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.
Due to the significance of the PC algorithm in the constraint based causal discovery approach, there have been several methods aiming to modify the procedure of the PC algorithm directly to improve the efficiency and or the accuracy of the algorithm. Steck and Tresp @cite_39 used the necessary path condition to reduce the number of CI tests in the PC algorithm. They have proved that when testing the edge between @math to @math , we do not need to condition on the nodes that are not in a path from @math to @math . This modification may help reduce the chance for making errors by conducting fewer tests. However, it requires more running time for finding the nodes that are not in the path. Other researchers @cite_56 @cite_45 proposed to replace the CI test, which is normally based on the Chi-square statistical test, with the Bayesian statistical tests. They aim to reduce the error rates made by the CI tests. However, there is still no clear evidence in real world datasets about the impacts of this replacement on the efficiency improvement of the PC algorithm.
@cite_56 @cite_45 @cite_39
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For many random constraint satisfaction problems, by now there exist asymptotically tight estimates of the largest constraint density for which solutions exist. At the same time, for many of these problems, all known polynomial-time algorithms stop finding solutions at much smaller densities. For example, it is well-known that it is easy to color a random graph using twice as many colors as its chromatic number. Indeed, some of the simplest possible coloring algorithms achieve this goal. Given the simplicity of those algorithms, one would expect room for improvement. Yet, to date, no algorithm is known that uses (2 - epsiv)chi colors, in spite of efforts by numerous researchers over the years. In view of the remarkable resilience of this factor of 2 against every algorithm hurled at it, we find it natural to inquire into its origin. We do so by analyzing the evolution of the set of k-colorings of a random graph, viewed as a subset of 1,...,k n, as edges are added. We prove that the factor of 2 corresponds in a precise mathematical sense to a phase transition in the geometry of this set. Roughly speaking, we prove that the set of k-colorings looks like a giant ball for k ges 2chi, but like an error-correcting code for k les (2 - epsiv)chi. We also prove that an analogous phase transition occurs both in random k-SAT and in random hypergraph 2-coloring. And that for each of these three problems, the location of the transition corresponds to the point where all known polynomial-time algorithms fail. To prove our results we develop a general technique that allows us to establish rigorously much of the celebrated 1-step replica-symmetry-breaking hypothesis of statistical physics for random CSPs. There are several existing algorithms that under appropriate assumptions can reliably identify a subset of the underlying causal relationships from observational data. This paper introduces the first computationally feasible score-based algorithm that can reliably identify causal relationships in the large sample limit for discrete models, while allowing for the possibility that there are unobserved common causes. In doing so, the algorithm does not ever need to assign scores to causal structures with unobserved common causes. The algorithm is based on the identification of so called Y substructures within Bayesian network structures that can be learned from observational data. An example of a Y substructure is A -> C, B -> C, C -> D. After providing background on causal discovery, the paper proves the conditions under which the algorithm is reliable in the large sample limit. Constraint-based causal discovery (CCD) algorithms require fast and accurate conditional independence (CI) testing. The Kernel Conditional Independence Test (KCIT) is currently one of the most popular CI tests in the non-parametric setting, but many investigators cannot use KCIT with large datasets because the test scales cubicly with sample size. We therefore devise two relaxations called the Randomized Conditional Independence Test (RCIT) and the Randomized conditional Correlation Test (RCoT) which both approximate KCIT by utilizing random Fourier features. In practice, both of the proposed tests scale linearly with sample size and return accurate p-values much faster than KCIT in the large sample size context. CCD algorithms run with RCIT or RCoT also return graphs at least as accurate as the same algorithms run with KCIT but with large reductions in run time. It is known that there exists a PCP characterization of NP where the verifier makes 3 queries and has a one-sided error that is bounded away from 1; and also that 2 queries do not suffice for such a characterization. Thus PCPs with 3 queries possess non-trivial verification power and motivate the task of determining the lowest error that can be achieved with a 3-query PCP. Recently, Hastad (1997) has shown a tight characterization of NP by constructing a 3-query PCP verifier with "error" arbitrarily close to 1 2. Unfortunately this verifier makes two-sided error and Hastad makes essential use of this feature. One-sided error, on the other hand, is a natural notion to associate with a proof system, since it has the desirable property that every rejected proof has a short counterexample. The question of determining the smallest error for which there exists a 3-query PCP verifier making one-sided error and accepting an NP-complete language, however, remained open. We resolve this question by showing that NP has a 3-query PCP with