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
1957379630 2110893740 1961009203 2066277072 2153037482 2060515712 1520257903 2051332471 2902208421 2085638007 1511277043 114321176 1961345416 1992862710 2112671715 1977455514 1492644044 2040825624 2112247328 1808652302
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. 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. Mining for association rules in market basket data has proved a fruitful area of research. Measures such as conditional probability (confidence) and correlation have been used to infer rules of the form “the existence of item A implies the existence of item B.” However, such rules indicate only a statistical relationship between A and B. They do not specify the nature of the relationship: whether the presence of A causes the presence of B, or the converse, or some other attribute or phenomenon causes both to appear together. In applications, knowing such causal relationships is extremely useful for enhancing understanding and effecting change. While distinguishing causality from correlation is a truly difficult problem, recent work in statistics and Bayesian learning provide some avenues of attack. In these fields, the goal has generally been to learn complete causal models, which are essentially impossible to learn in large-scale data mining applications with a large number of variables. In this paper, we consider the problem of determining casual relationships, instead of mere associations, when mining market basket data. We identify some problems with the direct application of Bayesian learning ideas to mining large databases, concerning both the scalability of algorithms and the appropriateness of the statistical techniques, and introduce some initial ideas for dealing with these problems. We present experimental results from applying our algorithms on several large, real-world data sets. The results indicate that the approach proposed here is both computationally feasible and successful in identifying interesting causal structures. An interesting outcome is that it is perhaps easier to infer the lack of causality than to infer causality, information that is useful in preventing erroneous decision making. Many techniques for association rule mining and feature selection require a suitable metric to capture the dependencies among variables in a data set. For example, metrics such as support, confidence, lift, correlation, and collective strength are often used to determine the interestingness of association patterns. However, many such measures provide conflicting information about the interestingness of a pattern, and the best metric to use for a given application domain is rarely known. In this paper, we present an overview of various measures proposed in the statistics, machine learning and data mining literature. We describe several key properties one should examine in order to select the right measure for a given application domain. A comparative study of these properties is made using twenty one of the existing measures. We show that each measure has different properties which make them useful for some application domains, but not for others. We also present two scenarios in which most of the existing measures agree with each other, namely, support-based pruning and table standardization. Finally, we present an algorithm to select a small set of tables such that an expert can select a desirable measure by looking at just this small set of tables. Motivation: Approaches for testing sets of variants, such as a set of rare or common variants within a gene or pathway, for association with complex traits are important. In particular, set tests allow for aggregation of weak signal within a set, can capture interplay among variants and reduce the burden of multiple hypothesis testing. Until now, these approaches did not address confounding by family relatedness and population structure, a problem that is becoming more important as larger datasets are used to increase power. Results: We introduce a new approach for set tests that handles confounders. Our model is based on the linear mixed model and uses two random effects—one to capture the set association signal and one to capture confounders. We also introduce a computational speedup for two random-effects models that makes this approach feasible even for extremely large cohorts. Using this model with both the likelihood ratio test and score test, we find that the former yields more power while controlling type I error. Application of our approach to richly structured Genetic Analysis Workshop 14 data demonstrates that our method successfully corrects for population structure and family relatedness, whereas application of our method to a 15 000 individual Crohn’s disease case–control cohort demonstrates that it additionally recovers genes not recoverable by univariate analysis. Availability: A Python-based library implementing our approach is available at http: mscompbio.codeplex.com. Contact:jennl@microsoft.com or lippert@microsoft.com or heckerma@microsoft.com Supplementary information:Supplementary data are available at Bioinformatics online. The wealth of interaction information provided in biomedical articles motivated the implementation of text mining approaches to automatically extract biomedical relations. This paper presents an unsupervised method based on pattern clustering and sentence parsing to deal with biomedical relation extraction. Pattern clustering algorithm is based on Polynomial Kernel method, which identifies interaction words from unlabeled data; these interaction words are then used in relation extraction between entity pairs. Dependency parsing and phrase structure parsing are combined for relation