Spatial Neighbours Research Articles

MorphoFeatures for unsupervised exploration of cell types, tissues, and organs in volume electron microscopy.

Electron microscopy (EM) provides a uniquely detailed view of cellular morphology, including organelles and fine subcellular ultrastructure. While the acquisition and (semi-)automatic segmentation of multicellular EM volumes are now becoming routine, large-scale analysis remains severely limited by the lack of generally applicable pipelines for automatic extraction of comprehensive morphological descriptors. Here, we present a novel unsupervised method for learning cellular morphology features directly from 3D EM data: a neural network delivers a representation of cells by shape and ultrastructure. Applied to the full volume of an entire three-segmented worm of the annelid Platynereis dumerilii, it yields a visually consistent grouping of cells supported by specific gene expression profiles. Integration of features across spatial neighbours can retrieve tissues and organs, revealing, for example, a detailed organisation of the animal foregut. We envision that the unbiased nature of the proposed morphological descriptors will enable rapid exploration of very different biological questions in large EM volumes, greatly increasing the impact of these invaluable, but costly resources.

Long short‐distance topology modelling of 3D point cloud segmentation with a graph convolution neural network

Abstract3D point cloud segmentation is a non‐trivial problem due to its irregular, sparse, and unordered data structure. Existing methods only consider structural relationships of a 3D point and its spatial neighbours. However, the inner‐point interactions and long‐distance context of a 3D point cloud have been less investigated. In this study, we propose an effective plug‐and‐play module called the Long Short‐Distance Topologically Modelled (LSDTM) Graph Convolutional Neural Network (GCNN) to learn the underlying structure of 3D point clouds. Specifically, we introduce the concept of subgraph to model the contextual‐point relationships within a short distance. Then the proposed topology can be reconstructed by recursive aggregation of subgraphs, and importantly, to propagate the contextual scope to a long range. The proposed LSDTM can parse the point cloud data with maximisation of preserving the geometric structure and contextual structure, and the topological graph can be trained end‐to‐end through a seamlessly integrated GCNN. We provide a case study of triple‐layer ternary topology and experimental results on ShapeNetPart, Stanford 3D Indoor Semantics and ScanNet datasets, indicating a significant improvement on the task of 3D point cloud segmentation and validating the effectiveness of our research.

Investigating Farm Fragmentation as a Risk Factor for Bovine Tuberculosis in Cattle Herds: A Matched Case-Control Study from Northern Ireland.

Bovine tuberculosis remains a challenging endemic pathogen of cattle in many parts of the globe. Spatial clustering of Mycoacterium bovis molecular types in cattle suggests that local factors are the primary drivers of spread. Northern Ireland’s agricultural landscape is comprised of highly fragmented farms, distributed across spatially discontinuous land parcels, and these highly fragmented farms are thought to facilitate localised spread. We conducted a matched case control study to quantify the risks of bovine tuberculosis breakdown with farm area, farm fragmentation, fragment dispersal, and contact with neighbouring herds. Whilst our results show small but significant increases in breakdown risk associated with each factor, these relationships were strongly confounded with the number of contiguous neighbours with bovine tuberculosis. Our key finding was that every infected neighbour led to an increase in the odds of breakdown by 40% to 50%, and that highly fragmented farms were almost twice as likely to have a bTB positive neighbour compared to nonfragmented farms. Our results suggest that after controlling for herd size, herd type, spatial and temporal factors, farm fragmentation increasingly exposes herds to infection originating from first-order spatial neighbours. Given Northern Ireland’s particularly fragmented landscape, and reliance on short-term leases, our data support the hypothesis that between-herd contiguous spread is a particularly important component of the region’s bovine tuberculosis disease system.

Nearest polarimetric and spatial neighbours for feature space projection and guidance image-based spatial filtering for PolSAR image classification

ABSTRACT A feature space projection based on the nearest polarimetric and spatial neighbours is proposed for polarimetric synthetic aperture radar (PolSAR) images. The objective function is designed such that increases the class discrimination while preserves the contextual properties. Each polarimetric or spatial neighbour is contributed proportional to with its Wishart distance to the given pixel. A guidance image, which involves all polarimetric channels, is also introduced for spatial filtering of the initial classification map, which is efficient for improving the final classification map. The proposed method shows high performance for PolSAR image classification using limited training samples.

