Effects of the lack of selective pressure on the expected run-time distribution in genetic programming

Personal use of this material is permitted. Permission from IEEE must be obtained for all other uses, in any current or future media, including reprinting/republishing this material for advertising or promotional purposes, creating new collective works, for resale or redistribution to servers or lists, or reuse of any copyrighted component of this work in other works. D. F. Barrero, M. D. R-Moreno, B. Castano, and D. Camacho, "Effects of the lack of selective pressure on the expected run-time distribution in genetic programming", in IEEE Congress on Evolutionary Computation, CEC 2013, pp. 1748 - 1755Run-time analysis is a powerful tool to analyze algorithms. It is focused on studying the time required by an algorithm to find a solution, the expected run-time, which is one of the most relevant algorithm attributes. Previous research has associated the expected run-time in GP with the lognormal distribution. In this paper we provide additional evidence in that regard and show how the algorithm parametrization may change the resulting run-time distribution. In particular, we explore the influence of the selective pressure on the run-time distribution in tree-based GP, finding that, at least in two problem instances, the lack of selective pressure generates an expected run-time distribution well described by the Weibull probability distribution.This work has been partly supported by Spanish Ministry of Science and Education under project ABANT (TIN2010- 19872)

An empirical study on the accuracy of computational effort in Genetic Programming

Personal use of this material is permitted. Permission from IEEE must be obtained for all other uses, in any current or future media, including reprinting/republishing this material for advertising or promotional purposes, creating new collective works, for resale or redistribution to servers or lists, or reuse of any copyrighted component of this work in other works. D. F. Barrero, M. D. R-Moreno, B. Castaño, and D. Camacho, "An empirical study on the accuracy of computational effort in Genetic Programming", in IEEE Congress on Evolutionary Computation (CEC), 2011, pp. 1164 - 1171Some commonly used performance measures in Genetic Programming are those defined by John Koza in his first book. These measures, mainly computational effort and number of individuals to be processed, estimate the performance of the algorithm as well as the difficulty of a problem. Although Koza's performance measures have been widely used in the literature, their behaviour is not well known. In this paper we study the accuracy of these measures and advance in the understanding of the factors that influence them. In order to achieve this goal, we report an empirical study that attempts to systematically measure the effects of two variability sources in the estimation of the number of individuals to be processed and the computational effort. The results obtained in those experiments suggests that these measures, in common experimental setups, and under certain circumstances, might have a high relative error.This work was partially supported by the MICYT project ABANT (TIN2010-19872) and Castilla-La Mancha project PEII09- 0266-664

Statistical distribution of generation-to-success in GP: Application to model accumulated success probability

The final publication is available at Springer via http://dx.doi.org/10.1007/978-3-642-20407-4_14Proceedings of the 14th European Conference, EuroGP 2011, Torino, Italy, April 27-29, 2011.Many different metrics have been defined in Genetic Programming. Depending on the experiment requirements and objectives, a collection of measures are selected in order to achieve an understanding of the algorithm behaviour. One of the most common metrics is the accumulated success probability, which evaluates the probability of an algorithm to achieve a solution in a certain generation. We propose a model of accumulated success probability composed by two parts, a binomial distribution that models the total number of success, and a lognormal approximation to the generation-to-success, that models the variation of the success probability with the generation.This work was partially supported by the MICYT project ABANT (TIN2010-19872) and Castilla-La Mancha project PEII09- 0266-664

Acidity and accessibility studies of desilicated ZSM-5 zeolites in terms of their effectiveness as catalysts in acid-catalyzed cracking processes

