Search

Blind image quality assessment can be modeled as feature extraction followed by score prediction. It necessitates considerable expertise and efforts to handcraft features for optimal representation of perceptual image quality. This paper addresses blind image sharpness assessment by using a shallow convolutional neural network (CNN). The network takes single feature layer to unearth intrinsic features for image sharpness representation and utilizes multilayer perceptron (MLP) to rate image quality. Different from traditional methods, CNN integrates feature extraction and score prediction into an optimization procedure and retrieves features automatically from raw images. Moreover, its prediction performance can be enhanced by replacing MLP with general regression neural network (GRNN) and support vector regression (SVR). Experiments on Gaussian blur images from LIVE-II, CSIQ, TID2008 and TID2013 demonstrate that CNN features with SVR achieves the best overall performance, indicating high correlation with human subjective judgment. [ABSTRACT FROM AUTHOR]

Driver behavior impacts traffic safety, fuel/energy consumption and gas emissions. Driver behavior profiling tries to understand and positively impact driver behavior. Usually driver behavior profiling tasks involve automated collection of driving data and application of computer models to generate a classification that characterizes the driver aggressiveness profile. Different sensors and classification methods have been employed in this task, however, low-cost solutions and high performance are still research targets. This paper presents an investigation with different Android smartphone sensors, and classification algorithms in order to assess which sensor/method assembly enables classification with higher performance. The results show that specific combinations of sensors and intelligent methods allow classification performance improvement. [ABSTRACT FROM AUTHOR]

This paper proposes a new support vector machine (SVM) optimization scheme based on an improved chaotic fly optimization algorithm (FOA) with a mutation strategy to simultaneously perform parameter setting turning for the SVM and feature selection. In the improved FOA, the chaotic particle initializes the fruit fly swarm location and replaces the expression of distance for the fruit fly to find the food source. However, the proposed mutation strategy uses two distinct generative mechanisms for new food sources at the osphresis phase, allowing the algorithm procedure to search for the optimal solution in both the whole solution space and within the local solution space containing the fruit fly swarm location. In an evaluation based on a group of ten benchmark problems, the proposed algorithm’s performance is compared with that of other well-known algorithms, and the results support the superiority of the proposed algorithm. Moreover, this algorithm is successfully applied in a SVM to perform both parameter setting turning for the SVM and feature selection to solve real-world classification problems. This method is called chaotic fruit fly optimization algorithm (CIFOA)-SVM and has been shown to be a more robust and effective optimization method than other well-known methods, particularly in terms of solving the medical diagnosis problem and the credit card problem. [ABSTRACT FROM AUTHOR]

Music emotion recognition (MER) field rapidly expanded in the last decade. Many new methods and new audio features are developed to improve the performance of MER algorithms. However, it is very difficult to compare the performance of the new methods because of the data representation diversity and scarcity of publicly available data. In this paper, we address these problems by creating a data set and a benchmark for MER. The data set that we release, a MediaEval Database for Emotional Analysis in Music (DEAM), is the largest available data set of dynamic annotations (valence and arousal annotations for 1,802 songs and song excerpts licensed under Creative Commons with 2Hz time resolution). Using DEAM, we organized the ‘Emotion in Music’ task at MediaEval Multimedia Evaluation Campaign from 2013 to 2015. The benchmark attracted, in total, 21 active teams to participate in the challenge. We analyze the results of the benchmark: the winning algorithms and feature-sets. We also describe the design of the benchmark, the evaluation procedures and the data cleaning and transformations that we suggest. The results from the benchmark suggest that the recurrent neural network based approaches combined with large feature-sets work best for dynamic MER. [ABSTRACT FROM AUTHOR]

Many biomedical relation extraction approaches are based on supervised machine learning, requiring an annotated corpus. Distant supervision aims at training a classifier by combining a knowledge base with a corpus, reducing the amount of manual effort necessary. This is particularly useful for biomedicine because many databases and ontologies have been made available for many biological processes, while the availability of annotated corpora is still limited. We studied the extraction of microRNA-gene relations from text. MicroRNA regulation is an important biological process due to its close association with human diseases. The proposed method, IBRel, is based on distantly supervised multi-instance learning. We evaluated IBRel on three datasets, and the results were compared with a co-occurrence approach as well as a supervised machine learning algorithm. While supervised learning outperformed on two of those datasets, IBRel obtained an F-score 28.3 percentage points higher on the dataset for which there was no training set developed specifically. To demonstrate the applicability of IBRel, we used it to extract 27 miRNA-gene relations from recently published papers about cystic fibrosis. Our results demonstrate that our method can be successfully used to extract relations from literature about a biological process without an annotated corpus. The source code and data used in this study are available at . [ABSTRACT FROM AUTHOR]