Lossless Coding of Light Fields Based on 4D Minimum Rate Predictors.

Common representations of light fields use four-dimensional data structures, where a given pixel is closely related not only to its spatial neighbours within the same view, but also to its angular neighbours, co-located in adjacent views. Such structure presents increased redundancy between pixels, when compared with regular single-view images. Then, these redundancies are exploited to obtain compressed representations of the light field, using prediction algorithms specifically tailored to estimate pixel values based on both spatial and angular references. This paper proposes new encoding schemes which take advantage of the four-dimensional light field data structures to improve the coding performance of Minimum Rate Predictors. The proposed methods expand previous research on lossless coding beyond the current state-of-the-art. The experimental results, obtained using both traditional datasets and others more challenging, show bit-rate savings no smaller than 10%, when compared with existing methods for lossless light field compression.

Automatic processing of time domain induced polarization data using supervised artificial neural networks

SUMMARYProcessing of geophysical data is a time consuming task involving many different steps. One approach for accelerating and automating processing of geophysical data is to look towards machine learning (ML). ML encompasses a wide range of tools, which can be used to automate complicated and/or tedious tasks. We present strategies for automating the processing of time-domain induced polarization (IP) data using ML. An IP data set from Grindsted in Denmark is used to investigate the applicability of neural networks for processing such data. The Grindsted data set consists of eight profiles, with approximately 2000 data curves per profile, on average. Each curve needs to be processed, which, using the manual approach, can take 1–2 hr per profile. Around 20 per cent of the curves were manually processed and used to train and validate an artificial neural network. Once trained, the network could process all curves, in 6–15 s for each profile. The accuracy of the neural network, when considering the manual processing as a reference, is 90.8 per cent. At first, the network could not detect outlier curves, that is where entire chargeability curves were significantly different from their spatial neighbours. Therefore, an outlier curve detection algorithm was developed and implemented to work in tandem with the network. The automatic processing approach developed here, involving the neural network and the outlier curve detection, leads to similar inversion results as the manual processing, with the two significant advantages of reduced processing times and enhanced processing consistency.

Modelling and predicting the spatio-temporal spread of COVID-19 in Italy

BackgroundThe Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) was first detected in China at the end of 2019 and it has since spread in few months all over the World. Italy was one of the first Western countries who faced the health emergency and is one of the countries most severely affected by the pandemic. The diffusion of Coronavirus disease 2019 (COVID-19) in Italy has followed a peculiar spatial pattern, however the attention of the scientific community has so far focussed almost exclusively on the prediction of the evolution of the disease over time.MethodsOfficial freely available data about the number of infected at the finest possible level of spatial areal aggregation (Italian provinces) are used to model the spatio-temporal distribution of COVID-19 infections at local level. An endemic-epidemic time-series mixed-effects generalized linear model for areal disease counts has been implemented to understand and predict spatio-temporal diffusion of the phenomenon.ResultsThree subcomponents characterize the fitted model. The first describes the transmission of the illness within provinces; the second accounts for the transmission between nearby provinces; the third is related to the evolution of the disease over time. At the local level, the provinces first concerned by containment measures are those that are not affected by the effects of spatial neighbours. On the other hand, the component accounting for the spatial interaction with surrounding areas is prevalent for provinces that are strongly involved by contagions. Moreover, the proposed model provides good forecasts for the number of infections at local level while controlling for delayed reporting.ConclusionsA strong evidence is found that strict control measures implemented in some provinces efficiently break contagions and limit the spread to nearby areas. While containment policies may potentially be more effective if planned considering the peculiarities of local territories, the effective and homogeneous enforcement of control measures at national level is needed to prevent the disease control being delayed or missed as a whole. This may also apply at international level where, as it is for the European Union or the United States, the internal border checks among states have largely been abolished.

