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Prediction of microbial communities for urban metagenomics using neural network approach.
BACKGROUND:Microbes are greatly associated with human health and disease, especially in densely populated cities. It is essential to understand the microbial ecosystem in an urban environment for cities to monitor the transmission of infectious diseases and detect potentially urgent threats. To achieve this goal, the DNA sample collection and analysis have been conducted at subway stations in major cities. However, city-scale sampling with the fine-grained geo-spatial resolution is expensive and laborious. In this paper, we introduce MetaMLAnn, a neural network based approach to infer microbial communities at unsampled locations given information reflecting different factors, including subway line networks, sampling material types, and microbial composition patterns. RESULTS:We evaluate the effectiveness of MetaMLAnn based on the public metagenomics dataset collected from multiple locations in the New York and Boston subway systems. The experimental results suggest that MetaMLAnn consistently performs better than other five conventional classifiers under different taxonomic ranks. At genus level, MetaMLAnn can achieve F1 scores of 0.63 and 0.72 on the New York and the Boston datasets, respectively. CONCLUSIONS:By exploiting heterogeneous features, MetaMLAnn captures the hidden interactions between microbial compositions and the urban environment, which enables precise predictions of microbial communities at unmeasured locations
Blockout: Dynamic Model Selection for Hierarchical Deep Networks
Most deep architectures for image classification--even those that are trained
to classify a large number of diverse categories--learn shared image
representations with a single model. Intuitively, however, categories that are
more similar should share more information than those that are very different.
While hierarchical deep networks address this problem by learning separate
features for subsets of related categories, current implementations require
simplified models using fixed architectures specified via heuristic clustering
methods. Instead, we propose Blockout, a method for regularization and model
selection that simultaneously learns both the model architecture and
parameters. A generalization of Dropout, our approach gives a novel
parametrization of hierarchical architectures that allows for structure
learning via back-propagation. To demonstrate its utility, we evaluate Blockout
on the CIFAR and ImageNet datasets, demonstrating improved classification
accuracy, better regularization performance, faster training, and the clear
emergence of hierarchical network structures
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