extraction. Based on the semi-supervised KNN algorithm, we extend the proposed unsupervised approach to a semi-supervised approach by combining pattern clustering, dependency parsing and phrase structure parsing rules. We evaluated the approaches on two different tasks: (1) Protein–protein interactions extraction, and (2) Gene–suicide association extraction. The evaluation of task (1) on the benchmark dataset (AImed corpus) showed that our proposed unsupervised approach outperformed three supervised methods. The three supervised methods are rule based, SVM based, and Kernel based separately. The proposed semi-supervised approach is superior to the existing semi-supervised methods. The evaluation on gene–suicide association extraction on a smaller dataset from Genetic Association Database and a larger dataset from publicly available PubMed showed that the proposed unsupervised and semi-supervised methods achieved much higher F-scores than co-occurrence based method. Finding interesting association rules is an important and active research field in data mining. The algorithms of the Apriori family are based on two rule extraction measures, support and confidence. Although these two measures have the virtue of being algorithmically fast, they generate a prohibitive number of rules most of which are redundant and irrelevant. It is therefore necessary to use further measures which filter uninteresting rules. Many synthesis studies were then realized on the interestingness measures according to several points of view. Different reported studies have been carried out to identify "good" properties of rule extraction measures and these properties have been assessed on 61 measures. The purpose of this paper is twofold. First to extend the number of the measures and properties to be studied, in addition to the formalization of the properties proposed in the literature. Second, in the light of this formal study, to categorize the studied measures. This paper leads then to identify categories of measures in order to help the users to efficiently select an appropriate measure by choosing one or more measure(s) during the knowledge extraction process. The properties evaluation on the 61 measures has enabled us to identify 7 classes of measures, classes that we obtained using two different clustering techniques. 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. Motivated by settings in which predictive models may be required to be non-discriminatory with respect to certain attributes (such as race), but even collecting the sensitive attribute may be forbidden or restricted, we initiate the study of fair learning under the constraint of differential privacy. We design two learning algorithms that simultaneously promise differential privacy and equalized odds, a 'fairness' condition that corresponds to equalizing false positive and negative rates across protected groups. Our first algorithm is a private implementation of the equalized odds post-processing approach of [, 2016]. This algorithm is appealingly simple, but must be able to use protected group membership explicitly at test time, which can be viewed as a form of 'disparate treatment'. Our second algorithm is a differentially private version of the oracle-efficient in-processing approach of [, 2018] that can be used to find the optimal fair classifier, given access to a subroutine that can solve the original (not necessarily fair) learning problem. This algorithm is more complex but need not have access to protected group membership at test time. We identify new tradeoffs between fairness, accuracy, and privacy that emerge only when requiring all three properties, and show that these tradeoffs can be milder if group membership may be used at test time. We conclude with a brief experimental evaluation. From the standpoint of supporting human-centered discovery of knowledge, the present-day model of mining association rules suffers from the following serious shortcomings: (i) lack of user exploration and control, (ii) lack of focus, and (iii) rigid notion of relationships. In effect, this model functions as a black-box, admitting little user interaction in between. We propose, in this paper, an architecture that opens up the black-box, and supports constraint-based, human-centered exploratory mining of associations. The foundation of this architecture is a rich set of constraint constructs, including domain, class, and SQL-style aggregate constraints, which enable users to clearly specify what associations are to be mined. We propose constrained association queries as a means of specifying the constraints to be satisfied by the antecedent and consequent of a mined association. In this paper, we mainly focus on the technical challenges in guaranteeing a level of performance that is commensurate with the selectivities of the constraints in an association query. To this end, we introduce and analyze two properties of constraints that are critical to pruning: anti-monotonicity and succinctness . We then develop characterizations of various constraints into four categories, according to these properties. Finally, we describe a mining algorithm called CAP, which achieves a maximized degree of pruning for all categories of constraints. Experimental results indicate that CAP can run much faster, in some cases as much as 80 times, than several basic algorithms. This demonstrates how important the succinctness and anti-monotonicity properties are, in delivering the performance guarantee. One of the more well-studied problems in data mining is the search for association rules in market basket data. Association rules are intended to identify patterns of the type: “A customer purchasing item A often also purchases item B.” Motivated partly