SPATIAL-SPECTRAL MANIFOLD EMBEDDING OF HYPERSPECTRAL DATA

Abstract. In recent years, hyperspectral imaging, also known as imaging spectroscopy, has been paid an increasing interest in geoscience and remote sensing community. Hyperspectral imagery is characterized by very rich spectral information, which enables us to recognize the materials of interest lying on the surface of the Earth more easier. We have to admit, however, that high spectral dimension inevitably brings some drawbacks, such as expensive data storage and transmission, information redundancy, etc. Therefore, to reduce the spectral dimensionality effectively and learn more discriminative spectral low-dimensional embedding, in this paper we propose a novel hyperspectral embedding approach by simultaneously considering spatial and spectral information, called spatial-spectral manifold embedding (SSME). Beyond the pixel-wise spectral embedding approaches, SSME models the spatial and spectral information jointly in a patch-based fashion. SSME not only learns the spectral embedding by using the adjacency matrix obtained by similarity measurement between spectral signatures, but also models the spatial neighbours of a target pixel in hyperspectral scene by sharing the same weights (or edges) in the process of learning embedding. Classification is explored as a potential strategy to quantitatively evaluate the performance of learned embedding representations. Classification is explored as a potential application for quantitatively evaluating the performance of these hyperspectral embedding algorithms. Extensive experiments conducted on the widely-used hyperspectral datasets demonstrate the superiority and effectiveness of the proposed SSME as compared to several state-of-the-art embedding methods.

Space-time analysis of ovarian cancer mortality rates by age groups in spanish provinces (1989\u20132015)

BackgroundOvarian cancer is a silent and largely asymptomatic cancer, leading to late diagnosis and worse prognosis. The late-stage detection and low survival rates, makes the study of the space-time evolution of ovarian cancer particularly relevant. In addition, research of this cancer in small areas (like provinces or counties) is still scarce.MethodsThe study presented here covers all ovarian cancer deaths for women over 50 years of age in the provinces of Spain during the period 1989-2015. Spatio-temporal models have been fitted to smooth ovarian cancer mortality rates in age groups [50,60), [60,70), [70,80), and [80,+), borrowing information from spatial and temporal neighbours. Model fitting and inference has been carried out using the Integrated Nested Laplace Approximation (INLA) technique.ResultsLarge differences in ovarian cancer mortality among the age groups have been found, with higher mortality rates in the older age groups. Striking differences are observed between northern and southern Spain. The global temporal trends (by age group) reveal that the evolution of ovarian cancer over the whole of Spain has remained nearly constant since the early 2000s.ConclusionDifferences in ovarian cancer mortality exist among the Spanish provinces, years, and age groups. As the exact causes of ovarian cancer remain unknown, spatio-temporal analyses by age groups are essential to discover inequalities in ovarian cancer mortality. Women over 60 years of age should be the focus of follow-up studies as the mortality rates remain constant since 2002. High-mortality provinces should also be monitored to look for specific risk factors.

Modelling and Predicting the Spatio-Temporal Spread of Coronavirus Disease 2019 (COVID-19) in Italy

Background: Severe acute respiratory syndrome Coronavirus 2019 (COVID-19) has been firstly detected in China at the end of 2019 and it spread in few months all over the world. Italy is the second country in the world for number of cases. In this country, the diffusion of COVID-19 has followed a peculiar spatial pattern. However, the interest of scientific community has been devoted almost exclusively to the prediction of the disease evolution over time so far. Methods: Official freely available data about the number of infected at the finest possible level of spatial areal aggregation (Italian provinces) are used to model the spatio-temporal distribution of COVID-19 infections at local level. Data time horizon ranges from 20 February 2020, which is the date when the first case not directly connected with China has been discovered in northern Italy, to 18 March 2020. An endemic-epidemic multivariate time-series mixed-effects generalized linear model for areal disease counts has been implemented to understand and predict spatio-temporal diffusion of the phenomenon. Previous literature has shown that these class of models provide reliable predictions of infectious diseases in time and space. Findings: Three subcomponents characterize the estimated model. The first is related to the evolution of the disease over time; the second is characterized by transmission of the illness among inhabitants of the same province; the third remarks the effects of spatial neighbourhood and try to capture the contagion effects of nearby areas. Focusing on the aggregated time-series of the daily counts in Italy, the contribution of any of the three subcomponents do not dominate on the others and our predictions are excellent for the whole country, with an error of 3 ‰ compared to the late available data. At local level, instead, interesting distinct patterns emerge. In particular, the provinces first concerned by containment measures are those that are not affected by the effects of spatial neighbours. On the other hand, for the provinces the are currently strongly affected by contagions, the component accounting for the spatial interaction with surrounding areas is prevalent. Moreover, the proposed model provides good forecasts of the number of infections at local level while controlling for delayed reporting. Interpretation: Social and demographic aspects can explain the dramatic involvement of some provinces. A strong evidence is found that strict control measures implemented in some provinces efficiently break contagions and limit the spread to nearby areas. While policies to contain the 1 spreading of the disease may potentially be more effective if planned considering the peculiarities of local territories, the effective and homogeneous enforcement of control measures at national level is imperative to prevent the disease control being delayed or missed as a whole. This may also apply at international level where, as it is for the EU or the USA, the internal border checks among states have largely been abolished. Funding Statement: None. Declaration of Interests: None of the authors of this paper has a financial or personal relationship with other people or organizations that could inappropriately influence or bias the content of the paper. No competing interests are at stake and there is no conflict of interest with other people or organizations that could inappropriately influence or bias the content of the paper. Ethics Approval Statement: Data is publicly available.

