aiagents4pharma 1.18.0__tar.gz → 1.19.1__tar.gz

{aiagents4pharma-1.18.0 → aiagents4pharma-1.19.1}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.2
 Name: aiagents4pharma
-Version: 1.18.0
+Version: 1.19.1
 Summary: AI Agents for drug discovery, drug development, and other pharmaceutical R&D.
 Classifier: Programming Language :: Python :: 3
 Classifier: License :: OSI Approved :: MIT License
@@ -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
@@ -27,6 +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

{aiagents4pharma-1.18.0 → aiagents4pharma-1.19.1}/aiagents4pharma/talk2knowledgegraphs/__init__.py

@@ -1,5 +1,8 @@
 '''
 This file is used to import the datasets and utils.
 '''
+from . import agents
 from . import datasets
+from . import states
+from . import tools
 from . import utils

aiagents4pharma-1.19.1/aiagents4pharma/talk2knowledgegraphs/agents/__init__.py

@@ -0,0 +1,4 @@
+'''
+This file is used to import all the models in the package.
+'''
+from . import t2kg_agent

aiagents4pharma-1.19.1/aiagents4pharma/talk2knowledgegraphs/agents/t2kg_agent.py

@@ -0,0 +1,85 @@
+'''
+This is the agent file for the Talk2KnowledgeGraphs agent.
+'''
+
+import logging
+from typing import Annotated
+import hydra
+from langchain_ollama import ChatOllama
+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
+from ..tools.subgraph_extraction import SubgraphExtractionTool
+from ..tools.subgraph_summarization import SubgraphSummarizationTool
+from ..tools.graphrag_reasoning import GraphRAGReasoningTool
+from ..states.state_talk2knowledgegraphs import Talk2KnowledgeGraphs
+
+# Initialize logger
+logging.basicConfig(level=logging.INFO)
+logger = logging.getLogger(__name__)
+
+def get_app(uniq_id, llm_model: BaseChatModel=ChatOllama(model='llama3.2:1b', temperature=0.0)):
+    '''
+    This function returns the langraph app.
+    '''
+    def agent_t2kg_node(state: Annotated[dict, InjectedState]):
+        '''
+        This function calls the model.
+        '''
+        logger.log(logging.INFO, "Calling t2kg_agent node with thread_id %s", uniq_id)
+        response = model.invoke(state, {"configurable": {"thread_id": uniq_id}})
+
+        return response
+
+    # Load hydra configuration
+    logger.log(logging.INFO, "Load Hydra configuration for Talk2KnowledgeGraphs agent.")
+    with hydra.initialize(version_base=None, config_path="../configs"):
+        cfg = hydra.compose(config_name='config',
+                            overrides=['agents/t2kg_agent=default'])
+        cfg = cfg.agents.t2kg_agent
+
+    # Define the tools
+    subgraph_extraction = SubgraphExtractionTool()
+    subgraph_summarization = SubgraphSummarizationTool()
+    graphrag_reasoning = GraphRAGReasoningTool()
+    tools = ToolNode([
+                    subgraph_extraction,
+                    subgraph_summarization,
+                    graphrag_reasoning,
+                    ])
+
+    # Create the agent
+    model = create_react_agent(
+                llm_model,
+                tools=tools,
+                state_schema=Talk2KnowledgeGraphs,
+                state_modifier=cfg.state_modifier,
+                checkpointer=MemorySaver()
+            )
+
+    # Define a new graph
+    workflow = StateGraph(Talk2KnowledgeGraphs)
+
+    # Define the two nodes we will cycle between
+    workflow.add_node("agent_t2kg", agent_t2kg_node)
+
+    # Set the entrypoint as the first node
+    # This means that this node is the first one called
+    workflow.add_edge(START, "agent_t2kg")
+
+    # Initialize memory to persist state between graph runs
+    checkpointer = MemorySaver()
+
+    # Finally, we compile it!
+    # This compiles it into a LangChain Runnable,
+    # meaning you can use it as you would any other runnable.
+    # Note that we're (optionally) passing the memory
+    # when compiling the graph
+    app = workflow.compile(checkpointer=checkpointer)
+    logger.log(logging.INFO,
+               "Compiled the graph with thread_id %s and llm_model %s",
+               uniq_id,
+               llm_model)
+
+    return app

aiagents4pharma-1.19.1/aiagents4pharma/talk2knowledgegraphs/configs/__init__.py

@@ -0,0 +1,7 @@
+'''
+Import all the modules in the package
+'''
+
+from . import agents
+from . import tools
+from . import app

aiagents4pharma-1.19.1/aiagents4pharma/talk2knowledgegraphs/configs/agents/t2kg_agent/__init__.py

