Spatial transcriptomics is a modern sequencing technology that allows the measurement of the activity of thousands of genes in a tissue sample and map where the activity is occurring. This technology has enabled the study of the so-called spatially expressed genes, i.e., genes which exhibit spatial variation across the tissue. Comprehending their functions and their interactions in different areas of the tissue is of great scientific interest, as it might lead to a deeper understanding of several key biological mechanisms. However, adequate statistical tools that exploit the newly spatial mapping information to reach more specific conclusions are still lacking. In this work, we introduce SpaRTaCo, a new statistical model that clusters the spatial expression profiles of the genes according to the areas of the tissue. This is accomplished by performing a co-clustering, i.e., inferring the latent block structure of the data and inducing two types of clustering: of the genes, using their expression across the tissue, and of the image areas, using the gene expression in the spots where the RNA is collected. Our proposed methodology is validated with a series of simulation experiments and its usefulness in responding to specific biological questions is illustrated with an application to a human brain tissue sample processed with the 10X-Visium protocol.
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Estimation of the spatial heterogeneity in crime incidence across an entire city is an important step towards reducing crime and increasing our understanding of the physical and social functioning of urban environments. This is a difficult modeling endeavor since crime incidence can vary smoothly across space and time but there also exist physical and social barriers that result in discontinuities in crime rates between different regions within a city. A further difficulty is that there are different levels of resolution that can be used for defining regions of a city in order to analyze crime. To address these challenges, we develop a Bayesian non-parametric approach for the clustering of urban areal units at different levels of resolution simultaneously. Our approach is evaluated with an extensive synthetic data study and then applied to the estimation of crime incidence at various levels of resolution in the city of Philadelphia.
The onset of rheumatic diseases such as rheumatoid arthritis is typically subclinical, which results in challenging early detection of the disease. However, characteristic changes in the anatomy can be detected using imaging techniques such as MRI or CT. Modern imaging techniques such as chemical exchange saturation transfer (CEST) MRI drive the hope to improve early detection even further through the imaging of metabolites in the body. To image small structures in the joints of patients, typically one of the first regions where changes due to the disease occur, a high resolution for the CEST MR imaging is necessary. Currently, however, CEST MR suffers from an inherently low resolution due to the underlying physical constraints of the acquisition. In this work we compared established up-sampling techniques to neural network-based super-resolution approaches. We could show, that neural networks are able to learn the mapping from low-resolution to high-resolution unsaturated CEST images considerably better than present methods. On the test set a PSNR of 32.29dB (+10%), a NRMSE of 0.14 (+28%), and a SSIM of 0.85 (+15%) could be achieved using a ResNet neural network, improving the baseline considerably. This work paves the way for the prospective investigation of neural networks for super-resolution CEST MRI and, followingly, might lead to a earlier detection of the onset of rheumatic diseases.
Graph Convolutional Network (GCN) has been widely applied in transportation demand prediction due to its excellent ability to capture non-Euclidean spatial dependence among station-level or regional transportation demands. However, in most of the existing research, the graph convolution was implemented on a heuristically generated adjacency matrix, which could neither reflect the real spatial relationships of stations accurately, nor capture the multi-level spatial dependence of demands adaptively. To cope with the above problems, this paper provides a novel graph convolutional network for transportation demand prediction. Firstly, a novel graph convolution architecture is proposed, which has different adjacency matrices in different layers and all the adjacency matrices are self-learned during the training process. Secondly, a layer-wise coupling mechanism is provided, which associates the upper-level adjacency matrix with the lower-level one. It also reduces the scale of parameters in our model. Lastly, a unitary network is constructed to give the final prediction result by integrating the hidden spatial states with gated recurrent unit, which could capture the multi-level spatial dependence and temporal dynamics simultaneously. Experiments have been conducted on two real-world datasets, NYC Citi Bike and NYC Taxi, and the results demonstrate the superiority of our model over the state-of-the-art ones.
Because of continuous advances in mathematical programing, Mix Integer Optimization has become a competitive vis-a-vis popular regularization method for selecting features in regression problems. The approach exhibits unquestionable foundational appeal and versatility, but also poses important challenges. We tackle these challenges, reducing computational burden when tuning the sparsity bound (a parameter which is critical for effectiveness) and improving performance in the presence of feature collinearity and of signals that vary in nature and strength. Importantly, we render the approach efficient and effective in applications of realistic size and complexity - without resorting to relaxations or heuristics in the optimization, or abandoning rigorous cross-validation tuning. Computational viability and improved performance in subtler scenarios is achieved with a multi-pronged blueprint, leveraging characteristics of the Mixed Integer Programming framework and by means of whitening, a data pre-processing step.
