Discovering causal relationships from observational data is a crucial problem and it has applications in many research areas. The PC algorithm is the state-of-the-art constraint based method for causal discovery. However, runtime of the PC algorithm, in the worst-case, is exponential to the number of nodes (variables), and thus it is inefficient when being applied to high dimensional data, e.g. gene expression datasets. On another note, the advancement of computer hardware in the last decade has resulted in the widespread availability of multi-core personal computers. There is a significant motivation for designing a parallelised PC algorithm that is suitable for personal computers and does not require end users’ parallel computing knowledge beyond their competency in using the PC algorithm. In this paper, we develop parallel-PC, a fast and memory efficient PC algorithm using the parallel computing technique. We apply our method to a range of synthetic and real-world high dimensional datasets. Experimental results on a dataset from the DREAM 5 challenge show that the original PC algorithm could not produce any results after running more than 24 hours; meanwhile, our parallel-PC algorithm managed to finish within around 12 hours with a 4-core CPU computer, and less than 6 hours with a 8-core CPU computer. Furthermore, we integrate parallel-PC into a causal inference method for inferring miRNA-mRNA regulatory relationships. The experimental results show that parallel-PC helps improve both the efficiency and accuracy of the causal inference algorithm.
Meanwhile, the other constraint based methods @cite_26 infer causal relationships by performing CI tests and searching for specific causal structures. For instance, Cooper @cite_56 proposed the LCD method to learn only a small portion of edges rather than the complete network. Specifically, the LCD algorithm searches for the CCC structures which consist of three pairs of correlated variables: ( @math , @math ), ( @math , @math ) and ( @math , @math ). If @math and @math become independent when conditioned on @math , we may infer that one of the following causal relations exists between @math , @math , and @math : @math ; @math ; and @math . @cite_28 proposed the similar method that focuses on the CCU structures. The CCU method searches for two correlated pairs @math and @math and an independent pair @math . When conditioning on @math , if @math becomes dependent then the causal relationships @math are concluded. Compared to the PC algorithm, such specific structure finding methods are more efficient, but the causal discoveries are incomplete.
@cite_28 @cite_26 @cite_56
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Motivated by online recommendation and advertising systems, we consider a causal model for stochastic contextual bandits with a latent low-dimensional confounder. In our model, there are @math observed contexts and @math arms of the bandit. The observed context influences the reward obtained through a latent confounder variable with cardinality @math ( @math ). The arm choice and the latent confounder causally determines the reward while the observed context is correlated with the confounder. Under this model, the @math mean reward matrix @math (for each context in @math and each arm in @math ) factorizes into non-negative factors @math ( @math ) and @math ( @math ). This insight enables us to propose an @math -greedy NMF-Bandit algorithm that designs a sequence of interventions (selecting specific arms), that achieves a balance between learning this low-dimensional structure and selecting the best arm to minimize regret. Our algorithm achieves a regret of @math at time @math , as compared to @math for conventional contextual bandits, assuming a constant gap between the best arm and the rest for each context. These guarantees are obtained under mild sufficiency conditions on the factors that are weaker versions of the well-known Statistical RIP condition. We further propose a class of generative models that satisfy our sufficient conditions, and derive a lower bound of @math . These are the first regret guarantees for online matrix completion with bandit feedback, when the rank is greater than one. We further compare the performance of our algorithm with the state of the art, on synthetic and real world data-sets. Let @math be a tree space (or tree network) represented by a weighted tree with @math vertices, and @math be a set of @math stochastic points in @math , each of which has a fixed location with an independent existence probability. We investigate two fundamental problems under such a stochastic setting, the closest-pair problem and the nearest-neighbor search. For the former, we study the computation of the @math -threshold probability and the expectation of the closest-pair distance of a realization of @math . We propose the first algorithm to compute the @math -threshold probability in @math time for any given threshold @math , which immediately results in an @math -time algorithm for computing the expected closest-pair distance. Based on this, we further show that one can compute a @math -approximation for the expected closest-pair distance in @math time, by arguing that the expected closest-pair distance can be approximated via @math threshold probability queries. For the latter, we study the @math most-likely nearest-neighbor