Deep neural nets with a large number of parameters are very powerful machine learning systems. However, overfitting is a serious problem in such networks. Large networks are also slow to use, making it difficult to deal with overfitting by combining the predictions of many different large neural nets at test time. Dropout is a technique for addressing this problem. The key idea is to randomly drop units (along with their connections) from the neural network during training. This prevents units from co-adapting too much. During training, dropout samples from an exponential number of different "thinned" networks. At test time, it is easy to approximate the effect of averaging the predictions of all these thinned networks by simply using a single unthinned network that has smaller weights. This significantly reduces overfitting and gives major improvements over other regularization methods. We show that dropout improves the performance of neural networks on supervised learning tasks in vision, speech recognition, document classification and computational biology, obtaining state-of-the-art results on many benchmark data sets.

/pdf/dropout-a-simple-way-to-prevent-neural-networks-from-4gtr92okhv.pdf

Dropout: a simple way to prevent neural networks from overfitting

抗原变异可使得多种致病微生物易于逃避宿主免疫应答。表达在感染红细胞表面的恶性疟原虫红细胞表面蛋白1（PfPMP1）与感染红细胞、内皮细胞、树突状细胞以及胎盘的单个或多个受体作用，在黏附及免疫逃避中起关键的作用。每个单倍体基因组var基因家族编码约60种成员，通过启动转录不同的var基因变异体为抗原变异提供了分子基础。

疟原虫var基因转换速率变化导致抗原变异[英]／Paul H, Robert P, Christodoulou Z, et al//Proc Natl Acad Sci U S A

The identification of genetically homogeneous groups of individuals is a long standing issue in population genetics. A recent Bayesian algorithm implemented in the software STRUCTURE allows the identification of such groups. However, the ability of this algorithm to detect the true number of clusters (K) in a sample of individuals when patterns of dispersal among populations are not homogeneous has not been tested. The goal of this study is to carry out such tests, using various dispersal scenarios from data generated with an individual-based model. We found that in most cases the estimated 'log probability of data' does not provide a correct estimation of the number of clusters, K. However, using an ad hoc statistic DeltaK based on the rate of change in the log probability of data between successive K values, we found that STRUCTURE accurately detects the uppermost hierarchical level of structure for the scenarios we tested. As might be expected, the results are sensitive to the type of genetic marker used (AFLP vs. microsatellite), the number of loci scored, the number of populations sampled, and the number of individuals typed in each sample.

/pdf/detecting-the-number-of-clusters-of-individuals-using-the-16mlx2qlv8.pdf

Detecting the number of clusters of individuals using the software STRUCTURE: a simulation study.

Arlequin ver 3.0 is a software package integrating several basic and advanced methods for population genetics data analysis, like the computation of standard genetic diversity indices, the estimation of allele and haplotype frequencies, tests of departure from linkage equilibrium, departure from selective neutrality and demographic equilibrium, estimation or parameters from past population expansions, and thorough analyses of population subdivision under the AMOVA framework. Arlequin 3 introduces a completely new graphical interface written in C++, a more robust semantic analysis of input files, and two new methods: a Bayesian estimation of gametic phase from multi-locus genotypes, and an estimation of the parameters of an instantaneous spatial expansion from DNA sequence polymorphism. Arlequin can handle several data types like DNA sequences, microsatellite data, or standard multi-locus genotypes. A Windows version of the software is freely available on http://cmpg.unibe.ch/software/arlequin3.

/pdf/arlequin-version-3-0-an-integrated-software-package-for-4cs6nd3y2p.pdf

Arlequin (version 3.0): An integrated software package for population genetics data analysis

We present here a new version of the Arlequin program available under three different forms: a Windows graphical version (Winarl35), a console version of Arlequin (arlecore), and a specific console version to compute summary statistics (arlsumstat). The command-line versions run under both Linux and Windows. The main innovations of the new version include enhanced outputs in XML format, the possibility to embed graphics displaying computation results directly into output files, and the implementation of a new method to detect loci under selection from genome scans. Command-line versions are designed to handle large series of files, and arlsumstat can be used to generate summary statistics from simulated data sets within an Approximate Bayesian Computation framework.

