The behaviour of random forest permutation-based variable importance measures under predictor correlation

Background  

Random forests (RF) have been increasingly used in applications such as genome-wide association and microarray studies where predictor correlation is frequently observed. Recent works on permutation-based variable importance measures (VIMs) used in RF have come to apparently contradictory conclusions. We present an extended simulation study to synthesize results.     

Letter to the editor: on the stability and ranking of predictors from random forest variable importance measures

A recent study examined the stability of rankings from random forests using two variable importance measures (mean decrease accuracy (MDA) and mean decrease Gini (MDG)) and concluded that rankings based on the MDG were more robust than MDA. However, studies examining data-specific characteristics on ranking stability have been few. Rankings based on the MDG measure showed sensitivity to within-predictor correlation and differences in category frequencies, even when the number of categories was held constant, and thus may produce spurious results. The MDA measure was robust to these data characteristics. Further, under strong within-predictor correlation, MDG rankings were less stable than those using MDA.     

Erratum to: Informative metabolites identification by variable importance analysis based on random variable combination

Metabolomics - The quality of rice in terms not only of its nutritional value but also in terms of its aroma and flavour is becoming increasingly important in modern rice breeding where global...     

Saproxylic beetle diversity in a managed boreal forest: importance of stand characteristics and forestry conservation measures

Saproxylic beetles constitute a significant proportion of boreal forest biodiversity. However, the long history of timber production in Fennoscandia has significantly reduced the availability of dead wood and is considered a threat to the conservation of saproxylic beetle assemblages. Therefore, since the mid‐1990s dead wood retention in harvested stands has formed an integral part of silvicultural practices. However, the contribution of this biodiversity‐orientated management approach to conserving saproxylic beetle assemblages in boreal forest landscapes that include production forestry remains largely untested. We examined differences in resident saproxylic beetle assemblages among stands under different management in a boreal forest landscape in Central Sweden, and in particular stands managed according to new conservation‐orientated practices. We also investigated the relationship between beetle diversity and forest stand characteristics. Bark of coarse woody debris (CWD) was sieved for beetles in old managed stands, unmanaged nature reserves, and set‐aside areas, and clear‐cut stands harvested according to certification guidelines [new forestry (NF) clear‐cuts]. All stand types contributed significantly to the total diversity of beetles found. While stand size, position, and distance to nearest reserve were unimportant, both the quality and the quantity of CWD in stands contributed significantly to explaining beetle abundance and species richness. This extends the previous findings for red‐listed invertebrates, and shows that heterogeneous substrate quality and a range of management practices are necessary to maintain saproxylic beetle diversity in boreal forest landscapes that include production forestry. The unique abiotic conditions in combination with the abundant and varied CWD associated with NF clear‐cuts form an important component of forest stand heterogeneity for saproxylic beetles. It is thus essential that sufficient, diverse, CWD is retained in managed boreal landscapes to ensure the conservation of boreal saproxylic beetle assemblages.     

Random forest Gini importance favours SNPs with large minor allele frequency: impact, sources and recommendations

The use of random forests is increasingly common in genetic association studies. The variable importance measure (VIM) that is automatically calculated as a by-product of the algorithm is often used to rank polymorphisms with respect to their ability to predict the investigated phenotype. Here, we investigate a characteristic of this methodology that may be considered as an important pitfall, namely that common variants are systematically favoured by the widely used Gini VIM. As a consequence, researchers may overlook rare variants that contribute to the missing heritability. The goal of the present article is 3-fold: (i) to assess this effect quantitatively using simulation studies for different types of random forests (classical random forests and conditional inference forests, that employ unbiased variable selection criteria) as well as for different importance measures (Gini and permutation based); (ii) to explore the trees and to compare the behaviour of random forests and the standard logistic regression model in order to understand the statistical mechanisms behind the preference for common variants; and (iii) to summarize these results and previously investigated properties of random forest VIMs in the context of genetic association studies and to make practical recommendations regarding the choice of the random forest and variable importance type. All our analyses can be reproduced using R code available from the companion website: http://www.ibe.med.uni-muenchen.de/organisation/mitarbeiter/020_professuren/boulesteix/ginibias/.     

Modeling a Poisson forest in variable elevations: a nonparametric Bayesian approach

A nonparametric Bayesian formulation is given to the problem of modeling nonhomogeneous spatial point patterns influenced by concomitant variables. Only incomplete information on the concomitant variables is assumed, consisting of a relatively small number of point measurements. Residual variation, caused by other unmeasured influential factors, is modeled in terms of a spatially varying baseline intensity function. A Markov chain Monte Carlo scheme is proposed for the simultaneous nonparametric estimation of each unknown function in the model. The suggested method is illustrated by reanalysing a data set in Rathbun (1996, Biometrics 52, 226-242), and the estimated models are compared with those obtained by Rathbun.     

