrings-python==1.12.2
+Requires-Dist: mkdocs-include-markdown-plugin==7.1.2
+Requires-Dist: mkdocstrings==0.27.0
+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)
+[![TESTS 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)
+
+
+## Introduction
+
+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.
+
+Our toolkit currently consists of the following agents:
+
+- **Talk2BioModels** _(v1 released; v2 in progress)_: Engage directly with mathematical models in systems biology.
+- **Talk2KnowledgeGraphs** _(v1 in progress)_: Access and explore complex biological knowledge graphs for insightful data connections.
+- **Talk2Scholars** _(v1 in progress)_: Get recommendations for articles related to your choice. Download, query, and write/retrieve them to your reference manager (currently supporting Zotero).
+- **Talk2Cells** _(v1 in progress)_: Query and analyze sequencing data with ease.
+
+![AIAgents4Pharma](docs/assets/AIAgents4Pharma.png)
+
+## Getting Started
+
+![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)
+
+### Installation
+
+#### Option 1: PyPI
+
+```bash
+pip install aiagents4pharma
+```
+
+Check out the tutorials on each agent for detailed instrcutions.
+
+#### Option 2: git
+
+1. **Clone the repository:**
+   ```bash
+   git clone https://github.com/VirtualPatientEngine/AIAgents4Pharma
+   cd AIAgents4Pharma
+   ```
+2. **Install dependencies:**
+   ```bash
+   pip install .
+   ```
+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
+   export LANGCHAIN_API_KEY=<your-api-key>
+   ```
+_Please note that this will create a new tracing project in your Langsmith
+account with the name `T2X-xxxx`, where `X` can be `B` (Biomodels), `S` (Scholars),
+`KG` (KnowledgeGraphs), or `C` (Cells). If you skip the previous step, it will
+default to the name `default`. `xxxx` will be the 4-digit ID created for the
+session._
+
+5. **Launch the app:**
+   ```bash
+   streamlit run app/frontend/streamlit_app_<agent>.py
+   ```
+_Replace <agent> with the agent name you are interested to launch._
+
+For detailed instructions on each agent, please refer to their respective modules.
+
+---
+
+## Contributing
+
+We welcome contributions to AIAgents4Pharma! Here’s how you can help:
+
+1. **Fork the repository**
+2. **Create a new branch** for your feature (`git checkout -b feat/feature-name`)
+3. **Commit your changes** (`git commit -m 'feat: Add new feature'`)
+4. **Push to the branch** (`git push origin feat/feature-name`)
+5. **Open a pull request** and reach out to any one of us below via Discussions:
+
+   _Note: We welcome all contributions, not just programming-related ones. Feel free to open bug reports, suggest new features, or participate as a beta tester. Your support is greatly appreciated!_
+
+- **Talk2Biomodels/Talk2Cells**: [@gurdeep330](https://github.com/gurdeep330) [@lilijap](https://github.com/lilijap) [@dmccloskey](https://github.com/dmccloskey)
+- **Talk2KnowledgeGraphs**: [@awmulyadi](https://github.com/awmulyadi) [@dmccloskey](https://github.com/dmccloskey)
+- **Talk2Scholars**: [@ansh-info](https://github.com/ansh-info) [@gurdeep330](https://github.com/gurdeep330) [@dmccloskey](https://github.com/dmccloskey)
+
+### Current Needs
+
+- **Beta testers** for Talk2BioModels and Talk2Scholars.
+- **Developers** with experience in Python and Bioinformatics and/or knowledge graphs for contributions to AIAgents4Pharma.
+
+Feel free to reach out to us via Discussions.
+
+Check out our [CONTRIBUTING.md](CONTRIBUTING.md) for more information.