a one-sided error that is arbitrarily close to 1 2. This characterization is tight, i.e., the error cannot be lower. This result is in seeming contradiction with the results of Trevisan (1997) and Zwick (1998) who show that in order to recognize an NP-complete language, the error probability of a PCP verifier making 3 non-adaptive queries and having one-sided error must be at least 5 8. We get around this bottleneck by designing an adaptive 3-query PCP for NP. Our result yields the first tight analysis of an adaptive PCP; and reveals a previously unsuspected separation between the powers of adaptive and non-adaptive PCPs. Our design and analysis of adaptive PCPs can be extended to higher number of queries as well and we give an example of such a proof system with 5 queries. Our adaptive verifiers yield proof systems whose error probabilities match those of previous constructions, while also achieving one-sidedness in the error. This raises new questions about the power of adaptive PCPs, which deserve further study. We introduce a new function-preserving transformation for efficient neural architecture search. This network transformation allows reusing previously trained networks and existing successful architectures that improves sample efficiency. We aim to address the limitation of current network transformation operations that can only perform layer-level architecture modifications, such as adding (pruning) filters or inserting (removing) a layer, which fails to change the topology of connection paths. Our proposed path-level transformation operations enable the meta-controller to modify the path topology of the given network while keeping the merits of reusing weights, and thus allow efficiently designing effective structures with complex path topologies like Inception models. We further propose a bidirectional tree-structured reinforcement learning meta-controller to explore a simple yet highly expressive tree-structured architecture space that can be viewed as a generalization of multi-branch architectures. We experimented on the image classification datasets with limited computational resources (about 200 GPU-hours), where we observed improved parameter efficiency and better test results (97.70 test accuracy on CIFAR-10 with 14.3M parameters and 74.6 top-1 accuracy on ImageNet in the mobile setting), demonstrating the effectiveness and transferability of our designed architectures. Fort now and Klivans proved the following relationship between efficient learning algorithms and circuit lower bounds: if a class of boolean circuits C contained in P poly of Boolean is exactly learnable with membership and equivalence queries in polynomial-time, then EXP^NP is not contained in C (the class EXP^NP was subsequently improved to EXP by Hitchcock and Harkins). In this paper, we improve on these results and show * If C is exactly learnable with membership and equivalence queries in polynomial-time, then DTIME(n^ (1) ) is not contained in C. We obtain even stronger consequences if C is learnable in the mistake-bounded model, in which case we prove an average-case hardness result against C. * If C is learnable in polynomial time in the PAC model then PSPACE is not contained in C, unless PSPACE is contained in BPP. Removing this extra assumption from the statement of the theorem would provide an unconditional separation of PSPACE and BPP. * If C is efficiently learnable in the Correlational Statistical Query (CSQ) model, we show that there exists an explicit function f that is average-case hard for circuits in C. This result provides stronger average-case hardness guarantees than those obtained by SQ-dimension arguments ( 1993). We also obtain a non-constructive extension of this result to the stronger Statistical Query (SQ) model. Similar results hold in the case where the learning algorithm runs in sub exponential time. Our proofs regarding exact and mistake-bounded learning are simple and self-contained, yield explicit hard functions, and show how to use mistake-bounded learners to "diagonalize"' over families of polynomial-size circuits. Our consequences for PAC learning lead to new proofs of Karp-Lipton-style collapse results, and the lower bounds from SQ learning make use of recent work relating combinatorial discrepancy to the existence of hard-on-average functions. When faced with high-dimensional data, one often uses principal component analysis (PCA) for dimension reduction. Classical PCA constructs a set of uncorrelated variables, which correspond to eigenvectors of the sample covariance matrix. However, it is well-known that this covariance matrix is strongly affected by anomalous observations. It is therefore necessary to apply robust methods that are resistant to possible outliers. Li and Chen [J. Am. Stat. Assoc. 80 (1985) 759] proposed a solution based on projection pursuit (PP). The idea is to search for the direction in which the projected observations have the largest robust scale. In subsequent steps, each new direction is constrained to be orthogonal to all previous directions. This method is very well suited for high-dimensional data, even when the number of variables p is higher than the number of observations n. However, the algorithm of Li and Chen has a high computational cost. In the references [C. Croux, A. Ruiz-Gazen, in COMPSTAT: Proceedings in Computational Statistics 1996, Physica-Verlag, Heidelberg, 1996, pp. 211–217; C. Croux and A. Ruiz-Gazen, High Breakdown Estimators for Principal Components: the Projection-Pursuit Approach Revisited, 2000, submitted for publication.], a computationally much more attractive method is presented, but in high dimensions (large p) it has a numerical accuracy problem