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.
In another direction, @cite_58 proposed an efficient method for testing the persistent associations between the target variable and its neighbours. The method is based on partial association tests and association rule mining framework to remove the spurious associations. In a similar fashion, @cite_4 @cite_20 integrated the ideas of retrospective cohort study with the association rule mining framework. They proposed to divide the samples into two groups of individuals, who share common characteristics but differ in regard to a certain factor of interest. The newly-designed dataset is called fair dataset" and is used to infer the level of influence that the factor of interest affects the target variable. These works were extended in @cite_61 , and the software tools were also provided. However, these methods are only applicable for binary datasets with a fixed target variable, and thus may not be suitable for high dimensional datasets, e.g. gene expression data.
@cite_61 @cite_58 @cite_4 @cite_20
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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. This brief presents four practical methods to effectively explore causal relationships, which are often used for explanation, prediction and decision making in medicine, epidemiology, biology, economics, physics and social sciences. The first two methods apply conditional independence tests for causal discovery. The last two methods employ association rule mining for efficient causal hypothesis generation, and a partial association test and retrospective cohort study for validating the hypotheses. All four methods are innovative and effective in identifying potential causal relationships around a given target, and each has its own strength and weakness. For each method, a software tool is provided along with examples demonstrating its use. Practical Approaches to Causal Relationship Exploration is designed for researchers and practitioners working in the areas of artificial intelligence, machine learning, data mining, and biomedical research. The material also benefits advanced students interested in causal relationship discovery. 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. Discovering causal relationships is the ultimate goal of many scientific explorations. Causal relationships can be identified with controlled experiments, but such experiments are often very expensive and sometimes impossible to conduct. On the other hand, the collection of observational data has increased dramatically in recent decades. Therefore it is desirable to find causal relationships from the data directly. Significant progress has been made in the field of discovering causal relationships using the Causal Bayesian Network (CBN) theory. The applications of CBNs, however, are greatly limited due to the high computational complexity. In another direction, association rule mining has been shown to be an efficient data mining means for relationship discovery. However, although causal relationships imply associations, the reverse does not always hold. In this paper we study how to use an efficient association mining approach to discover potential causal rules in observational data. We make use of the idea of retrospective cohort studies, a widely used approach in medical and social research, to detect causal association rules. In comparison with the constraint-based methods within the CBN paradigm, the proposed approach is faster and is capable of finding a cause consisting of combined variables. In a document network such as a citation network of scientific documents, web-logs, etc., the content produced by authors exhibits their interest in certain topics. In addition some authors influence other authors' interests. In this work, we propose to model the influence of cited authors along with the interests of citing authors. Moreover, we hypothesize that apart from the citations present in documents, the context surrounding the citation mention provides extra topical information about the cited authors. However, associating terms in the context to the cited authors remains an open problem. We propose novel document generation schemes that incorporate the context while simultaneously modeling the interests of citing authors and influence of the cited authors. Our experiments show significant improvements over baseline models for various evaluation criteria such as link prediction between document and cited author, and quantitatively explaining unseen text. In this paper we propose to use association rules to mine the association relationships among different genes under the same experimental conditions. These kinds of relations may also exist across many different experiments with various experimental conditions. In this paper, a new approach, called FIS-tree mining, is proposed for mining the microarray data. Our approach uses two new data structures, BSC-tree and FIS-tree, and a data partition format for gene expression level data. Based on these two new data structures it is possible to mine the association rules efficiently and quickly from the gene expression database. Our algorithm was tested using the two real-life gene expression databases available at Stanford University and Harvard Medical School and was shown to perform better than the two existing algorithms, Apriori and FP-Growth. Association rules discovered through attribute-oriented induction are commonly used in data mining tools to express relationships between variables. However, causal inference algorithms discover more concise relationships between variables, namely, relations of direct cause. These algorithms produce regressive structured equation models for continuous linear data and Bayes networks for discrete data. This work compares the effectiveness of causal inference algorithms with association rule induction for discovering patterns in discrete data. Classification rule mining aims to discover a small set of rules in the database that forms an accurate classifier. Association rule mining finds all the rules existing in the database that satisfy some minimum support and minimum confidence constraints. For association rule mining, the target of discovery is not pre-determined, while for classification rule mining there is one and only one predetermined target. In this paper, we propose to integrate these two mining techniques. The integration is done by focusing on mining a special subset of association rules, called class association rules (CARs). An efficient algorithm is also given for building a classifier based on the set of discovered CARs. Experimental results show that the classifier built this way is, in general, more accurate than that produced by the state-of-the-art classification system C4.5. In addition, this integration helps to solve a number of problems that exist in the current classification systems. Motivation: