Modeling of evolving textures using granulometries

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Interpretable multiclass classification by MDL-based rule lists

Interpretable classifiers have recently witnessed an increase in attention from the data mining community because they are inherently easier to understand and explain than their more complex counterparts. Examples of interpretable classification models include decision trees, rule sets, and rule lists. Learning such models often involves optimizing hyperparameters, which typically requires substantial amounts of data and may result in relatively large models. In this paper, we consider the problem of learning compact yet accurate probabilistic rule lists for multiclass classification. Specifically, we propose a novel formalization based on probabilistic rule lists and the minimum description length (MDL) principle. This results in virtually parameter-free model selection that naturally allows to trade-off model complexity with goodness of fit, by which overfitting and the need for hyperparameter tuning are effectively avoided. Finally, we introduce the Classy algorithm, which greedily finds rule lists according to the proposed criterion. We empirically demonstrate that Classy selects small probabilistic rule lists that outperform state-of-the-art classifiers when it comes to the combination of predictive performance and interpretability. We show that Classy is insensitive to its only parameter, i.e., the candidate set, and that compression on the training set correlates with classification performance, validating our MDL-based selection criterion

Probabilistic Anomaly Detection in Natural Gas Time Series Data

This paper introduces a probabilistic approach to anomaly detection, specifically in natural gas time series data. In the natural gas field, there are various types of anomalies, each of which is induced by a range of causes and sources. The causes of a set of anomalies are examined and categorized, and a Bayesian maximum likelihood classifier learns the temporal structures of known anomalies. Given previously unseen time series data, the system detects anomalies using a linear regression model with weather inputs, after which the anomalies are tested for false positives and classified using a Bayesian classifier. The method can also identify anomalies of an unknown origin. Thus, the likelihood of a data point being anomalous is given for anomalies of both known and unknown origins. This probabilistic anomaly detection method is tested on a reported natural gas consumption data set

Classification of airborne laser scanning point clouds based on binomial logistic regression analysis

This article presents a newly developed procedure for the classification of airborne laser scanning (ALS) point clouds, based on binomial logistic regression analysis. By using a feature space containing a large number of adaptable geometrical parameters, this new procedure can be applied to point clouds covering different types of topography and variable point densities. Besides, the procedure can be adapted to different user requirements. A binomial logistic model is estimated for all a priori defined classes, using a training set of manually classified points. For each point, a value is calculated defining the probability that this point belongs to a certain class. The class with the highest probability will be used for the final point classification. Besides, the use of statistical methods enables a thorough model evaluation by the implementation of well-founded inference criteria. If necessary, the interpretation of these inference analyses also enables the possible definition of more sub-classes. The use of a large number of geometrical parameters is an important advantage of this procedure in comparison with current classification algorithms. It allows more user modifications for the large variety of types of ALS point clouds, while still achieving comparable classification results. It is indeed possible to evaluate parameters as degrees of freedom and remove or add parameters as a function of the type of study area. The performance of this procedure is successfully demonstrated by classifying two different ALS point sets from an urban and a rural area. Moreover, the potential of the proposed classification procedure is explored for terrestrial data

Microarray Data Mining and Gene Regulatory Network Analysis

The novel molecular biological technology, microarray, makes it feasible to obtain quantitative measurements of expression of thousands of genes present in a biological sample simultaneously. Genome-wide expression data generated from this technology are promising to uncover the implicit, previously unknown biological knowledge. In this study, several problems about microarray data mining techniques were investigated, including feature(gene) selection, classifier genes identification, generation of reference genetic interaction network for non-model organisms and gene regulatory network reconstruction using time-series gene expression data. The limitations of most of the existing computational models employed to infer gene regulatory network lie in that they either suffer from low accuracy or computational complexity. To overcome such limitations, the following strategies were proposed to integrate bioinformatics data mining techniques with existing GRN inference algorithms, which enables the discovery of novel biological knowledge. An integrated statistical and machine learning (ISML) pipeline was developed for feature selection and classifier genes identification to solve the challenges of the curse of dimensionality problem as well as the huge search space. Using the selected classifier genes as seeds, a scale-up technique is applied to search through major databases of genetic interaction networks, metabolic pathways, etc. By curating relevant genes and blasting genomic sequences of non-model organisms against well-studied genetic model organisms, a reference gene regulatory network for less-studied organisms was built and used both as prior knowledge and model validation for GRN reconstructions. Networks of gene interactions were inferred using a Dynamic Bayesian Network (DBN) approach and were analyzed for elucidating the dynamics caused by perturbations. Our proposed pipelines were applied to investigate molecular mechanisms for chemical-induced reversible neurotoxicity

Machine-Learning-based Prediction of Sepsis Events from Vertical Clinical Trial Data: a Naïve Approach

Sepsis is a potentially life-threatening condition characterized by a dysregulated, disproportionate immune response to infection by which the afflicted body attacks its own tissues, sometimes to the point of organ failure, and in the worst cases, death. According to the Centers for Disease Control and Prevention (CDC) Sepsis is reported to kill upwards of 270,000 Americans annually, though this figure may be greater given certain ambiguities in the current accepted diagnostic framework of the disease. This study attempted to first establish an understanding of past definitions of sepsis, and to then recommend use of machine learning as integral in an eventual amended disease definition. Longitudinal clinical trial data (ntrials=30,915) were vectorized into a machine-readable format compatible with predictive modeling, selected and reduced in dimension, and used to predict incidences of sepsis via application of several machine learning models: logistic regression, support vector machines (SVM), naïve Bayes Classifier, decision trees, and random forests. The intent of the study was to identify possible predictive features for sepsis via comparative analysis of different machine learning models, and to recommend subsequent study of sepsis prediction using the training model on new data (non-clinical-trial-derived) in the same format. If the models can be generalized to new data, it stands to assume they could eventually become clinically useful. In referencing F1 scores and recall scores, the random forest classifier was the best performer among this cohort of models

Unconventional machine learning of genome-wide human cancer data

Recent advances in high-throughput genomic technologies coupled with exponential increases in computer processing and memory have allowed us to interrogate the complex aberrant molecular underpinnings of human disease from a genome-wide perspective. While the deluge of genomic information is expected to increase, a bottleneck in conventional high-performance computing is rapidly approaching. Inspired in part by recent advances in physical quantum processors, we evaluated several unconventional machine learning (ML) strategies on actual human tumor data. Here we show for the first time the efficacy of multiple annealing-based ML algorithms for classification of high-dimensional, multi-omics human cancer data from the Cancer Genome Atlas. To assess algorithm performance, we compared these classifiers to a variety of standard ML methods. Our results indicate the feasibility of using annealing-based ML to provide competitive classification of human cancer types and associated molecular subtypes and superior performance with smaller training datasets, thus providing compelling empirical evidence for the potential future application of unconventional computing architectures in the biomedical sciences