and still consumes much computation time. In this paper, we construct a faster two-step algorithm that is more stable numerically. The new algorithm is illustrated on a data set with four dimensions and on two chemometrical data sets with 1200 and 600 dimensions. We present a hybrid constraint-based Bayesian algorithm for learning causal networks in the presence of sparse data. The algorithm searches the space of equivalence classes of models (essential graphs) using a heuristic based on conventional constraint-based techniques. Each essential graph is then converted into a directed acyclic graph and scored using a Bayesian scoring metric. Two variants of the algorithm are developed and tested using data from randomly generated networks of sizes from 15 to 45 nodes with data sizes ranging from 250 to 2000 records. Both variations are compared to, and found to consistently outperform two variations of greedy search with restarts. The discovery of causal relationships from purely observational data is a fundamental problem in science. The most elementary form of such a causal discovery problem is to decide whether X causes Y or, alternatively, Y causes X, given joint observations of two variables X,Y. An example is to decide whether altitude causes temperature, or vice versa, given only joint measurements of both variables. Even under the simplifying assumptions of no confounding, no feedback loops, and no selection bias, such bivariate causal discovery problems are challenging. Nevertheless, several approaches for addressing those problems have been proposed in recent years. We review two families of such methods: methods based on Additive Noise Models (ANMs) and Information Geometric Causal Inference (IGCI). We present the benchmark CAUSEEFFECTPAIRS that consists of data for 100 different causee ffect pairs selected from 37 data sets from various domains (e.g., meteorology, biology, medicine, engineering, economy, etc.) and motivate our decisions regarding the "ground truth" causal directions of all pairs. We evaluate the performance of several bivariate causal discovery methods on these real-world benchmark data and in addition on artificially simulated data. Our empirical results on real-world data indicate that certain methods are indeed able to distinguish cause from effect using only purely observational data, although more benchmark data would be needed to obtain statistically significant conclusions. One of the best performing methods overall is the method based on Additive Noise Models that has originally been proposed by (2009), which obtains an accuracy of 63 ± 10 and an AUC of 0.74 ± 0.05 on the real-world benchmark. As the main theoretical contribution of this work we prove the consistency of that method. We introduce a novel generative model for interpretable subgroup analysis for causal inference applications, Causal Rule Sets (CRS). A CRS model uses a small set of short rules to capture a subgroup where the average treatment effect is elevated compared to the entire population. We present a Bayesian framework for learning a causal rule set. The Bayesian framework consists of a prior that favors simpler models and a Bayesian logistic regression that characterizes the relation between outcomes, attributes and subgroup membership. We find maximum a posteriori models using discrete Monte Carlo steps in the joint solution space of rules sets and parameters. We provide theoretically grounded heuristics and bounding strategies to improve search efficiency. Experiments show that the search algorithm can efficiently recover a true underlying subgroup and CRS shows consistently competitive performance compared to other state-of-the-art baseline methods. We show that, under a standard hardness assumption, there is no computationally efficient algorithm that given @math samples from an unknown distribution can give valid answers to @math adaptively chosen statistical queries. A statistical query asks for the expectation of a predicate over the underlying distribution, and an answer to a statistical query is valid if it is "close" to the correct expectation over the distribution. Our result stands in stark contrast to the well known fact that exponentially many statistical queries can be answered validly and efficiently if the queries are chosen non-adaptively (no query may depend on the answers to previous queries). Moreover, a recent work by shows how to accurately answer exponentially many adaptively chosen statistical queries via a computationally inefficient algorithm; and how to answer a quadratic number of adaptive queries via a computationally efficient algorithm. The latter result implies that our result is tight up to a linear factor in @math Conceptually, our result demonstrates that achieving statistical validity alone can be a source of computational intractability in adaptive settings. For example, in the modern large collaborative research environment, data analysts typically choose a particular approach based on previous findings. False discovery occurs if a research finding is supported by the data but not by the underlying distribution. While the study of preventing false discovery in Statistics is decades old, to the best of our knowledge our result is the first to demonstrate a computational barrier. In particular, our result suggests that the perceived difficulty of preventing false discovery in today's collaborative research environment may be inherent. We show that the Graph Isomorphism (GI) problem and the more general problems of String Isomorphism (SI) andCoset Intersection (CI) can be solved in quasipolynomial(exp((logn)O(1))) time. The best previous bound for GI was exp(O( √n log n)), where n is