Set-based variance component tests have been identified as a way to increase power in association studies by aggregating weak individual effects. However, the choice of test statistic has been largely ignored even though it may play an important role in obtaining optimal power. We compared a standard statistical test— a score test—with a recently developed likelihood ratio (LR) test. Further, when correction for hidden structure is needed, or gene– gene interactions are sought, state-of-the art algorithms for both the score and LR tests can be computationally impractical. Thus we develop new computationally efficient methods. Results: After reviewing theoretical differences in performance between the score and LR tests, we find empirically on real data that the LR test generally has more power. In particular, on 15 of 17 real datasets, the LR test yielded at least as many associations as the score test—up to 23 more associations—whereas the score test yielded at most one more association than the LR test in the two remaining datasets. On synthetic data, we find that the LR test yielded up to 12 more associations, consistent with our results on real data, but also observe a regime of extremely small signal where the score test yielded up to 25 more associations than the LR test, consistent with theory. Finally, our computational speedups now enable (i) efficient LR testing when the background kernel is full rank, and (ii) efficient score testing when the background kernel changes with each test, as for gene–gene interaction tests. The latter yielded a factor of 2000 speedup on a cohort of size 13 500. Availability: Software available at http: research.microsoft.com enus um redmond projects MSCompBio Fastlmm . A logistic regression model for application in retrospective studies is described and a study of the association of postmenopausal estrogen therapy with the incidence of endometrial cancer is given as an illustration. The method accounts for factors that may confound the association between a dichotomous exposure variable and a disease and allows for a quantitative study of the influence of factors which are related to the strength of the association. Associative classification is a rule-based approach to classify data relying on association rule mining by discovering associations between a set of features and a class label. Support and confidence are the de-facto "interestingness measures" used for discovering relevant association rules. The support-confidence framework has also been used in most, if not all, associative classifiers. Although support and confidence are appropriate measures for building a strong model in many cases, they are still not the ideal measures and other measures could be better suited. There are many other rule interestingness measures already used in machine learning, data mining and statistics. This work focuses on using 53 different objective measures for associative classification rules. A wide range of UCI datasets are used to study the impact of different "inter-estingness measures" on different phases of associative classifiers based on the number of rules generated and the accuracy obtained. The results show that there are interesting-ness measures that can significantly reduce the number of rules for almost all datasets while the accuracy of the model is hardly jeopardized or even improved. However, no single measure can be introduced as an obvious winner. Classification, which involves finding rules that partition a given da.ta set into disjoint groups, is one class of data mining problems. Approaches proposed so far for mining classification rules for large databases are mainly decision tree based symbolic learning methods. The connectionist approach based on neura.l networks has been thought not well suited for data mining. One of the major reasons cited is that knowledge generated by neural networks is not explicitly represented in the form of rules suitable for verification or interpretation by humans. This paper examines this issue. With our newly developed algorithms, rules which are similar to, or more concise than those generated by the symbolic methods can be extracted from the neural networks. The data mining process using neural networks with the emphasis on rule extraction is described. ExperimenM results and comparison with previously published works are presented. In this paper we discuss our study of the problems 12 software companies experienced in software development. In total we present qualitative data collected from 45 focus groups that involved over 200 software staff. We look at how different practitioner groups respond to software process improvement problems. We show our classification and analysis of this data using correspondence analysis. Correspondence analysis is a graphical data representation method new to software development research. The aim of the work we present is to develop a more holistic understanding of the problems practitioners are experiencing in their attempts to improve their software processes. Our main finding is that there is an association between a company’s capability maturity and patterns of reported problems. Organizational problems are more associated with high maturity companies than with low maturity companies. Low maturity companies are closely linked to problems relating directly to projects such as documentation, timescales, tools and technology. Our findings also confirm differences in practitioner group problems. Senior managers cite problems with goals, culture and politics. Project managers are concerned with timescales, change management, budgets and estimates. Developers are experiencing problems with requirements, testing, documentation, communication, tools and technology. These associations are displayed graphically through correspondence analysis maps. Due to the simplicity and efficiency, many hashing methods have recently been developed for large-scale similarity search. Most of the existing hashing methods focus on mapping low-level features to binary codes, but neglect attributes that are commonly associated with data samples. Attribute data, such as image tag, product brand, and user profile, can represent human recognition better than low-level features. However, attributes have specific characteristics, including high-dimensional, sparse and categorical properties, which is hardly leveraged into the existing hashing learning frameworks. In this paper, we propose a hashing learning framework, Probabilistic Attributed Hashing (PAH), to integrate attributes with low-level features. The connections between attributes and low-level features are built through sharing a common set of latent binary variables, i.e. hash codes, through which attributes and features can complement each other. Finally, we develop an efficient iterative learning algorithm, which is generally feasible for large-scale applications. Extensive experiments and comparison