Browsing by Subject "RANDOM FORESTS"

Sort by: Order: Results:

Now showing items 1-4 of 4
  • Lammel, Daniel R.; Barth, Gabriel; Ovaskainen, Otso; Cruz, Leonardo M.; Zanatta, Josileia A.; Ryo, Masahiro; de Souza, Emanuel M.; Pedrosa, Fabio O. (2018)
    Background: pH is frequently reported as the main driver for prokaryotic community structure in soils. However, pH changes are also linked to "spillover effects" on other chemical parameters (e.g., availability of Al, Fe, Mn, Zn, and Cu) and plant growth, but these indirect effects on the microbial communities are rarely investigated. Usually, pH also co-varies with some confounding factors, such as land use, soil management (e.g., tillage and chemical inputs), plant cover, and/or edapho-climatic conditions. So, a more comprehensive analysis of the direct and indirect effects of pH brings a better understanding of the mechanisms driving prokaryotic (archaeal and bacterial) community structures. Results: We evaluated an agricultural soil pH gradient (from 4 to 6, the typical range for tropical farms), in a liming gradient with confounding factors minimized, investigating relationships between prokaryotic communities (16S rRNA) and physical-chemical parameters (indirect effects). Correlations, hierarchical modeling of species communities (HMSC), and random forest (RF) modeling indicated that both direct and indirect effects of the pH gradient affected the prokaryotic communities. Some OTUs were more affected by the pH changes (e.g., some Actinobacteria), while others were more affected by the indirect pH effects (e.g., some Proteobacteria). HMSC detected a phylogenetic signal related to the effects. Both HMSC and RF indicated that the main indirect effect was the pH changes on the availability of some elements (e.g., Al, Fe, and Cu), and secondarily, effects on plant growth and nutrient cycling also affected the OTUs. Additionally, we found that some of the OTUs that responded to pH also correlated with CO2, CH4, and N2O greenhouse gas fluxes. Conclusions: Our results indicate that there are two distinct pH-related mechanisms driving prokaryotic community structures, the direct effect and "spillover effects" of pH (indirect effects). Moreover, the indirect effects are highly relevant for some OTUs and consequently for the community structure; therefore, it is a mechanism that should be further investigated in microbial ecology.
  • Haukka, Jani K.; Sandholm, Niina; Forsblom, Carol; Cobb, Jeffrey E.; Groop, Per-Henrik; Ferrannini, Ele (2018)
    Elevated urinary albumin excretion (microalbuminuria) is an early marker of diabetic nephropathy, but there is an unmet need for better biomarkers that capture the individuals at risk with higher accuracy and earlier than the current markers do. We performed an untargeted metabolomic study to assess baseline differences between individuals with type 1 diabetes who either developed microalbuminuria or remained normoalbuminuric. A total of 102 individuals progressed to microalbuminuria during a median follow-up of 3.2 years, whereas 98 sex-, age- and body mass index (BMI) matched nonprogressors remained normoalbuminuric during a median follow-up of 7.1 years. Metabolomic screening identified 1,242 metabolites, out of which 111 differed significantly between progressors and non-progressors after adjustment for age of diabetes onset, baseline glycosylated hemoglobin A1c (HbA(1c)), and albumin excretion rate (AER). The metabolites that predicted development of microalbumiuria included several uremic toxins and carnitine metabolism related molecules. Iterative variable selection indicated erythritol, 3-phenylpropionate, and N-trimethyl-5-aminovalerate as the best set of variables to predict development of microalbuminuria. A metabolomic index based on these metabolites improved the prediction of incident microalbuminuria on top of the clinical variables age of diabetes onset, baseline HbA1c and AER (ROCAUC = 0.842 vs 0.797), highlighting their ability to predict early-phase diabetic nephropathy.
  • Yu, Xiaowei; Hyyppa, Juha; Litkey, Paula; Kaartinen, Harri; Vastaranta, Mikko; Holopainen, Markus (2017)
    This paper investigated the potential of multispectral airborne laser scanning (ALS) data for individual tree detection and tree species classification. The aim was to develop a single-sensor solution for forest mapping that is capable of providing species-specific information, required for forest management and planning purposes. Experiments were conducted using 1903 ground measured trees from 22 sample plots and multispectral ALS data, acquired with an Optech Titan scanner over a boreal forest, mainly consisting of Scots pine (Pinus Sylvestris), Norway spruce (Picea Abies), and birch (Betula sp.), in southern Finland. ALS-features used as predictors for tree species were extracted from segmented tree objects and used in random forest classification. Different combinations of features, including point cloud features, and intensity features of single and multiple channels, were tested. Among the field-measured trees, 61.3% were correctly detected. The best overall accuracy (OA) of tree species classification achieved for correctly-detected trees was 85.9% (Kappa = 0.75), using a point cloud and single-channel intensity features combination, which was not significantly different from the ones that were obtained either using all features (OA = 85.6%, Kappa = 0.75), or single-channel intensity features alone (OA = 85.4%, Kappa = 0.75). Point cloud features alone achieved the lowest accuracy, with an OA of 76.0%. Field-measured trees were also divided into four categories. An examination of the classification accuracy for four categories of trees showed that isolated and dominant trees can be detected with a detection rate of 91.9%, and classified with a high overall accuracy of 90.5%. The corresponding detection rate and accuracy were 81.5% and 89.8% for a group of trees, 26.4% and 79.1% for trees next to a larger tree, and 7.2% and 53.9% for trees situated under a larger tree, respectively. The results suggest that Channel 2 (1064 nm) contains more information for separating pine, spruce, and birch, followed by channel 1 (1550 nm) and channel 3 (532 nm) with an overall accuracy of 81.9%, 78.3%, and 69.1%, respectively. Our results indicate that the use of multispectral ALS data has great potential to lead to a single-sensor solution for forest mapping.
  • Imangholiloo, Mohammad; Rasinmaki, Jussi; Rauste, Yrjo; Holopainen, Markus (2019)
    Land use and land cover maps are vital sources of information for many applications. Recently, using high-resolution and open-access satellite images has become a preferred method for mapping land cover, especially over large areas. This study was designed to map the land cover and agricultural fields of a large area using Sentinel-1A synthetic aperture radar (SAR) images. Seven machine-learning methods were employed for image analyses. The Random Forest classifier algorithm outperformed the other machine-learning methods in the training step; thus, we selected it for further use and tuned its parameters. After several image processing steps, we classified the final image into 23 land cover classes and achieved an overall accuracy of 42% for all classes, and 57% for agricultural fields. This research note highlights some characteristics and advantages of using Sentinel-1A images and provides novel methods for nation-wide large-area mapping applications.