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

aiagents4pharma-1.19.1/aiagents4pharma/talk2knowledgegraphs/configs/agents/t2kg_agent/default.yaml

@@ -0,0 +1,62 @@
+_target_: agents.t2kg_agent.get_app
+state_modifier: >
+  You are talk2knowledgegraphs agent, a helpful assistant for reasoning over knowledge graphs.
+  User can ask questions related to the knowledge graphs, and you will provide the answers using 
+  the provided tools as follows (if necessary):
+  [`subgraph_extraction`, `subgraph_summarization`, `graphrag_reasoning`].
+
+  **Tools Descriptions**:
+  - `subgraph_extraction`: Extract a subgraph from the knowledge graph that contains the relevant
+    information to answer the user's query. This tool can be used to provide a subgraph context
+    as a part of the reasoning process. The extracted subgraph should contain the most relevant
+    nodes and edges to the user's query in the form of a textualized subgraph.
+  - `subgraph_summarization`: Summarize the extracted textualized subgraph obtained from the
+    `subgraph_extraction` tool. This tool can be used to provide a concise and informative summary
+    of the subgraph to be used for reasoning as subgraph context. This tool highlights the most
+    important nodes and edges in the subgraph to respond to the user's request.
+  - `graphrag_reasoning`: Reason over the extracted textualized subgraph to answer the user's
+    prompt by also considering the context from the extracted subgraph and the retrieved
+    documents. User may also have a set of uploaded files that can be used to provide additional
+    information for reasoning. The history of previous conversations should be considered as well, 
+    and you as an agent should provide which conversations can be included as chat history.
+
+  As an agent, you should approach each request by first understanding the user's query and then 
+  following the appropriate steps to provide the best answer possible. 
+
+  **Execution Steps**:
+  - Understand thoroughly the user's query and think over the best approach to answer it.
+  - You may not need to call any tool for each user's query. Use the related tool(s) as needed. 
+    Think deeply whether it is necessary to call any tool to respond to the user's request.
+  - Call `subgraph_extraction` if there is any indication that the user needs to get the
+    information from the knowledge graph, which is not directly available as context in the prompt or
+    in the previous extracted subgraph. 
+    If the user asks for subgraph extraction, suggest a value for the `extraction_name` argument.
+    You should always follow it with `subgraph_summarization` as the next tool to be invoked.
+  - Call `subgraph_summarization` tool to summarize the extracted subgraph and provide
+    a useful insights over the subgraph. This tool also has the ability to filter endotypes
+    in the forms of differentially expressed genes that are relevant to the input query. Make sure
+    to include the most relevant genes if the user provides endotype-related documents.
+    The summary of the subgraph will be stored as `graph_summary` in the state in which you can use
+    it for reasoning over the subgraph in the `graphrag_reasoning` tool afterwards.
+  - If the user asks follow-up questions related to the extracted subgraph, you should
+    call `subgraph_summarization` followed by `graphrag_reasoning` tools if you think
+    the answer can be retrieved from the previously extracted subgraph.
+  - Call `graphrag_reasoning` tool to reason over the extracted subgraph and documents.
+    Always perform reasoning over the extracted subgraph and documents to provide
+    the best possible answer to the user's query. Before calling this tool, 
+    make sure you have access to the summarized subgraph obtained from `subgraph_summarization` tool.
+  - By default, if the user asks for a specific question about the extracted graph, you should
+    call `subgraph_summarization` followed by `graphrag_reasoning` if the most recent subgraphs
+    contain the relevant information to answer the user's question.
+    Use the summarized subgraph as the subgraph context in the `graphrag_reasoning` tool.
+  - It is strongly recommended to avoid calling the same tool multiple times unless
+    it is necessary to get the correct and thorough answer to the user's request.
+
+  **Tool Calling Workflow Examples**:
+  - `subgraph_extraction` -> `subgraph_summarization` -> `graphrag_reasoning` when the user asks
+  for specific instructions to extract the subgraph and reason over it. Follow this order to
+  provide the most accurate and relevant information if you think the currently available context
+  is not enough to answer the user's question.
+  - `subgraph_summarization` -> `graphrag_reasoning` when the user asks for the previously extracted
+  subgraph. Use the summarized subgraph as the subgraph context in the `graphrag_reasoning` tool.
+  - Do not call `graphrag_reasoning` tool without calling `subgraph_summarization` tool first.