Arlequin suite ver 3.5: a new series of programs to perform population genetics analyses under Linux and Windows

We examine how genomic imprinting may have evolved at an X-linked locus, using six diallelic models of selection in which one allele is imprintable and the other is not. Selection pressures are generated by genetic conflict between mothers and their offspring. The various models describe cases of maternal and paternal inactivation, in which females may be monogamous or bigamous. When inactivation is maternal, we examine the situations in which only female offspring exhibit imprinting as well as when both sexes do. We compare our results to those previously obtained for an autosomal locus and to four models in which a dominant modifier of biallelic expression is subjected to the same selection pressures. We find that, in accord with verbal predictions, maternal inactivation of growth enhancers and paternal inactivation of growth inhibitors are more likely than imprinting in the respective opposite directions, although these latter outcomes are possible for certain parameter combinations. The expected outcomes are easier to evolve than the same outcomes for autosomal loci, contradicting the available evidence concerning the direction of imprinting on mammalian sex chromosomes. In most of our models stable polymorphism of imprinting status is possible, a behavior not predicted by verbal accounts.

https://www.genetics.org/content/genetics/166/1/565.full.pdf

The effect of genetic conflict on genomic imprinting and modification of expression at a sex-linked locus.

Son Preference, Marriage, and Intergenerational Transfer in Rural China

Structural balance plays an important role in the dynamics of signed networks. Based on structural balance, we generalize the evolution of cooperation in signed networks. Here we develop a new simulation model to study the impact of structural balance on the evolution of cooperation in signed networks. The simulation shows that cooperation prevails when an individual has a higher probability of adjusting the signs of its relations. We also find that structural balance forces the coexistence of cooperators and defectors, while the initial attributes of networks have little impact on the evolution of cooperation in the presence of structural balance, although they have a strong effect on the evolution of structural balance.

/pdf/the-evolution-of-cooperation-in-signed-networks-under-the-2s9673ec8p.pdf

The evolution of cooperation in signed networks under the impact of structural balance.

Node attributes play an important role in shaping network structures, but are generally ignored in transformations of structural balance. A fully signed network consisting of signs of edges and nodes expresses both properties of relationship and node attributes. In this article, we generalize the definition of structural balance in fully signed networks. We transform the unbalanced fully signed network by not only changing signs of edges but also changing the signs of nodes. We propose a memetic algorithm to transform unbalanced networks at the lowest cost. Experiments show that our algorithm can solve this problem efficiently, and different node attribute assignments may lead to different optimized structures. © 2016 Wiley Periodicals, Inc. Complexity, 2016

Structural balance in fully signed networks

China is facing a male marriage squeeze, as there are more men in the marriage market than potential female partners. As a consequence, some men may fail to ever marry. However, while some studies have suggested that most unmarried men affected by the marriage squeeze in rural China feel a sense of failure, the quality of life of the men who remain unmarried against their will remains largely unexplored. Using data collected in rural Hanbin district of Ankang City (Shaanxi, China), this study analyzes the relationship between the marriage squeeze and the quality of life among rural men. Descriptive analyses indicate that the quality of life of unmarried men aged 28 years and older tends to be worse than for both younger unmarried men and married men. Also, the quality of life of men who perceive the marriage squeeze appears to be worse than that of those who do not. Regression analyses reveal that the perceived marriage squeeze and age independently have a significant negative relationship with the quality of life of rural men.

https://journals.sagepub.com/doi/pdf/10.1177/1557988316681220

Marcus W. Feldman

Papers

The effect of genetic conflict on genomic imprinting and modification of expression at a sex-linked locus.

Son Preference, Marriage, and Intergenerational Transfer in Rural China

The evolution of cooperation in signed networks under the impact of structural balance.

Structural balance in fully signed networks

On the Relationship Between the Marriage Squeeze and the Quality of Life of Rural Men in China.