search ( @math -LNN) via a notion called @math most-likely Voronoi Diagram ( @math -LVD). We show that the size of the @math -LVD @math of @math on @math is bounded by @math if the existence probabilities of the points in @math are constant-far from 0. Furthermore, we establish an @math average-case upper bound for the size of @math , by regarding the existence probabilities as i.i.d. random variables drawn from some fixed distribution. Our results imply the existence of an LVD data structure which answers @math -LNN queries in @math time using average-case @math space, and worst-case @math space if the existence probabilities are constant-far from 0. Finally, we also give an @math -time algorithm to construct the LVD data structure. Let @math be an @math real random matrix whose elements are independent and identically distributed standard normal random variables, and let @math be the 2-norm condition number of @math . We prove that, for any @math , @math , and @math , @math satisfies @math where @math and @math @math are universal positive constants independent of @math , @math , and @math . Moreover, for any @math and @math , @math A similar pair of results for complex Gaussian random matrices is also established. State-of-the-art semantic image segmentation methods are mostly based on training deep convolutional neural networks (CNNs). In this work, we proffer to improve semantic segmentation with the use of contextual information. In particular, we explore patch-patch' context and patch-background' context in deep CNNs. We formulate deep structured models by combining CNNs and Conditional Random Fields (CRFs) for learning the patch-patch context between image regions. Specifically, we formulate CNN-based pairwise potential functions to capture semantic correlations between neighboring patches. Efficient piecewise training of the proposed deep structured model is then applied in order to avoid repeated expensive CRF inference during the course of back propagation. For capturing the patch-background context, we show that a network design with traditional multi-scale image inputs and sliding pyramid pooling is very effective for improving performance. We perform comprehensive evaluation of the proposed method. We achieve new state-of-the-art performance on a number of challenging semantic segmentation datasets including @math , @math - @math , @math , @math - @math , @math - @math , @math - @math , and @math datasets. Particularly, we report an intersection-over-union score of @math on the @math - @math dataset. In the range closest pair problem, we want to construct a data structure storing a set @math of @math points in the plane, such that for any axes-parallel query rectangle @math , the closest pair in the set @math can be reported. The currently best result for this problem is by (SoCG 2018). Their data structure has size @math and query time @math . We show that a data structure of size @math can be constructed in @math time, such that queries can be answered in @math time, where @math is the aspect ratio of @math . Thus, for fat query rectangles, the query time is @math . This result is obtained by reducing the range closest pair problem to standard range searching problems on the points of @math . Given a set of @math @math -dimensional Boolean vectors with the promise that the vectors are chosen uniformly at random with the exception of two vectors that have Pearson -- correlation @math (Hamming distance @math ), how quickly can one find the two correlated vectors? We present an algorithm which, for any constants @math and @math finds the correlated pair with high probability, and runs in time @math given @math vectors in @math , our algorithm returns a pair of vectors whose Euclidean distance differs from that of the closest pair by a factor of at most @math and runs in time @math . The best previous algorithms (including LSH) have runtime @math Learning Sparse Parity with Noise: Given samples from an instance of the learning parity with noise problem where each example has length @math , the true parity set has size at most @math . Learning @math -Juntas without Noise: Our results for learning sparse parities with noise imply an algorithm for learning juntas without noise with runtime $n^ + 4 k poly(n) which improves on the runtime n !+1 ! poly(n) n0:7kpoly(n) of [13]. Given an undirected graph @math , it is known that its edge-connectivity @math can be computed by solving @math max-flow problems. The best time bounds known for the problem are @math , due to Matula (28th IEEE Symposium on the Foundations of Computer Science, 1987, pp. 249–251) if G is simple, and @math , due to Even and Tarjan (SIAM J. Comput., 4 (1975), pp. 507–518) if G is multiple.An @math time algorithm for computing the edge-connectivity @math of a multigraph @math , where @math is the number of pairs of nodes between which G has an edge, is proposed. This algorithm does not use any max-flow algorithm but consists only of @math times of graph searches and edge contractions. This method is then extended to a capacitated network to compute its minimum cut capacity in @math time. Complex information-processing systems, for example, quantum circuits, cryptographic protocols, or multi-player games, are naturally described as networks composed of more basic information-processing systems. A modular analysis of such systems