Space-efficient Feature Maps for String Alignment Kernels

String kernels are attractive data analysis tools for analyzing string data. Among them, alignment kernels are known for their high prediction accuracies in string classifications when tested in combination with SVM in various applications. However, alignment kernels have a crucial drawback in that they scale poorly due to their quadratic computation complexity in the number of input strings, which limits large-scale applications in practice. We address this need by presenting the first approximation for string alignment kernels, which we call space-efficient feature maps for edit distance with moves (SFMEDM), by leveraging a metric embedding named edit sensitive parsing (ESP) and feature maps (FMs) of random Fourier features (RFFs) for large-scale string analyses. The original FMs for RFFs consume a huge amount of memory proportional to the dimension d of input vectors and the dimension D of output vectors, which prohibits its large-scale applications. We present novel space-efficient feature maps (SFMs) of RFFs for a space reduction from O(dD) of the original FMs to O(d) of SFMs with a theoretical guarantee with respect to concentration bounds. We experimentally test SFMEDM on its ability to learn SVM for large-scale string classifications with various massive string data, and we demonstrate the superior performance of SFMEDM with respect to prediction accuracy, scalability and computation efficiency.Comment: Full version for ICDM'19 pape

Reduced tillage, but not organic matter input, increased nematode diversity and food web stability in European long‐term field experiments

Soil nematode communities and food web indices can inform about the complexity, nutrient flows and decomposition pathways of soil food webs, reflecting soil quality. Relative abundance of nematode feeding and life‐history groups are used for calculating food web indices, i.e., maturity index (MI), enrichment index (EI), structure index (SI) and channel index (CI). Molecular methods to study nematode communities potentially offer advantages compared to traditional methods in terms of resolution, throughput, cost and time. In spite of such advantages, molecular data have not often been adopted so far to assess the effects of soil management on nematode communities and to calculate these food web indices. Here, we used high‐throughput amplicon sequencing to investigate the effects of tillage (conventional vs. reduced) and organic matter addition (low vs. high) on nematode communities and food web indices in 10 European long‐term field experiments and we assessed the relationship between nematode communities and soil parameters. We found that nematode communities were more strongly affected by tillage than by organic matter addition. Compared to conventional tillage, reduced tillage increased nematode diversity (23% higher Shannon diversity index), nematode community stability (12% higher MI), structure (24% higher SI), and the fungal decomposition channel (59% higher CI), and also the number of herbivorous nematodes (70% higher). Total and labile organic carbon, available K and microbial parameters explained nematode community structure. Our findings show that nematode communities are sensitive indicators of soil quality and that molecular profiling of nematode communities has the potential to reveal the effects of soil management on soil quality

Tide-induced head fluctuations in coastal aquifers of variable thickness

In this work, a new analytical solution to describe tide-induced head fluctuations in aquifers of variable thickness is presented. The proposed model assumes a finite and confined aquifer with a thickness that increases or decreases quadratically with the distance to the coast. A closed-form analytical solution is obtained by solving a boundary-value problem with both a separation of variables method and a change of variables method. This solution is a generalization of the solution obtained by Cuello et al., Hydrogeological Journal, 2017, 25, 1509–1515. The analytical solution is expressed in terms of the wedging parameter, a parameter that depends on the length and thicknesses at the coast and at the inland edge of the aquifer. Positive values of the wedging parameter describe aquifers with increasing thickness towards land and negative values describe aquifers with a decreasing thickness in the inland direction. The comparison of the new solution and the solution for a finite aquifer with constant thickness indicates that the sign of the wedging parameter enhances or decreases the amplitude of the tide-induced signal. However, the differences in time-lag between both solutions are negligible near the coast. The slope factor, which quantifies the inconsistencies between aquifer diffusivities estimated from attenuation and time-lag data, is computed and analysed. Near the coast, slope factor values greater than one are obtained for negative wedging parameters while slope factor values less than one are obtained for positive wedging parameters. The analysis of the new solution also indicates that more reliable estimates of the hydraulic diffusivity can be obtained from time-lag data.Fil: Cuello, Julián Eduardo. Universidad Nacional de La Plata. Facultad de Ciencias Astronómicas y Geofísicas. Departamento de Geofísica Aplicada; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - La Plata; ArgentinaFil: Guarracino, Luis. Universidad Nacional de La Plata. Facultad de Ciencias Astronómicas y Geofísicas. Departamento de Geofísica Aplicada; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - La Plata; Argentina. Universidad Nacional de La Plata. Facultad de Ciencias Naturales y Museo; Argentin

