scholarly journals spiralize: an R Package for Visualizing Data on Spirals

2021 ◽  
Author(s):  
Zuguang Gu ◽  
Daniel Huebschmann

Spiral layout has two major advantages for data visualization. First, it is able to visualize data with long axes, which greatly improves the resolution of visualization. Second, it is efficient for time series data to reveal periodic patterns. Here we present the R package spiralize that provides a general solution for visualizing data on spirals. spiralize implements numerous graphics functions so that self-defined high-level graphics can be easily implemented by users. The power of spiralize is demonstrated by five real world datasets.

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Alaa Sagheer ◽  
Mostafa Kotb

AbstractCurrently, most real-world time series datasets are multivariate and are rich in dynamical information of the underlying system. Such datasets are attracting much attention; therefore, the need for accurate modelling of such high-dimensional datasets is increasing. Recently, the deep architecture of the recurrent neural network (RNN) and its variant long short-term memory (LSTM) have been proven to be more accurate than traditional statistical methods in modelling time series data. Despite the reported advantages of the deep LSTM model, its performance in modelling multivariate time series (MTS) data has not been satisfactory, particularly when attempting to process highly non-linear and long-interval MTS datasets. The reason is that the supervised learning approach initializes the neurons randomly in such recurrent networks, disabling the neurons that ultimately must properly learn the latent features of the correlated variables included in the MTS dataset. In this paper, we propose a pre-trained LSTM-based stacked autoencoder (LSTM-SAE) approach in an unsupervised learning fashion to replace the random weight initialization strategy adopted in deep LSTM recurrent networks. For evaluation purposes, two different case studies that include real-world datasets are investigated, where the performance of the proposed approach compares favourably with the deep LSTM approach. In addition, the proposed approach outperforms several reference models investigating the same case studies. Overall, the experimental results clearly show that the unsupervised pre-training approach improves the performance of deep LSTM and leads to better and faster convergence than other models.


Longitudinal Time Series data visualization plays important role in all sector of business decision making [9]. With enormous amount of complex data [11] from cloud and business requirement, number of graphs needed for decision making increased many folds. Generating enormous number of plots manually with more human input is tedious, time consuming and error prone. To avoid these issues, suitable visualization techniques with solid design principles become very important. We conceptualized and designed a novel method for automation of these processes. R-GGPLOT2[7] package and XL specifications file were primarily used to achieve this goal. We here show as how we can create multiple plots from time series data, plots specifications-XL file and R package GGPLOT2[7] in a single run. Since all required information are entered in XL sheet, R function can be run with no modification. Multiple plots can be generated by using enormous data available in production and service sectors such as finance, healthcare, transportation and food industries etc.


Author(s):  
Chenxi Sun ◽  
Shenda Hong ◽  
Moxian Song ◽  
Yen-Hsiu Chou ◽  
Yongyue Sun ◽  
...  

Prediction based on Irregularly Sampled Time Series (ISTS) is of wide concern in real-world applications. For more accurate prediction, methods had better grasp more data characteristics. Different from ordinary time series, ISTS is characterized by irregular time intervals of intra-series and different sampling rates of inter-series. However, existing methods have suboptimal predictions due to artificially introducing new dependencies in a time series and biasedly learning relations among time series when modeling these two characteristics. In this work, we propose a novel Time Encoding (TE) mechanism. TE can embed the time information as time vectors in the complex domain. It has the properties of absolute distance and relative distance under different sampling rates, which helps to represent two irregularities. Meanwhile, we create a new model named Time Encoding Echo State Network (TE-ESN). It is the first ESNs-based model that can process ISTS data. Besides, TE-ESN incorporates long short-term memories and series fusion to grasp horizontal and vertical relations. Experiments on one chaos system and three real-world datasets show that TE-ESN performs better than all baselines and has better reservoir property.


2017 ◽  
Vol 33 (20) ◽  
pp. 3308-3310 ◽  
Author(s):  
Wenbin Guo ◽  
Cristiane P G Calixto ◽  
John W S Brown ◽  
Runxuan Zhang

2015 ◽  
Vol 51 (3) ◽  
pp. 200-218 ◽  
Author(s):  
Carissa Sparkes ◽  
Leonard M. Lye ◽  
Susan Richter

Time series data such as monthly stream flows can be modelled using time series methods and then used to simulate or forecast flows for short term planning. Two methods of time series modelling were reviewed and compared: the well-known auto regressive moving average (ARMA) method and the state-space time-series (SSTS) method. ARMA has been used in hydrology to model and simulate flows with good results and is widely accepted for this purpose. SSTS modelling is a more recently developed method that is relatively unused for hydrologic modelling. This paper focuses on modelling the stream flows from basins of different sizes using these two time series modelling methods and comparing the results. Three rivers in Labrador and South-East Quebec were modelled: the Romaine, Ugjoktok and Alexis Rivers. Both models were compared for accuracy of prediction, ease of software use and simplicity of model to determine the preferred time series methodology approach for modelling these rivers. The SSTS was considered very easy to use but model diagnostics were found to require a high level of statistical understanding. Ultimately, the ARMA method was determined to be the better method for the typical engineer to use, considering the diagnostics were simple and the monthly flows could be easily simulated to verify results.


