SUMMARY: Inferring genetic or transcriptional interactions, when done successfully, may provide insights into biological processes or biochemical pathways of interest. Unfortunately, most computational algorithms require a certain level of programming expertise. To provide a simple web interface for users to infer interactions from time course gene expression data, we present WebPARE, which is based on the pattern recognition algorithm (PARE). For expression data, in which each type of interaction (e.g. activator target) and the corresponding paired gene expression pattern are significantly associated, PARE uses a non-linear score to classify gene pairs of interest into a few subclasses of various time lags. In each subclass, PARE learns the parameters in the decision score using known interactions from biological experiments or published literature. Subsequently, the trained algorithm predicts interactions of a similar nature. Previously, PARE was shown to infer two sets of interactions in yeast successfully. Moreover, several predicted genetic interactions coincided with existing pathways; this indicates the potential of PARE in predicting partial pathway components. Given a list of gene pairs or genes of interest and expression data, WebPARE invokes PARE and outputs predicted interactions and their networks in directed graphs.

Domain-specific features are important in representing problem structure throughout machine learning and decision-theoretic planning. In planning, once state features are provided, domain-independent algorithms such as approximate value iteration can learn weighted combinations of those features that often perform well as heuristic estimates of state value (e.g., distance to the goal). Successful applications in real-world domains often require features crafted by human experts. Here, we propose automatic processes for learning useful domain-specific feature sets with little or no human intervention. Our methods select and add features that describe state-space regions of high inconsistency in the Bellman equation (statewise Bellman error) during approximate value iteration. Our method can be applied using any real-valued-feature hypothesis space and corresponding learning method for selecting features from training sets of state-value pairs. We evaluate the method with hypothesis spaces defined by both relational and propositional feature languages, using nine probabilistic planning domains. We show that approximate value iteration using a relational feature space performs at the state-of-the-art in domain-independent stochastic relational planning. Our method provides the first domain-independent approach that plays Tetris successfully (without human-engineered features).

In this work, we develop a statistical thermal simulator including the effect of spatial correlation under within-die process variations. This method utilizes the Karhunen-Loève (KL) expansion to model the physical parameters, and apply the Polynomial Chaoses (PCs) and the stochastic Galerkin method to tackle stochastic heat transfer equations. We demonstrate the accuracy and efficiency of our simulator by comparing with the Monte Carlo simulation, and point out that the stochastic thermal analysis is essential to provide a robust estimation of temperature distribution for the thermal-aware design flow.