Fast robust estimation of prediction error based on resampling

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fDETECT webserver: fast predictor of propensity for protein production, purification, and crystallization

Background: Development of predictors of propensity of protein sequences for successful crystallization has been actively pursued for over a decade. A few novel methods that expanded the scope of these predictions to address additional steps of protein production and structure determination pipelines were released in recent years. The predictive performance of the current methods is modest. This is because the only input that they use is the protein sequence and since the experimental annotations of these data might be inconsistent given that they were collected across many laboratories and centers. However, even these modest levels of predictive quality are still practical compared to the reported low success rates of crystallization, which are below 10%. We focus on another important aspect related to a high computational cost of running the predictors that offer the expanded scope. Results: We introduce a novel fDETECT webserver that provides very fast and modestly accurate predictions of the success of protein production, purification, crystallization, and structure determination. Empirical tests on two datasets demonstrate that fDETECT is more accurate than the only other similarly fast method, and similarly accurate and three orders of magnitude faster than the currently most accurate predictors. Our method predicts a single protein in about 120 milliseconds and needs less than an hour to generate the four predictions for an entire human proteome. Moreover, we empirically show that fDETECT secures similar levels of predictive performance when compared with four representative methods that only predict success of crystallization, while it also provides the other three predictions. A webserver that implements fDETECT is available at http://biomine.cs.vcu.edu/servers/ fDETECT/. Conclusions: fDETECT is a computational tool that supports target selection for protein production and X-ray crystallography-based structure determination. It offers predictive quality that matches or exceeds other state-ofthe-art tools and is especially suitable for the analysis of large protein sets

A highly modular adaptive lattice algorithm for multichannel least squares filtering

In this paper a highly modular adaptive lattice algorithm for multichannel least squares FIR filtering and multivariable system identification is presented. Multichannel filters with different number of delay elements per input channel are allowed. The main features of the proposed multichannel adaptive lattice least squares algorithm is the use of scalar only operations, multiplications/divisions and additions, and the local communication which enables the development of a fully pipelining architecture. The tracking capability and the numerical stability and accuracy of the proposed technique are illustrated by simulations

Emotion and language: valence and arousal affect word recognition

Emotion influences most aspects of cognition and behavior, but emotional factors are conspicuously absent from current models of word recognition. The influence of emotion on word recognition has mostly been reported in prior studies on the automatic vigilance for negative stimuli, but the precise nature of this relationship is unclear. Various models of automatic vigilance have claimed that the effect of valence on response times is categorical, an inverted U, or interactive with arousal. In the present study, we used a sample of 12,658 words and included many lexical and semantic control factors to determine the precise nature of the effects of arousal and valence on word recognition. Converging empirical patterns observed in word-level and trial-level data from lexical decision and naming indicate that valence and arousal exert independent monotonic effects: Negative words are recognized more slowly than positive words, and arousing words are recognized more slowly than calming words. Valence explained about 2% of the variance in word recognition latencies, whereas the effect of arousal was smaller. Valence and arousal do not interact, but both interact with word frequency, such that valence and arousal exert larger effects among low-frequency words than among high-frequency words. These results necessitate a new model of affective word processing whereby the degree of negativity monotonically and independently predicts the speed of responding. This research also demonstrates that incorporating emotional factors, especially valence, improves the performance of models of word recognition