The structural, textural and acidic characteristics of hierarchical ZSM-5 (Si/Al = 18-32), obtained with two desilication approaches, and the effect of these treatments on the reactivity in various cracking reactions of variable feedstock size and severity have been investigated. Emphasis is given to understanding the accessibility of acid sites; this was investigated by textural analysis, FTIR probe molecules (pyridine, trimethylacetonitrile and 2,4,6-trimethylpyridine) and reactions involving n-decane, 1,3,5-triisopropylbenzene (TIPB), and low and high-density polyethylene, LDPE and HDPE, respectively. Higher surface areas and a narrower pore size distribution were obtained for NaOH&TBAOH-treated materials, comparing to NaOH-treated ones. FTIR studies of pivalonitrile and collidine adsorption correlate well with the mesopore surface area. For n-decane cracking activity, the acid strength is a determining factor, revealing that the NaOH&TBAOH treatment gave stronger sites than NaOH, but lower than the native zeolite. In contrast, the TIPB cracking activity was improved by the developed mesoporosity of the alkaline treated zeolites, and this was correlated to the pivalonitrile and collidine accessibility factors. During the n-decane and TIPB cracking, hydrogen transfer reactions were reduced, leading to high olefin production for the NaOH&TBAOH materials due to the shorter microporous paths after desilication. The increased accessibility of the acid sites also leads to an enhanced cracking activity of polyethylenes at low conversions, as determined by a decrease in the T5% and T50%; both parameters are linearly dependent on the pivalonitrile and collidine accessibility factors, for LDPE and HDPE. The T5% for HDPE is more influenced by the accessibility factors than it is for the LDPE. This is interpreted to be the result of the branching degree of HDPE and LDPE; linear HDPE is more sensitive to the enhanced number of pore mouths of ZSM-5 channels on the mesopores. At high conversion, the influence on the T50% of the accessibility factors for HDPE and LDPE is weaker, suggesting that the cracking at this stage involves intermediate molecules of smaller size with fewer diffusional limitations. With respect to our own prior work, the chosen zeolite and the cracking of polyolefins gave more pronounced differences for the hierarchical ZSM-5

Rarity of monodominance in hyperdiverse Amazonian forests.

Tropical forests are known for their high diversity. Yet, forest patches do occur in the tropics where a single tree species is dominant. Such "monodominant" forests are known from all of the main tropical regions. For Amazonia, we sampled the occurrence of monodominance in a massive, basin-wide database of forest-inventory plots from the Amazon Tree Diversity Network (ATDN). Utilizing a simple defining metric of at least half of the trees ≥ 10 cm diameter belonging to one species, we found only a few occurrences of monodominance in Amazonia, and the phenomenon was not significantly linked to previously hypothesized life history traits such wood density, seed mass, ectomycorrhizal associations, or Rhizobium nodulation. In our analysis, coppicing (the formation of sprouts at the base of the tree or on roots) was the only trait significantly linked to monodominance. While at specific locales coppicing or ectomycorrhizal associations may confer a considerable advantage to a tree species and lead to its monodominance, very few species have these traits. Mining of the ATDN dataset suggests that monodominance is quite rare in Amazonia, and may be linked primarily to edaphic factors

Local hydrological conditions influence tree diversity and composition across the Amazon basin

Tree diversity and composition in Amazonia are known to be strongly determined by the water supplied by precipitation. Nevertheless, within the same climatic regime, water availability is modulated by local topography and soil characteristics (hereafter referred to as local hydrological conditions), varying from saturated and poorly drained to well-drained and potentially dry areas. While these conditions may be expected to influence species distribution, the impacts of local hydrological conditions on tree diversity and composition remain poorly understood at the whole Amazon basin scale. Using a dataset of 443 1-ha non-flooded forest plots distributed across the basin, we investigate how local hydrological conditions influence 1) tree alpha diversity, 2) the community-weighted wood density mean (CWM-wd) – a proxy for hydraulic resistance and 3) tree species composition. We find that the effect of local hydrological conditions on tree diversity depends on climate, being more evident in wetter forests, where diversity increases towards locations with well-drained soils. CWM-wd increased towards better drained soils in Southern and Western Amazonia. Tree species composition changed along local soil hydrological gradients in Central-Eastern, Western and Southern Amazonia, and those changes were correlated with changes in the mean wood density of plots. Our results suggest that local hydrological gradients filter species, influencing the diversity and composition of Amazonian forests. Overall, this study shows that the effect of local hydrological conditions is pervasive, extending over wide Amazonian regions, and reinforces the importance of accounting for local topography and hydrology to better understand the likely response and resilience of forests to increased frequency of extreme climate events and rising temperatures

Estimating the global conservation status of more than 15,000 Amazonian tree species

