Exploiting Event Log Event Attributes in RNN Based Prediction

In predictive process analytics, current and historical process data in event logs are used to predict future. E.g., to predict the next activity or how long a process will still require to complete. Recurrent neural networks (RNN) and its subclasses have been demonstrated to be well suited for creating prediction models. Thus far, event attributes have not been fully utilized in these models. The biggest challenge in exploiting them in prediction models is the potentially large amount of event attributes and attribute values. We present a novel clustering technique which allows for trade-offs between prediction accuracy and the time needed for model training and prediction. As an additional finding, we also find that this clustering method combined with having raw event attribute values in some cases provides even better prediction accuracy at the cost of additional time required for training and prediction.Peer reviewe

Evaluation of clustering algorithms for gene expression data

BACKGROUND: Cluster analysis is an integral part of high dimensional data analysis. In the context of large scale gene expression data, a filtered set of genes are grouped together according to their expression profiles using one of numerous clustering algorithms that exist in the statistics and machine learning literature. A closely related problem is that of selecting a clustering algorithm that is "optimal" in some sense from a rather impressive list of clustering algorithms that currently exist. RESULTS: In this paper, we propose two validation measures each with two parts: one measuring the statistical consistency (stability) of the clusters produced and the other representing their biological functional congruence. Smaller values of these indices indicate better performance for a clustering algorithm. We illustrate this approach using two case studies with publicly available gene expression data sets: one involving a SAGE data of breast cancer patients and the other involving a time course cDNA microarray data on yeast. Six well known clustering algorithms UPGMA, K-Means, Diana, Fanny, Model-Based and SOM were evaluated. CONCLUSION: No single clustering algorithm may be best suited for clustering genes into functional groups via expression profiles for all data sets. The validation measures introduced in this paper can aid in the selection of an optimal algorithm, for a given data set, from a collection of available clustering algorithms

Female homicide in Rio Grande do Sul, Brazil

This study aimed to assess the female homicide rate due to aggression in Rio Grande do Sul, Brazil, using this as a "proxy" of femicide. This was an ecological study which correlated the female homicide rate due to aggression in Rio Grande do Sul, according to the 35 microregions defined by the Brazilian Institute of Geography and Statistics (IBGE), with socioeconomic and demographic variables access and health indicators. Pearson's correlation test was performed with the selected variables. After this, multiple linear regressions were performed with variables with p < 0.20. The standardized average of female homicide rate due to aggression in the period from 2003 to 2007 was 3.1 obits per 100 thousand. After multiple regression analysis, the final model included male mortality due to aggression (p = 0.016), the percentage of hospital admissions for alcohol (p = 0.005) and the proportion of ill-defined deaths (p = 0.015). The model have an explanatory power of 39% (adjusted r2 = 0.391). The results are consistent with other studies and indicate a strong relationship between structural violence in society and violence against women, in addition to a higher incidence of female deaths in places with high alcohol hospitalization

Randomization in Laboratory Procedure Is Key to Obtaining Reproducible Microarray Results

The quality of gene expression microarray data has improved dramatically since the first arrays were introduced in the late 1990s. However, the reproducibility of data generated at multiple laboratory sites remains a matter of concern, especially for scientists who are attempting to combine and analyze data from public repositories. We have carried out a study in which a common set of RNA samples was assayed five times in four different laboratories using Affymetrix GeneChip arrays. We observed dramatic differences in the results across laboratories and identified batch effects in array processing as one of the primary causes for these differences. When batch processing of samples is confounded with experimental factors of interest it is not possible to separate their effects, and lists of differentially expressed genes may include many artifacts. This study demonstrates the substantial impact of sample processing on microarray analysis results and underscores the need for randomization in the laboratory as a means to avoid confounding of biological factors with procedural effects

Randomization in Laboratory Procedure Is Key to Obtaining Reproducible Microarray Results

