diff --git a/api/configs/feature/__init__.py b/api/configs/feature/__init__.py
index 4890b5f746..a3da5c1b49 100644
--- a/api/configs/feature/__init__.py
+++ b/api/configs/feature/__init__.py
@@ -74,7 +74,7 @@ class CodeExecutionSandboxConfig(BaseSettings):
 
     CODE_EXECUTION_ENDPOINT: HttpUrl = Field(
         description="URL endpoint for the code execution service",
-        default="http://sandbox:8194",
+        default=HttpUrl("http://sandbox:8194"),
     )
 
     CODE_EXECUTION_API_KEY: str = Field(
@@ -145,7 +145,7 @@ class PluginConfig(BaseSettings):
 
     PLUGIN_DAEMON_URL: HttpUrl = Field(
         description="Plugin API URL",
-        default="http://localhost:5002",
+        default=HttpUrl("http://localhost:5002"),
     )
 
     PLUGIN_DAEMON_KEY: str = Field(
@@ -188,7 +188,7 @@ class MarketplaceConfig(BaseSettings):
 
     MARKETPLACE_API_URL: HttpUrl = Field(
         description="Marketplace API URL",
-        default="https://marketplace.dify.ai",
+        default=HttpUrl("https://marketplace.dify.ai"),
     )
 
 
diff --git a/api/configs/middleware/__init__.py b/api/configs/middleware/__init__.py
index d285515998..9d30badb3d 100644
--- a/api/configs/middleware/__init__.py
+++ b/api/configs/middleware/__init__.py
@@ -173,7 +173,7 @@ class DatabaseConfig(BaseSettings):
 
     RETRIEVAL_SERVICE_EXECUTORS: NonNegativeInt = Field(
         description="Number of processes for the retrieval service, default to CPU cores.",
-        default=os.cpu_count(),
+        default=os.cpu_count() or 1,
     )
 
     @computed_field
diff --git a/api/core/plugin/entities/endpoint.py b/api/core/plugin/entities/endpoint.py
index 6c6c8bf9bc..d7ba75bb4f 100644
--- a/api/core/plugin/entities/endpoint.py
+++ b/api/core/plugin/entities/endpoint.py
@@ -24,7 +24,7 @@ class EndpointProviderDeclaration(BaseModel):
     """
 
     settings: list[ProviderConfig] = Field(default_factory=list)
-    endpoints: Optional[list[EndpointDeclaration]] = Field(default_factory=list)
+    endpoints: Optional[list[EndpointDeclaration]] = Field(default_factory=list[EndpointDeclaration])
 
 
 class EndpointEntity(BasePluginEntity):
diff --git a/api/core/plugin/entities/plugin.py b/api/core/plugin/entities/plugin.py
index 07ed94380a..edce905075 100644
--- a/api/core/plugin/entities/plugin.py
+++ b/api/core/plugin/entities/plugin.py
@@ -52,7 +52,7 @@ class PluginResourceRequirements(BaseModel):
         model: Optional[Model] = Field(default=None)
         node: Optional[Node] = Field(default=None)
         endpoint: Optional[Endpoint] = Field(default=None)
-        storage: Storage = Field(default=None)
+        storage: Optional[Storage] = Field(default=None)
 
     permission: Optional[Permission] = Field(default=None)
 
@@ -66,9 +66,9 @@ class PluginCategory(enum.StrEnum):
 
 class PluginDeclaration(BaseModel):
     class Plugins(BaseModel):
-        tools: Optional[list[str]] = Field(default_factory=list)
-        models: Optional[list[str]] = Field(default_factory=list)
-        endpoints: Optional[list[str]] = Field(default_factory=list)
+        tools: Optional[list[str]] = Field(default_factory=list[str])
+        models: Optional[list[str]] = Field(default_factory=list[str])
+        endpoints: Optional[list[str]] = Field(default_factory=list[str])
 