Biological organization,Jarkievich measures and asymmetric random walks

In this paper we analyze the organization imposed by the energy input during the migration of enzymes on DNA. We attempt to measure that organization by means of a concept proposed by A.A. Jarkievich in 1961. We found relationships among a Jarkievich measure, the energy dissipation, and the fluctuations in the kinematic velocity of the enzyme on the DNA.     

Bias, precision and accuracy in the estimation of cuticular and respiratory water loss: a case study from a highly variable cockroach, Perisphaeria sp

We compared the precision, bias and accuracy of two techniques that were recently proposed to estimate the contributions of cuticular and respiratory water loss to total water loss in insects. We performed measurements of VCO2 and VH2O in normoxia, hyperoxia and anoxia using flow through respirometry on single individuals of the highly variable cockroach Perisphaeria sp. to compare estimates of cuticular and respiratory water loss (CWL and RWL) obtained by the VH2O-VCO2 y-intercept method with those obtained by the hyperoxic switch method. Precision was determined by assessing the repeatability of values obtained whereas bias was assessed by comparing the methods' results to each other and to values for other species found in the literature. We found that CWL was highly repeatable by both methods (R0.88) and resulted in similar values to measures of CWL determined during the closed-phase of discontinuous gas exchange (DGE). Repeatability of RWL was much lower (R=0.40) and significant only in the case of the hyperoxic method. RWL derived from the hyperoxic method is higher (by 0.044 micromol min(-1)) than that obtained from the method traditionally used for measuring water loss during the closed-phase of DGE, suggesting that in the past RWL may have been underestimated. The very low cuticular permeability of this species (3.88 microg cm(-2) h(-1) Torr(-1)) is reasonable given the seasonally hot and dry habitat where it lives. We also tested the hygric hypothesis proposed to account for the evolution of discontinuous gas exchange cycles and found no effect of respiratory pattern on RWL, although the ratio of mean VH2O to VCO2 was higher for continuous patterns compared with discontinuous ones.     

Breeding systems in a secondary deciduous forest in Venezuela: The importance of life form, habitat, and pollination specificity

Breeding systems and mating systems of plants in a previously studied secondary deciduous forest were reanalysed in the context of new data. In this analysis, we increased the number of plant species (up to approximately 25% of the plant species in the community), included other life forms (23 annual and perennial species, plus habitat disturbance categories), and considered information about pollinator specificity. The frequencies of species with different sexual systems in a sample of 51 species were 82% hermaphrodite, 14% monoecious, and 4% dioecious. The frequencies of breeding systems in the sample of 49 hermaphroditic and monoecious species were 53% self-incompatible and 47% self-compatible. Self-compatible species included seven partially self-compatible, three self-compatible non-autogamous, and 13 self-compatible autogamous species. None of the species evaluated proved to be agamospermous. Fifty-five percent of the species tested were obligate outbreeders. The proportion of self-incompatible species was higher among trees and shrubs than among annual herbs. The proportion of self-compatible species for perennial herbs and lianas was not different. The association between annual herbs and autogamy was not strong: seven of 13 species were autogamous, five were partially self-compatible, and one was self-incompatible. The main characteristics or factors associated with breeding system were life cycle and successional stage. Short-lived species were mostly self-compatible, and xenogamy tended to be associated with forest and forest-border. In contrast, pollination specificity and life form were not consistently related to breeding system (self-compatibility or self-incompatibility) and mating system (xenogamy or autogamy).     

Ecological importance of large-diameter trees in a temperate mixed-conifer forest

Large-diameter trees dominate the structure, dynamics and function of many temperate and tropical forests. Although both scaling theory and competition theory make predictions about the relative composition and spatial patterns of large-diameter trees compared to smaller diameter trees, these predictions are rarely tested. We established a 25.6 ha permanent plot within which we tagged and mapped all trees ≥1 cm dbh, all snags ≥10 cm dbh, and all shrub patches ≥2 m(2). We sampled downed woody debris, litter, and duff with line intercept transects. Aboveground live biomass of the 23 woody species was 507.9 Mg/ha, of which 503.8 Mg/ha was trees (SD?=?114.3 Mg/ha) and 4.1 Mg/ha was shrubs. Aboveground live and dead biomass was 652.0 Mg/ha. Large-diameter trees comprised 1.4% of individuals but 49.4% of biomass, with biomass dominated by Abies concolor and Pinus lambertiana (93.0% of tree biomass). The large-diameter component dominated the biomass of snags (59.5%) and contributed significantly to that of woody debris (36.6%). Traditional scaling theory was not a good model for either the relationship between tree radii and tree abundance or tree biomass. Spatial patterning of large-diameter trees of the three most abundant species differed from that of small-diameter conspecifics. For A. concolor and P. lambertiana, as well as all trees pooled, large-diameter and small-diameter trees were spatially segregated through inter-tree distances <10 m. Competition alone was insufficient to explain the spatial patterns of large-diameter trees and spatial relationships between large-diameter and small-diameter trees. Long-term observations may reveal regulation of forest biomass and spatial structure by fire, wind, pathogens, and insects in Sierra Nevada mixed-conifer forests. Sustaining ecosystem functions such as carbon storage or provision of specialist species habitat will likely require different management strategies when the functions are performed primarily by a few large trees as opposed to many smaller trees.     