+
+---
+
+## Feedback
+
+Questions/Bug reports/Feature requests/Comments/Suggestions? We welcome all. Please use `Isssues` or `Discussions` 😀

{aiagents4pharma-1.17.0.dist-info → aiagents4pharma-1.18.0.dist-info}/RECORD

@@ -1,50 +1,48 @@
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-aiagents4pharma/configs/__init__.py,sha256=hNkSrXw1Ix1HhkGn_aaidr2coBYySfM0Hm_pMeRcX7k,76
-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=B08KWjj7bpizuTETGnnngrEVK4nzdWGREdoCCSw1Sm4,102
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-aiagents4pharma/talk2biomodels/__init__.py,sha256=2ICwVh1u07SZv31Jd2DKHobauOxWNWY29_Gqq3kOnNQ,159
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 aiagents4pharma/talk2biomodels/agents/__init__.py,sha256=sn5-fREjMdEvb-OUan3iOqrgYGjplNx3J8hYOaW0Po8,128
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 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
 aiagents4pharma/talk2biomodels/api/uniprot.py,sha256=aPUAVBR7UYXDuuhDpKezAK2aTMzo-NxFYFq6C0W5u6U,1175
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-aiagents4pharma/talk2biomodels/tools/search_models.py,sha256=Iq2ddofOOfZYtAurCISq3bAq5rbwB3l_rL1lgEFyFCI,2653
+aiagents4pharma/talk2biomodels/tools/query_article.py,sha256=6xfirRRMXN-wxqZxYYbKeEMXLMAHKl5IPShfpoOEBcc,2268
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 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
@@ -114,8 +112,8 @@ 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
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aiagents4pharma/configs/__init__.py

@@ -1,5 +0,0 @@
-'''
-Import all the modules in the package
-'''
-
-from . import talk2biomodels

aiagents4pharma/configs/config.yaml

@@ -1,5 +0,0 @@
-defaults:
-  - _self_
-  - talk2biomodels/agents/t2b_agent: default
-  - talk2biomodels/tools/ask_question: default
-  - talk2biomodels/tools/get_annotation: default

aiagents4pharma-1.17.0.dist-info/METADATA

@@ -1,212 +0,0 @@
-Metadata-Version: 2.2
-Name: aiagents4pharma
-Version: 1.17.0
-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
-Requires-Python: >=3.12
-Description-Content-Type: text/markdown
-License-File: LICENSE
-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: huggingface_hub==0.26.5
-Requires-Dist: hydra-core==1.3.2
-Requires-Dist: joblib==1.4.2
-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-openai==0.2.5
-Requires-Dist: langchain_ollama==0.2.2
-Requires-Dist: langgraph==0.2.66
-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: plotly==5.24.1
-Requires-Dist: pydantic==2.9.2
-Requires-Dist: pylint==3.3.1
-Requires-Dist: pypdf==5.2.0
-Requires-Dist: pytest==8.3.3
-Requires-Dist: pytest-asyncio==0.25.2
-Requires-Dist: streamlit==1.39.0
-Requires-Dist: sentence_transformers==3.3.1
-Requires-Dist: tabulate==0.9.0
-Requires-Dist: torch==2.2.2
-Requires-Dist: torch_geometric==2.6.1
-Requires-Dist: tqdm==4.66.6
-Requires-Dist: transformers==4.48.0
-Requires-Dist: mkdocs==1.6.1
-Requires-Dist: mkdocs-jupyter==0.25.1
-Requires-Dist: mkdocs-material==9.5.47
-Requires-Dist: mkdocstrings-python==1.12.2
-Requires-Dist: mkdocs-include-markdown-plugin==7.1.2
-Requires-Dist: mkdocstrings==0.27.0
-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)
-[![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.
-
-Our toolkit currently consists of three intelligent agents, each designed to simplify and enhance access to specialized data in biology:
-
-- **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.
-- **Talk2Scholars** _(Coming soon)_: Get recommendations for articles related to your choice. Download, query, and write/retrieve them to your reference manager (currently supporting Zotero).
