An intuitionistic approach to scoring DNA sequences against transcription factor binding site motifs

Background: Transcription factors (TFs) control transcription by binding to specific regions of DNA called transcription factor binding sites (TFBSs). The identification of TFBSs is a crucial problem in computational biology and includes the subtask of predicting the location of known TFBS motifs in a given DNA sequence. It has previously been shown that, when scoring matches to known TFBS motifs, interdependencies between positions within a motif should be taken into account. However, this remains a challenging task owing to the fact that sequences similar to those of known TFBSs can occur by chance with a relatively high frequency. Here we present a new method for matching sequences to TFBS motifs based on intuitionistic fuzzy sets (IFS) theory, an approach that has been shown to be particularly appropriate for tackling problems that embody a high degree of uncertainty. Results: We propose SCintuit, a new scoring method for measuring sequence-motif affinity based on IFS theory. Unlike existing methods that consider dependencies between positions, SCintuit is designed to prevent overestimation of less conserved positions of TFBSs. For a given pair of bases, SCintuit is computed not only as a function of their combined probability of occurrence, but also taking into account the individual importance of each single base at its corresponding position. We used SCintuit to identify known TFBSs in DNA sequences. Our method provides excellent results when dealing with both synthetic and real data, outperforming the sensitivity and the specificity of two existing methods in all the experiments we performed. Conclusions: The results show that SCintuit improves the prediction quality for TFs of the existing approaches without compromising sensitivity. In addition, we show how SCintuit can be successfully applied to real research problems. In this study the reliability of the IFS theory for motif discovery tasks is proven

Advanced analytical methods for fraud detection: a systematic literature review

The developments of the digital era demand new ways of producing goods and rendering services. This fast-paced evolution in the companies implies a new approach from the auditors, who must keep up with the constant transformation. With the dynamic dimensions of data, it is important to seize the opportunity to add value to the companies. The need to apply more robust methods to detect fraud is evident. In this thesis the use of advanced analytical methods for fraud detection will be investigated, through the analysis of the existent literature on this topic. Both a systematic review of the literature and a bibliometric approach will be applied to the most appropriate database to measure the scientific production and current trends. This study intends to contribute to the academic research that have been conducted, in order to centralize the existing information on this topic

Predicting software project effort: A grey relational analysis based method

This is the post-print version of the final paper published in Expert Systems with Applications. The published article is available from the link below. Changes resulting from the publishing process, such as peer review, editing, corrections, structural formatting, and other quality control mechanisms may not be reflected in this document. Changes may have been made to this work since it was submitted for publication. Copyright @ 2011 Elsevier B.V.The inherent uncertainty of the software development process presents particular challenges for software effort prediction. We need to systematically address missing data values, outlier detection, feature subset selection and the continuous evolution of predictions as the project unfolds, and all of this in the context of data-starvation and noisy data. However, in this paper, we particularly focus on outlier detection, feature subset selection, and effort prediction at an early stage of a project. We propose a novel approach of using grey relational analysis (GRA) from grey system theory (GST), which is a recently developed system engineering theory based on the uncertainty of small samples. In this work we address some of the theoretical challenges in applying GRA to outlier detection, feature subset selection, and effort prediction, and then evaluate our approach on five publicly available industrial data sets using both stepwise regression and Analogy as benchmarks. The results are very encouraging in the sense of being comparable or better than other machine learning techniques and thus indicate that the method has considerable potential.National Natural Science Foundation of Chin

Video Registration in Egocentric Vision under Day and Night Illumination Changes

With the spread of wearable devices and head mounted cameras, a wide range of application requiring precise user localization is now possible. In this paper we propose to treat the problem of obtaining the user position with respect to a known environment as a video registration problem. Video registration, i.e. the task of aligning an input video sequence to a pre-built 3D model, relies on a matching process of local keypoints extracted on the query sequence to a 3D point cloud. The overall registration performance is strictly tied to the actual quality of this 2D-3D matching, and can degrade if environmental conditions such as steep changes in lighting like the ones between day and night occur. To effectively register an egocentric video sequence under these conditions, we propose to tackle the source of the problem: the matching process. To overcome the shortcomings of standard matching techniques, we introduce a novel embedding space that allows us to obtain robust matches by jointly taking into account local descriptors, their spatial arrangement and their temporal robustness. The proposal is evaluated using unconstrained egocentric video sequences both in terms of matching quality and resulting registration performance using different 3D models of historical landmarks. The results show that the proposed method can outperform state of the art registration algorithms, in particular when dealing with the challenges of night and day sequences