Using the 6,638 case descriptions of societal impact submitted for evaluation in the Research Excellence Framework (REF 2014), we replicate the topic model (Latent Dirichlet Allocation or LDA) made in this context and compare the results with factor-analytic results using a traditional word-document matrix (Principal Component Analysis or PCA). Removing a small fraction of documents from the sample, for example, has on average a much larger impact on LDA than on PCA-based models to the extent that the largest distortion in the case of PCA has less effect than the smallest distortion of LDA-based models. In terms of semantic coherence, however, LDA models outperform PCA-based models. The topic models inform us about the statistical properties of the document sets under study, but the results are statistical and should not be used for a semantic interpretation - for example, in grant selections and micro-decision making, or scholarly work-without follow-up using domain-specific semantic maps.
For extracting meaningful topics from texts, their structures should be considered properly. In this paper, we aim to analyze structured time-series documents such as a collection of news articles and a series of scientific papers, wherein topics evolve along time depending on multiple topics in the past and are also related to each other at each time. To this end, we propose a dynamic and static topic model, which simultaneously considers the dynamic structures of the temporal topic evolution and the static structures of the topic hierarchy at each time. We show the results of experiments on collections of scientific papers, in which the proposed method outperformed conventional models. Moreover, we show an example of extracted topic structures, which we found helpful for analyzing research activities.
A recent research trend has emerged to identify developers' emotions, by applying sentiment analysis to the content of communication traces left in collaborative development environments. Trying to overcome the limitations posed by using off-the-shelf sentiment analysis tools, researchers recently started to develop their own tools for the software engineering domain. In this paper, we report a benchmark study to assess the performance and reliability of three sentiment analysis tools specifically customized for software engineering. Furthermore, we offer a reflection on the open challenges, as they emerge from a qualitative analysis of misclassified texts.
In this paper we propose a new parallel architecture based on Big Data technologies for real-time sentiment analysis on microblogging posts. Polypus is a modular framework that provides the following functionalities: (1) massive text extraction from Twitter, (2) distributed non-relational storage optimized for time range queries, (3) memory-based intermodule buffering, (4) real-time sentiment classification, (5) near real-time keyword sentiment aggregation in time series, (6) a HTTP API to interact with the Polypus cluster and (7) a web interface to analyze results visually. The whole architecture is self-deployable and based on Docker containers.
Steve Jobs, one of the greatest visionaries of our time was quoted in 1996 saying "a lot of times, people do not know what they want until you show it to them" [38] indicating he advocated products to be developed based on human intuition rather than research. With the advancements of mobile devices, social networks and the Internet of Things, enormous amounts of complex data, both structured and unstructured are being captured in hope to allow organizations to make better business decisions as data is now vital for an organizations success. These enormous amounts of data are referred to as Big Data, which enables a competitive advantage over rivals when processed and analyzed appropriately. However Big Data Analytics has a few concerns including Management of Data-lifecycle, Privacy & Security, and Data Representation. This paper reviews the fundamental concept of Big Data, the Data Storage domain, the MapReduce programming paradigm used in processing these large datasets, and focuses on two case studies showing the effectiveness of Big Data Analytics and presents how it could be of greater good in the future if handled appropriately.
In this paper we introduce a covariance framework for the analysis of EEG and MEG data that takes into account observed temporal stationarity on small time scales and trial-to-trial variations. We formulate a model for the covariance matrix, which is a Kronecker product of three components that correspond to space, time and epochs/trials, and consider maximum likelihood estimation of the unknown parameter values. An iterative algorithm that finds approximations of the maximum likelihood estimates is proposed. We perform a simulation study to assess the performance of the estimator and investigate the influence of different assumptions about the covariance factors on the estimated covariance matrix and on its components. Apart from that, we illustrate our method on real EEG and MEG data sets. The proposed covariance model is applicable in a variety of cases where spontaneous EEG or MEG acts as source of noise and realistic noise covariance estimates are needed for accurate dipole localization, such as in evoked activity studies, or where the properties of spontaneous EEG or MEG are themselves the topic of interest, such as in combined EEG/fMRI experiments in which the correlation between EEG and fMRI signals is investigated.
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