requires a mathematical model of systems that is closed under composition, i.e., a network of these objects is again an object of the same type. We propose such a model and call the corresponding systems causal boxes . Causal boxes capture superpositions of causal structures, e.g., messages sent by a causal box @math can be in a superposition of different orders or in a superposition of being sent to box @math and box @math . Furthermore, causal boxes can model systems whose behavior depends on time. By instantiating the abstract cryptography framework with causal boxes, we obtain the first composable security framework that can handle arbitrary quantum protocols and relativistic protocols. Let @math be any undirected graph on @math vertices and @math edges. A path @math between any two vertices @math is said to be @math -approximate shortest path if its length is at most @math times the length of the shortest path between @math and @math . We consider the problem of building a compact data structure for a given graph @math which is capable of answering the following query for any @math and @math . report @math -approximate shortest path between @math and @math when vertex @math fails We present data structures for the single source as well all-pairs versions of this problem. Our data structures guarantee optimal query time. Most impressive feature of our data structures is that their size nearly match the size of their best static counterparts. Given a dataset @math of points in @math , the range closest-pair (RCP) problem aims to preprocess @math into a data structure such that when a query range @math is specified, the closest-pair in @math can be reported efficiently. The RCP problem can be viewed as a range-search version of the classical closest-pair problem, and finds applications in many areas. Due to its non-decomposability, the RCP problem is much more challenging than many traditional range-search problems. This paper revisits the RCP problem, and proposes new data structures for various query types including quadrants, strips, rectangles, and halfplanes. Both worst-case and average-case analyses (in the sense that the data points are drawn uniformly and independently from the unit square) are applied to these new data structures, which result in new bounds for the RCP problem. Some of the new bounds significantly improve the previous results, while the others are entirely new. Understanding the local behaviour of structured multi-dimensional data is a fundamental problem in various areas of computer science. As the amount of data is often huge, it is desirable to obtain sublinear time algorithms, and specifically property testers, to understand local properties of the data. We focus on the natural local problem of testing pattern freeness: given a large @math -dimensional array @math and a fixed @math -dimensional pattern @math over a finite alphabet, we say that @math is @math -free if it does not contain a copy of the forbidden pattern @math as a consecutive subarray. The distance of @math to @math -freeness is the fraction of entries of @math that need to be modified to make it @math -free. For any @math and any large enough pattern @math over any alphabet, other than a very small set of exceptional patterns, we design a tolerant tester that distinguishes between the case that the distance is at least @math and the case that it is at most @math , with query complexity and running time @math , where @math and @math depend only on @math . To analyze the testers we establish several combinatorial results, including the following @math -dimensional modification lemma, which might be of independent interest: for any large enough pattern @math over any alphabet (excluding a small set of exceptional patterns for the binary case), and any array @math containing a copy of @math , one can delete this copy by modifying one of its locations without creating new @math -copies in @math . Our results address an open question of Fischer and Newman, who asked whether there exist efficient testers for properties related to tight substructures in multi-dimensional structured data. They serve as a first step towards a general understanding of local properties of multi-dimensional arrays, as any such property can be characterized by a fixed family of forbidden patterns. We consider the problem of clustering a graph @math into two communities by observing a subset of the vertex correlations. Specifically, we consider the inverse problem with observed variables @math , where @math is the incidence matrix of a graph @math , @math is the vector of unknown vertex variables (with a uniform prior), and @math is a noise vector with Bernoulli @math i.i.d. entries. All variables and operations are Boolean. This model is motivated by coding, synchronization, and community detection problems. In particular, it corresponds to a stochastic block model or a correlation clustering problem with two communities and censored edges. Without noise, exact recovery (up to global flip) of @math is possible if and only the graph @math is connected, with a sharp threshold at the edge probability @math for Erdős-Renyi random graphs. The first goal of this paper is to determine how the edge probability @math needs to scale to allow exact recovery in the presence of noise. Defining the degree rate of the graph by @math , it is shown that exact