Sequence Classification Based on Delta-Free Sequential Pattern

International audienceSequential pattern mining is one of the most studied and challenging tasks in data mining. However, the extension of well-known methods from many other classical patterns to sequences is not a trivial task. In this paper we study the notion of δ-freeness for sequences. While this notion has extensively been discussed for itemsets, this work is the first to extend it to sequences. We define an efficient algorithm devoted to the extraction of δ-free sequential patterns. Furthermore, we show the advantage of the δ-free sequences and highlight their importance when building sequence classifiers, and we show how they can be used to address the feature selection problem in statistical classifiers, as well as to build symbolic classifiers which optimizes both accuracy and earliness of predictions

A Training Sample Sequence Planning Method for Pattern Recognition Problems

In solving pattern recognition problems, many classification methods, such as the nearest-neighbor (NN) rule, need to determine prototypes from a training set. To improve the performance of these classifiers in finding an efficient set of prototypes, this paper introduces a training sample sequence planning method. In particular, by estimating the relative nearness of the training samples to the decision boundary, the approach proposed here incrementally increases the number of prototypes until the desired classification accuracy has been reached. This approach has been tested with a NN classification method and a neural network training approach. Studies based on both artificial and real data demonstrate that higher classification accuracy can be achieved with fewer prototypes

RasBhari: optimizing spaced seeds for database searching, read mapping and alignment-free sequence comparison

Many algorithms for sequence analysis rely on word matching or word statistics. Often, these approaches can be improved if binary patterns representing match and don't-care positions are used as a filter, such that only those positions of words are considered that correspond to the match positions of the patterns. The performance of these approaches, however, depends on the underlying patterns. Herein, we show that the overlap complexity of a pattern set that was introduced by Ilie and Ilie is closely related to the variance of the number of matches between two evolutionarily related sequences with respect to this pattern set. We propose a modified hill-climbing algorithm to optimize pattern sets for database searching, read mapping and alignment-free sequence comparison of nucleic-acid sequences; our implementation of this algorithm is called rasbhari. Depending on the application at hand, rasbhari can either minimize the overlap complexity of pattern sets, maximize their sensitivity in database searching or minimize the variance of the number of pattern-based matches in alignment-free sequence comparison. We show that, for database searching, rasbhari generates pattern sets with slightly higher sensitivity than existing approaches. In our Spaced Words approach to alignment-free sequence comparison, pattern sets calculated with rasbhari led to more accurate estimates of phylogenetic distances than the randomly generated pattern sets that we previously used. Finally, we used rasbhari to generate patterns for short read classification with CLARK-S. Here too, the sensitivity of the results could be improved, compared to the default patterns of the program. We integrated rasbhari into Spaced Words; the source code of rasbhari is freely available at http://rasbhari.gobics.de

A multi-granularity pattern-based sequence classification framework for educational data

In many application domains, such as education, sequences of events occurring over time need to be studied in order to understand the generative process behind these sequences, and hence classify new examples. In this paper, we propose a novel multi-granularity sequence lassification framework that generates features based on frequent patterns at multiple levels of time granularity. Feature selection techniques are applied to identify the most informative features that are then used to construct the classification model. We show the applicability and suitability of the proposed framework to the area of educational data mining by experimenting on an educational dataset collected from an asynchronous communication tool in which students interact to accomplish an underlying group project. The experimental results showed that our model can achieve competitive performance in detecting the students' roles in their corresponding projects, compared to a baseline similarity-based approach

Anomaly Detection for Human Home Activities Using Pattern Based Sequence Classification

In most countries, the old-age people population continues to rise. Because young adults are busy with their work engagements, they have to let the elderly stay at home alone. This is quite dangerous, as accidents at home may happen anytime without anyone knowing. Although sending elderly relatives to an elderly care center or hiring a caregiver are good solutions, they may not be feasible since it may be too expensive over a long-term period. The behavior patterns of elderly people during daily activities can give hints about their health condition. If an abnormal behavior pattern can be detected in advance, then precautions can be taken at an early stage. Previous studies have suggested machine learning techniques for such anomaly detection but most of the techniques are complicated. In this paper, a simple model for detecting anomaly patterns in human activity sequences using Random forest (RF) and K-nearest neighbor (KNN) classifiers is presented. The model was implemented on a public dataset and it showed that the RF classifier performed better, with an accuracy of 85%, compared to the KNN classifier, which achieved 73%

DeepSF: deep convolutional neural network for mapping protein sequences to folds

Motivation Protein fold recognition is an important problem in structural bioinformatics. Almost all traditional fold recognition methods use sequence (homology) comparison to indirectly predict the fold of a tar get protein based on the fold of a template protein with known structure, which cannot explain the relationship between sequence and fold. Only a few methods had been developed to classify protein sequences into a small number of folds due to methodological limitations, which are not generally useful in practice. Results We develop a deep 1D-convolution neural network (DeepSF) to directly classify any protein se quence into one of 1195 known folds, which is useful for both fold recognition and the study of se quence-structure relationship. Different from traditional sequence alignment (comparison) based methods, our method automatically extracts fold-related features from a protein sequence of any length and map it to the fold space. We train and test our method on the datasets curated from SCOP1.75, yielding a classification accuracy of 80.4%. On the independent testing dataset curated from SCOP2.06, the classification accuracy is 77.0%. We compare our method with a top profile profile alignment method - HHSearch on hard template-based and template-free modeling targets of CASP9-12 in terms of fold recognition accuracy. The accuracy of our method is 14.5%-29.1% higher than HHSearch on template-free modeling targets and 4.5%-16.7% higher on hard template-based modeling targets for top 1, 5, and 10 predicted folds. The hidden features extracted from sequence by our method is robust against sequence mutation, insertion, deletion and truncation, and can be used for other protein pattern recognition problems such as protein clustering, comparison and ranking.Comment: 28 pages, 13 figure

VTOL shipboard letdown guidance system analysis

Alternative letdown guidance strategies are examined for landing of a VTOL aircraft onboard a small aviation ship under adverse environmental conditions. Off line computer simulation of shipboard landing task is utilized for assessing the relative merits of the proposed guidance schemes. The touchdown performance of a nominal constant rate of descent (CROD) letdown strategy serves as a benchmark for ranking the performance of the alternative letdown schemes. Analysis of ship motion time histories indicates the existence of an alternating sequence of quiescent and rough motions called lulls and swells. A real time algorithms lull/swell classification based upon ship motion pattern features is developed. The classification algorithm is used to command a go/no go signal to indicate the initiation and termination of an acceptable landing window. Simulation results show that such a go/no go pattern based letdown guidance strategy improves touchdown performance