A ship power equipments’ fault monitoring signal usually provides few samples and the data’s feature is non-linear in practical situation. This paper adopts the method of the least squares support vector machine (LSSVM) to deal with the problem of fault pattern identification in the case of small sample data. Meanwhile, in order to avoid involving a local extremum and poor convergence precision which are induced by optimizing the kernel function parameter and penalty factor of LSSVM, an improved Cuckoo Search (CS) algorithm is proposed for the purpose of parameter optimization. Based on the dynamic adaptive strategy, the newly proposed algorithm improves the recognition probability and the searching step length, which can effectively solve the problems of slow searching speed and low calculation accuracy of the CS algorithm. A benchmark example demonstrates that the CS-LSSVM algorithm can accurately and effectively identify the fault pattern types of ship power equipments. [ABSTRACT FROM AUTHOR]

Artificial neural networks (ANNs) have been employed to solve a broad variety of tasks. The selection of an ANN model with appropriate weights is important in achieving accurate results. This paper presents an optimization strategy for ANN model selection based on the cuckoo search (CS) algorithm, which is rooted in the obligate brood parasitic actions of some cuckoo species. In order to enhance the convergence ability of basic CS, some modifications are proposed. The fraction Pa of the n nests replaced by new nests is a fixed parameter in basic CS. As the selection of Pa is a challenging issue and has a direct effect on exploration and therefore on convergence ability, in this work the Pa is set to a maximum value at initialization to achieve more exploration in early iterations and it is decreased during the search to achieve more exploitation in later iterations until it reaches the minimum value in the final iteration. In addition, a novel master-leader-slave multi-population strategy is used where the slaves employ the best fitness function among all slaves, which is selected by the leader under a certain condition. This fitness function is used for subsequent Lévy flights. In each iteration a copy of the best solution of each slave is migrated to the master and then the best solution is found by the master. The method is tested on benchmark classification and time series prediction problems and the statistical analysis proves the ability of the method. This method is also applied to a real-world water quality prediction problem with promising results. [ABSTRACT FROM AUTHOR]

In the sparse representation model, the design of overcomplete dictionaries plays a key role for the effectiveness and applicability in different domains. Recent research has produced several dictionary learning approaches, being proven that dictionaries learnt by data examples significantly outperform structured ones, e.g. wavelet transforms. In this context, learning consists in adapting the dictionary atoms to a set of training signals in order to promote a sparse representation that minimizes the reconstruction error. Finding the best fitting dictionary remains a very difficult task, leaving the question still open. A well-established heuristic method for tackling this problem is an iterative alternating scheme, adopted for instance in the well-known K-SVD algorithm. Essentially, it consists in repeating two stages; the former promotes sparse coding of the training set and the latter adapts the dictionary to reduce the error. In this paper we present R-SVD, a new method that, while maintaining the alternating scheme, adopts the Orthogonal Procrustes analysis to update the dictionary atoms suitably arranged into groups. Comparative experiments on synthetic data prove the effectiveness of R-SVD with respect to well known dictionary learning algorithms such as K-SVD, ILS-DLA and the online method OSDL. Moreover, experiments on natural data such as ECG compression, EEG sparse representation, and image modeling confirm R-SVD’s robustness and wide applicability. [ABSTRACT FROM AUTHOR]

Breast cancer is an all too common disease in women, making how to effectively predict it an active research problem. A number of statistical and machine learning techniques have been employed to develop various breast cancer prediction models. Among them, support vector machines (SVM) have been shown to outperform many related techniques. To construct the SVM classifier, it is first necessary to decide the kernel function, and different kernel functions can result in different prediction performance. However, there have been very few studies focused on examining the prediction performances of SVM based on different kernel functions. Moreover, it is unknown whether SVM classifier ensembles which have been proposed to improve the performance of single classifiers can outperform single SVM classifiers in terms of breast cancer prediction. Therefore, the aim of this paper is to fully assess the prediction performance of SVM and SVM ensembles over small and large scale breast cancer datasets. The classification accuracy, ROC, F-measure, and computational times of training SVM and SVM ensembles are compared. The experimental results show that linear kernel based SVM ensembles based on the bagging method and RBF kernel based SVM ensembles with the boosting method can be the better choices for a small scale dataset, where feature selection should be performed in the data pre-processing stage. For a large scale dataset, RBF kernel based SVM ensembles based on boosting perform better than the other classifiers. [ABSTRACT FROM AUTHOR]