Do sequence neighbours of intrinsically disordered regions promote structural flexibility in intrinsically disordered proteins?

Intrinsically disordered proteins (IDPs) are crucial players in various cellular activities. Several experimental and computational analyses have been conducted to study structural pliability and functional potential of IDPs. In spite of active research in past few decades, what induces structural disorder in IDPs and how is still elusive. Many studies testify that sequential and spatial neighbours often play important roles in determining structural and functional behaviour of proteins. Considering this fact, we assessed sequence neighbours of intrinsically disordered regions (IDRs) to understand if they have any role to play in inducing structural flexibility in IDPs. Our analysis includes 97% eukaryotic IDPs and 3% from bacteria and viruses. Physicochemical and structural parameters including amino acid propensity, hydrophobicity, secondary structure propensity, relative solvent accessibility, B-factor and atomic packing density are used to characterise the neighbouring residues of IDRs (NRIs). We show that NRIs exhibit a unique nature, which makes them stand out from both ordered and disordered residues. They show correlative occurrences of residue pairs like Ser-Thr and Gln-Asn, indicating their tendency to avoid strong biases of order or disorder promoting amino acids. We also find differential preferences of amino acids between N- and C-terminal neighbours, which might indicate a plausible directional effect on the dynamics of adjacent IDRs. We designed an efficient prediction tool using Random Forest to distinguish the NRIs from the ordered residues. Our findings will contribute to understand the behaviour of IDPs, and may provide potential lead in deciphering the role of IDRs in protein folding and assembly.

Spectral dimension on spatial hypersurfaces in causal set quantum gravity

An important probe of quantum geometry is its spectral dimension, defined via a spatial diffusion process. In this work we study the spectral dimension of a ‘spatial hypersurface’ in a manifoldlike causal set using the induced spatial distance function. In previous work, the diffusion was taken on the full causal set, where the nearest neighbours are unbounded in number. The resulting super-diffusion leads to an increase in the spectral dimension at short diffusion times, in contrast to other approaches to quantum gravity. In the current work, by using a temporal localisation in the causal set, the number of nearest spatial neighbours is rendered finite. Using numerical simulations of causal sets obtained from d = 3 Minkowski spacetime, we find that for a flat spatial hypersurface, the spectral dimension agrees with the Hausdorff dimension at intermediate scales, but shows clear indications of dimensional reduction at small scales, i.e. in the ultraviolet. The latter is a direct consequence of ‘discrete asymptotic silence’ at small scales in causal sets.

