SMRUCC.genomics.Analysis.BNLearn 1.0.9753.40023.

Namespaces 13 Types 49 Members 515

01 Namespaces

SMRUCC.genomics.Analysis.BNLearn

Type	Summary	Members
Effector	effects of the effector to the TF protein	3
RegulatoryLink	Gene regulatory network	8

SMRUCC.genomics.Analysis.BNLearn.Core

Type	Summary	Members
BayesianNetwork	贝叶斯网络 —— DAG 结构	23
BnCPD	高斯条件概率分布参数 Xi \| Pa(Xi) ~ N(β0 + β1·Pa1 + β2·Pa2 + ...	14
BNLearnWorkflow	BNLearn 工作流 —— 基因表达调控网络建模与虚拟干扰分析	52
BnNode	贝叶斯网络节点 —— 对应一个基因	7
GeneExpressionData	基因表达矩阵行 = 基因，列 = 样本（可能包含多个时间点）	16
InterventionCPD	被干预节点的 CPD —— 用于虚拟敲除/过表达将节点值固定为常数，忽略所有父节点	6
PriorNetwork	先验调控网络	8
RegulatoryEdge	转录调控关系	6

SMRUCC.genomics.Analysis.BNLearn.Core.InterventionCPD

Type	Summary	Members
InterventionMode		4

SMRUCC.genomics.Analysis.BNLearn.DBN

Type	Summary	Members
ActivationModel	节点激活模型的预计算结果：把 TF / effector 的父下标与调控方向解析成定长数组。原始实现在每一个父配置里都要对 ParentIds 做 IndexOf 字符串查找，单次 O(P) 比较 × 每个配置 O(P) 次 = O(P²)，在 3^P 个配置上总复杂度为 O(3^P·P²)。预计算之后每个配置只需 O(P) 次数组取值，无字…	4
ConditionalProbabilityTable	Conditional Probability Table (CPT) for a DBN node.	11
DBNConfig	Configuration options for the Dynamic Bayesian Network.	19
DBNNode	A node in the Dynamic Bayesian Network.	10
DBNNodeType	Type of node in the Dynamic Bayesian Network.	6
DBNODECoupler	Coupling interface between the DBN and metabolic network ODEs.	7
DBNPredictionResult	Result of a DBN prediction step.	7
DynamicBayesianNetwork	Dynamic Bayesian Network for gene regulatory network simulation.	34

SMRUCC.genomics.Analysis.BNLearn.Inference

Type	Summary	Members
BnInferenceEngine	概率推断引擎	7
Extensions		2

SMRUCC.genomics.Analysis.BNLearn.Intervention

Type	Summary	Members
BnInterventionAnalyzer	虚拟干扰分析引擎	8
InterventionComparisonExporter	虚拟扰动结果比较分析导出器	20
InterventionMode	干预模式	8
InterventionResult	干预分析结果	14
InterventionSpec	单次干预定义	6

SMRUCC.genomics.Analysis.BNLearn.Intervention.InterventionComparisonExporter

Type	Summary	Members
ComparisonMatrix	比较矩阵数据结构	4
ComparisonMetric	比较指标枚举	7

SMRUCC.genomics.Analysis.BNLearn.IO

Type	Summary	Members
BnIO	数据读写工具	5
WriteModel		2

SMRUCC.genomics.Analysis.BNLearn.ModularNetwork

Type	Summary	Members
BlockBayesianNetwork		31
BlockDynamics		2
BlockModules		12
BlockNetwork		10
BlockPropagate		7
BlockResponseResult		6
GlobalPerturbationResult	单个扰动源在全局网络上传播后的结果	10
ModularNetworkPipeline	基于 WGCNA 模块划分的贝叶斯子网络训练 + 全局虚拟扰动流水线	36
ModuleDBN	单个 WGCNA 模块的 DBN 子网络训练结果容器（模块内部使用，不污染公共 API）。	6
PropagationMethod	全局虚拟扰动的传播方法	4

SMRUCC.genomics.Analysis.BNLearn.ModularNetwork.WGCNA

Type	Summary	Members
GeneModuleColor	WGCNA gene module color assignment result	4
WGCNAFiles	WGCNA module block extensions	2

SMRUCC.genomics.Analysis.BNLearn.ParameterLearning

Type	Summary	Members
BnParameterLearner	贝叶斯网络参数学习器	1
ParameterLearningResult	参数学习结果	5

SMRUCC.genomics.Analysis.BNLearn.StructureLearning

Type	Summary	Members
BnStructureLearner	贝叶斯网络结构学习器	30
StructureAlgorithm	结构学习算法类型	6
StructureLearningParams	结构学习参数	9
StructureLearningResult	结构学习结果	5

SMRUCC.genomics.Analysis.BNLearn.StructureLearning.BnStructureLearner

Type	Summary	Members
EdgeCandidate	边操作候选项 —— 供外层并行搜索的 thread-local 局部最优归约使用	1