Bearing failure is one of the dominant causes of failure and breakdowns in rotating machinery, leading to huge economic loss. Aiming at the nonstationary and nonlinear characteristics of bearing vibration signals as well as the complexity of condition-indicating information distribution in the signals, a novel rolling element bearing fault diagnosis method based on multifractal theory and gray relation theory was proposed in the paper. Firstly, a generalized multifractal dimension algorithm was developed to extract the characteristic vectors of fault features from the bearing vibration signals, which can offer more meaningful and distinguishing information reflecting different bearing health status in comparison with conventional single fractal dimension. After feature extraction by multifractal dimensions, an adaptive gray relation algorithm was applied to implement an automated bearing fault pattern recognition. The experimental results show that the proposed method can identify various bearing fault types as well as severities effectively and accurately. [ABSTRACT FROM AUTHOR]

Over the history of mankind, textual records change. Sometimes due to mistakes during transcription, sometimes on purpose, as a way to rewrite facts and reinterpret history. There are several classical cases, such as the logarithmic tables, and the transmission of antique and medieval scholarship. Today, text documents are largely edited and redistributed on the Web. Articles on news portals and collaborative platforms (such as Wikipedia), source code, posts on social networks, and even scientific publications or literary works are some examples in which textual content can be subject to changes in an evolutionary process. In this scenario, given a set of near-duplicate documents, it is worthwhile to find which one is the original and the history of changes that created the whole set. Such functionality would have immediate applications on news tracking services, detection of plagiarism, textual criticism, and copyright enforcement, for instance. However, this is not an easy task, as textual features pointing to the documents’ evolutionary direction may not be evident and are often dataset dependent. Moreover, side information, such as time stamps, are neither always available nor reliable. In this paper, we propose a framework for reliably reconstructing text phylogeny trees, and seamlessly exploring new approaches on a wide range of scenarios of text reusage. We employ and evaluate distinct combinations of dissimilarity measures and reconstruction strategies within the proposed framework, and evaluate each approach with extensive experiments, including a set of artificial near-duplicate documents with known phylogeny, and from documents collected from Wikipedia, whose modifications were made by Internet users. We also present results from qualitative experiments in two different applications: text plagiarism and reconstruction of evolutionary trees for manuscripts (stemmatology). [ABSTRACT FROM AUTHOR]

Prediction of memory performance (remembered or forgotten) has various potential applications not only for knowledge learning but also for disease diagnosis. Recently, subsequent memory effects (SMEs)—the statistical differences in electroencephalography (EEG) signals before or during learning between subsequently remembered and forgotten events—have been found. This finding indicates that EEG signals convey the information relevant to memory performance. In this paper, based on SMEs we propose a computational approach to predict memory performance of an event from EEG signals. We devise a convolutional neural network for EEG, called ConvEEGNN, to predict subsequently remembered and forgotten events from EEG recorded during memory process. With the ConvEEGNN, prediction of memory performance can be achieved by integrating two main stages: feature extraction and classification. To verify the proposed approach, we employ an auditory memory task to collect EEG signals from scalp electrodes. For ConvEEGNN, the average prediction accuracy was 72.07% by using EEG data from pre-stimulus and during-stimulus periods, outperforming other approaches. It was observed that signals from pre-stimulus period and those from during-stimulus period had comparable contributions to memory performance. Furthermore, the connection weights of ConvEEGNN network can reveal prominent channels, which are consistent with the distribution of SME studied previously. [ABSTRACT FROM AUTHOR]

Railway and metro transport systems (RS) are becoming one of the popular choices of transportation among people, especially those who live in urban cities. Urbanization and increasing population due to rapid development of economy in many cities are leading to a bigger demand for urban rail transit. Despite being a popular variant of Traveling Salesman Problem (TSP), it appears that the universal formula or techniques to solve the problem are yet to be found. This paper aims to develop an optimization algorithm for optimum route selection to multiple destinations in RS before returning to the starting point. Bee foraging behaviour is examined to generate a reliable algorithm in railway TSP. The algorithm is then verified by comparing the results with the exact solutions in 10 test cases, and a numerical case study is designed to demonstrate the application with large size sample. It is tested to be efficient and effective in railway route planning as the tour can be completed within a certain period of time by using minimal resources. The findings further support the reliability of the algorithm and capability to solve the problems with different complexity. This algorithm can be used as a method to assist business practitioners making better decision in route planning. [ABSTRACT FROM AUTHOR]

During the last years, many research efforts have been devoted to the definition of Fall Detection Systems (FDSs) that benefit from the inherent computing, communication and sensing capabilities of smartphones. However, employing a smartphone as the unique sensor in a FDS application entails several disadvantages as long as an accurate characterization of the patient’s mobility may force to transport this personal device on an unnatural position. This paper presents a smartphone-based architecture for the automatic detection of falls. The system incorporates a set of small sensing motes that can communicate with the smartphone to help in the fall detection decision. The deployed architecture is systematically evaluated in a testbed with experimental users in order to determine the number and positions of the sensors that optimize the effectiveness of the FDS, as well as to assess the most convenient role of the smartphone in the architecture. [ABSTRACT FROM AUTHOR]