by the goal of generalizing beyond market basket data and partly by the goal of ironing out some problems in the definition of association rules, we develop the notion of dependence rules that identify statistical dependence in both the presence and absence of items in itemsets. We propose measuring significance of dependence via the chi-squared test for independence from classical statistics. This leads to a measure that is upward-closed in the itemset lattice, enabling us to reduce the mining problem to the search for a border between dependent and independent itemsets in the lattice. We develop pruning strategies based on the closure property and thereby devise an efficient algorithm for discovering dependence rules. We demonstrate our algorithm‘s effectiveness by testing it on census data, text data (wherein we seek term dependence), and synthetic data. An unsupervised iterative approach for extracting a new lexicon (or unknown words) from a Chinese text corpus is proposed in this paper. Instead of using a non-iterative segmentation-merging-filtering-and-disambiguation approach, the proposed method iteratively integrates the contextual constraints (among word candidates) and a joint character association metric to progressively improve the segmentation results of the input corpus (and thus the new word list.) An augmented dictionary, which includes potential unknown words (in addition to known words), is used to segment the input corpus, unlike traditional approaches which use only known words for segmentation. In the segmentation process, the augmented dictionary is used to impose contextual constraints over known words and potential unknown words within input sentences; an unsupervised Viterbi Training process is then applied to ensure that the selected potential unknown words (and known words) maximize the likelihood of the input corpus. On the other hand, the joint character association metric (which reflects the global character association characteristics across the corpus) is derived by integrating several commonly used word association metrics, such as mutual information and entropy, with a joint Gaussian mixture density function; such integration allows the filter to use multiple features simultaneously to evaluate character association, unlike traditional filters which apply multiple features independently. The proposed method then allows the contextual constraints and the joint character association metric to enhance each other; this is achieved by iteratively applying the joint association metric to truncate unlikely unknown words in the augmented dictionary and using the segmentation result to improve the estimation of the joint association metric. The refined augmented dictionary and improved estimation are then used in the next iteration to acquire better segmentation and carry out more reliable filtering. Experiments show that both the precision and recall rates are improved almost monotonically, in contrast to non-iterative segmentation-merging-filtering-and-disambiguation approaches, which often sacrifice precision for recall or vice versa. With a corpus of 311,591 sentences, the performance is 76 (bigram), 54 (trigram), and 70 (quadragram) in F-measure, which is significantly better than using the non-iterative approach with F-measures of 74 (bigram), 46 (trigram), and 58 (quadragram). With the spread of data mining technologies and the accumulation of social data, such technologies and data are being used for determinations that seriously affect individuals' lives. For example, credit scoring is frequently determined based on the records of past credit data together with statistical prediction techniques. Needless to say, such determinations must be nondiscriminatory and fair in sensitive features, such as race, gender, religion, and so on. Several researchers have recently begun to attempt the development of analysis techniques that are aware of social fairness or discrimination. They have shown that simply avoiding the use of sensitive features is insufficient for eliminating biases in determinations, due to the indirect influence of sensitive information. In this paper, we first discuss three causes of unfairness in machine learning. We then propose a regularization approach that is applicable to any prediction algorithm with probabilistic discriminative models. We further apply this approach to logistic regression and empirically show its effectiveness and efficiency. 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. Traditional text mining techniques transform free text into flat bags of words representation, which does not preserve sufficient semantics for the purpose of knowledge discovery. In this paper, we present a two-step procedure to mine generalized associations of semantic relations conveyed by the textual content of Web documents. First, RDF (resource description framework) metadata representing semantic relations are extracted from raw text using a myriad of natural language processing techniques. The relation extraction process also creates a term taxonomy in the form of a sense hierarchy inferred from WordNet. Then, a novel generalized association pattern mining algorithm (GP-Close) is applied to discover the underlying relation association patterns on RDF metadata. For pruning the large number of redundant overgeneralized patterns in relation pattern search space, the GP-Close algorithm adopts the notion of generalization closure for systematic overgeneralization reduction. The efficacy of our approach is demonstrated through empirical experiments conducted on an online database of terrorist activities Data association is a fundamental problem in multisensor fusion, tracking, and localization. The joint