Texas A&M University

About: Texas A&M University is a education organization based out in College Station, Texas, United States. It is known for research contribution in the topics: Population & Gene. The organization has 72169 authors who have published 164372 publications receiving 5764236 citations.

Auto-Keras: An Efficient Neural Architecture Search System

Abstract: Neural architecture search (NAS) has been proposed to automatically tune deep neural networks, but existing search algorithms, e.g., NASNet, PNAS, usually suffer from expensive computational cost. Network morphism, which keeps the functionality of a neural network while changing its neural architecture, could be helpful for NAS by enabling more efficient training during the search. In this paper, we propose a novel framework enabling Bayesian optimization to guide the network morphism for efficient neural architecture search. The framework develops a neural network kernel and a tree-structured acquisition function optimization algorithm to efficiently explores the search space. Extensive experiments on real-world benchmark datasets have been done to demonstrate the superior performance of the developed framework over the state-of-the-art methods. Moreover, we build an open-source AutoML system based on our method, namely Auto-Keras. The code and documentation are available at https://autokeras.com. The system runs in parallel on CPU and GPU, with an adaptive search strategy for different GPU memory limits.

Extensive introgression in a malaria vector species complex revealed by phylogenomics

Abstract: Introgressive hybridization is now recognized as a widespread phenomenon, but its role in evolution remains contested. Here, we use newly available reference genome assemblies to investigate phylogenetic relationships and introgression in a medically important group of Afrotropical mosquito sibling species. We have identified the correct species branching order to resolve a contentious phylogeny and show that lineages leading to the principal vectors of human malaria were among the first to split. Pervasive autosomal introgression between these malaria vectors means that only a small fraction of the genome, mainly on the X chromosome, has not crossed species boundaries. Our results suggest that traits enhancing vectorial capacity may be gained through interspecific gene flow, including between nonsister species.

Mapping QTLs with epistatic effects and QTL×environment interactions by mixed linear model approaches

Abstract: A new methodology based on mixed linear models was developed for mapping QTLs with digenic epistasis and QTL×environment (QE) interactions. Reliable estimates of QTL main effects (additive and epistasis effects) can be obtained by the maximum-likelihood estimation method, while QE interaction effects (additive×environment interaction and epistasis×environment interaction) can be predicted by the-best-linear-unbiased-prediction (BLUP) method. Likelihood ratio and t statistics were combined for testing hypotheses about QTL effects and QE interactions. Monte Carlo simulations were conducted for evaluating the unbiasedness, accuracy, and power for parameter estimation in QTL mapping. The results indicated that the mixed-model approaches could provide unbiased estimates for both positions and effects of QTLs, as well as unbiased predicted values for QE interactions. Additionally, the mixed-model approaches also showed high accuracy and power in mapping QTLs with epistatic effects and QE interactions. Based on the models and the methodology, a computer software program (QTLMapper version 1.0) was developed, which is suitable for interval mapping of QTLs with additive, additive×additive epistasis, and their environment interactions.

Redefining the age of Clovis: implications for the peopling of the Americas.

Abstract: The Clovis complex is considered to be the oldest unequivocal evidence of humans in the Americas, dating between 11,500 and 10,900 radiocarbon years before the present ( 14 C yr B.P.). Adjusted 14 C dates and a reevaluation of the existing Clovis date record revise the Clovis time range to 11,050 to 10,800 14 C yr B.P. In as few as 200 calendar years, Clovis technology originated and spread throughout North America. The revised age range for Clovis overlaps non-Clovis sites in North and South America. This and other evidence imply that humans already lived in the Americas before Clovis.