Endophytic fungi as novel sources of biopesticides: the Macaronesian Laurel forest,a case study

Endophytes fungi have been widely bioprospected to find new drugs and drug leads including antimicrobial agents and antifungals. However, an important role in host plant protection has been suggested for their presence and their metabolites. Therefore, nematicidal and insecticidal effects of their metabolites should be expected. In this review, the literature data available on insecicidal and nematicidal compounds identified from fungal endophytes are presented. Additionally we present a recent study on the endophytic biodiversity of a unique paleoflora, the Macaronesian laurel forest, in the light of their role in plant protection.     

Oxidation of methane in boreal forest soils: a comparison of seven measures

Methane oxidation rates were measured in boreal forest soils using seven techniques that provide a range of information on soil CH₄ oxidation. These include: (a) short-term static chamber experiments with a free-air (1.7 ppm CH₄) headspace, (b) estimating CH₄ oxidation rates from soil CH₄ distributions and (c)²²²Rn-calibrated flux measurements, (d) day-long static chamber experiments with free-air and amended (+20 to 2000 PPM CH₄) headspaces, (e) jar experiments on soil core sections using free-air and (f) amended (+500 ppm CH₄) headspaces, and (g) jar experiments on core sections involving tracer additions of¹⁴CH₄. Short-term unamended chamber measurements,²²²Rn-calibrated flux measurements, and soil CH₄ distributions show independently that the soils are capable of oxidizing atmospheric CH₄ at rates ranging to < 2 mg m^–2 d^–1. Jar experiments with free-air headspaces and soil CH₄ profiles show that CH₄ oxidation occurs to a soil depth of 60 cm and is maximum in the 10 to 20 cm zone. Jar experiments and chamber measurements with free-air headspaces show that CH₄ oxidation occurs at low (< 0.9 ppm) thresholds. The¹⁴CH₄-amended jar experiments show the distribution of end products of CH₄ oxidation; 60% is transformed to CO₂ and the remainder is incorporated in biomass. Chamber and jar experiments under amended atmospheres show that these soils have a high capacity for CH₄ oxidation and indicate potential CH₄ oxidation rates as high as 867 mg m^–2 d^–1. Methane oxidation in moist soils modulates CH₄ emission and can serve as a negative feedback on atmospheric CH₄ increases.     

Conifer seedling recruitment in a southeastern Canadian boreal forest: the importance of substrate

Abstract. In order to explain conifer species recruitment in Canada's southeastern boreal forest, we characterized conifer regeneration microsites and determined how these microsites vary in abundance during succession. Microsite abundance was evaluated in deciduous, mixed and coniferous stands along a 234-yr postfire chronosequence. Conifers were most often found in relatively well-illuminated microsites, devoid of litter, especially broad-leaf litter, and with a reduced cover of lower vegetation (< 50 cm tall). Although associated with moss-rich forest floor substrates, Abies balsamea was the most ubiquitously distributed species. Picea glauca and especially Thuja occidentalis seedlings were frequently found on rotten logs. Light measurements did not show differences among seedling species nor between stand types. The percentage cover of broad-leaf litter decreased significantly during succession. Also, rotten logs covered with moss occupied a significantly larger area in the mid-successionnal stands than in early successional deciduous or late successional coniferous stands. The results suggest that the presence of specific forest floor substrate types is a factor explaining low conifer recruitment under deciduous stands, conifer codominance in the mid-successional stage, and delayed Thuja recolonization after fire. Results also suggest that some facilitation mechanism is responsible for the observed directional succession.     

Regeneration failure and the potential importance of human disturbance in a subtropical forest

Abstract. A lack of regeneration of shade‐intolerant canopy species has been reported in several subtropical South African forests. The subtropical forest of Hluhluwe‐Umfolozi Park, KwaZulu‐Natal, was examined in order to determine the extent of regeneration, the forest grain, dynamics and conservation value. Field sampling took the form of recording DBH for all woody species in 29 0.04‐ha circular plots, walking 5‐m wide transects in mature and marginal forest to record size classes of important species and analysis of 20 gaps. A community analysis was performed using the multivariate program TWINSPAN. Size‐class distributions indicate a lack of regeneration and suggest a prevalence of shade‐intolerant species in the canopy. The composition of the canopy and subcanopy are distinct from one another and the forest is coarse‐grained. Conservation of the present species composition could be aided by encouraging patch‐scale disturbance. It is hypothesized that swidden agriculture may have favoured the formation of the present forest canopy structure.     

