Understanding the movement of animals is crucial to conservation efforts. Past research often focuses on factors affecting movement, rather than locations of interest that animals return to or habitat. We explore the use of clustering to identify locations of interest to African Elephants in regions of Sub-Saharan Africa. Our analysis was performed using publicly available datasets for tracking African elephants at Kruger National Park (KNP), South Africa; Etosha National Park, Namibia; as well as areas in Burkina Faso and the Congo. Using the DBSCAN and KMeans clustering algorithms, we calculate clusters and centroids to simplify elephant movement data and highlight important locations of interest. Through a comparison of feature spaces with and without temperature, we show that temperature is an important feature to explain movement clustering. Recognizing the importance of temperature, we develop a technique to add external temperature data from an API to other geospatial datasets that would otherwise not have temperature data. After addressing the hurdles of using external data with marginally different timestamps, we consider the quality of this data, and the quality of the centroids of the clusters calculated based on this external temperature data. Finally, we overlay these centroids onto satellite imagery and locations of human settlements to validate the real-life applications of the calculated centroids to identify locations of interest for elephants. As expected, we confirmed that elephants tend to cluster their movement around sources of water as well as some human settlements, especially those with water holes. Identifying key locations of interest for elephants is beneficial in predicting the movement of elephants and preventing poaching. These methods may in the future be applied to other animals beyond elephants to identify locations of interests for them.
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Inherent in virtually every iterative machine learning algorithm is the problem of hyper-parameter tuning, which includes three major design parameters: (a) the complexity of the model, e.g., the number of neurons in a neural network, (b) the initial conditions, which heavily affect the behavior of the algorithm, and (c) the dissimilarity measure used to quantify its performance. We introduce an online prototype-based learning algorithm that can be viewed as a progressively growing competitive-learning neural network architecture for classification and clustering. The learning rule of the proposed approach is formulated as an online gradient-free stochastic approximation algorithm that solves a sequence of appropriately defined optimization problems, simulating an annealing process. The annealing nature of the algorithm contributes to avoiding poor local minima, offers robustness with respect to the initial conditions, and provides a means to progressively increase the complexity of the learning model, through an intuitive bifurcation phenomenon. The proposed approach is interpretable, requires minimal hyper-parameter tuning, and allows online control over the performance-complexity trade-off. Finally, we show that Bregman divergences appear naturally as a family of dissimilarity measures that play a central role in both the performance and the computational complexity of the learning algorithm.
Cluster analysis refers to a wide range of data analytic techniques for class discovery and is popular in many application fields. To judge the quality of a clustering result, different cluster validation procedures have been proposed in the literature. While there is extensive work on classical validation techniques, such as internal and external validation, less attention has been given to validating and replicating a clustering result using a validation dataset. Such a dataset may be part of the original dataset, which is separated before analysis begins, or it could be an independently collected dataset. We present a systematic structured framework for validating clustering results on validation data that includes most existing validation approaches. In particular, we review classical validation techniques such as internal and external validation, stability analysis, hypothesis testing, and visual validation, and show how they can be interpreted in terms of our framework. We precisely define and formalise different types of validation of clustering results on a validation dataset and explain how each type can be implemented in practice. Furthermore, we give examples of how clustering studies from the applied literature that used a validation dataset can be classified into the framework.
Epistasis is a phenomenon in which a phenotype outcome is determined by the interaction of genetic variation at two or more loci and it cannot be attributed to the additive combination of effects corresponding to the individual loci. Although it has been more than 100 years since William Bateson introduced this concept, it still is a topic under active research. Locating epistatic interactions is a computationally expensive challenge that involves analyzing an exponentially growing number of combinations. Authors in this field have resorted to a multitude of hardware architectures in order to speed up the search, but little to no attention has been paid to the vector instructions that current CPUs include in their instruction sets. This work extends an existing third-order exhaustive algorithm to support the search of epistasis interactions of any order and discusses multiple SIMD implementations of the different functions that compose the search using Intel AVX Intrinsics. Results using the GCC and the Intel compiler show that the 512-bit explicit vector implementation proposed here performs the best out of all of the other implementations evaluated. The proposed 512-bit vectorization accelerates the original implementation of the algorithm by an average factor of 7 and 12, for GCC and the Intel Compiler, respectively, in the scenarios tested.
High-resolution spectroscopic surveys of the Milky Way have entered the Big Data regime and have opened avenues for solving outstanding questions in Galactic archaeology. However, exploiting their full potential is limited by complex systematics, whose characterization has not received much attention in modern spectroscopic analyses. In this work, we present a novel method to disentangle the component of spectral data space intrinsic to the stars from that due to systematics. Using functional principal component analysis on a sample of $18,933$ giant spectra from APOGEE, we find that the intrinsic structure above the level of observational uncertainties requires ${\approx}$10 functional principal components (FPCs). Our FPCs can reduce the dimensionality of spectra, remove systematics, and impute masked wavelengths, thereby enabling accurate studies of stellar populations. To demonstrate the applicability of our FPCs, we use them to infer stellar parameters and abundances of 28 giants in the open cluster M67. We employ Sequential Neural Likelihood, a simulation-based Bayesian inference method that learns likelihood functions using neural density estimators, to incorporate non-Gaussian effects in spectral likelihoods. By hierarchically combining the inferred abundances, we limit the spread of the following elements in M67: $\mathrm{Fe} \lesssim 0.02$ dex; $\mathrm{C} \lesssim 0.03$ dex; $\mathrm{O}, \mathrm{Mg}, \mathrm{Si}, \mathrm{Ni} \lesssim 0.04$ dex; $\mathrm{Ca} \lesssim 0.05$ dex; $\mathrm{N}, \mathrm{Al} \lesssim 0.07$ dex (at 68% confidence). Our constraints suggest a lack of self-pollution by core-collapse supernovae in M67, which has promising implications for the future of chemical tagging to understand the star formation history and dynamical evolution of the Milky Way.