compatibility test is commonly regarded as the true solution to the problem. However, traditional joint compatibility tests are computationally expensive, are sensitive to linearization errors, and require the knowledge of the full covariance matrix of state variables. The paper proposes a posterior-based joint compatibility test scheme to conquer the three problems mentioned above. The posterior-based test naturally separates the test of state variables from the test of observations. Therefore, through the introduction of the robot movement and proper approximation, the joint test process is sequentialized to the sum of individual tests; therefore, the test has O(n) complexity (compared with O(n2) for traditional tests), where n denotes the total number of related observations. At the same time, the sequentialized test neither requires the knowledge to the full covariance matrix of state variables nor is sensitive to linearization errors caused by poor pose estimates. The paper also shows how to apply the proposed method to various simultaneous localization and mapping (SLAM) algorithms. Theoretical analysis and experiments on both simulated data and popular datasets show the proposed method outperforms some classical algorithms, including sequential compatibility nearest neighbor (SCNN), random sample consensus (RANSAC), and joint compatibility branch and bound (JCBB), on precision, efficiency, and robustness. 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. With the spread of data mining technologies and the accumulation of social data, such technologies and data are being used for determinations that seriously affect people's lives. For example, credit scoring is frequently determined based on the records of past credit data together with statistical prediction techniques. Needless to say, such determinations must be socially and legally fair from a viewpoint of social responsibility, namely, it must be unbiased and nondiscriminatory in sensitive features, such as race, gender, religion, and so on. Several researchers have recently begun to attempt the development of analysis techniques that are aware of social fairness or discrimination. They have shown that simply avoiding the use of sensitive features is insufficient for eliminating biases in determinations, due to the indirect influence of sensitive information. From a privacy-preserving viewpoint, this can be interpreted as hiding sensitive information when classification results are observed. In this paper, we first discuss three causes of unfairness in machine learning. We then propose a regularization approach that is applicable to any prediction algorithm with probabilistic discriminative models. We further apply this approach to logistic regression and empirically show its effectiveness and efficiency. In this paper, we define and study a novel text mining problem, which we refer to as Comparative Text Mining (CTM). Given a set of comparable text collections, the task of comparative text mining is to discover any latent common themes across all collections as well as summarize the similarity and differences of these collections along each common theme. This general problem subsumes many interesting applications, including business intelligence and opinion summarization. We propose a generative probabilistic mixture model for comparative text mining. The model simultaneously performs cross-collection clustering and within-collection clustering, and can be applied to an arbitrary set of comparable text collections. The model can be estimated efficiently using the Expectation-Maximization (EM) algorithm. We evaluate the model on two different text data sets (i.e., a news article data set and a laptop review data set), and compare it with a baseline clustering method also based on a mixture model. Experiment results show that the model is quite effective in discovering the latent common themes across collections and performs significantly better than our baseline mixture model. Objective To summarize literature describing approaches aimed at automatically identifying patients with a common phenotype. @PARASPLIT Materials and methods We performed a review of studies describing systems or reporting techniques developed for identifying cohorts of patients with specific phenotypes. Every full text article published in (1) Journal of American Medical Informatics Association , (2) Journal of Biomedical Informatics , (3) Proceedings of the Annual American Medical Informatics Association Symposium , and (4) Proceedings of Clinical Research Informatics Conference within the past 3 years was assessed for inclusion in the review. Only articles using automated techniques were included. @PARASPLIT Results Ninety-seven articles met our inclusion criteria. Forty-six used natural language processing (NLP)-based techniques, 24 described rule-based systems, 41 used statistical analyses, data mining, or machine learning techniques, while 22 described hybrid systems. Nine articles described the architecture of large-scale systems developed for determining cohort eligibility of patients. @PARASPLIT Discussion We observe that there is a rise in the number of studies associated with cohort identification using electronic medical records. Statistical analyses or machine learning, followed by NLP techniques, are gaining popularity over the years in comparison with rule-based systems. @PARASPLIT Conclusions There are a variety of approaches for classifying patients into a particular phenotype. Different techniques and data sources are used, and good performance is reported on datasets at respective institutions. However, no system makes comprehensive use of electronic medical records addressing all of their known weaknesses.