Simulation and Application to learn gene causal relationships了解基因的因果关系的仿真与应用.pptVIP

Simulation and Application on learning gene causal relationships Xin Zhang Introduction High-throughput genetic technologies empowers to study how genes interact with each other; Simulation to evaluate how well IC algorithm learns gene causal relationships; We present an algorithm (mIC algorithm) for learning causal relationship with knowledge of topological ordering information, and apply it on Melanoma dataset; Apply mIC algorithm on Melanoma dataset; Steps for Simulation Study Construct a causal network N; Generate datasets based on the causal network; Learning the simulated data using causal algorithms (e.g. IC algorithm) to obtain network N′; Compare the original network N with obtained network N′ w.r.t precision and recall; Modeling and simulation of a causal Boolean network (BN) Boolean network: Constructing Boolean Network 1. Generate M BNs with up to 3 causal parents for each node; 2. For each BN, generate a random proper function for each node; 3. Assign random probabilities for the root gene(s); 4. Given one configuration, get probability distribution; 5. Collect 200 data points for each network; 6. Repeat above steps 3-5 for all M networks. Constructing Causal Structure Steps for constructing causal structure Proper function (1) Proper function (2) Definition: Probability Distribution Generating dataset Steps of learning gene causal relationships Step1: obtain the probability distribution and data sampling; Step2: apply algorithms to find causal relations; Step3: compare the original and obtained networks based on the two notions of precision and recall; Step4: repeat step 1-3 for every random network; Comparing two networks Precision and Recall Original graph is a DAG, while obtained graph has both directed and undirected edges; Observational equivalence and Transitive Closure Two DAGs are said to be observational equivalent (OE) if they have the same skeleton and the same set of v-structure; Result for IC algorithm How to improve IC algorithm The ori