Big Data Analytics in Bioinformatics: A Machine Learning Perspective

Bioinformatics research is characterized by voluminous and incremental datasets and complex data analytics methods. The machine learning methods used in bioinformatics are iterative and parallel. These methods can be scaled to handle big data using the distributed and parallel computing technologies. Usually big data tools perform computation in batch-mode and are not optimized for iterative processing and high data dependency among operations. In the recent years, parallel, incremental, and multi-view machine learning algorithms have been proposed. Similarly, graph-based architectures and in-memory big data tools have been developed to minimize I/O cost and optimize iterative processing. However, there lack standard big data architectures and tools for many important bioinformatics problems, such as fast construction of co-expression and regulatory networks and salient module identification, detection of complexes over growing protein-protein interaction data, fast analysis of massive DNA, RNA, and protein sequence data, and fast querying on incremental and heterogeneous disease networks. This paper addresses the issues and challenges posed by several big data problems in bioinformatics, and gives an overview of the state of the art and the future research opportunities.Comment: 20 pages survey paper on Big data analytics in Bioinformatic

Scalable Prototype Selection by Genetic Algorithms and Hashing

Classification in the dissimilarity space has become a very active research area since it provides a possibility to learn from data given in the form of pairwise non-metric dissimilarities, which otherwise would be difficult to cope with. The selection of prototypes is a key step for the further creation of the space. However, despite previous efforts to find good prototypes, how to select the best representation set remains an open issue. In this paper we proposed scalable methods to select the set of prototypes out of very large datasets. The methods are based on genetic algorithms, dissimilarity-based hashing, and two different unsupervised and supervised scalable criteria. The unsupervised criterion is based on the Minimum Spanning Tree of the graph created by the prototypes as nodes and the dissimilarities as edges. The supervised criterion is based on counting matching labels of objects and their closest prototypes. The suitability of these type of algorithms is analyzed for the specific case of dissimilarity representations. The experimental results showed that the methods select good prototypes taking advantage of the large datasets, and they do so at low runtimes.Comment: 26 pages, 8 figure

Clustering Time Series Data Stream - A Literature Survey

Mining Time Series data has a tremendous growth of interest in today's world. To provide an indication various implementations are studied and summarized to identify the different problems in existing applications. Clustering time series is a trouble that has applications in an extensive assortment of fields and has recently attracted a large amount of research. Time series data are frequently large and may contain outliers. In addition, time series are a special type of data set where elements have a temporal ordering. Therefore clustering of such data stream is an important issue in the data mining process. Numerous techniques and clustering algorithms have been proposed earlier to assist clustering of time series data streams. The clustering algorithms and its effectiveness on various applications are compared to develop a new method to solve the existing problem. This paper presents a survey on various clustering algorithms available for time series datasets. Moreover, the distinctiveness and restriction of previous research are discussed and several achievable topics for future study are recognized. Furthermore the areas that utilize time series clustering are also summarized.Comment: IEEE Publication format, International Journal of Computer Science and Information Security, IJCSIS, Vol. 8 No. 1, April 2010, USA. ISSN 1947 5500, http://sites.google.com/site/ijcsis

Unsupervised Assignment Flow: Label Learning on Feature Manifolds by Spatially Regularized Geometric Assignment

This paper introduces the unsupervised assignment flow that couples the assignment flow for supervised image labeling with Riemannian gradient flows for label evolution on feature manifolds. The latter component of the approach encompasses extensions of state-of-the-art clustering approaches to manifold-valued data. Coupling label evolution with the spatially regularized assignment flow induces a sparsifying effect that enables to learn compact label dictionaries in an unsupervised manner. Our approach alleviates the requirement for supervised labeling to have proper labels at hand, because an initial set of labels can evolve and adapt to better values while being assigned to given data. The separation between feature and assignment manifolds enables the flexible application which is demonstrated for three scenarios with manifold-valued features. Experiments demonstrate a beneficial effect in both directions: adaptivity of labels improves image labeling, and steering label evolution by spatially regularized assignments leads to proper labels, because the assignment flow for supervised labeling is exactly used without any approximation for label learning.Comment: 34 pages, 13 figures, published in Journal of Mathematical Imaging and Vision (JMIV

Using real-time cluster configurations of streaming asynchronous features as online state descriptors in financial markets

We present a scheme for online, unsupervised state discovery and detection from streaming, multi-featured, asynchronous data in high-frequency financial markets. Online feature correlations are computed using an unbiased, lossless Fourier estimator. A high-speed maximum likelihood clustering algorithm is then used to find the feature cluster configuration which best explains the structure in the correlation matrix. We conjecture that this feature configuration is a candidate descriptor for the temporal state of the system. Using a simple cluster configuration similarity metric, we are able to enumerate the state space based on prevailing feature configurations. The proposed state representation removes the need for human-driven data pre-processing for state attribute specification, allowing a learning agent to find structure in streaming data, discern changes in the system, enumerate its perceived state space and learn suitable action-selection policies.Comment: 19 pages, 6 figures, 3 tables, under review at Pattern Recognition Letter

