update

Author: WuJunde

.gitignore

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+*.txt
+dataset
+dataset_paper
+dataset_test
+test*

README.md

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 # Medical-Graph-RAG
+We build a Graph RAG System specifically for the medical domain.
 
-paper: https://arxiv.org/html/2408.04187v1
+Check our paper here: https://arxiv.org/html/2408.04187v1
 
-code comming soon
+# Quick Start
+1. conda env create -f medgraphrag.yml
+
+2. export OPENAI_API_KEY = <your OPENAI_API_KEY>
+
+3. python run.py -simple True (now using ./dataset_ex/report_0.txt as RAG doc, "What is the main symptom of the patient?" as the prompt, change the prompt in run.py as you like.)
+
+# Build from scratch
+## Prepare Neo4j and LLM: 
+prepare neo4j and LLM (using ChatGPT here for an example), you need to export:
+export OPENAI_API_KEY = <your OPENAI_API_KEY>
+export NEO4J_URL= <your NEO4J_URL>
+export NEO4J_USERNAME= <your NEO4J_USERNAME>
+export NEO4J_PASSWORD=<your NEO4J_PASSWORD>
+
+## Construct the graph (use "mimic_ex" dataset as an example): 
+1. Download mimic_ex here, put that under your data path, like ./dataset/mimic_ex
+
+2. python run.py -dataset mimic_ex -data_path ./dataset/mimic_ex(where you put the dataset) -grained_chunk True -ingraphmerge True -construct_graph True
+
+## Model Inference: 
+1. put your prompt to ./prompt.txt
+
+2. python run.py -dataset mimic_ex -data_path ./dataset/mimic_ex(where you put the dataset) -inference True

__pycache__/agentic_chunker.cpython-310.pyc

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+# =========== Copyright 2023 @ CAMEL-AI.org. All Rights Reserved. ===========
+# Licensed under the Apache License, Version 2.0 (the “License”);
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#     http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an “AS IS” BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+# =========== Copyright 2023 @ CAMEL-AI.org. All Rights Reserved. ===========
+
+__version__ = '0.1.6.2'
+
+__all__ = [
+    '__version__',
+    'camel',
+]

__pycache__/creat_graph.cpython-310.pyc

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+# =========== Copyright 2023 @ CAMEL-AI.org. All Rights Reserved. ===========
+# Licensed under the Apache License, Version 2.0 (the “License”);
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#     http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an “AS IS” BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+# =========== Copyright 2023 @ CAMEL-AI.org. All Rights Reserved. ===========
+from .base import BaseAgent
+from .chat_agent import ChatAgent
+from .critic_agent import CriticAgent
+from .embodied_agent import EmbodiedAgent
+from .knowledge_graph_agent import KnowledgeGraphAgent
+from .role_assignment_agent import RoleAssignmentAgent
+from .search_agent import SearchAgent
+from .task_agent import (
+    TaskCreationAgent,
+    TaskPlannerAgent,
+    TaskPrioritizationAgent,
+    TaskSpecifyAgent,
+)
+from .tool_agents.base import BaseToolAgent
+from .tool_agents.hugging_face_tool_agent import HuggingFaceToolAgent
+
+__all__ = [
+    'BaseAgent',
+    'ChatAgent',
+    'TaskSpecifyAgent',
+    'TaskPlannerAgent',
+    'TaskCreationAgent',
+    'TaskPrioritizationAgent',
+    'CriticAgent',
+    'BaseToolAgent',
+    'HuggingFaceToolAgent',
+    'EmbodiedAgent',
+    'RoleAssignmentAgent',
+    'SearchAgent',
+    'KnowledgeGraphAgent',
+]

__pycache__/data_chunk.cpython-310.pyc

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+# =========== Copyright 2023 @ CAMEL-AI.org. All Rights Reserved. ===========
+# Licensed under the Apache License, Version 2.0 (the “License”);
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#     http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an “AS IS” BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+# =========== Copyright 2023 @ CAMEL-AI.org. All Rights Reserved. ===========
+from abc import ABC, abstractmethod
+from typing import Any
+
+
+class BaseAgent(ABC):
+    r"""An abstract base class for all CAMEL agents."""
+
+    @abstractmethod
+    def reset(self, *args: Any, **kwargs: Any) -> Any:
+        r"""Resets the agent to its initial state."""
+        pass
+
+    @abstractmethod
+    def step(self, *args: Any, **kwargs: Any) -> Any:
+        r"""Performs a single step of the agent."""
+        pass