the number of vertices (Luks, 1983); for the other two problems, the bound was similar, exp(O (√ n)), where n is the size of the permutation domain (Babai, 1983). Following the approach of Luks’s seminal 1980 82 paper, the problem we actually address is SI. This problem takes two strings of length n and a permutation group G of degree n (the “ambient group”) as input (G is given by a list of generators) and asks whether or not one of the strings can be transformed into the other by some element of G. Luks’s divide-and-conquer algorithm for SI proceeds by recursion on the ambient group. We build on Luks’s framework and attack the obstructions to efficient Luks recurrence via an interplay between local and global symmetry. We construct group theoretic “local certificates” to certify the presence or absence of local symmetry, aggregate the negative certificates to canonical k-ary relations where k = O(log n), and employ combinatorial canonical partitioning techniques to split the k-ary relational structure for efficient divide-and- conquer. We show that in a well–defined sense, Johnson graphs are the only obstructions to effective canonical partitioning. The central element of the algorithm is the “local certificates” routine which is based on a new group theoretic result, the “Unaffected stabilizers lemma,” that allows us to construct global automorphisms out of local information. Randomised controlled trials (RCTs) are the most effective approach to causal discovery, but in many circumstances it is impossible to conduct RCTs. Therefore, observational studies based on passively observed data are widely accepted as an alternative to RCTs. However, in observational studies, prior knowledge is required to generate the hypotheses about the cause-effect relationships to be tested, and hence they can only be applied to problems with available domain knowledge and a handful of variables. In practice, many datasets are of high dimensionality, which leaves observational studies out of the opportunities for causal discovery from such a wealth of data sources. In another direction, many efficient data mining methods have been developed to identify associations among variables in large datasets. The problem is that causal relationships imply associations, but the reverse is not always true. However, we can see the synergy between the two paradigms here. Specifically, association rule mining can be used to deal with the high-dimensionality problem, whereas observational studies can be utilised to eliminate noncausal associations. In this article, we propose the concept of causal rules (CRs) and develop an algorithm for mining CRs in large datasets. We use the idea of retrospective cohort studies to detect CRs based on the results of association rule mining. Experiments with both synthetic and real-world datasets have demonstrated the effectiveness and efficiency of CR mining. In comparison with the commonly used causal discovery methods, the proposed approach generally is faster and has better or competitive performance in finding correct or sensible causes. It is also capable of finding a cause consisting of multiple variables—a feature that other causal discovery methods do not possess. We introduce a 2-round stochastic constraint-satisfaction problem, and show that its approximation version is complete for (the promise version of) the complexity class AM. This gives a PCP characterization' of AM analogous to the PCP Theorem for NP. Similar characterizations have been given for higher levels of the Polynomial Hierarchy, and for PSPACE; however, we suggest that the result for AM might be of particular significance for attempts to derandomize this class. To test this notion, we pose some Randomized Optimization Hypotheses' related to our stochastic CSPs that (in light of our result) would imply collapse results for AM. Unfortunately, the hypotheses appear over-strong, and we present evidence against them. In the process we show that, if some language in NP is hard-on-average against circuits of size 2^ Omega(n) , then there exist hard-on-average optimization problems of a particularly elegant form. All our proofs use a powerful form of PCPs known as Probabilistically Checkable Proofs of Proximity, and demonstrate their versatility. We also use known results on randomness-efficient soundness- and hardness-amplification. In particular, we make essential use of the Impagliazzo-Wigderson generator; our analysis relies on a recent Chernoff-type theorem for expander walks. In the conclusion of his monumental paper on optimal inapproximability results, Hastad [13] suggested that Fourier analysis of Dictator (Long Code) Tests may not be universally applicable in the study of CSPs. His main open question was to determine if the technique could resolve the approximability of satisfiable 3-bit constraint satisfaction problems. In particular, he asked if the "Not Two" (NTW) predicate is non-approximable beyond the random assignment threshold of 5 8 on satisfiable instances. Around the same time, Zwick [30] showed that all satisfiable 3-CSPs are 5 8-approximable and conjectured that the 5 8 is optimal. In this work we show that Fourier analysis techniques can produce a Dictator Test based on NTW with completeness 1 and soundness 5 8. Our test's analysis uses the Bonami-Gross-Beckner hypercontractive inequality. We also show a soundness lower bound of 5 8 for all 3-query Dictator Tests with perfect completeness. This lower bound for Property Testing is proved in part via a semidefinite programming algorithm of Zwick [30]. Our work precisely determines the 3-query "Dictatorship Testing gap". Although this represents progress on Zwick's conjecture, current PCP "outer verifier" technology is insufficient to convert our Dictator Test into an NP-hardness-of-approximation result. 