Wireless Data Acquisition for Edge Learning: Data-Importance Aware Retransmission

By deploying machine-learning algorithms at the network edge, edge learning can leverage the enormous real-time data generated by billions of mobile devices to train AI models, which enable intelligent mobile applications. In this emerging research area, one key direction is to efficiently utilize radio resources for wireless data acquisition to minimize the latency of executing a learning task at an edge server. Along this direction, we consider the specific problem of retransmission decision in each communication round to ensure both reliability and quantity of those training data for accelerating model convergence. To solve the problem, a new retransmission protocol called data-importance aware automatic-repeat-request (importance ARQ) is proposed. Unlike the classic ARQ focusing merely on reliability, importance ARQ selectively retransmits a data sample based on its uncertainty which helps learning and can be measured using the model under training. Underpinning the proposed protocol is a derived elegant communication-learning relation between two corresponding metrics, i.e., signal-to-noise ratio (SNR) and data uncertainty. This relation facilitates the design of a simple threshold based policy for importance ARQ. The policy is first derived based on the classic classifier model of support vector machine (SVM), where the uncertainty of a data sample is measured by its distance to the decision boundary. The policy is then extended to the more complex model of convolutional neural networks (CNN) where data uncertainty is measured by entropy. Extensive experiments have been conducted for both the SVM and CNN using real datasets with balanced and imbalanced distributions. Experimental results demonstrate that importance ARQ effectively copes with channel fading and noise in wireless data acquisition to achieve faster model convergence than the conventional channel-aware ARQ.Comment: This is an updated version: 1) extension to general classifiers; 2) consideration of imbalanced classification in the experiments. Submitted to IEEE Journal for possible publicatio

Cost-Quality Trade-Offs in One-Class Active Learning

Active learning is a paradigm to involve users in a machine learning process. The core idea of active learning is to ask a user to annotate a specific observation to improve the classification performance. One important application of active learning is detecting outliers, i.e., unusual observations that deviate from the regular ones in a data set. Applying active learning for outlier detection in practice requires to design a system that consists of several components: the data, the classifier that discerns between inliers and outliers, the query strategy that selects the observations for feedback collection, and an oracle, e.g., the human expert that annotates the queries. Each of these components and their interplay influences the classification quality. Naturally, there are cost budgets limiting certain parts of the system, e.g., the number of queries one can ask a human. Thus, to configure efficient active learning systems, one must decide on several trade-offs between costs and quality. The existing literature on active learning systems does not provide an overview nor a formal description of the cost-quality trade-offs of active learning. All this makes the configuration of efficient active learning systems in practice difficult. In this thesis, we study different cost-quality trade-offs that are pivotal for configuring an active learning system for outlier detection. We first provide an overview of the costs of an active learning system. Then, we analyze three important trade-offs and propose ways to model and quantify them. In our first contribution, we study how one can reduce classification training costs by training only on a sample of the data set. We formalize the sampling trade-off between classifier training costs and resulting quality as an optimization problem and propose an efficient algorithm to solve it. Compared to the existing sampling methods in literature, our approach guarantees that a classifier trained on our sample makes the same predictions as if trained on the complete data set. We can therefore reduce the classification training costs without a loss of classification quality. In our second contribution, we investigate how selecting multiple queries allows trading off costs against quality. So-called batch queries reduce classifier training costs because the system only updates the classifier once for each batch. But the annotation of a batch may give redundant information, which reduces the achievable quality with a fixed query budget. We are the first to consider batch queries for outlier detection, a generalization of the more common case to query sequentially. We formalize batch active learning and propose several strategies to construct batches by modeling the expected utility of a batch. In our third contribution, we propose query synthesis for outlier detection. Query synthesis allows to artificially generate queries at any point in the data space without being restricted by a pool of query candidates. We propose a framework to efficiently synthesize queries and develop a novel query strategy to improve the generalization of a classifier beyond a biased data set with active learning. For all contributions, we derive recommendations for the cost-quality trade-offs from formal investigations and empirical studies to facilitate the configuration of robust and efficient active learning systems for outlier detection