The quality of gene expression microarray data has improved dramatically since the first arrays were introduced in the late 1990s. However, the reproducibility of data generated at multiple laboratory sites remains a matter of concern, especially for scientists who are attempting to combine and analyze data from public repositories. We have carried out a study in which a common set of RNA samples was assayed five times in four different laboratories using Affymetrix GeneChip arrays. We observed dramatic differences in the results across laboratories and identified batch effects in array processing as one of the primary causes for these differences. When batch processing of samples is confounded with experimental factors of interest it is not possible to separate their effects, and lists of differentially expressed genes may include many artifacts. This study demonstrates the substantial impact of sample processing on microarray analysis results and underscores the need for randomization in the laboratory as a means to avoid confounding of biological factors with procedural effects

Methods for evaluating clustering algorithms for gene expression data using a reference set of functional classes

BACKGROUND: A cluster analysis is the most commonly performed procedure (often regarded as a first step) on a set of gene expression profiles. In most cases, a post hoc analysis is done to see if the genes in the same clusters can be functionally correlated. While past successes of such analyses have often been reported in a number of microarray studies (most of which used the standard hierarchical clustering, UPGMA, with one minus the Pearson's correlation coefficient as a measure of dissimilarity), often times such groupings could be misleading. More importantly, a systematic evaluation of the entire set of clusters produced by such unsupervised procedures is necessary since they also contain genes that are seemingly unrelated or may have more than one common function. Here we quantify the performance of a given unsupervised clustering algorithm applied to a given microarray study in terms of its ability to produce biologically meaningful clusters using a reference set of functional classes. Such a reference set may come from prior biological knowledge specific to a microarray study or may be formed using the growing databases of gene ontologies (GO) for the annotated genes of the relevant species. RESULTS: In this paper, we introduce two performance measures for evaluating the results of a clustering algorithm in its ability to produce biologically meaningful clusters. The first measure is a biological homogeneity index (BHI). As the name suggests, it is a measure of how biologically homogeneous the clusters are. This can be used to quantify the performance of a given clustering algorithm such as UPGMA in grouping genes for a particular data set and also for comparing the performance of a number of competing clustering algorithms applied to the same data set. The second performance measure is called a biological stability index (BSI). For a given clustering algorithm and an expression data set, it measures the consistency of the clustering algorithm's ability to produce biologically meaningful clusters when applied repeatedly to similar data sets. A good clustering algorithm should have high BHI and moderate to high BSI. We evaluated the performance of ten well known clustering algorithms on two gene expression data sets and identified the optimal algorithm in each case. The first data set deals with SAGE profiles of differentially expressed tags between normal and ductal carcinoma in situ samples of breast cancer patients. The second data set contains the expression profiles over time of positively expressed genes (ORF's) during sporulation of budding yeast. Two separate choices of the functional classes were used for this data set and the results were compared for consistency. CONCLUSION: Functional information of annotated genes available from various GO databases mined using ontology tools can be used to systematically judge the results of an unsupervised clustering algorithm as applied to a gene expression data set in clustering genes. This information could be used to select the right algorithm from a class of clustering algorithms for the given data set

Exhaled nitric oxide and clinical phenotypes of childhood asthma

Whether exhaled NO helps to identify a specific phenotype of asthmatic patients remains debated. Our aims were to evaluate whether exhaled NO (FENO0.05) is independently associated (1) with underlying pathophysiological characteristics of asthma such as airway tone (bronchodilator response) and airway inflammation (inhaled corticosteroid [ICS]-dependant inflammation), and (2) with clinical phenotypes of asthma

Exhaled nitric oxide and clinical phenotypes of childhood asthma

Whether exhaled NO helps to identify a specific phenotype of asthmatic patients remains debated. Our aims were to evaluate whether exhaled NO (FENO0.05) is independently associated (1) with underlying pathophysiological characteristics of asthma such as airway tone (bronchodilator response) and airway inflammation (inhaled corticosteroid [ICS]-dependant inflammation), and (2) with clinical phenotypes of asthma

Biclustering models for two-mode ordinal data

The work in this paper introduces finite mixture models that can be used to simul- taneously cluster the rows and columns of two-mode ordinal categorical response data, such as those resulting from Likert scale responses. We use the popular proportional odds parameterisation and propose models which provide insights into major patterns in the data. Model-fitting is performed using the EM algorithm and a fuzzy allocation of rows and columns to corresponding clusters is obtained. The clustering ability of the models is evaluated in a simulation study and demonstrated using two real data sets