Aspen lichens in agricultural and forest landscapes: the importance of habitat quality

The amount of aspen Populus tremula , has declined in the boreal forest landscape. This decline is especially marked in young and intermediate stands due to the lack of regeneration. Aspen regeneration is nowadays mainly restricted to abandoned agricultural land. The decrease of aspen is of particular concern as it has more host-specific species than any other boreal tree species. The main question addressed is whether regenerating aspen stands in agricultural habitats can compensate for the deficiency of young stands in the forest. Data on epiphytic macrolichens show that cyanolichens increased, in number and frequency, with stand age in the forest landscape, and that there was a striking difference in species composition between stands in the two landscapes. Lichens with cyanobacterial and green-algal photobionts dominated in the forest and agricultural stands, respectively. Notably, cyanolichens were not found in stands younger than 50 yr in the forest, and stands younger than 100 yr in the agricultural landscape. This difference between the landscapes cannot be explained by stand age, stand size or isolation. Instead, differences in habitat quality, due to differences in the physical environment associated with the presence of conifers in the older forest stands, appear to be involved. We suggest that in order to conserve cyanolichens that are confined to aspen, active management practices have to be adopted that promote the regeneration of aspen in the forest landscape, and the establishment of conifers in areas where aspen regeneration is confined to the agricultural landscape. In addition, until new aspen stands with appropriate physical environments have been established, these measures must be combined with the preservation of existing old-growth stands, which can provide appropriate source populations.     

Topological keystone species: measures of positional importance in food webs

The local extinction or large fluctuation in abundance of a species may seriously affect other species in the community. The effects spread through the community by direct and indirect interactions. The network perspective on ecology can help map the pathways of these effects, for food webs, the pathways of indirect trophic interactions. Indirect interactions typically decay in intensity as they spread. Therefore, there is a conceptual maximum range in topological space beyond which interactions have no effects, even though all species remain connected. Neither the local characteristics of species, nor the global characteristics of entire webs, suitably quantify this range. We therefore apply intermediate scale indices that reflect the limitations imposed by effect damping in networks. We present a complex analysis of the topological positional importance of species in the Chesapeake Bay web. This web is a carbon-flow network that represents trophic interactions. We present several different indices reflecting different properties and discuss which questions the different indices best answer. We look for the best indices for identifying the key players in ecosystem functioning. Our study contributes to the quantification of relative species importance and provides an exact and a priori determination of a class of candidate keystone species that can inform applied and conservation ecology as well as theoretical concerns.     

Pentapeptide scanning mutagenesis: random insertion of a variable five amino acid cassette in a target protein.

A new insertion method for probing protein functional organization was developed. The method relies on the random insertion of transposon Tn 4430 and subsequent in vitro deletion of the bulk of the transposon after which a 15 bp insertion remains within the target gene. This results in pentapeptide insertions randomly distributed in the target protein. Characterization of 23 pentapeptide insertions in TEM-1beta-lactamase demonstrated the utility of the method. The phenotypes associated with the mutated beta-lactamase proteins equated both with the sorts of local peptide structures in which the pentapeptide insertions occurred and their position in the three-dimensional structure of the enzyme.     

Mosquito diversity (Diptera: Culicidae) and medical importance,in a bird sanctuary inside the flooded forest of Prek Toal,Cambodia

Wild birds have been identified as reservoirs of many pathogens transmissible to humans through bird-biting mosquitoes. Understanding the diversity of vector fauna in bird-conservation areas, is a cornerstone to later develop early detection systems and reduce the risk of emerging disease incidence. Prek Toal is a bird Sanctuary in the Tonle-Sap area in Cambodia hosting the largest migratory bird colony of southeast Asia. The Culicidae fauna was investigated during both dry and rainy seasons. In total, 8,224 mosquitoes from 6 genera and 25 species were collected. The two most represented genera were Anopheles (8 species) and Culex (11 species), while the dominant species was Culex vishnui (58.8%). During the rainy season, 1.6 fold more mosquitoes were caught and the number of species doubled. One of the most notable feature is the absence of any Aedinii mosquito which could be attributed to the low human density around the area, and the large populations of migratory birds. A total of 13 species from 3 genera are reported to be of medical importance. 6 medically-important species were collected in all 3 sites, and are known to bite both wild birds and humans: An. barbirostris, An. campestris, Cx. bitaeniorhynchus, Cx. vishnui, Ma. indiana and Ma. uniformis. One of the most important feature is the over-abundance of Culex vishnui, largely dominant in Prek Toal throughout the seasons and the sites, and being present everywhere in Cambodia. This finding stresses its potentiality to act as bridge vectors in the case of new disease emergence.