'Put Your Money Where Your Mouth Is!': Effects of Streaks on Confidence and Betting in a Binary Choice Task.

This is the final published version. It first appeared at http://onlinelibrary.wiley.com/doi/10.1002/bdm.1844/abstract.Human choice under uncertainty is influenced by erroneous beliefs about randomness. In simple binary choice tasks, such as red/black predictions in roulette, long outcome runs (e.g. red, red, red) typically increase the tendency to predict the other outcome (i.e. black), an effect labeled the "gambler's fallacy." In these settings, participants may also attend to streaks in their predictive performance. Winning and losing streaks are thought to affect decision confidence, although prior work indicates conflicting directions. Over three laboratory experiments involving red/black predictions in a sequential roulette task, we sought to identify the effects of outcome runs and winning/losing streaks upon color predictions, decision confidence and betting behavior. Experiments 1 (n = 40) and 3 (n = 40) obtained trial-by-trial confidence ratings, with a win/no win payoff and a no loss/loss payoff, respectively. Experiment 2 (n = 39) obtained a trial-by-trial bet amount on an equivalent scale. In each experiment, the gambler's fallacy was observed on choice behavior after color runs and, in experiment 2, on betting behavior after color runs. Feedback streaks exerted no reliable influence on confidence ratings, in either payoff condition. Betting behavior, on the other hand, increased as a function of losing streaks. The increase in betting on losing streaks is interpreted as a manifestation of loss chasing; these data help clarify the psychological mechanisms underlying loss chasing and caution against the use of betting measures ("post-decision wagering") as a straightforward index of decision confidence. © 2014 The Authors. Journal of Behavioral Decision Making published by John Wiley & Sons Ltd

Large-scale analysis of protein expression changes in human keratinocytes immortalized by human papilloma virus type 16 E6 and E7 oncogenes

<p>Abstract</p> <p>Background</p> <p>Infection with high-risk type human papilloma viruses (HPVs) is associated with cervical carcinomas and with a subset of head and neck squamous cell carcinomas. Viral E6 and E7 oncogenes cooperate to achieve cell immortalization by a mechanism that is not yet fully understood. Here, human keratinocytes were immortalized by long-term expression of HPV type 16 E6 or E7 oncoproteins, or both. Proteomic profiling was used to compare expression levels for 741 discrete protein features.</p> <p>Results</p> <p>Six replicate measurements were performed for each group using two-dimensional difference gel electrophoresis (2D-DIGE). The median within-group coefficient of variation was 19–21%. Significance of between-group differences was tested based on Significance Analysis of Microarray and fold change. Expression of 170 (23%) of the protein features changed significantly in immortalized cells compared to primary keratinocytes. Most of these changes were qualitatively similar in cells immortalized by E6, E7, or E6/7 expression, indicating convergence on a common phenotype, but fifteen proteins (~2%) were outliers in this regulatory pattern. Ten demonstrated opposite regulation in E6- and E7-expressing cells, including the cell cycle regulator p16^INK4a; the carbohydrate binding protein Galectin-7; two differentially migrating forms of the intermediate filament protein Cytokeratin-7; HSPA1A (Hsp70-1); and five unidentified proteins. Five others had a pattern of expression that suggested cooperativity between the co-expressed oncoproteins. Two of these were identified as forms of the small heat shock protein HSPB1 (Hsp27).</p> <p>Conclusion</p> <p>This large-scale analysis provides a framework for understanding the cooperation between E6 and E7 oncoproteins in HPV-driven carcinogenesis.</p