aiagents4pharma-1.19.1/aiagents4pharma/talk2knowledgegraphs/configs/app/__init__.py

@@ -0,0 +1,4 @@
+'''
+Import all the modules in the package
+'''
+from . import frontend

aiagents4pharma-1.19.1/aiagents4pharma/talk2knowledgegraphs/configs/app/frontend/__init__.py

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

aiagents4pharma-1.19.1/aiagents4pharma/talk2knowledgegraphs/configs/app/frontend/default.yaml

@@ -0,0 +1,31 @@
+_target_: app.frontend.streamlit_app_talk2knowledgegraphs
+default_user: "talk2kg_user"
+data_package_allowed_file_types:
+  - "pdf"
+endotype_allowed_file_types:
+  - "pdf"
+upload_data_dir: "../files"
+kg_name: "PrimeKG"
+kg_pyg_path: "aiagents4pharma/talk2knowledgegraphs/tests/files/primekg_ibd_pyg_graph.pkl"
+kg_text_path: "aiagents4pharma/talk2knowledgegraphs/tests/files/primekg_ibd_text_graph.pkl"
+openai_api_key: ${oc.env:OPENAI_API_KEY}
+openai_llms:
+  - "gpt-4o-mini"
+  - "gpt-4-turbo"
+  - "gpt-3.5-turbo"
+openai_embeddings:
+  - "text-embedding-3-small"
+ollama_llms:
+  - "llama3.2:1b"
+  - "llama3.2"
+  - "llama3.1"
+ollama_embeddings:
+  - "nomic-embed-text"
+temperature: 0.1
+streaming: False
+reasoning_subgraph_topk_nodes: 10
+reasoning_subgraph_topk_nodes_min: 1
+reasoning_subgraph_topk_nodes_max: 100
+reasoning_subgraph_topk_edges: 10
+reasoning_subgraph_topk_edges_min: 1
+reasoning_subgraph_topk_edges_max: 100

aiagents4pharma-1.19.1/aiagents4pharma/talk2knowledgegraphs/configs/config.yaml

@@ -0,0 +1,7 @@
+defaults:
+  - _self_
+  - agents/t2kg_agent: default
+  - tools/subgraph_extraction: default
+  - tools/subgraph_summarization: default
+  - tools/graphrag_reasoning: default
+  - app/frontend: default

aiagents4pharma-1.19.1/aiagents4pharma/talk2knowledgegraphs/configs/tools/__init__.py

@@ -0,0 +1,6 @@
+'''
+Import all the modules in the package
+'''
+from . import subgraph_extraction
+from . import subgraph_summarization
+from . import graphrag_reasoning

aiagents4pharma-1.19.1/aiagents4pharma/talk2knowledgegraphs/configs/tools/graphrag_reasoning/__init__.py

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

aiagents4pharma-1.19.1/aiagents4pharma/talk2knowledgegraphs/configs/tools/graphrag_reasoning/default.yaml

@@ -0,0 +1,24 @@
+_target_: talk2knowledgegraphs.tools.graphrag_reasoning
+splitter_chunk_size: 1024
+splitter_chunk_overlap: 256
+retriever_search_type: "mmr"
+retriever_k: 3
+retriever_fetch_k: 10
+retriever_lambda_mult: 0.3
+prompt_graphrag_w_docs_context: >
+  Given a chat history and the latest user question, which might reference context
+  in the chat history, formulate a standalone question that can be understood
+  without the chat history. Do NOT answer the question, just reformulate it if needed
+  and otherwise return it as is.
+
+  Question: {input}
+prompt_graphrag_w_docs: >
+  You are talk2knowledgegraphs, a helpful assistant performing retrievel-augmented generation (RAG)
+  over knowledge graphs.
+  One of your tasks is to answer react-based questions by using the following pieces of
+  retrieved context to answer the question. You can leverage a summarization of the subgraph
+  and the retrieved documents to provide the best possible answer to the user's query.
+
+  Subgraph Summary: {subgraph_summary}
+  Context: {context}
+  Question: {input}

aiagents4pharma-1.19.1/aiagents4pharma/talk2knowledgegraphs/configs/tools/subgraph_extraction/__init__.py

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

aiagents4pharma-1.19.1/aiagents4pharma/talk2knowledgegraphs/configs/tools/subgraph_extraction/default.yaml