Early childhood anxiety disorders are common, impairing, and predictive of anxiety and mood disorders later in childhood. Epidemiological studies over the last decade find that the prevalence of impairing anxiety disorders in preschool children ranges from 0.3% to 6.5%. Yet, less than 15% of young children with an impairing anxiety disorder receive a mental health evaluation or treatment. One possible reason for the low rate of care for anxious preschoolers is the lack of affordable, timely, reliable and valid tools for identifying young children with clinically significant anxiety. Diagnostic interviews assessing psychopathology in young children require intensive training, take hours to administer and code, and are not available for use outside of research settings. The Preschool Age Psychiatric Assessment (PAPA) is a reliable and valid structured diagnostic parent-report interview for assessing psychopathology, including anxiety disorders, in 2 to 5 year old children. In this paper, we apply machine-learning tools to already collected PAPA data from two large community studies to identify sub-sets of PAPA items that could be developed into an efficient, reliable, and valid screening tool to assess a young child’s risk for an anxiety disorder. Using machine learning, we were able to decrease by an order of magnitude the number of items needed to identify a child who is at risk for an anxiety disorder with an accuracy of over 96% for both generalized anxiety disorder (GAD) and separation anxiety disorder (SAD). Additionally, rather than considering GAD or SAD as discrete/binary entities, we present a continuous risk score representing the child’s risk of meeting criteria for GAD or SAD. Identification of a short question-set that assesses risk for an anxiety disorder could be a first step toward development and validation of a relatively short screening tool feasible for use in pediatric clinics and daycare/preschool settings. [ABSTRACT FROM AUTHOR]

Traffic identification of the target category is currently a significant challenge for network monitoring and management. To identify the target category with pertinence, a feature extraction algorithm based on the subset with highest proportion is presented in this paper. The method is proposed to be applied to the identification of any category that is assigned as the target one, but not restricted to certain specific category. We divide the process of feature extraction into two stages. In the stage of primary feature extraction, the feature subset is extracted from the dataset which has the highest proportion of the target category. In the stage of secondary feature extraction, the features that can distinguish the target and interfering categories are added to the feature subset. Our theoretical analysis and experimental observations reveal that the proposed algorithm is able to extract fewer features with greater identification ability of the target category. Moreover, the universality of the proposed algorithm proves to be available with the experiment that every category is set to be the target one. [ABSTRACT FROM AUTHOR]

Understanding the relationship between physiological measurements from human subjects and their demographic data is important within both the biometric and forensic domains. In this paper we explore the relationship between measurements of the human hand and a range of demographic features. We assess the ability of linear regression and machine learning classifiers to predict demographics from hand features, thereby providing evidence on both the strength of relationship and the key features underpinning this relationship. Our results show that we are able to predict sex, height, weight and foot size accurately within various data-range bin sizes, with machine learning classification algorithms out-performing linear regression in most situations. In addition, we identify the features used to provide these relationships applicable across multiple applications. [ABSTRACT FROM AUTHOR]

Malaria detection through microscopic examination of stained blood smears is a diagnostic challenge that heavily relies on the expertise of trained microscopists. This paper presents an automated analysis method for detection and staging of red blood cells infected by the malaria parasite Plasmodium falciparum at trophozoite or schizont stage. Unlike previous efforts in this area, this study uses quantitative phase images of unstained cells. Erythrocytes are automatically segmented using thresholds of optical phase and refocused to enable quantitative comparison of phase images. Refocused images are analyzed to extract 23 morphological descriptors based on the phase information. While all individual descriptors are highly statistically different between infected and uninfected cells, each descriptor does not enable separation of populations at a level satisfactory for clinical utility. To improve the diagnostic capacity, we applied various machine learning techniques, including linear discriminant classification (LDC), logistic regression (LR), and k-nearest neighbor classification (NNC), to formulate algorithms that combine all of the calculated physical parameters to distinguish cells more effectively. Results show that LDC provides the highest accuracy of up to 99.7% in detecting schizont stage infected cells compared to uninfected RBCs. NNC showed slightly better accuracy (99.5%) than either LDC (99.0%) or LR (99.1%) for discriminating late trophozoites from uninfected RBCs. However, for early trophozoites, LDC produced the best accuracy of 98%. Discrimination of infection stage was less accurate, producing high specificity (99.8%) but only 45.0%-66.8% sensitivity with early trophozoites most often mistaken for late trophozoite or schizont stage and late trophozoite and schizont stage most often confused for each other. Overall, this methodology points to a significant clinical potential of using quantitative phase imaging to detect and stage malaria infection without staining or expert analysis. [ABSTRACT FROM AUTHOR]