A novel approach for modelling pattern and spatial dependence structures between climate variables by combining mixture models with copula models

AbstractSpatiotemporal dependence structures play a pivotal role in understanding the meteorological characteristics of a basin or subbasin. This further affects the hydrological conditions and, consequently, will provide misleading results if these structures are not taken into account properly. In this study, we modelled the spatial dependence structure of three climate variables, maximum and minimum temperature and precipitation, throughout the Monsoon‐dominated zone of Pakistan. For temperature, six meteorological stations have been considered, for precipitation we used the results of four meteorological stations. For modelling the dependence structure between temperature and precipitation at multiple sites, we utilized C‐Vine, D‐Vine and student t‐copula models. For temperature, multivariate mixture normal distributions, and for precipitation, the gamma distribution, have been used as marginals under the copula models. The models were calibrated by utilizing the 20 years daily data from 1981 to 2000, and for validation, we used the data for 10‐year period from 2001 to 2010. The simulations were performed for each variable separately, conditioned on spatial neighbours. A comparison was made between the different copula models, on the basis of observational and simulated patterns and spatial dependence structures, the performance was evaluated for the validation period. The results show that all copula models performed well; however, there are subtle differences between them. The copula models captured the patterns and spatial dependence structures between climate variables, however, the t‐copula showed poor performance in reproducing the dependence structure with respect to magnitude. It was observed that important statistics of observed data have been closely approximated except a few maximum values for maximum temperature and minimum values for minimum temperature. Probability density functions of simulated data follow closely the pattern of observational data. These methods can be combined with statistical downscaling models to improve their performance, particularly in modelling the dependence structure between climate variables at multiple sites.

A collaborative representation-based approximation method for remote sensing image fusion

ABSTRACTA collaborative representation-based approximation (CRA) for the fusion of low resolution multispectral (MS) image and high-resolution Panchromatic (Pan) image is proposed in this paper. To approximate each pixel of the high-resolution MS, the corresponding pixel in MS and the surrounding neighbours in its associated local window of Pan are contributed. Moreover, for increasing the spatial details in the final fused product, the spatial details of Pan are added to the fused image. The CRA method simply uses the spatial neighbours in the local regions and has no need to compose any appropriate dictionary for image representation. Moreover, it involves a -norm optimization problem which results in a closed-form solution. Various experiments visually and numerically show the superior performance of the proposed CRA method compared to several popular and recent pansharpening methods.

Wild zebra finches choose neighbours for synchronized breeding

Organisms should aim to time their reproduction to match the optimal ecological conditions and thus maximize their fitness. However, social cues have been identified as determinants of reproductive decisions and might also be involved in coordinating the timing of reproduction. Breeding synchronously with other individuals can bring several advantages, including a reduced individual predation risk and an increased opportunity for social foraging. The behavioural mechanisms underlying reproductive synchrony are versatile and not well understood, particularly in species inhabiting unpredictable environments. In contrast to highly seasonal environments, more variable and unpredictable environments can support periods of extended breeding with lower levels of synchronous breeding overall, but opportunities for individuals to breed synchronously at a finer temporal and spatial scale. Zebra finches, Taeniopygia guttata, are a highly social species, naturally inhabiting the ecologically unpredictable arid zone of Australia. In the wild, reproduction at a broad population level is not highly synchronized and, at any time during a period of breeding activity, reproductive attempts can be found at different stages. However, previous work has suggested that at a finer spatial scale neighbours tend to breed at approximately the same time. Using nestboxes, we tested whether wild zebra finches preferentially seek to settle and initiate a breeding attempt adjacent to conspecifics at an early stage of breeding (nest building), as opposed to others at later stages of breeding and with which the opportunity to breed synchronously was reduced or absent. Pairs were more likely to initiate egg laying in nestboxes close to conspecifics at an early stage of breeding, suggesting that they do try to maximize the level of synchronicity with neighbours. Our results indicate the importance of social effects on both the phenology and spatial distribution of breeding.

Grouping-based adaptive spatial formation of swarm robots in a dynamic environment

Spatial formations of swarm robots are increasingly applied in many domains in which the environments are dynamic and unpredictable. The autonomy of the individual robots and decentralization of the entire system increase the complexity of the response to environmental changes, which could prolong the formation convergence and significantly increase the communication cost. To address these issues, we propose an adaptive mechanism with three basic behaviours for each individual robot and design a grouping-based spatial formation algorithm for swarm robots to respond to changes and accomplish shape formation. Specifically, the robots are automatically partitioned into several groups based on their spatial neighbours. In this manner, the interactions and self-organization of robots are primarily performed at the intra-group rather than inter-group level, leading to decreased communication costs. Furthermore, this grouping mechanism naturally supports parallel formation and therefore improves the convergence speed. Our simulation and experimental results demonstrate that the proposed method significantly improves the convergence speed and decreases the communication cost, thus validating the effectiveness of the proposed adaptive mechanism.