-
----
-
-## Overview of Agents
-
-### 1. Talk2BioModels
-
-**Talk2BioModels** is an AI agent designed to facilitate interaction with mathematical models in systems biology. Systems biology models are critical in understanding complex biological mechanisms, but they’re often inaccessible to those without coding or mathematical expertise. Talk2BioModels simplifies this, enabling researchers to focus on analysis and interpretation rather than on programming. With Talk2BioModels, users can interact directly with these models through natural language. By simply asking questions or making requests, users can:
-
-- Forward simulation of both internal and open-source models (BioModels).
-- Adjust parameters within the model to simulate different conditions.
-- Query simulation results.
-- Extract model information such as species, parameters, units and description.
-
-### 2. Talk2Cells _(Work in Progress)_
-
-**Talk2Cells** is being developed to provide direct access to and analysis of sequencing data, such as RNA-Seq or DNA-Seq, using natural language.
-
-### 3. Talk2KnowledgeGraphs _(Work in Progress)_
-
-**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. 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
-
-![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)
-
-### Installation
-
-#### Option 1: PyPI
-
-```bash
-pip install aiagents4pharma
-```
-
-Check out the tutorials on each agent for detailed instrcutions.
-
-#### Option 2: git
-
-1. **Clone the repository:**
-
-   ```bash
-   git clone https://github.com/VirtualPatientEngine/AIAgents4Pharma
-   cd AIAgents4Pharma
-   ```
-
-2. **Install dependencies:**
-
-   ```bash
-   pip install .
-   ```
-
-3. **Initialize OPENAI_API_KEY**
-
-   ```bash
-   export OPENAI_API_KEY=....
-   ```
-
-4. **[Optional] Set up login credentials**
-
-   ```bash
-   vi .streamlit/secrets.toml
-   ```
-
-   and enter
-
-   ```
-   password='XXX'
-   ```
-
-   Please note that the passoword will be same for all the users.
-
-5. **[Optional] Initialize LANGSMITH_API_KEY**
-
-   ```bash
-   export LANGCHAIN_TRACING_V2=true
-   export LANGCHAIN_API_KEY=<your-api-key>
-   ```
-
-   Please note that this will create a new tracing project in your Langsmith
-   account with the name `<user_name>@<uuid>`, where `user_name` is the name
-   you provided in the previous step. If you skip the previous step, it will
-   default to `default`. <uuid> will be the 128 bit unique ID created for the
-   session.
-
-6. **Launch the app:**
-   ```bash
-   streamlit run app/frontend/streamlit_app.py
-   ```
-
-For detailed instructions on each agent, please refer to their respective folders.
-
----
-
-## Usage
-
-**Talk2BioModels** currently provides an interactive console where you can enter natural language queries to simulate models, adjust parameters, and query the simulated results.
-
-More detailed usage examples, including sample data for Talk2Cells and Talk2KnowledgeGraphs, will be provided as development progresses.
-
----
-
-## Contributing
-
-We welcome contributions to AIAgents4Pharma! Here’s how you can help:
-
-1. **Fork the repository**
-2. **Create a new branch** for your feature (`git checkout -b feat/feature-name`)
-3. **Commit your changes** (`git commit -m 'feat: Add new feature'`)
-4. **Push to the branch** (`git push origin feat/feature-name`)
-5. **Open a pull request**
-
-### Current Needs
-
-- **Beta testers** for Talk2BioModels.
-- **Developers** with experience in natural language processing, bioinformatics, or knowledge graphs for contributions to AIAgents4Pharma.
-
-Check out our [CONTRIBUTING.md](CONTRIBUTING.md) for more information.
-
----
-
-## Roadmap
-
-### Completed
-
-- **Talk2BioModels**: Initial release with core capabilities for interacting with systems biology models.
-
-### Planned
-
-- **User Interface**: Interactive web UI for all agents.
-- **Talk2Cells**: Integration of sequencing data analysis tools.
-- **Talk2KnowledgeGraphs**: Interface for biological knowledge graph interaction.
-- **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.
-
-**Get Started** with AIAgents4Pharma today and transform the way you interact with biological data.
-
----
-
-## Feedback
-
-Questions/Bug reports/Feature requests/Comments/Suggestions? We welcome all. Please use the `Isssues` tab 😀