2017 ◽  
Author(s):  
María José Nueda ◽  
Jordi Martorell-Marugan ◽  
Cristina Martí ◽  
Sonia Tarazona ◽  
Ana Conesa

AbstractAs sequencing technologies improve their capacity to detect distinct transcripts of the same gene and to address complex experimental designs such as longitudinal studies, there is a need to develop statistical methods for the analysis of isoform expression changes in time series data. Iso-maSigPro is a new functionality of the R package maSigPro for transcriptomics time series data analysis. Iso-maSigPro identifies genes with a differential isoform usage across time. The package also includes new clustering and visualization functions that allow grouping of genes with similar expression patterns at the isoform level, as well as those genes with a shift in major expressed isoform. The package is freely available under the LGPL license from the Bioconductor web site (http://bioconductor.org).


2021 ◽  
Author(s):  
◽  
Ali Alqahtani

The use of deep learning has grown increasingly in recent years, thereby becoming a much-discussed topic across a diverse range of fields, especially in computer vision, text mining, and speech recognition. Deep learning methods have proven to be robust in representation learning and attained extraordinary achievement. Their success is primarily due to the ability of deep learning to discover and automatically learn feature representations by mapping input data into abstract and composite representations in a latent space. Deep learning’s ability to deal with high-level representations from data has inspired us to make use of learned representations, aiming to enhance unsupervised clustering and evaluate the characteristic strength of internal representations to compress and accelerate deep neural networks.Traditional clustering algorithms attain a limited performance as the dimensionality in-creases. Therefore, the ability to extract high-level representations provides beneficial components that can support such clustering algorithms. In this work, we first present DeepCluster, a clustering approach embedded in a deep convolutional auto-encoder. We introduce two clustering methods, namely DCAE-Kmeans and DCAE-GMM. The DeepCluster allows for data points to be grouped into their identical cluster, in the latent space, in a joint-cost function by simultaneously optimizing the clustering objective and the DCAE objective, producing stable representations, which is appropriate for the clustering process. Both qualitative and quantitative evaluations of proposed methods are reported, showing the efficiency of deep clustering on several public datasets in comparison to the previous state-of-the-art methods.Following this, we propose a new version of the DeepCluster model to include varying degrees of discriminative power. This introduces a mechanism which enables the imposition of regularization techniques and the involvement of a supervision component. The key idea of our approach is to distinguish the discriminatory power of numerous structures when searching for a compact structure to form robust clusters. The effectiveness of injecting various levels of discriminatory powers into the learning process is investigated alongside the exploration and analytical study of the discriminatory power obtained through the use of two discriminative attributes: data-driven discriminative attributes with the support of regularization techniques, and supervision discriminative attributes with the support of the supervision component. An evaluation is provided on four different datasets.The use of neural networks in various applications is accompanied by a dramatic increase in computational costs and memory requirements. Making use of the characteristic strength of learned representations, we propose an iterative pruning method that simultaneously identifies the critical neurons and prunes the model during training without involving any pre-training or fine-tuning procedures. We introduce a majority voting technique to compare the activation values among neurons and assign a voting score to evaluate their importance quantitatively. This mechanism effectively reduces model complexity by eliminating the less influential neurons and aims to determine a subset of the whole model that can represent the reference model with much fewer parameters within the training process. Empirically, we demonstrate that our pruning method is robust across various scenarios, including fully-connected networks (FCNs), sparsely-connected networks (SCNs), and Convolutional neural networks (CNNs), using two public datasets.Moreover, we also propose a novel framework to measure the importance of individual hidden units by computing a measure of relevance to identify the most critical filters and prune them to compress and accelerate CNNs. Unlike existing methods, we introduce the use of the activation of feature maps to detect valuable information and the essential semantic parts, with the aim of evaluating the importance of feature maps, inspired by novel neural network interpretability. A majority voting technique based on the degree of alignment between a se-mantic concept and individual hidden unit representations is utilized to evaluate feature maps’ importance quantitatively. We also propose a simple yet effective method to estimate new convolution kernels based on the remaining crucial channels to accomplish effective CNN compression. Experimental results show the effectiveness of our filter selection criteria, which outperforms the state-of-the-art baselines.To conclude, we present a comprehensive, detailed review of time-series data analysis, with emphasis on deep time-series clustering (DTSC), and a founding contribution to the area of applying deep clustering to time-series data by presenting the first case study in the context of movement behavior clustering utilizing the DeepCluster method. The results are promising, showing that the latent space encodes sufficient patterns to facilitate accurate clustering of movement behaviors. Finally, we identify state-of-the-art and present an outlook on this important field of DTSC from five important perspectives.


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