     class Meta(BaseModel):
         minimum_dify_version: Optional[str] = Field(default=None, pattern=r"^\d{1,4}(\.\d{1,4}){1,3}(-\w{1,16})?$")
diff --git a/api/core/plugin/entities/request.py b/api/core/plugin/entities/request.py
index 6c0c7f2868..1692020ec8 100644
--- a/api/core/plugin/entities/request.py
+++ b/api/core/plugin/entities/request.py
@@ -55,8 +55,8 @@ class RequestInvokeLLM(BaseRequestInvokeModel):
     mode: str
     completion_params: dict[str, Any] = Field(default_factory=dict)
     prompt_messages: list[PromptMessage] = Field(default_factory=list)
-    tools: Optional[list[PromptMessageTool]] = Field(default_factory=list)
-    stop: Optional[list[str]] = Field(default_factory=list)
+    tools: Optional[list[PromptMessageTool]] = Field(default_factory=list[PromptMessageTool])
+    stop: Optional[list[str]] = Field(default_factory=list[str])
     stream: Optional[bool] = False
 
     model_config = ConfigDict(protected_namespaces=())
diff --git a/api/core/variables/variables.py b/api/core/variables/variables.py
index c32815b24d..b650b1682e 100644
--- a/api/core/variables/variables.py
+++ b/api/core/variables/variables.py
@@ -30,7 +30,7 @@ class Variable(Segment):
     """
 
     id: str = Field(
-        default=lambda _: str(uuid4()),
+        default_factory=lambda: str(uuid4()),
         description="Unique identity for variable.",
     )
     name: str
diff --git a/api/core/workflow/graph_engine/entities/graph.py b/api/core/workflow/graph_engine/entities/graph.py
index 5c672c985b..8e5b1e7142 100644
--- a/api/core/workflow/graph_engine/entities/graph.py
+++ b/api/core/workflow/graph_engine/entities/graph.py
@@ -36,7 +36,7 @@ class Graph(BaseModel):
     root_node_id: str = Field(..., description="root node id of the graph")
     node_ids: list[str] = Field(default_factory=list, description="graph node ids")
     node_id_config_mapping: dict[str, dict] = Field(
-        default_factory=list, description="node configs mapping (node id: node config)"
+        default_factory=dict, description="node configs mapping (node id: node config)"
     )
     edge_mapping: dict[str, list[GraphEdge]] = Field(
         default_factory=dict, description="graph edge mapping (source node id: edges)"
diff --git a/api/core/workflow/nodes/loop/entities.py b/api/core/workflow/nodes/loop/entities.py
index 16802311dc..3f4a5edab9 100644
--- a/api/core/workflow/nodes/loop/entities.py
+++ b/api/core/workflow/nodes/loop/entities.py
@@ -26,7 +26,7 @@ class LoopNodeData(BaseLoopNodeData):
     loop_count: int  # Maximum number of loops
     break_conditions: list[Condition]  # Conditions to break the loop
     logical_operator: Literal["and", "or"]
-    loop_variables: Optional[list[LoopVariableData]] = Field(default_factory=list)
+    loop_variables: Optional[list[LoopVariableData]] = Field(default_factory=list[LoopVariableData])
     outputs: Optional[Mapping[str, Any]] = None
 
 
diff --git a/api/core/workflow/utils/condition/entities.py b/api/core/workflow/utils/condition/entities.py
index 799c735f54..56871a15d8 100644
--- a/api/core/workflow/utils/condition/entities.py
+++ b/api/core/workflow/utils/condition/entities.py
@@ -39,7 +39,7 @@ class SubCondition(BaseModel):
 
 class SubVariableCondition(BaseModel):
     logical_operator: Literal["and", "or"]
-    conditions: list[SubCondition] = Field(default=list)
+    conditions: list[SubCondition] = Field(default_factory=list)
 
 
 class Condition(BaseModel):
diff --git a/api/pyproject.toml b/api/pyproject.toml
index 65315e9be7..4cdae173dd 100644
--- a/api/pyproject.toml
+++ b/api/pyproject.toml
@@ -63,9 +63,9 @@ dependencies = [
     "psycogreen~=1.0.2",
     "psycopg2-binary~=2.9.6",
     "pycryptodome==3.19.1",
-    "pydantic~=2.9.2",
-    "pydantic-extra-types~=2.9.0",
-    "pydantic-settings~=2.6.0",
+    "pydantic~=2.11.4",
+    "pydantic-extra-types~=2.10.3",
+    "pydantic-settings~=2.9.1",
     "pyjwt~=2.8.0",
     "pypdfium2~=4.30.0",
     "python-docx~=1.1.0",