Methods for Joint Normalization and Comparison of Hi-C data

The development of chromatin conformation capture technology has opened new avenues of study into the 3D structure and function of the genome. Chromatin structure is known to influence gene regulation, and differences in structure are now emerging as a mechanism of regulation between, e.g., cell differentiation and disease vs. normal states. Hi-C sequencing technology now provides a way to study the 3D interactions of the chromatin over the whole genome. However, like all sequencing technologies, Hi-C suffers from several forms of bias stemming from both the technology and the DNA sequence itself. Several normalization methods have been developed for normalizing individual Hi-C datasets, but little work has been done on developing joint normalization methods for comparing two or more Hi-C datasets. To make full use of Hi-C data, joint normalization and statistical comparison techniques are needed to carry out experiments to identify regions where chromatin structure differs between conditions. We develop methods for the joint normalization and comparison of two Hi-C datasets, which we then extended to more complex experimental designs. Our normalization method is novel in that it makes use of the distance-dependent nature of chromatin interactions. Our modification of the Minus vs. Average (MA) plot to the Minus vs. Distance (MD) plot allows for a nonparametric data-driven normalization technique using loess smoothing. Additionally, we present a simple statistical method using Z-scores for detecting differentially interacting regions between two datasets. Our initial method was published as the Bioconductor R package HiCcompare [http://bioconductor.org/packages/HiCcompare/](http://bioconductor.org/packages/HiCcompare/). We then further extended our normalization and comparison method for use in complex Hi-C experiments with more than two datasets and optional covariates. We extended the normalization method to jointly normalize any number of Hi-C datasets by using a cyclic loess procedure on the MD plot. The cyclic loess normalization technique can remove between dataset biases efficiently and effectively even when several datasets are analyzed at one time. Our comparison method implements a generalized linear model-based approach for comparing complex Hi-C experiments, which may have more than two groups and additional covariates. The extended methods are also available as a Bioconductor R package [http://bioconductor.org/packages/multiHiCcompare/](http://bioconductor.org/packages/multiHiCcompare/). Finally, we demonstrate the use of HiCcompare and multiHiCcompare in several test cases on real data in addition to comparing them to other similar methods (https://doi.org/10.1002/cpbi.76)

Mechanical MNIST: A benchmark dataset for mechanical metamodels

Metamodels, or models of models, map defined model inputs to defined model outputs. Typically, metamodels are constructed by generating a dataset through sampling a direct model and training a machine learning algorithm to predict a limited number of model outputs from varying model inputs. When metamodels are constructed to be computationally cheap, they are an invaluable tool for applications ranging from topology optimization, to uncertainty quantification, to multi-scale simulation. By nature, a given metamodel will be tailored to a specific dataset. However, the most pragmatic metamodel type and structure will often be general to larger classes of problems. At present, the most pragmatic metamodel selection for dealing with mechanical data has not been thoroughly explored. Drawing inspiration from the benchmark datasets available to the computer vision research community, we introduce a benchmark data set (Mechanical MNIST) for constructing metamodels of heterogeneous material undergoing large deformation. We then show examples of how our benchmark dataset can be used, and establish baseline metamodel performance. Because our dataset is readily available, it will enable the direct quantitative comparison between different metamodeling approaches in a pragmatic manner. We anticipate that it will enable the broader community of researchers to develop improved metamodeling techniques for mechanical data that will surpass the baseline performance that we show here.Accepted manuscrip

A Multi-Gene Genetic Programming Application for Predicting Students Failure at School

Several efforts to predict student failure rate (SFR) at school accurately still remains a core problem area faced by many in the educational sector. The procedure for forecasting SFR are rigid and most often times require data scaling or conversion into binary form such as is the case of the logistic model which may lead to lose of information and effect size attenuation. Also, the high number of factors, incomplete and unbalanced dataset, and black boxing issues as in Artificial Neural Networks and Fuzzy logic systems exposes the need for more efficient tools. Currently the application of Genetic Programming (GP) holds great promises and has produced tremendous positive results in different sectors. In this regard, this study developed GPSFARPS, a software application to provide a robust solution to the prediction of SFR using an evolutionary algorithm known as multi-gene genetic programming. The approach is validated by feeding a testing data set to the evolved GP models. Result obtained from GPSFARPS simulations show its unique ability to evolve a suitable failure rate expression with a fast convergence at 30 generations from a maximum specified generation of 500. The multi-gene system was also able to minimize the evolved model expression and accurately predict student failure rate using a subset of the original expressionComment: 14 pages, 9 figures, Journal paper. arXiv admin note: text overlap with arXiv:1403.0623 by other author

Distributed multinomial regression

This article introduces a model-based approach to distributed computing for multinomial logistic (softmax) regression. We treat counts for each response category as independent Poisson regressions via plug-in estimates for fixed effects shared across categories. The work is driven by the high-dimensional-response multinomial models that are used in analysis of a large number of random counts. Our motivating applications are in text analysis, where documents are tokenized and the token counts are modeled as arising from a multinomial dependent upon document attributes. We estimate such models for a publicly available data set of reviews from Yelp, with text regressed onto a large set of explanatory variables (user, business, and rating information). The fitted models serve as a basis for exploring the connection between words and variables of interest, for reducing dimension into supervised factor scores, and for prediction. We argue that the approach herein provides an attractive option for social scientists and other text analysts who wish to bring familiar regression tools to bear on text data.Comment: Published at http://dx.doi.org/10.1214/15-AOAS831 in the Annals of Applied Statistics (http://www.imstat.org/aoas/) by the Institute of Mathematical Statistics (http://www.imstat.org

Computing server power modeling in a data center: survey,taxonomy and performance evaluation

Data centers are large scale, energy-hungry infrastructure serving the increasing computational demands as the world is becoming more connected in smart cities. The emergence of advanced technologies such as cloud-based services, internet of things (IoT) and big data analytics has augmented the growth of global data centers, leading to high energy consumption. This upsurge in energy consumption of the data centers not only incurs the issue of surging high cost (operational and maintenance) but also has an adverse effect on the environment. Dynamic power management in a data center environment requires the cognizance of the correlation between the system and hardware level performance counters and the power consumption. Power consumption modeling exhibits this correlation and is crucial in designing energy-efficient optimization strategies based on resource utilization. Several works in power modeling are proposed and used in the literature. However, these power models have been evaluated using different benchmarking applications, power measurement techniques and error calculation formula on different machines. In this work, we present a taxonomy and evaluation of 24 software-based power models using a unified environment, benchmarking applications, power measurement technique and error formula, with the aim of achieving an objective comparison. We use different servers architectures to assess the impact of heterogeneity on the models' comparison. The performance analysis of these models is elaborated in the paper

Theoretical Interpretations and Applications of Radial Basis Function Networks

Medical applications usually used Radial Basis Function Networks just as Artificial Neural Networks. However, RBFNs are Knowledge-Based Networks that can be interpreted in several way: Artificial Neural Networks, Regularization Networks, Support Vector Machines, Wavelet Networks, Fuzzy Controllers, Kernel Estimators, Instanced-Based Learners. A survey of their interpretations and of their corresponding learning algorithms is provided as well as a brief survey on dynamic learning algorithms. RBFNs' interpretations can suggest applications that are particularly interesting in medical domains