A note on the complexity of the causal ordering problem

In this note we provide a concise report on the complexity of the causal ordering problem, originally introduced by Simon to reason about causal dependencies implicit in systems of mathematical equations. We show that Simon’s classical algorithm to infer causal ordering is NP-Hard—an intractability previously guessed but never proven. We present then a detailed account based on Nayak’s suggested algorithmic solution (the best available), which is dominated by computing transitive closure—bounded in time by O(|V|·|S|), where S(E, V) is the input system structure composed of a set E of equations over a set V of variables with number of variable appearances (density) |S|. We also comment on the potential of causal ordering for emerging applications in large-scale hypothesis management and analytics

Structure and Complexity in Planning with Unary Operators

Unary operator domains -- i.e., domains in which operators have a single effect -- arise naturally in many control problems. In its most general form, the problem of STRIPS planning in unary operator domains is known to be as hard as the general STRIPS planning problem -- both are PSPACE-complete. However, unary operator domains induce a natural structure, called the domain's causal graph. This graph relates between the preconditions and effect of each domain operator. Causal graphs were exploited by Williams and Nayak in order to analyze plan generation for one of the controllers in NASA's Deep-Space One spacecraft. There, they utilized the fact that when this graph is acyclic, a serialization ordering over any subgoal can be obtained quickly. In this paper we conduct a comprehensive study of the relationship between the structure of a domain's causal graph and the complexity of planning in this domain. On the positive side, we show that a non-trivial polynomial time plan generation algorithm exists for domains whose causal graph induces a polytree with a constant bound on its node indegree. On the negative side, we show that even plan existence is hard when the graph is a directed-path singly connected DAG. More generally, we show that the number of paths in the causal graph is closely related to the complexity of planning in the associated domain. Finally we relate our results to the question of complexity of planning with serializable subgoals

Inferring Regulatory Networks by Combining Perturbation Screens and Steady State Gene Expression Profiles

Reconstructing transcriptional regulatory networks is an important task in functional genomics. Data obtained from experiments that perturb genes by knockouts or RNA interference contain useful information for addressing this reconstruction problem. However, such data can be limited in size and/or are expensive to acquire. On the other hand, observational data of the organism in steady state (e.g. wild-type) are more readily available, but their informational content is inadequate for the task at hand. We develop a computational approach to appropriately utilize both data sources for estimating a regulatory network. The proposed approach is based on a three-step algorithm to estimate the underlying directed but cyclic network, that uses as input both perturbation screens and steady state gene expression data. In the first step, the algorithm determines causal orderings of the genes that are consistent with the perturbation data, by combining an exhaustive search method with a fast heuristic that in turn couples a Monte Carlo technique with a fast search algorithm. In the second step, for each obtained causal ordering, a regulatory network is estimated using a penalized likelihood based method, while in the third step a consensus network is constructed from the highest scored ones. Extensive computational experiments show that the algorithm performs well in reconstructing the underlying network and clearly outperforms competing approaches that rely only on a single data source. Further, it is established that the algorithm produces a consistent estimate of the regulatory network.Comment: 24 pages, 4 figures, 6 table

Penalized Likelihood Methods for Estimation of Sparse High Dimensional Directed Acyclic Graphs

Directed acyclic graphs (DAGs) are commonly used to represent causal relationships among random variables in graphical models. Applications of these models arise in the study of physical, as well as biological systems, where directed edges between nodes represent the influence of components of the system on each other. The general problem of estimating DAGs from observed data is computationally NP-hard, Moreover two directed graphs may be observationally equivalent. When the nodes exhibit a natural ordering, the problem of estimating directed graphs reduces to the problem of estimating the structure of the network. In this paper, we propose a penalized likelihood approach that directly estimates the adjacency matrix of DAGs. Both lasso and adaptive lasso penalties are considered and an efficient algorithm is proposed for estimation of high dimensional DAGs. We study variable selection consistency of the two penalties when the number of variables grows to infinity with the sample size. We show that although lasso can only consistently estimate the true network under stringent assumptions, adaptive lasso achieves this task under mild regularity conditions. The performance of the proposed methods is compared to alternative methods in simulated, as well as real, data examples.Comment: 19 pages, 8 figure