Local Aggregation for Unsupervised Learning of Visual Embeddings

Unsupervised approaches to learning in neural networks are of substantial interest for furthering artificial intelligence, both because they would enable the training of networks without the need for large numbers of expensive annotations, and because they would be better models of the kind of general-purpose learning deployed by humans. However, unsupervised networks have long lagged behind the performance of their supervised counterparts, especially in the domain of large-scale visual recognition. Recent developments in training deep convolutional embeddings to maximize non-parametric instance separation and clustering objectives have shown promise in closing this gap. Here, we describe a method that trains an embedding function to maximize a metric of local aggregation, causing similar data instances to move together in the embedding space, while allowing dissimilar instances to separate. This aggregation metric is dynamic, allowing soft clusters of different scales to emerge. We evaluate our procedure on several large-scale visual recognition datasets, achieving state-of-the-art unsupervised transfer learning performance on object recognition in ImageNet, scene recognition in Places 205, and object detection in PASCAL VOC

Julia Language in Machine Learning: Algorithms, Applications, and Open Issues

Machine learning is driving development across many fields in science and engineering. A simple and efficient programming language could accelerate applications of machine learning in various fields. Currently, the programming languages most commonly used to develop machine learning algorithms include Python, MATLAB, and C/C ++. However, none of these languages well balance both efficiency and simplicity. The Julia language is a fast, easy-to-use, and open-source programming language that was originally designed for high-performance computing, which can well balance the efficiency and simplicity. This paper summarizes the related research work and developments in the application of the Julia language in machine learning. It first surveys the popular machine learning algorithms that are developed in the Julia language. Then, it investigates applications of the machine learning algorithms implemented with the Julia language. Finally, it discusses the open issues and the potential future directions that arise in the use of the Julia language in machine learning.Comment: Published in Computer Science Revie

A survey on trajectory clustering analysis

This paper comprehensively surveys the development of trajectory clustering. Considering the critical role of trajectory data mining in modern intelligent systems for surveillance security, abnormal behavior detection, crowd behavior analysis, and traffic control, trajectory clustering has attracted growing attention. Existing trajectory clustering methods can be grouped into three categories: unsupervised, supervised and semi-supervised algorithms. In spite of achieving a certain level of development, trajectory clustering is limited in its success by complex conditions such as application scenarios and data dimensions. This paper provides a holistic understanding and deep insight into trajectory clustering, and presents a comprehensive analysis of representative methods and promising future directions

Application of Machine Learning in Wireless Networks: Key Techniques and Open Issues

As a key technique for enabling artificial intelligence, machine learning (ML) is capable of solving complex problems without explicit programming. Motivated by its successful applications to many practical tasks like image recognition, both industry and the research community have advocated the applications of ML in wireless communication. This paper comprehensively surveys the recent advances of the applications of ML in wireless communication, which are classified as: resource management in the MAC layer, networking and mobility management in the network layer, and localization in the application layer. The applications in resource management further include power control, spectrum management, backhaul management, cache management, beamformer design and computation resource management, while ML based networking focuses on the applications in clustering, base station switching control, user association and routing. Moreover, literatures in each aspect is organized according to the adopted ML techniques. In addition, several conditions for applying ML to wireless communication are identified to help readers decide whether to use ML and which kind of ML techniques to use, and traditional approaches are also summarized together with their performance comparison with ML based approaches, based on which the motivations of surveyed literatures to adopt ML are clarified. Given the extensiveness of the research area, challenges and unresolved issues are presented to facilitate future studies, where ML based network slicing, infrastructure update to support ML based paradigms, open data sets and platforms for researchers, theoretical guidance for ML implementation and so on are discussed.Comment: 34 pages,8 figure

Training a Restricted Boltzmann Machine for Classification by Labeling Model Samples

We propose an alternative method for training a classification model. Using the MNIST set of handwritten digits and Restricted Boltzmann Machines, it is possible to reach a classification performance competitive to semi-supervised learning if we first train a model in an unsupervised fashion on unlabeled data only, and then manually add labels to model samples instead of training data samples with the help of a GUI. This approach can benefit from the fact that model samples can be presented to the human labeler in a video-like fashion, resulting in a higher number of labeled examples. Also, after some initial training, hard-to-classify examples can be distinguished from easy ones automatically, saving manual work