Machine Learning for the Estimation of Diameter Increment in Mixed and Uneven-Aged Forests

Estimating the diameter increment of forests is one of the most important relationships in forest management and planning. The aim of this study was to provide insight into the application of two machine learning methods, i.e., the multilayer perceptron artificial neural network (MLP) and adaptive neuro-fuzzy inference system (ANFIS), for developing diameter increment models for the Hyrcanian forests. For this purpose, the diameters at breast height (DBH) of seven tree species were recorded during two inventory periods. The trees were divided into four broad species groups, including beech (Fagus orientalis), chestnut-leaved oak (Quercus castaneifolia), hornbeam (Carpinus betulus), and other species. For each group, a separate model was developed. The k-fold strategy was used to evaluate these models. The Pearson correlation coefficient (r), coefficient of determination (R2), root mean square error (RMSE), Akaike information criterion (AIC), and Bayesian information criterion (BIC) were utilized to evaluate the models. RMSE and R2 of the MLP and ANFIS models were estimated for the four groups of beech ((1.61 and 0.23) and (1.57 and 0.26)), hornbeam ((1.42 and 0.13) and (1.49 and 0.10)), chestnut-leaved oak ((1.55 and 0.28) and (1.47 and 0.39)), and other species ((1.44 and 0.32) and (1.5 and 0.24)), respectively. Despite the low coefficient of determination, the correlation test in both techniques was significant at a 0.01 level for all four groups. In this study, we also determined optimal network parameters such as number of nodes of one or multiple hidden layers and the type of membership functions for modeling the diameter increment in the Hyrcanian forests. Comparison of the results of the two techniques showed that for the groups of beech and chestnut-leaved oak, the ANFIS technique performed better and that the modeling techniques have a deep relationship with the nature of the tree species

Machine Learning for the Estimation of Diameter Increment in Mixed and Uneven-Aged Forests

Estimating the diameter increment of forests is one of the most important relationships in forest management and planning. The aim of this study was to provide insight into the application of two machine learning methods, i.e., the multilayer perceptron artificial neural network (MLP) and adaptive neuro-fuzzy inference system (ANFIS), for developing diameter increment models for the Hyrcanian forests. For this purpose, the diameters at breast height (DBH) of seven tree species were recorded during two inventory periods. The trees were divided into four broad species groups, including beech (Fagus orientalis), chestnut-leaved oak (Quercus castaneifolia), hornbeam (Carpinus betulus), and other species. For each group, a separate model was developed. The k-fold strategy was used to evaluate these models. The Pearson correlation coefficient (r), coefficient of determination (R2), root mean square error (RMSE), Akaike information criterion (AIC), and Bayesian information criterion (BIC) were utilized to evaluate the models. RMSE and R2 of the MLP and ANFIS models were estimated for the four groups of beech ((1.61 and 0.23) and (1.57 and 0.26)), hornbeam ((1.42 and 0.13) and (1.49 and 0.10)), chestnut-leaved oak ((1.55 and 0.28) and (1.47 and 0.39)), and other species ((1.44 and 0.32) and (1.5 and 0.24)), respectively. Despite the low coefficient of determination, the correlation test in both techniques was significant at a 0.01 level for all four groups. In this study, we also determined optimal network parameters such as number of nodes of one or multiple hidden layers and the type of membership functions for modeling the diameter increment in the Hyrcanian forests. Comparison of the results of the two techniques showed that for the groups of beech and chestnut-leaved oak, the ANFIS technique performed better and that the modeling techniques have a deep relationship with the nature of the tree species

The evolving SARS-CoV-2 epidemic in Africa: Insights from rapidly expanding genomic surveillance

INTRODUCTION Investment in Africa over the past year with regard to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) sequencing has led to a massive increase in the number of sequences, which, to date, exceeds 100,000 sequences generated to track the pandemic on the continent. These sequences have profoundly affected how public health officials in Africa have navigated the COVID-19 pandemic. RATIONALE We demonstrate how the first 100,000 SARS-CoV-2 sequences from Africa have helped monitor the epidemic on the continent, how genomic surveillance expanded over the course of the pandemic, and how we adapted our sequencing methods to deal with an evolving virus. Finally, we also examine how viral lineages have spread across the continent in a phylogeographic framework to gain insights into the underlying temporal and spatial transmission dynamics for several variants of concern (VOCs). RESULTS Our results indicate that the number of countries in Africa that can sequence the virus within their own borders is growing and that this is coupled with a shorter turnaround time from the time of sampling to sequence submission. Ongoing evolution necessitated the continual updating of primer sets, and, as a result, eight primer sets were designed in tandem with viral evolution and used to ensure effective sequencing of the virus. The pandemic unfolded through multiple waves of infection that were each driven by distinct genetic lineages, with B.1-like ancestral strains associated with the first pandemic wave of infections in 2020. Successive waves on the continent were fueled by different VOCs, with Alpha and Beta cocirculating in distinct spatial patterns during the second wave and Delta and Omicron affecting the whole continent during the third and fourth waves, respectively. Phylogeographic reconstruction points toward distinct differences in viral importation and exportation patterns associated with the Alpha, Beta, Delta, and Omicron variants and subvariants, when considering both Africa versus the rest of the world and viral dissemination within the continent. Our epidemiological and phylogenetic inferences therefore underscore the heterogeneous nature of the pandemic on the continent and highlight key insights and challenges, for instance, recognizing the limitations of low testing proportions. We also highlight the early warning capacity that genomic surveillance in Africa has had for the rest of the world with the detection of new lineages and variants, the most recent being the characterization of various Omicron subvariants. CONCLUSION Sustained investment for diagnostics and genomic surveillance in Africa is needed as the virus continues to evolve. This is important not only to help combat SARS-CoV-2 on the continent but also because it can be used as a platform to help address the many emerging and reemerging infectious disease threats in Africa. In particular, capacity building for local sequencing within countries or within the continent should be prioritized because this is generally associated with shorter turnaround times, providing the most benefit to local public health authorities tasked with pandemic response and mitigation and allowing for the fastest reaction to localized outbreaks. These investments are crucial for pandemic preparedness and response and will serve the health of the continent well into the 21st century