The remaining useful life (RUL) prediction of Lithium-ion batteries is closely related to the capacity degeneration trajectories. Due to the self-charging and the capacity regeneration, the trajectories have the property of multimodality. Traditional prediction models such as the support vector machines (SVM) or the Gaussian Process regression (GPR) cannot accurately characterize this multimodality. This paper proposes a novel RUL prediction method based on the Gaussian Process Mixture (GPM). It can process multimodality by fitting different segments of trajectories with different GPR models separately, such that the tiny differences among these segments can be revealed. The method is demonstrated to be effective for prediction by the excellent predictive result of the experiments on the two commercial and chargeable Type 1850 Lithium-ion batteries, provided by NASA. The performance comparison among the models illustrates that the GPM is more accurate than the SVM and the GPR. In addition, GPM can yield the predictive confidence interval, which makes the prediction more reliable than that of traditional models. [ABSTRACT FROM AUTHOR]

Coping with scarcity of labeled data is a common problem in sound classification tasks. Approaches for classifying sounds are commonly based on supervised learning algorithms, which require labeled data which is often scarce and leads to models that do not generalize well. In this paper, we make an efficient combination of confidence-based Active Learning and Self-Training with the aim of minimizing the need for human annotation for sound classification model training. The proposed method pre-processes the instances that are ready for labeling by calculating their classifier confidence scores, and then delivers the candidates with lower scores to human annotators, and those with high scores are automatically labeled by the machine. We demonstrate the feasibility and efficacy of this method in two practical scenarios: pool-based and stream-based processing. Extensive experimental results indicate that our approach requires significantly less labeled instances to reach the same performance in both scenarios compared to Passive Learning, Active Learning and Self-Training. A reduction of 52.2% in human labeled instances is achieved in both of the pool-based and stream-based scenarios on a sound classification task considering 16,930 sound instances. [ABSTRACT FROM AUTHOR]

Simultaneous and proportional myocontrol of dexterous hand prostheses is to a large extent still an open problem. With the advent of commercially and clinically available multi-fingered hand prostheses there are now more independent degrees of freedom (DOFs) in prostheses than can be effectively controlled using surface electromyography (sEMG), the current standard human-machine interface for hand amputees. In particular, it is uncertain, whether several DOFs can be controlled simultaneously and proportionally by exclusively calibrating the intended activation of single DOFs. The problem is currently solved by training on all required combinations. However, as the number of available DOFs grows, this approach becomes overly long and poses a high cognitive burden on the subject. In this paper we present a novel approach to overcome this problem. Multi-DOF activations are artificially modelled from single-DOF ones using a simple linear combination of sEMG signals, which are then added to the training set. This procedure, which we named LET (Linearly Enhanced Training), provides an augmented data set to any machine-learning-based intent detection system. In two experiments involving intact subjects, one offline and one online, we trained a standard machine learning approach using the full data set containing single- and multi-DOF activations as well as using the LET-augmented data set in order to evaluate the performance of the LET procedure. The results indicate that the machine trained on the latter data set obtains worse results in the offline experiment compared to the full data set. However, the online implementation enables the user to perform multi-DOF tasks with almost the same precision as single-DOF tasks without the need of explicitly training multi-DOF activations. Moreover, the parameters involved in the system are statistically uniform across subjects. [ABSTRACT FROM AUTHOR]

One of fundamental challenges in cancer studies is that varying molecular characteristics of different tumor types may lead to resistance to certain drugs. As a result, the same drug can lead to significantly different results in different types of cancer thus emphasizing the need for individualized medicine. Individual prediction of drug response has great potential to aid in improving the clinical outcome and reduce the financial costs associated with prescribing chemotherapy drugs to which the patient’s tumor might be resistant. In this paper we develop a network based classifier (NBC) method for predicting sensitivity of cell lines to anticancer drugs from transcriptome data. In the literature, this strategy has been used for predicting cancer types. Here, we extend it to estimate sensitivity of cells from different tumor types to various anticancer drugs. Furthermore, we incorporate domain specific knowledge such as the use of apoptotic gene list and clinical dose information in our method to impart biological significance to the prediction. Our experimental results suggest that our network based classifier (NBC) method outperforms existing classifiers in estimating sensitivity of cell lines for different drugs. [ABSTRACT FROM AUTHOR]

