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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
Network Model Selection Using Task-Focused Minimum Description Length
Networks are fundamental models for data used in practically every
application domain. In most instances, several implicit or explicit choices
about the network definition impact the translation of underlying data to a
network representation, and the subsequent question(s) about the underlying
system being represented. Users of downstream network data may not even be
aware of these choices or their impacts. We propose a task-focused network
model selection methodology which addresses several key challenges. Our
approach constructs network models from underlying data and uses minimum
description length (MDL) criteria for selection. Our methodology measures
efficiency, a general and comparable measure of the network's performance of a
local (i.e. node-level) predictive task of interest. Selection on efficiency
favors parsimonious (e.g. sparse) models to avoid overfitting and can be
applied across arbitrary tasks and representations. We show stability,
sensitivity, and significance testing in our methodology
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