recovery is possible if and only if @math . In other words, @math is the information theoretic threshold for exact recovery at low-SNR. In addition, an efficient recovery algorithm based on semidefinite programming is proposed and shown to succeed in the threshold regime up to twice the optimal rate. For a deterministic graph @math , defining the degree rate as @math , where @math is the minimum degree of the graph, it is shown that the proposed method achieves the rate @math , where @math is the spectral gap of the graph @math . For an unweighted graph @math , @math is a subgraph if @math , and @math is a Steiner graph if @math , and for any pair of vertices @math , the distance between them in @math (denoted @math ) is at least the distance between them in @math (denoted @math ). In this paper we introduce the notion of distance preserver. A subgraph (resp., Steiner graph) @math of a graph @math is a subgraph (resp., Steiner) @math -preserver of @math if for every pair of vertices @math with @math , @math . We show that any graph (resp., digraph) has a subgraph @math -preserver with at most @math edges (resp., arcs), and there are graphs and digraphs for which any undirected Steiner @math -preserver contains @math edges. However, we show that if one allows a directed Steiner (diSteiner) @math -preserver, then these bounds can be improved. Specifically, we show that for any graph or digraph there exists a diSteiner @math -preserver with @math arcs, and that this result is tight up to a constant factor. We also study @math -preserving distance labeling schemes, that are labeling schemes that guarantee precise calculation of distances between pairs of vertices that are at a distance of at least @math one from another. We show that there exists a @math -preserving labeling scheme with labels of size @math , and that labels of size @math are required for any @math -preserving labeling scheme. In this paper we study noisy sorting without re-sampling. In this problem there is an unknown order @math for all pairs @math , where @math is a constant and @math for all @math and @math . It is assumed that the errors are independent. Given the status of the queries the goal is to find the maximum likelihood order. In other words, the goal is find a permutation @math that minimizes the number of pairs @math where @math . The problem so defined is the feedback arc set problem on distributions of inputs, each of which is a tournament obtained as a noisy perturbations of a linear order. Note that when @math and @math is large, it is impossible to recover the original order @math . It is known that the weighted feedback are set problem on tournaments is NP-hard in general. Here we present an algorithm of running time @math and sampling complexity @math that with high probability solves the noisy sorting without re-sampling problem. We also show that if @math is an optimal solution of the problem then it is close'' to the original order. More formally, with high probability it holds that @math and @math . Our results are of interest in applications to ranking, such as ranking in sports, or ranking of search items based on comparisons by experts. In this paper, we show that many graph search problems can be solved quite efficiently for a geometric intersection graph of horizontal and vertical line segments. We first extract several basic operations for depth first search and breadth first search on a graph. Then we present data structures for the intersection graph in terms of which those operations can be implemented in an efficient manner. The data structures enable us to solve various graph search problems besides depth first search and breadth first search. Specifying the results obtained in this paper for an intersection graph of n horizontal and vertical segments with m pairs of intersecting segments, we obtain algorithms with the following complexity, where @math . (i) Depth first search and breadth first search can be executed in @math time and @math space. (ii) The biconnected components can be found in @math time and @math space. (iii) A maximum matching and a maximum independent set can be found in $O... Let @math be a @math -ary predicate over a finite alphabet. Consider a random CSP @math instance @math over @math variables with @math constraints. When @math the instance @math will be unsatisfiable with high probability, and we want to find a refutation - i.e., a certificate of unsatisfiability. When @math is the @math -ary OR predicate, this is the well studied problem of refuting random @math -SAT formulas, and an efficient algorithm is known only when @math . Understanding the density required for refutation of other predicates is important in cryptography, proof complexity, and learning theory. Previously, it was known that for a @math -ary predicate, having @math constraints suffices for refutation. We give a criterion for predicates that often yields efficient refutation algorithms at much lower densities. Specifically, if @math fails to support a @math -wise uniform distribution, then there is an efficient algorithm that refutes random CSP @math instances @math whp when @math . Indeed, our algorithm will "somewhat strongly" refute @math , certifying @math , if @math then we get the strongest possible refutation, certifying @math . This last result is new even in the context of random @math -SAT. Regarding