Background: Identifying conserved regions in protein sequences is a fundamental operation, occurring in numerous sequence-driven analysis pipelines. It is used as a way to decode domain-rich regions within proteins, to compute protein clusters, to annotate sequence function, and to compute evolutionary relationships among protein sequences. A number of approaches exist for identifying and characterizing protein families based on their domains, and because domains represent conserved portions of a protein sequence, the primary computation involved in protein family characterization is identification of such conserved regions. However, identifying conserved regions from large collections (millions) of protein sequences presents significant challenges. Methods: In this paper we present a new, alignment-free method for detecting conserved regions in protein sequences called NADDA (No-Alignment Domain Detection Algorithm). Our method exploits the abundance of exact matching short subsequences (k-mers) to quickly detect conserved regions, and the power of machine learning is used to improve the prediction accuracy of detection. We present a parallel implementation of NADDA using the MapReduce framework and show that our method is highly scalable. Results: We have compared NADDA with Pfam and InterPro databases. For known domains annotated by Pfam, accuracy is 83%, sensitivity 96%, and specificity 44%. For sequences with new domains not present in the training set an average accuracy of 63% is achieved when compared to Pfam. A boost in results in comparison with InterPro demonstrates the ability of NADDA to capture conserved regions beyond those present in Pfam. We have also compared NADDA with ADDA and MKDOM2, assuming Pfam as ground-truth. On average NADDA shows comparable accuracy, more balanced sensitivity and specificity, and being alignment-free, is significantly faster. Excluding the one-time cost of training, runtimes on a single processor were 49s, 10,566s, and 456s for NADDA, ADDA, and MKDOM2, respectively, for a data set comprised of approximately 2500 sequences. [ABSTRACT FROM AUTHOR]

For the purposes of information retrieval, users must find highly relevant documents from within a system (and often a quite large one comprised of many individual documents) based on input query. Ranking the documents according to their relevance within the system to meet user needs is a challenging endeavor, and a hot research topic–there already exist several rank-learning methods based on machine learning techniques which can generate ranking functions automatically. This paper proposes a parallel B cell algorithm, RankBCA, for rank learning which utilizes a clonal selection mechanism based on biological immunity. The novel algorithm is compared with traditional rank-learning algorithms through experimentation and shown to outperform the others in respect to accuracy, learning time, and convergence rate; taken together, the experimental results show that the proposed algorithm indeed effectively and rapidly identifies optimal ranking functions. [ABSTRACT FROM AUTHOR]

In this paper we apply machine learning methods for predicting protein interactions in fungal secretion pathways. We assume an inter-species transfer setting, where training data is obtained from a single species and the objective is to predict protein interactions in other, related species. In our methodology, we combine several state of the art machine learning approaches, namely, multiple kernel learning (MKL), pairwise kernels and kernelized structured output prediction in the supervised graph inference framework. For MKL, we apply recently proposed centered kernel alignment and p-norm path following approaches to integrate several feature sets describing the proteins, demonstrating improved performance. For graph inference, we apply input-output kernel regression (IOKR) in supervised and semi-supervised modes as well as output kernel trees (OK3). In our experiments simulating increasing genetic distance, Input-Output Kernel Regression proved to be the most robust prediction approach. We also show that the MKL approaches improve the predictions compared to uniform combination of the kernels. We evaluate the methods on the task of predicting protein-protein-interactions in the secretion pathways in fungi, S.cerevisiae, baker’s yeast, being the source, T. reesei being the target of the inter-species transfer learning. We identify completely novel candidate secretion proteins conserved in filamentous fungi. These proteins could contribute to their unique secretion capabilities. [ABSTRACT FROM AUTHOR]

Bioimpedance spectroscopy (BIS) measurement errors may be caused by parasitic stray capacitance, impedance mismatch, cross-talking or their very likely combination. An accurate detection and identification is of extreme importance for further analysis because in some cases and for some applications, certain measurement artifacts can be corrected, minimized or even avoided. In this paper we present a robust method to detect the presence of measurement artifacts and identify what kind of measurement error is present in BIS measurements. The method is based on supervised machine learning and uses a novel set of generalist features for measurement characterization in different immittance planes. Experimental validation has been carried out using a database of complex spectra BIS measurements obtained from different BIS applications and containing six different types of errors, as well as error-free measurements. The method obtained a low classification error (0.33%) and has shown good generalization. Since both the features and the classification schema are relatively simple, the implementation of this pre-processing task in the current hardware of bioimpedance spectrometers is possible. [ABSTRACT FROM AUTHOR]