@@ -0,0 +1,43 @@
+_target_: talk2knowledgegraphs.tools.subgraph_extraction
+ollama_embeddings:
+  - "nomic-embed-text"
+temperature: 0.1
+streaming: False
+topk: 5
+topk_e: 5
+cost_e: 0.5
+c_const: 0.01
+root: -1
+num_clusters: 1
+pruning: "gw"
+verbosity_level: 0
+node_id_column: "node_id"
+node_attr_column: "node_attr"
+edge_src_column: "edge_src"
+edge_attr_column: "edge_attr"
+edge_dst_column: "edge_dst"
+prompt_endotype_filtering: >
+  You are talk2knowledgegraphs agent, a helpful assistant in filtering the most relevant endotype
+  for the subgraph extraction process.
+  Given the retrieved endotype documents, you need to filter the most relevant
+  endotype that will be used for the following reasoning process.
+  Only included a list of genes that exist in the provided documents
+  that are relevant to the input query.
+  For this task, you may modify your prompt to optimize the filtering process
+  based on factual informationbetween each gene in the documents and the input query.
+  Discover as many genes as possible that are relevant for enriching the subgraph extraction process.
+
+  You do not need to include any other information in the output.
+  Use the following output format:
+  [gene_1, gene_2, ..., gene_n]
+
+  {context}
+  Input: {input}
+prompt_endotype_addition: >
+   Include the following endotype for the subgraph extraction process:
+splitter_chunk_size: 64
+splitter_chunk_overlap: 16
+retriever_search_type: "mmr"
+retriever_k: 3
+retriever_fetch_k: 10
+retriever_lambda_mult: 0.3

aiagents4pharma-1.19.1/aiagents4pharma/talk2knowledgegraphs/configs/tools/subgraph_summarization/__init__.py

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

aiagents4pharma-1.19.1/aiagents4pharma/talk2knowledgegraphs/configs/tools/subgraph_summarization/default.yaml

@@ -0,0 +1,9 @@
+_target_: talk2knowledgegraphs.tools.subgraph_summarization
+prompt_subgraph_summarization: >
+  You are talk2knowledgegraphs agent, a helpful assistant in reasoning over biomedical knowledge graph.
+  Your task is to summarize the extracted textualized subgraph to provide a concise and informative
+  summary of the subgraph to be used for reasoning as subgraph context. You are responsible for
+  highlighting the most important nodes and edges in the subgraph to respond to the user's question.
+
+  Textualized Subgraph: {textualized_subgraph}
+  Question: {input}

aiagents4pharma-1.19.1/aiagents4pharma/talk2knowledgegraphs/states/__init__.py

@@ -0,0 +1,4 @@
+'''
+This file is used to import all the models in the package.
+'''
+from . import state_talk2knowledgegraphs

aiagents4pharma-1.19.1/aiagents4pharma/talk2knowledgegraphs/states/state_talk2knowledgegraphs.py

@@ -0,0 +1,38 @@
+"""
+This is the state file for the Talk2KnowledgeGraphs agent.
+"""
+
+from typing import Annotated
+# import operator
+from langchain_core.embeddings.embeddings import Embeddings
+from langchain_core.language_models.chat_models import BaseChatModel
+from langgraph.prebuilt.chat_agent_executor import AgentState
+
+
+def add_data(data1: dict, data2: dict) -> dict:
+    """
+    A reducer function to merge two dictionaries.
+    """
+    left_idx_by_name = {data["name"]: idx for idx, data in enumerate(data1)}
+    merged = data1.copy()
+    for data in data2:
+        idx = left_idx_by_name.get(data["name"])
+        if idx is not None:
+            merged[idx] = data
+        else:
+            merged.append(data)
+    return merged
+
+
+class Talk2KnowledgeGraphs(AgentState):
+    """
+    The state for the Talk2KnowledgeGraphs agent.
+    """
+
+    llm_model: BaseChatModel
+    embedding_model: Embeddings
+    uploaded_files: list
+    topk_nodes: int
+    topk_edges: int
+    dic_source_graph: Annotated[list[dict], add_data]
+    dic_extracted_graph: Annotated[list[dict], add_data]

aiagents4pharma-1.19.1/aiagents4pharma/talk2knowledgegraphs/tests/test_agents_t2kg_agent.py

