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Code for BIBM-18 paper Inferring Microbial Communities for City Scale Metagenomics Using Neural Networks

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MetaMLAnn

This repository includes the code of MetaMLAnn (see paper).

File discription:

  1. MetaMLAnn folder contains the core code for our model.

  2. naive_model.py: Evaluate baseline models. It will print out the result for 4 baseline models under K fold. you can change it. parameters: '--KFold' Number of Fold. '--embedding' 0 to use stations feature only; 1 to use embedding; 2 to use both (default)

  3. feature_extraction.py: Functions to extract embedding features/ subway line features

  4. gen_data.py: construct species matrix (label) from files or by loading from src/tmp/pic_spec_vec.data

  5. vectorize.py: exploration function for species distribuion similarity v.s. distance. Generate the matrix. Similar as part of function in the gen_data.py.

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Code for BIBM-18 paper Inferring Microbial Communities for City Scale Metagenomics Using Neural Networks

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