Spillover effects in local public spending

ABSTRACTThis paper investigated the fiscal interactions between Italian municipalities over the period 2001–11 and found a positive horizontal interdependence in spending decisions. The results are robust to different specifications of the spatial neighbours and are confirmed by a natural experiment (an earthquake in the Abruzzo region of Italy in 2009) that creates an exogenous variation in the neighbours’ spending. Furthermore, there is no evidence of yardstick competition when one considers political effects, while a negative relationship is found between spatial interaction and the size of the municipality. Thus, it can be concluded that spillover effects drive the strategic interactions in spending decisions.

Exploring spatial patterns of sudden cardiac arrests in the city of Toronto using Poisson kriging and Hot Spot analyses.

IntroductionOur study looked at out-of-hospital sudden cardiac arrest events in the City of Toronto. These are relatively rare events, yet present a serious global clinical and public health problem. We report on the application of spatial methods and tools that, although relatively well known to geographers and natural resource scientists, need to become better known and used more frequently by health care researchers.Materials and methodsOur data came from the population-based Rescu Epistry cardiac arrest database. We limited it to the residents of the City of Toronto who experienced sudden arrest in 2010. The data was aggregated at the Dissemination Area level, and population rates were calculated. Poisson kriging was carried out on one year of data using three different spatial weights. Kriging estimates were then compared in Hot Spot analyses.ResultsSpatial analysis revealed that Poisson kriging can yield reliable rates using limited data of high quality. We observed the highest rates of sudden arrests in the north and central parts of Etobicoke, western parts of North York as well as the central and southwestern parts of Scarborough while the lowest rates were found in north and eastern parts of Scarborough, downtown Toronto, and East York as well as east central parts of North York. Influence of spatial neighbours on the results did not extend past two rings of adjacent units.ConclusionsPoisson kriging has the potential to be applied to a wide range of healthcare research, particularly on rare events. This approach can be successfully combined with other spatial methods. More applied research, is needed to establish a wider acceptance for this method, especially among healthcare researchers and epidemiologists.

Local histogram and discriminative learning-based hyperspectral data classification

ABSTRACTA spectral–spatial hyperspectral image classification method is proposed in this article. The proposed method is local histogram and discriminative based classification (LHD). It is implemented in two steps. In the first step, a projection matrix is obtained by maximizing the class discrimination and preserving the local structure of data using both the spectral and spatial neighbours. In the second step, the contextual features are extracted from the local regions using the histogram as a nonparametric statistical estimate. Finally, with incorporating spectral and spatial features, the classification map is obtained. The experimental results demonstrate that the proposed method is superior to some state-of-the-art alternatives.

A label propagation method using spatial-spectral consistency for hyperspectral image classification

ABSTRACTIn this article, a label propagation approach with automatic seed selection is developed for hyperspectral image classification. The core idea is to combine pixel-wise classification results with spatial information described by a data graph. Using only the support vector machine (SVM) classifier on spectral features to tackle the hyperspectral classification task will produce results with a salt-and-pepper appearance. To overcome this limitation, the spatial information is incorporated by label propagation. The performance of label propagation is dependent on two points: the seeds and the connection graph. Generally, a limited number of labelled samples are available, which are considered as seeds in label propagation. However, the limited seeds will result in bad label propagation. Therefore, pseudo-seeds are automatically selected in local windows. Specifically, the pixels whose initial labels according to SVM are consistent with their most spatial neighbours are selected as seeds. Through seed selection, the number of seeds is greatly increased. Then, the label information of the selected seeds is propagated to their spatial neighbours using a data graph which is constructed according to the local structures in the image. Through seed selection and label propagation on the graph, the problem of salt-and-pepper appearance is solved elegantly – the noisy labels are highly suppressed and most of the structures are preserved. Competitive experimental results on a variety of hyperspectral data sets demonstrate the effectiveness of the proposed method.