This review article focuses on regularised estimation procedures applicable to geostatistical and spatial econometric models. These methods are particularly relevant in the case of big geospatial data for dimensionality reduction or model selection. To structure the review, we initially consider the most general case of multivariate spatiotemporal processes (i.e., $g > 1$ dimensions of the spatial domain, a one-dimensional temporal domain, and $q \geq 1$ random variables). Then, the idea of regularised/penalised estimation procedures and different choices of shrinkage targets are discussed. Finally, guided by the elements of a mixed-effects model, which allows for a variety of spatiotemporal models, we show different regularisation procedures and how they can be used for the analysis of geo-referenced data, e.g. for selection of relevant regressors, dimensionality reduction of the covariance matrices, detection of conditionally independent locations, or the estimation of a full spatial interaction matrix.
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Clustering of publication networks is an efficient way to obtain classifications of large collections of research publications. Such classifications can be used to, e.g., detect research topics, normalize citation relations, or explore the publication output of a unit. Citation networks can be created using a variety of approaches. Best practices to obtain classifications using clustering have been investigated, in particular the performance of different publication-publication relatedness measures. However, evaluation of different approaches to normalization of citation relations have not been explored to the same extent. In this paper, we evaluate five approaches to normalization of direct citation relations with respect to clustering solution quality in four data sets. A sixth approach is evaluated using no normalization. To assess the quality of clustering solutions, we use three measures. (1) We compare the clustering solution to the reference lists of a set of publications using the Adjusted Rand Index. (2) Using the Sihouette width measure, we quantity to which extent the publications have relations to other clusters than the one they have been assigned to. (3) We propose a measure that captures publications that have probably been inaccurately assigned. The results clearly show that normalization is preferred over unnormalized direct citation relations. Furthermore, the results indicate that the fractional normalization approach, which can be considered the standard approach, causes inaccurate assignments. The geometric normalization approach has a similar performance as the fractional approach regarding Adjusted Rand Index and Silhouette width but leads to fewer inaccurate assignments. We therefore believe that the geometric approach may be preferred over the fractional approach.
In this contribution, we deal with seed-based information retrieval in networks of research publications. Using systematic reviews as a baseline, and publication data from the NIH Open Citation Collection, we compare the performance of the three citation-based approaches direct citation, co-citation, and bibliographic coupling with respect to recall and precision measures. In addition, we include the PubMed Related Article score as well as combined approaches in the comparison. We also provide a fairly comprehensive review of earlier research in which citation relations have been used for information retrieval purposes. The results show an advantage for co-citation over bibliographic coupling and direct citation. However, combining the three approaches outperforms the exclusive use of co-citation in the study. The results further indicate, in line with previous research, that combining citation-based approaches with textual approaches enhances the performance of seed-based information retrieval. The results from the study may guide approaches combining citation-based and textual approaches in their choice of citation similarity measures. We suggest that future research use more structured approaches to evaluate methods for seed-based retrieval of publications, including comparative approaches as well as the elaboration of common data sets and baselines for evaluation.
Marginal structural models have been increasingly used by analysts in recent years to account for confounding bias in studies with time-varying treatments. The parameters of these models are often estimated using inverse probability of treatment weighting. To ensure that the estimated weights adequately control confounding, it is possible to check for residual imbalance between treatment groups in the weighted data. Several balance metrics have been developed and compared in the cross-sectional case but have not yet been evaluated and compared in longitudinal studies with time-varying treatment. We have first extended the definition of several balance metrics to the case of a time-varying treatment, with or without censoring. We then compared the performance of these balance metrics in a simulation study by assessing the strength of the association between their estimated level of imbalance and bias. We found that the Mahalanobis balance performed best.Finally, the method was illustrated for estimating the cumulative effect of statins exposure over one year on the risk of cardiovascular disease or death in people aged 65 and over in population-wide administrative data. This illustration confirms the feasibility of employing our proposed metrics in large databases with multiple time-points.
Systematic Literature Reviews (SLRs) have become the foundation of evidence-based studies, enabling researchers to identify, classify, and combine existing studies based on specific research questions. Conducting an SLR is largely a manual process. Over the previous years, researchers have made significant progress in automating certain phases of the SLR process, aiming to reduce the effort and time needed to carry out high-quality SLRs. However, there is still a lack of AI agent-based models that automate the entire SLR process. To this end, we introduce a novel multi-AI agent model designed to fully automate the process of conducting an SLR. By utilizing the capabilities of Large Language Models (LLMs), our proposed model streamlines the review process, enhancing efficiency and accuracy. The model operates through a user-friendly interface where researchers input their topic, and in response, the model generates a search string used to retrieve relevant academic papers. Subsequently, an inclusive and exclusive filtering process is applied, focusing on titles relevant to the specific research area. The model then autonomously summarizes the abstracts of these papers, retaining only those directly related to the field of study. In the final phase, the model conducts a thorough analysis of the selected papers concerning predefined research questions. We also evaluated the proposed model by sharing it with ten competent software engineering researchers for testing and analysis. The researchers expressed strong satisfaction with the proposed model and provided feedback for further improvement. The code for this project can be found on the GitHub repository at //github.com/GPT-Laboratory/SLR-automation.
