avsecz/concise

CONCISE (COnvolutional neural Networks for CIS-regulatory Elements)

concise's Issues

add method to ConciseCV - get_performance(type = "mse") or similar

type = "mse", "r-squared", "variance explained"

Update sklearn/cross_validation.py to model_selection

sklearn/cross_validation.py:44: DeprecationWarning: This module was deprecated in version 0.18 in favor of the model_selection module into which all the refactored classes and functions are moved. Also note that the interface of the new CV iterators are different from that of this module. This module will be removed in 0.20.
"This module will be removed in 0.20.", DeprecationWarning)

Ranking Metrics

I think it's good to have these in concise: https://gist.github.com/nkhuyu/ab5b0b29d55bcd6b80b8f11c2933636c

feature: remove regress_out_feat feature

fix: don't install tensorflow if tensorflow-gpu is installed

Asked in this thread:
http://stackoverflow.com/questions/41956902/how-to-declare-or-dependence-in-setup-py

update tensorflow compatibility

WARNING:tensorflow:tf.op_scope(values, name, default_name) is deprecated, use tf.name_scope(name, default_name, values) _build_graph.: initialize_all_variables (from tensorflow.python.ops.variables) is deprecated and will be removed after 2017-03-02. Usetf.global_variables_initializerinstead.

fix: readthedocs build

feature: multi-task learning

• w_motif -> matrix
• b -> vector
• optional w_feat -> matrix
• y -> matrix

feature: conciseCV global model - train for optimal number of epochs

At each fold, store the number of optimal epochs and train the global model for so many