Estimates of extinction risk for Amazonian plant and animal species are rare and not often incorporated into land-use policy and conservation planning. We overlay spatial distribution models with historical and projected deforestation to show that at least 36% and up to 57% of all Amazonian tree species are likely to qualify as globally threatened under International Union for Conservation of Nature (IUCN) Red List criteria. If confirmed, these results would increase the number of threatened plant species on Earth by 22%. We show that the trends observed in Amazonia apply to trees throughout the tropics, and we predict thatmost of the world’s >40,000 tropical tree species now qualify as globally threatened. A gap analysis suggests that existing Amazonian protected areas and indigenous territories will protect viable populations of most threatened species if these areas suffer no further degradation, highlighting the key roles that protected areas, indigenous peoples, and improved governance can play in preventing large-scale extinctions in the tropics in this century

Geographic patterns of tree dispersal modes in Amazonia and their ecological correlates

Aim: To investigate the geographic patterns and ecological correlates in the geographic distribution of the most common tree dispersal modes in Amazonia (endozoochory, synzoochory, anemochory and hydrochory). We examined if the proportional abundance of these dispersal modes could be explained by the availability of dispersal agents (disperser-availability hypothesis) and/or the availability of resources for constructing zoochorous fruits (resource-availability hypothesis). Time period: Tree-inventory plots established between 1934 and 2019. Major taxa studied: Trees with a diameter at breast height (DBH) ≥ 9.55 cm. Location: Amazonia, here defined as the lowland rain forests of the Amazon River basin and the Guiana Shield. Methods: We assigned dispersal modes to a total of 5433 species and morphospecies within 1877 tree-inventory plots across terra-firme, seasonally flooded, and permanently flooded forests. We investigated geographic patterns in the proportional abundance of dispersal modes. We performed an abundance-weighted mean pairwise distance (MPD) test and fit generalized linear models (GLMs) to explain the geographic distribution of dispersal modes. Results: Anemochory was significantly, positively associated with mean annual wind speed, and hydrochory was significantly higher in flooded forests. Dispersal modes did not consistently show significant associations with the availability of resources for constructing zoochorous fruits. A lower dissimilarity in dispersal modes, resulting from a higher dominance of endozoochory, occurred in terra-firme forests (excluding podzols) compared to flooded forests. Main conclusions: The disperser-availability hypothesis was well supported for abiotic dispersal modes (anemochory and hydrochory). The availability of resources for constructing zoochorous fruits seems an unlikely explanation for the distribution of dispersal modes in Amazonia. The association between frugivores and the proportional abundance of zoochory requires further research, as tree recruitment not only depends on dispersal vectors but also on conditions that favour or limit seedling recruitment across forest types

Geography and ecology shape the phylogenetic composition of Amazonian tree communities

AimAmazonia hosts more tree species from numerous evolutionary lineages, both young and ancient, than any other biogeographic region. Previous studies have shown that tree lineages colonized multiple edaphic environments and dispersed widely across Amazonia, leading to a hypothesis, which we test, that lineages should not be strongly associated with either geographic regions or edaphic forest types.LocationAmazonia.TaxonAngiosperms (Magnoliids; Monocots; Eudicots).MethodsData for the abundance of 5082 tree species in 1989 plots were combined with a mega-phylogeny. We applied evolutionary ordination to assess how phylogenetic composition varies across Amazonia. We used variation partitioning and Moran's eigenvector maps (MEM) to test and quantify the separate and joint contributions of spatial and environmental variables to explain the phylogenetic composition of plots. We tested the indicator value of lineages for geographic regions and edaphic forest types and mapped associations onto the phylogeny.ResultsIn the terra firme and várzea forest types, the phylogenetic composition varies by geographic region, but the igapó and white-sand forest types retain a unique evolutionary signature regardless of region. Overall, we find that soil chemistry, climate and topography explain 24% of the variation in phylogenetic composition, with 79% of that variation being spatially structured (R2 = 19% overall for combined spatial/environmental effects). The phylogenetic composition also shows substantial spatial patterns not related to the environmental variables we quantified (R2 = 28%). A greater number of lineages were significant indicators of geographic regions than forest types.Main ConclusionNumerous tree lineages, including some ancient ones (>66 Ma), show strong associations with geographic regions and edaphic forest types of Amazonia. This shows that specialization in specific edaphic environments has played a long-standing role in the evolutionary assembly of Amazonian forests. Furthermore, many lineages, even those that have dispersed across Amazonia, dominate within a specific region, likely because of phylogenetically conserved niches for environmental conditions that are prevalent within regions