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ericmjl / flu-sequence-predictor

An experimental deep learning & genotype network-based system for predicting new influenza protein sequences.
https://fluforecaster.herokuapp.com/
BSD 3-Clause "New" or "Revised" License
37 stars 12 forks source link

errors occur when importing objectives and pymc3 #2

Closed Spheluo closed 2 years ago

Spheluo commented 2 years ago

Dear @ericmjl : We would like to use the forecaster as Covid-19 forecaster. However, when I ran the codes in flu-forecaster with jupyter notebook, some errors occurred:

  1. from keras import objectives ImportError: cannot import name 'objectives' from 'keras'
  2. import pymc3 as pm AttributeError: 'TheanoConfigParser' object has no attribute 'gcc__cxxflags' I have no idea what's wrong with it and don't know how to fix it.
ericmjl commented 2 years ago

@Spheluo this is a pretty old codebase and I wouldn't recommend using it anymore. Thanks for your interest, though.

watercyn commented 2 years ago

Dear @ericmjl : it is such a pity to know that you personally do not recommend to use this codebase, as we found that the visualization of the forecaster helps illustrate the flu development in an effective and easily understanding manner. May i know you have other recommendation of similar codebase of newer version or more updated codebase for similar forecaster purpose?

ericmjl commented 2 years ago

Hi @watercyn! Much agreed, it is a pity as I don't have the time to keep it up-to-date anymore.

More modern efforts at doing flu sequence forecasting include those by:

  1. Eli Weinstein (Debora Marks' lab at Harvard Medical School): http://proceedings.mlr.press/v139/weinstein21a.html
  2. Brian Hie's Evolocity: https://github.com/brianhie/evolocity

Each have their own assumptions, so be sure to consider that too :).