Road casualties represent an alarming concern for modern societies, especially in poor and developing countries. In the last years, several authors developed sophisticated statistical approaches to help local authorities implement new policies and mitigate the problem. These models are typically developed taking into account a set of socio-economic or demographic variables, such as population density and traffic volumes. However, they usually ignore that the external factors may be suffering from measurement errors, which can severely bias the statistical inference. This paper presents a Bayesian hierarchical model to analyse car crashes occurrences at the network lattice level taking into account measurement error in the spatial covariates. The suggested methodology is exemplified considering all road collisions in the road network of Leeds (UK) from 2011 to 2019. Traffic volumes are approximated at the street segment level using an extensive set of road counts obtained from mobile devices, and the estimates are corrected using a measurement error model. Our results show that omitting measurement error considerably worsens the model's fit and attenuates the effects of imprecise covariates.
Advances in satellite imaging and GPS tracking devices have given rise to a new era of remote sensing and geospatial analysis. In environmental science and conservation ecology, biotelemetric data is often high-dimensional, spatially and/or temporally, and functional in nature, meaning that there is an underlying continuity to the biological process of interest. GPS-tracking of animal movement is commonly characterized by irregular time-recording of animal position, and the movement relationships between animals are prone to sudden change. In this paper, I propose a measure of localized mutual information (LMI) to derive a correlation function for monitoring changes in the pairwise association between animal movement trajectories. The properties of the LMI measure are assessed analytically and by simulation under a variety of circumstances. Advantages and disadvantages of the LMI measure are assessed and an alternate measure of LMI is proposed to handle potential disadvantages. The measure of LMI is shown to be an effective tool for detecting shifts in the correlation of animal movements, and seasonal/phasal correlatory structure.
Object-oriented programming (OOP) is one of the most popular paradigms used for building software systems. However, despite its industrial and academic popularity, OOP is still missing a formal apparatus similar to lambda-calculus, which functional programming is based on. There were a number of attempts to formalize OOP, but none of them managed to cover all the features available in modern OO programming languages, such as C++ or Java. We have made yet another attempt and created phi-calculus. We also created EOLANG (also called EO), an experimental programming language based on phi-calculus.
Modelling and forecasting homogeneous age-specific mortality rates of multiple countries could lead to improvements in long-term forecasting. Data fed into joint models are often grouped according to nominal attributes, such as geographic regions, ethnic groups, and socioeconomic status, which may still contain heterogeneity and deteriorate the forecast results. Our paper proposes a novel clustering technique to pursue homogeneity among multiple functional time series based on functional panel data modelling to address this issue. Using a functional panel data model with fixed effects, we can extract common functional time series features. These common features could be decomposed into two components: the functional time trend and the mode of variations of functions (functional pattern). The functional time trend reflects the dynamics across time, while the functional pattern captures the fluctuations within curves. The proposed clustering method searches for homogeneous age-specific mortality rates of multiple countries by accounting for both the modes of variations and the temporal dynamics among curves. We demonstrate that the proposed clustering technique outperforms other existing methods through a Monte Carlo simulation and could handle complicated cases with slow decaying eigenvalues. In empirical data analysis, we find that the clustering results of age-specific mortality rates can be explained by the combination of geographic region, ethnic groups, and socioeconomic status. We further show that our model produces more accurate forecasts than several benchmark methods in forecasting age-specific mortality rates.
Clustering is an essential data mining tool that aims to discover inherent cluster structure in data. For most applications, applying clustering is only appropriate when cluster structure is present. As such, the study of clusterability, which evaluates whether data possesses such structure, is an integral part of cluster analysis. However, methods for evaluating clusterability vary radically, making it challenging to select a suitable measure. In this paper, we perform an extensive comparison of measures of clusterability and provide guidelines that clustering users can reference to select suitable measures for their applications.
Discrete correlation filter (DCF) based trackers have shown considerable success in visual object tracking. These trackers often make use of low to mid level features such as histogram of gradients (HoG) and mid-layer activations from convolution neural networks (CNNs). We argue that including semantically higher level information to the tracked features may provide further robustness to challenging cases such as viewpoint changes. Deep salient object detection is one example of such high level features, as it make use of semantic information to highlight the important regions in the given scene. In this work, we propose an improvement over DCF based trackers by combining saliency based and other features based filter responses. This combination is performed with an adaptive weight on the saliency based filter responses, which is automatically selected according to the temporal consistency of visual saliency. We show that our method consistently improves a baseline DCF based tracker especially in challenging cases and performs superior to the state-of-the-art. Our improved tracker operates at 9.3 fps, introducing a small computational burden over the baseline which operates at 11 fps.
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