The identification of a subset of genes having the ability to capture the necessary information to distinguish classes of patients is crucial in bioinformatics applications. Ensemble and bagging methods have been shown to work effectively in the process of gene selection and classification. Testament to that is random forest which combines random decision trees with bagging to improve overall feature selection and classification accuracy. Surprisingly, the adoption of these methods in support vector machines has only recently received attention but mostly on classification not gene selection. This paper introduces an ensemble SVM-Recursive Feature Elimination (ESVM-RFE) for gene selection that follows the concepts of ensemble and bagging used in random forest but adopts the backward elimination strategy which is the rationale of RFE algorithm. The rationale behind this is, building ensemble SVM models using randomly drawn bootstrap samples from the training set, will produce different feature rankings which will be subsequently aggregated as one feature ranking. As a result, the decision for elimination of features is based upon the ranking of multiple SVM models instead of choosing one particular model. Moreover, this approach will address the problem of imbalanced datasets by constructing a nearly balanced bootstrap sample. Our experiments show that ESVM-RFE for gene selection substantially increased the classification performance on five microarray datasets compared to state-of-the-art methods. Experiments on the childhood leukaemia dataset show that an average 9% better accuracy is achieved by ESVM-RFE over SVM-RFE, and 5% over random forest based approach. The selected genes by the ESVM-RFE algorithm were further explored with Singular Value Decomposition (SVD) which reveals significant clusters with the selected data. [ABSTRACT FROM AUTHOR]

This paper presents a machine learning based approach for analyses of photos collected from laboratory experiments conducted to assess the potential impact of water-based drill cuttings on deep-water rhodolith-forming calcareous algae. This pilot study uses imaging technology to quantify and monitor the stress levels of the calcareous algae Mesophyllum engelhartii (Foslie) Adey caused by various degrees of light exposure, flow intensity and amount of sediment. A machine learning based algorithm was applied to assess the temporal variation of the calcareous algae size (∼ mass) and color automatically. Measured size and color were correlated to the photosynthetic efficiency (maximum quantum yield of charge separation in photosystem II, ) and degree of sediment coverage using multivariate regression. The multivariate regression showed correlations between time and calcareous algae sizes, as well as correlations between fluorescence and calcareous algae colors. [ABSTRACT FROM AUTHOR]

This work is motivated by the needs of predictive analytics on healthcare data as represented by Electronic Medical Records. Such data is invariably problematic: noisy, with missing entries, with imbalance in classes of interests, leading to serious bias in predictive modeling. Since standard data mining methods often produce poor performance measures, we argue for development of specialized techniques of data-preprocessing and classification. In this paper, we propose a new method to simultaneously classify large datasets and reduce the effects of missing values. It is based on a multilevel framework of the cost-sensitive SVM and the expected maximization imputation method for missing values, which relies on iterated regression analyses. We compare classification results of multilevel SVM-based algorithms on public benchmark datasets with imbalanced classes and missing values as well as real data in health applications, and show that our multilevel SVM-based method produces fast, and more accurate and robust classification results. [ABSTRACT FROM AUTHOR]

Anomaly detection is the process of identifying unexpected items or events in datasets, which differ from the norm. In contrast to standard classification tasks, anomaly detection is often applied on unlabeled data, taking only the internal structure of the dataset into account. This challenge is known as unsupervised anomaly detection and is addressed in many practical applications, for example in network intrusion detection, fraud detection as well as in the life science and medical domain. Dozens of algorithms have been proposed in this area, but unfortunately the research community still lacks a comparative universal evaluation as well as common publicly available datasets. These shortcomings are addressed in this study, where 19 different unsupervised anomaly detection algorithms are evaluated on 10 different datasets from multiple application domains. By publishing the source code and the datasets, this paper aims to be a new well-funded basis for unsupervised anomaly detection research. Additionally, this evaluation reveals the strengths and weaknesses of the different approaches for the first time. Besides the anomaly detection performance, computational effort, the impact of parameter settings as well as the global/local anomaly detection behavior is outlined. As a conclusion, we give an advise on algorithm selection for typical real-world tasks. [ABSTRACT FROM AUTHOR]

Classification based on social dimensions is commonly used to handle the multi-label classification task in heterogeneous networks. However, traditional methods, which mostly rely on the community detection algorithms to extract the latent social dimensions, produce unsatisfactory performance when community detection algorithms fail. In this paper, we propose a novel behavior based social dimensions extraction method to improve the classification performance in multi-label heterogeneous networks. In our method, nodes’ behavior features, instead of community memberships, are used to extract social dimensions. By introducing Latent Dirichlet Allocation (LDA) to model the network generation process, nodes’ connection behaviors with different communities can be extracted accurately, which are applied as latent social dimensions for classification. Experiments on various public datasets reveal that the proposed method can obtain satisfactory classification results in comparison to other state-of-the-art methods on smaller social dimensions. [ABSTRACT FROM AUTHOR]