Since coral reef ecosystems face threats from human activities and climate change, coral conservation programs are implemented worldwide. Monitoring coral health provides references for guiding conservation activities. However, current labor-intensive methods result in a backlog of unsorted images, highlighting the need for automated classification. Few studies have simultaneously utilized accurate annotations along with updated algorithms and datasets. This study aimed to create a dataset representing common coral conditions and associated stressors in the Indo-Pacific. Concurrently, it assessed existing classification algorithms and proposed a new multi-label method for automatically detecting coral conditions and extracting ecological information. A dataset containing over 20,000 high-resolution coral images of different health conditions and stressors was constructed based on the field survey. Seven representative deep learning architectures were tested on this dataset, and their performance was quantitatively evaluated using the F1 metric and the match ratio. Based on this evaluation, a new method utilizing the ensemble learning approach was proposed. The proposed method accurately classified coral conditions as healthy, compromised, dead, and rubble; it also identified corresponding stressors, including competition, disease, predation, and physical issues. This method can help develop the coral image archive, guide conservation activities, and provide references for decision-making for reef managers and conservationists. The proposed ensemble learning approach outperforms others on the dataset, showing State-Of-The-Art (SOTA) performance. Future research should improve its generalizability and accuracy to support global coral conservation efforts.
Signed graphs are an emergent way of representing data in a variety of contexts were conflicting interactions exist. These include data from biological, ecological, and social systems. Here we propose the concept of communicability geometry for signed graphs, proving that metrics in this space, such as the communicability distance and angles, are Euclidean and spherical. We then apply these metrics to solve several problems in data analysis of signed graphs in a unified way. They include the partitioning of signed graphs, dimensionality reduction, finding hierarchies of alliances in signed networks as well as the quantification of the degree of polarization between the existing factions in systems represented by this type of graphs.
Periodic autoregressive (PAR) time series with finite variance is considered as one of the most common models of second-order cyclostationary processes. However, in the real applications, the signals with periodic characteristics may be disturbed by additional noise related to measurement device disturbances or to other external sources. Thus, the known estimation techniques dedicated for PAR models may be inefficient for such cases. When the variance of the additive noise is relatively small, it can be ignored and the classical estimation techniques can be applied. However, for extreme cases, the additive noise can have a significant influence on the estimation results. In this paper, we propose four estimation techniques for the noise-corrupted PAR models with finite variance distributions. The methodology is based on Yule-Walker equations utilizing the autocovariance function. It can be used for any type of the finite variance additive noise. The presented simulation study clearly indicates the efficiency of the proposed techniques, also for extreme case, when the additive noise is a sum of the Gaussian additive noise and additive outliers. The proposed estimation techniques are also applied for testing if the data corresponds to noise-corrupted PAR model. This issue is strongly related to the identification of informative component in the data in case when the model is disturbed by additive non-informative noise. The power of the test is studied for simulated data. Finally, the testing procedure is applied for two real time series describing particulate matter concentration in the air.
We tackle covariance estimation in low-sample scenarios, employing a structured covariance matrix with shrinkage methods. These involve convexly combining a low-bias/high-variance empirical estimate with a biased regularization estimator, striking a bias-variance trade-off. Literature provides optimal settings of the regularization amount through risk minimization between the true covariance and its shrunk counterpart. Such estimators were derived for zero-mean statistics with i.i.d. diagonal regularization matrices accounting for the average sample variance solely. We extend these results to regularization matrices accounting for the sample variances both for centered and non-centered samples. In the latter case, the empirical estimate of the true mean is incorporated into our shrinkage estimators. Introducing confidence weights into the statistics also enhance estimator robustness against outliers. We compare our estimators to other shrinkage methods both on numerical simulations and on real data to solve a detection problem in astronomy.
This paper introduces a Bayesian framework designed to measure the degree of association between categorical random variables. The method is grounded in the formal definition of variable independence and is implemented using Markov Chain Monte Carlo (MCMC) techniques. Unlike commonly employed techniques in Association Rule Learning, this approach enables a clear and precise estimation of confidence intervals and the statistical significance of the measured degree of association. We applied the method to non-exclusive emotions identified by annotators in 4,613 tweets written in Portuguese. This analysis revealed pairs of emotions that exhibit associations and mutually opposed pairs. Moreover, the method identifies hierarchical relations between categories, a feature observed in our data, and is utilized to cluster emotions into basic-level groups.
Knowledge graphs (KGs) of real-world facts about entities and their relationships are useful resources for a variety of natural language processing tasks. However, because knowledge graphs are typically incomplete, it is useful to perform knowledge graph completion or link prediction, i.e. predict whether a relationship not in the knowledge graph is likely to be true. This paper serves as a comprehensive survey of embedding models of entities and relationships for knowledge graph completion, summarizing up-to-date experimental results on standard benchmark datasets and pointing out potential future research directions.
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