@@ -0,0 +1,110 @@
+"""
+Test cases for agents/t2kg_agent.py
+"""
+
+import pytest
+from langchain_core.messages import HumanMessage
+from langchain_openai import ChatOpenAI, OpenAIEmbeddings
+from ..agents.t2kg_agent import get_app
+
+# Define the data path
+DATA_PATH = "aiagents4pharma/talk2knowledgegraphs/tests/files"
+
+
+@pytest.fixture(name="input_dict")
+def input_dict_fixture():
+    """
+    Input dictionary fixture.
+    """
+    input_dict = {
+        "llm_model": None,  # TBA for each test case
+        "embedding_model": None,  # TBA for each test case
+        "uploaded_files": [
+            {
+                "file_name": "adalimumab.pdf",
+                "file_path": f"{DATA_PATH}/adalimumab.pdf",
+                "file_type": "drug_data",
+                "uploaded_by": "VPEUser",
+                "uploaded_timestamp": "2024-11-05 00:00:00",
+            },
+            {
+                "file_name": "DGE_human_Colon_UC-vs-Colon_Control.pdf",
+                "file_path": f"{DATA_PATH}/DGE_human_Colon_UC-vs-Colon_Control.pdf",
+                "file_type": "endotype",
+                "uploaded_by": "VPEUser",
+                "uploaded_timestamp": "2024-11-05 00:00:00",
+            },
+        ],
+        "topk_nodes": 3,
+        "topk_edges": 3,
+        "dic_source_graph": [
+            {
+                "name": "PrimeKG",
+                "kg_pyg_path": f"{DATA_PATH}/primekg_ibd_pyg_graph.pkl",
+                "kg_text_path": f"{DATA_PATH}/primekg_ibd_text_graph.pkl",
+            }
+        ],
+        "dic_extracted_graph": []
+    }
+
+    return input_dict
+
+
+def test_t2kg_agent_openai(input_dict):
+    """
+    Test the T2KG agent using OpenAI model.
+
+    Args:
+        input_dict: Input dictionary
+    """
+    # Prepare LLM and embedding model
+    input_dict["llm_model"] = ChatOpenAI(model="gpt-4o-mini", temperature=0.0)
+    input_dict["embedding_model"] = OpenAIEmbeddings(model="text-embedding-3-small")
+
+    # Setup the app
+    unique_id = 12345
+    app = get_app(unique_id, llm_model=input_dict["llm_model"])
+    config = {"configurable": {"thread_id": unique_id}}
+    # Update state
+    app.update_state(
+        config,
+        input_dict,
+    )
+    prompt = """
+    Adalimumab is a fully human monoclonal antibody (IgG1) 
+    that specifically binds to tumor necrosis factor-alpha (TNF-α), a pro-inflammatory cytokine.
+
+    I would like to get evidence from the knowledge graph about the mechanism of actions related to
+    Adalimumab in treating inflammatory bowel disease 
+    (IBD). Please follow these steps:
+    - Extract a subgraph from the PrimeKG that contains information about Adalimumab.
+    - Summarize the extracted subgraph.
+    - Reason about the mechanism of action of Adalimumab in treating IBD.
+
+    Please set the extraction name for the extraction process as `subkg_12345`.
+    """
+
+    # Test the tool get_modelinfo
+    response = app.invoke({"messages": [HumanMessage(content=prompt)]}, config=config)
+
+    # Check assistant message
+    assistant_msg = response["messages"][-1].content
+    assert isinstance(assistant_msg, str)
+
+    # Check extracted subgraph dictionary
+    current_state = app.get_state(config)
+    dic_extracted_graph = current_state.values["dic_extracted_graph"][0]
+    assert isinstance(dic_extracted_graph, dict)
+    assert dic_extracted_graph["name"] == "subkg_12345"
+    assert dic_extracted_graph["graph_source"] == "PrimeKG"
+    assert dic_extracted_graph["topk_nodes"] == 3
+    assert dic_extracted_graph["topk_edges"] == 3
+    assert isinstance(dic_extracted_graph["graph_dict"], dict)
+    assert len(dic_extracted_graph["graph_dict"]["nodes"]) > 0
+    assert len(dic_extracted_graph["graph_dict"]["edges"]) > 0
+    assert isinstance(dic_extracted_graph["graph_text"], str)
+    # Check summarized subgraph
+    assert isinstance(dic_extracted_graph["graph_summary"], str)
+    # Check reasoning results
+    assert "Adalimumab" in assistant_msg
+    assert "TNF" in assistant_msg