study are conducted on two public datasets, i.e., DBLP and NUS-WIDE. The results clearly demonstrate that the proposed PAH method substantially outperforms the peer methods. This article presents the design and implementation of a software tool, PROXIMUS, for error-bounded approximation of high-dimensional binary attributed datasets based on nonorthogonal decomposition of binary matrices. This tool can be used for analyzing data arising in a variety of domains ranging from commercial to scientific applications. Using a combination of innovative algorithms, novel data structures, and efficient implementation, PROXIMUS demonstrates excellent accuracy, performance, and scalability to large datasets. We experimentally demonstrate these on diverse applications in association rule mining and DNA microarray analysis. In limited beta release, PROXIMUS currently has over 300 installations in over 10 countries. The problem of discovering association rules has received considerable research attention and several fast algorithms for mining association rules have been developed. In practice, users are often interested in a subset of association rules. For example, they may only want rules that contain a specific item or rules that contain children of a specific item in a hierarchy. While such constraints can be applied as a post-processing step, integrating them into the mining algorithm can dramatically reduce the execution time. We consider the problem of integrating constraints that are Boolean expressions over the presence or absence of items into the association discovery algorithm. We present three integrated algorithms for mining association rules with item constraints and discuss their tradeoffs. Data mining services require accurate input data for their results to be meaningful, but privacy concerns may influence users to provide spurious information. We investigate here, with respect to mining association rules, whether users can be encouraged to provide correct information by ensuring that the mining process cannot, with any reasonable degree of certainty, violate their privacy. We present a scheme, based on probabilistic distortion of user data, that can simultaneously provide a high degree of privacy to the user and retain a high level of accuracy in the mining results. The performance of the scheme is validated against representative real and synthetic datasets. We propose an efficient frequent activity patterns mining in smart environments.We build an accurate activity classifier based on the mined frequent patterns.We distinguish overlapped activities with global and local weights of sensor events.We use publicly available dataset of smart environments to validate our methods. In the past decades, activity recognition has aroused a great interest for the research groups majoring in context-awareness computing and human behaviours monitoring. However, the correlations between the activities and their frequent patterns have never been directly addressed by traditional activity recognition techniques. As a result, activities that trigger the same set of sensors are difficult to differentiate, even though they present different patterns such as different frequencies of the sensor events. In this paper, we propose an efficient association rule mining technique to find the association rules between the activities and their frequent patterns, and build an activity classifier based on these association rules. We also address the classification of overlapped activities by incorporating the global and local weight of the patterns. The experiment results using publicly available dataset demonstrate that our method is able to achieve better performance than traditional recognition methods such as Decision Tree, Naive Bayesian and HMM. Comparison studies show that the proposed association rule mining method is efficient, and we can further improve the activity recognition accuracy by considering global and local weight of frequent patterns of activities. Background and objective Detecting complex patterns of association between genetic or environmental risk factors and disease risk has become an important target for epidemiological research. In particular, strategies that provide multifactor interactions or heterogeneous patterns of association can offer new insights into association studies for which traditional analytic tools have had limited success. Materials and methods To concurrently examine these phenomena, previous work has successfully considered the application of learning classifier systems (LCSs), a flexible class of evolutionary algorithms that distributes learned associations over a population of rules. Subsequent work dealt with the inherent problems of knowledge discovery and interpretation within these algorithms, allowing for the characterization of heterogeneous patterns of association. Whereas these previous advancements were evaluated using complex simulation studies, this study applied these collective works to a ‘real-world’ genetic epidemiology study of bladder cancer susceptibility. Results and discussion We replicated the identification of previously characterized factors that modify bladder cancer risk—namely, single nucleotide polymorphisms from a DNA repair gene, and smoking. Furthermore, we identified potentially heterogeneous groups of subjects characterized by distinct patterns of association. Cox proportional hazard models comparing clinical outcome variables between the cases of the two largest groups yielded a significant, meaningful difference in survival time in years (survivorship). A marginally significant difference in recurrence time was also noted. These results support the hypothesis that an LCS approach can offer greater insight into complex patterns of association. Conclusions This methodology appears to be well suited to the dissection of disease heterogeneity, a key component in the advancement of personalized medicine. A citing sentence is one that appears in a scientific article and cites previous work. Citing sentences have been studied and used in many applications. For example, they have been used in scientific paper summarization, automatic survey generation, paraphrase identification, and citation function classification. Citing sentences that cite multiple papers are common in scientific writing. This observation should be taken into consideration when using citing sentences in applications. For instance, when a citing sentence is used in a summary of a scientific paper, only the fragments of the sentence that are relevant to the summarized paper should be included in the summary. In this paper, we present and compare three different approaches for identifying the fragments of a citing sentence that are related to a given target reference. Our methods are: word classification, sequence labeling, and segment classification. Our experiments show that segment classification achieves the best results.