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. Machine learning is now being used to make crucial decisions about people's lives. For nearly all of these decisions there is a risk that individuals of a certain race, gender, sexual orientation, or any other subpopulation are unfairly discriminated against. Our recent method has demonstrated how to use techniques from counterfactual inference to make predictions fair across different subpopulations. This method requires that one provides the causal model that generated the data at hand. In general, validating all causal implications of the model is not possible without further assumptions. Hence, it is desirable to integrate competing causal models to provide counterfactually fair decisions, regardless of which causal "world" is the correct one. In this paper, we show how it is possible to make predictions that are approximately fair with respect to multiple possible causal models at once, thus mitigating the problem of exact causal specification. We frame the goal of learning a fair classifier as an optimization problem with fairness constraints entailed by competing causal explanations. We show how this optimization problem can be efficiently solved using gradient-based methods. We demonstrate the flexibility of our model on two real-world fair classification problems. We show that our model can seamlessly balance fairness in multiple worlds with prediction accuracy. Discovering causal relationships in large databases of observational data is challenging. The pioneering work in this area was rooted in the theory of Bayesian network (BN) learning, which however, is a NP-complete problem. Hence several constraint-based algorithms have been developed to efficiently discover causations in large databases. These methods usually use the idea of BN learning, directly or indirectly, and are focused on causal relationships with single cause variables. In this paper, we propose an approach to mine causal rules in large databases of binary variables. Our method expands the scope of causality discovery to causal relationships with multiple cause variables, and we utilise partial association tests to exclude noncausal associations, to ensure the high reliability of discovered causal rules. Furthermore an efficient algorithm is designed for the tests in large databases. We assess the method with a set of real-world diagnostic data. The results show that our method can effectively discover interesting causal rules in large databases. We show a new way to round vector solutions of semidefinite programming (SDP) hierarchies into integral solutions, based on a connection between these hierarchies and the spectrum of the input graph. We demonstrate the utility of our method by providing a new SDP-hierarchy based algorithm for constraint satisfaction problems with 2-variable constraints (2-CSP's). More concretely, we show for every 2-CSP instance I a rounding algorithm for r rounds of the Lasserre SDP hierarchy for I that obtains an integral solution that is at most worse than the relaxation's value (normalized to lie in [0,1]), as long as r > k ( ) ( ) ;, where k is the alphabet size of I, @math , and @math denotes the number of eigenvalues larger than @math in the normalized adjacency matrix of the constraint graph of @math . In the case that @math is a instance, the threshold @math is only a polynomial in @math , and is independent of the alphabet size. Also in this case, we can give a non-trivial bound on the number of rounds for instance. In particular our result yields an SDP-hierarchy based algorithm that matches the performance of the recent subexponential algorithm of Arora, Barak and Steurer (FOCS 2010) in the worst case, but runs faster on a natural family of instances, thus further restricting the set of possible hard instances for Khot's Unique Games Conjecture. Our algorithm actually requires less than the @math constraints specified by the @math level of the Lasserre hierarchy, and in some cases @math rounds of our program can be evaluated in time @math . For the tensor PCA (principal component analysis) problem, we propose a new hierarchy of algorithms that are increasingly powerful yet require increasing runtime. Our hierarchy is analogous to the sum-of-squares (SOS) hierarchy but is instead inspired by statistical physics and related algorithms such as belief propagation and AMP (approximate message passing). Our level- @math algorithm can be thought of as a (linearized) message-passing algorithm that keeps track of @math -wise dependencies among the hidden variables. Specifically, our algorithms are spectral methods based on the Kikuchi Hessian matrix, which generalizes the well-studied Bethe Hessian matrix to the higher-order Kikuchi free energies. It is known that AMP, the flagship algorithm of statistical physics, has substantially worse performance than SOS for tensor PCA. In this work we redeem' the statistical physics approach by showing that our hierarchy gives a polynomial-time algorithm matching the performance of SOS. Our hierarchy also yields a continuum of subexponential-time algorithms, and we prove that these achieve the same (conjecturally optimal) tradeoff between runtime and statistical power as SOS. Our results hold for even-order tensors, and we conjecture that they also hold for odd-order tensors. Our methods suggest a new avenue for systematically obtaining optimal algorithms for Bayesian inference problems, and our results constitute a step toward unifying the statistical physics and sum-of-squares approaches to algorithm design.