51,447 research outputs found
User-profile-based analytics for detecting cloud security breaches
While the growth of cloud-based technologies has benefited the society tremendously, it has also increased the surface area for cyber attacks. Given that cloud services are prevalent today, it is critical to devise systems that detect intrusions. One form of security breach in the cloud is when cyber-criminals compromise Virtual Machines (VMs) of unwitting users and, then, utilize user resources to run time-consuming, malicious, or illegal applications for their own benefit. This work proposes a method to detect unusual resource usage trends and alert the user and the administrator in real time. We experiment with three categories of methods: simple statistical techniques, unsupervised classification, and regression. So far, our approach successfully detects anomalous resource usage when experimenting with typical trends synthesized from published real-world web server logs and cluster traces. We observe the best results with unsupervised classification, which gives an average F1-score of 0.83 for web server logs and 0.95 for the cluster traces
Selection of sequence motifs and generative Hopfield-Potts models for protein familiesilies
Statistical models for families of evolutionary related proteins have
recently gained interest: in particular pairwise Potts models, as those
inferred by the Direct-Coupling Analysis, have been able to extract information
about the three-dimensional structure of folded proteins, and about the effect
of amino-acid substitutions in proteins. These models are typically requested
to reproduce the one- and two-point statistics of the amino-acid usage in a
protein family, {\em i.e.}~to capture the so-called residue conservation and
covariation statistics of proteins of common evolutionary origin. Pairwise
Potts models are the maximum-entropy models achieving this. While being
successful, these models depend on huge numbers of {\em ad hoc} introduced
parameters, which have to be estimated from finite amount of data and whose
biophysical interpretation remains unclear. Here we propose an approach to
parameter reduction, which is based on selecting collective sequence motifs. It
naturally leads to the formulation of statistical sequence models in terms of
Hopfield-Potts models. These models can be accurately inferred using a mapping
to restricted Boltzmann machines and persistent contrastive divergence. We show
that, when applied to protein data, even 20-40 patterns are sufficient to
obtain statistically close-to-generative models. The Hopfield patterns form
interpretable sequence motifs and may be used to clusterize amino-acid
sequences into functional sub-families. However, the distributed collective
nature of these motifs intrinsically limits the ability of Hopfield-Potts
models in predicting contact maps, showing the necessity of developing models
going beyond the Hopfield-Potts models discussed here.Comment: 26 pages, 16 figures, to app. in PR
DNA ANALYSIS USING GRAMMATICAL INFERENCE
An accurate language definition capable of distinguishing between coding and non-coding DNA has important applications and analytical significance to the field of computational biology. The method proposed here uses positive sample grammatical inference and statistical information to infer languages for coding DNA.
An algorithm is proposed for the searching of an optimal subset of input sequences for the inference of regular grammars by optimizing a relevant accuracy metric. The algorithm does not guarantee the finding of the optimal subset; however, testing shows improvement in accuracy and performance over the basis algorithm.
Testing shows that the accuracy of inferred languages for components of DNA are consistently accurate. By using the proposed algorithm languages are inferred for coding DNA with average conditional probability over 80%. This reveals that languages for components of DNA can be inferred and are useful independent of the process that created them. These languages can then be analyzed or used for other tasks in computational biology.
To illustrate potential applications of regular grammars for DNA components, an inferred language for exon sequences is applied as post processing to Hidden Markov exon prediction to reduce the number of wrong exons detected and improve the specificity of the model significantly
Training Support Vector Machines Using Frank-Wolfe Optimization Methods
Training a Support Vector Machine (SVM) requires the solution of a quadratic
programming problem (QP) whose computational complexity becomes prohibitively
expensive for large scale datasets. Traditional optimization methods cannot be
directly applied in these cases, mainly due to memory restrictions.
By adopting a slightly different objective function and under mild conditions
on the kernel used within the model, efficient algorithms to train SVMs have
been devised under the name of Core Vector Machines (CVMs). This framework
exploits the equivalence of the resulting learning problem with the task of
building a Minimal Enclosing Ball (MEB) problem in a feature space, where data
is implicitly embedded by a kernel function.
In this paper, we improve on the CVM approach by proposing two novel methods
to build SVMs based on the Frank-Wolfe algorithm, recently revisited as a fast
method to approximate the solution of a MEB problem. In contrast to CVMs, our
algorithms do not require to compute the solutions of a sequence of
increasingly complex QPs and are defined by using only analytic optimization
steps. Experiments on a large collection of datasets show that our methods
scale better than CVMs in most cases, sometimes at the price of a slightly
lower accuracy. As CVMs, the proposed methods can be easily extended to machine
learning problems other than binary classification. However, effective
classifiers are also obtained using kernels which do not satisfy the condition
required by CVMs and can thus be used for a wider set of problems
Memory-Based Shallow Parsing
We present memory-based learning approaches to shallow parsing and apply
these to five tasks: base noun phrase identification, arbitrary base phrase
recognition, clause detection, noun phrase parsing and full parsing. We use
feature selection techniques and system combination methods for improving the
performance of the memory-based learner. Our approach is evaluated on standard
data sets and the results are compared with that of other systems. This reveals
that our approach works well for base phrase identification while its
application towards recognizing embedded structures leaves some room for
improvement
Information Extraction, Data Integration, and Uncertain Data Management: The State of The Art
Information Extraction, data Integration, and uncertain data management are different areas of research that got vast focus in the last two decades. Many researches tackled those areas of research individually. However, information extraction systems should have integrated with data integration methods to make use of the extracted information. Handling uncertainty in extraction and integration process is an important issue to enhance the quality of the data in such integrated systems. This article presents the state of the art of the mentioned areas of research and shows the common grounds and how to integrate information extraction and data integration under uncertainty management cover
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