The user-based collaborative filtering (CF) algorithm is one of the most popular approaches for making recommendation. Despite its success, the traditional user-based CF algorithm suffers one serious problem that it only measures the influence between two users based on their symmetric similarities calculated by their consumption histories. It means that, for a pair of users, the influences on each other are the same, which however may not be true. Intuitively, an expert may have an impact on a novice user but a novice user may not affect an expert at all. Besides, each user may possess a global importance factor that affects his/her influence to the remaining users. To this end, in this paper, we propose an asymmetric user influence model to measure the directed influence between two users and adopt the PageRank algorithm to calculate the global importance value of each user. And then the directed influence values and the global importance values are integrated to deduce the final influence values between two users. Finally, we use the final influence values to improve the performance of the traditional user-based CF algorithm. Extensive experiments have been conducted, the results of which have confirmed that both the asymmetric user influence model and global importance value play key roles in improving recommendation accuracy, and hence the proposed method significantly outperforms the existing recommendation algorithms, in particular the user-based CF algorithm on the datasets of high rating density. [ABSTRACT FROM AUTHOR]

Background: Source localization algorithms often show multiple active cortical areas as the source of electroencephalography (EEG). Yet, there is little data quantifying the accuracy of these results. In this paper, the performance of current source density source localization algorithms for the detection of multiple cortical sources of EEG data has been characterized. Methods: EEG data were generated by simulating multiple cortical sources (2–4) with the same strength or two sources with relative strength ratios of 1:1 to 4:1, and adding noise. These data were used to reconstruct the cortical sources using current source density (CSD) algorithms: sLORETA, MNLS, and LORETA using a p-norm with p equal to 1, 1.5 and 2. Precision (percentage of the reconstructed activity corresponding to simulated activity) and Recall (percentage of the simulated sources reconstructed) of each of the CSD algorithms were calculated. Results: While sLORETA has the best performance when only one source is present, when two or more sources are present LORETA with p equal to 1.5 performs better. When the relative strength of one of the sources is decreased, all algorithms have more difficulty reconstructing that source. However, LORETA 1.5 continues to outperform other algorithms. If only the strongest source is of interest sLORETA is recommended, while LORETA with p equal to 1.5 is recommended if two or more of the cortical sources are of interest. These results provide guidance for choosing a CSD algorithm to locate multiple cortical sources of EEG and for interpreting the results of these algorithms. [ABSTRACT FROM AUTHOR]

Community structure detection is of great importance because it can help in discovering the relationship between the function and the topology structure of a network. Many community detection algorithms have been proposed, but how to incorporate the prior knowledge in the detection process remains a challenging problem. In this paper, we propose a semi-supervised community detection algorithm, which makes full utilization of the must-link and cannot-link constraints to guide the process of community detection and thereby extracts high-quality community structures from networks. To acquire the high-quality must-link and cannot-link constraints, we also propose a semi-supervised component generation algorithm based on active learning, which actively selects nodes with maximum utility for the proposed semi-supervised community detection algorithm step by step, and then generates the must-link and cannot-link constraints by accessing a noiseless oracle. Extensive experiments were carried out, and the experimental results show that the introduction of active learning into the problem of community detection makes a success. Our proposed method can extract high-quality community structures from networks, and significantly outperforms other comparison methods. [ABSTRACT FROM AUTHOR]

An increasing number of genes have been experimentally confirmed in recent years as causative genes to various human diseases. The newly available knowledge can be exploited by machine learning methods to discover additional unknown genes that are likely to be associated with diseases. In particular, positive unlabeled learning (PU learning) methods, which require only a positive training set P (confirmed disease genes) and an unlabeled set U (the unknown candidate genes) instead of a negative training set N, have been shown to be effective in uncovering new disease genes in the current scenario. Using only a single source of data for prediction can be susceptible to bias due to incompleteness and noise in the genomic data and a single machine learning predictor prone to bias caused by inherent limitations of individual methods. In this paper, we propose an effective PU learning framework that integrates multiple biological data sources and an ensemble of powerful machine learning classifiers for disease gene identification. Our proposed method integrates data from multiple biological sources for training PU learning classifiers. A novel ensemble-based PU learning method EPU is then used to integrate multiple PU learning classifiers to achieve accurate and robust disease gene predictions. Our evaluation experiments across six disease groups showed that EPU achieved significantly better results compared with various state-of-the-art prediction methods as well as ensemble learning classifiers. Through integrating multiple biological data sources for training and the outputs of an ensemble of PU learning classifiers for prediction, we are able to minimize the potential bias and errors in individual data sources and machine learning algorithms to achieve more accurate and robust disease gene predictions. In the future, our EPU method provides an effective framework to integrate the additional biological and computational resources for better disease gene predictions. [ABSTRACT FROM AUTHOR]