the optimality of our @math requirement, prior work on SDP hierarchies has given some evidence that efficient refutation of random CSP @math may be impossible when @math . Thus there is an indication our algorithm's dependence on @math is optimal for every @math , at least in the context of SDP hierarchies. Along these lines, we show that our refutation algorithm can be carried out by the @math -round SOS SDP hierarchy. Finally, as an application of our result, we falsify assumptions used to show hardness-of-learning results in recent work of Daniely, Linial, and Shalev-Shwartz. A sensor node that is sending measurement updates regarding some physical phenomenon to a destination is considered. The sensor relies on energy harvested from nature to transmit its updates, and is equipped with a finite @math -sized battery to save its harvested energy. Energy recharges the battery incrementally in units, according to a Poisson process, and one update consumes one energy unit to reach the destination. The setting is online, where the energy arrival times are revealed causally after the energy is harvested. The goal is to update the destination in a timely manner, namely, such that the long term average age of information is minimized, subject to energy causality constraints. The age of information at a given time is defined as the time spent since the latest update has reached the destination. It is shown that the optimal update policy follows a renewal structure, where the inter-update times are independent, and the time durations between any two consecutive events of submitting an update and having @math units of energy remaining in the battery are independent and identically distributed for a given @math . The optimal renewal policy for the case of @math energy units is explicitly characterized, and it is shown that it has an energy-dependent threshold structure, where the sensor updates only if the age grows above a certain threshold that is a function of the amount of energy in its battery. This paper studies problems of inferring order given noisy information. In these problems there is an unknown order (permutation) @math on @math elements denoted by @math . We assume that information is generated in a way correlated with @math . The goal is to find a maximum likelihood @math given the information observed. We will consider two different types of observations: noisy comparisons and noisy orders. The data in Noisy orders are permutations given from an exponential distribution correlated with (this is also called the Mallow's model). The data in Noisy Comparisons is a signal given for each pair of elements which is correlated with their true ordering. In this paper we present polynomial time algorithms for solving both problems with high probability. As part of our proof we show that for both models the maximum likelihood solution @math is close to the original permutation @math . Our results are of interest in applications to ranking, such as ranking in sports, or ranking of search items based on comparisons by experts. We consider the problem of community detection in the Stochastic Block Model with a finite number @math of communities of sizes linearly growing with the network size @math . This model consists in a random graph such that each pair of vertices is connected independently with probability @math within communities and @math across communities. One observes a realization of this random graph, and the objective is to reconstruct the communities from this observation. We show that under spectral algorithms, the number of misclassified vertices does not exceed @math with high probability as @math grows large, whenever @math , @math and where @math and @math denote the (fixed) proportions of vertices in the two smallest communities. In view of recent work by and , this establishes that the proposed spectral algorithms are able to exactly recover communities whenever this is at all possible in the case of networks with two communities with equal sizes. We conjecture that condition (1) is actually necessary to obtain less than @math misclassified vertices asymptotically, which would establish the optimality of spectral method in more general scenarios. We study the aggregate group nearest neighbor searching for the MAX operator in the plane. For a set @math of @math points and a query set @math of @math points, the query asks for a point of @math whose maximum distance to the points in @math is minimized. We present data structures for answering such queries for both @math and @math distance measures. Previously, only heuristic and approximation algorithms were given for both versions. For the @math version, we build a data structure of O(n) size in @math time, such that each query can be answered in @math time. For the @math version, we build a data structure in @math time and @math space, such that each query can be answered in @math time, and alternatively, we build a data structure in @math time and space for any @math , such that each query can be answered in @math time. Further, we extend our result for the @math version to the top- @math queries where each query asks for the @math points of @math whose maximum distances to @math are the smallest for any @math with @math : We build a data structure of O(n) size in @math time, such that each top- @math query can be answered in @math time.