Performing GMRQ

[drdoppio]

At the stage of Gmrq.ipynb of your tutorial I have gotten the following errors:

Input In [1], in <cell line: 87>() 84 no_clusters=[700,800,900] 85 tica_lagtime=[2,4,6] ---> 87 GMRQ(no_of_features,no_of_components,no_clusters,tica_lagtime)

Input In [1], in GMRQ(no_of_features, no_of_components, no_clusters, tica_lagtime, parameter, gmrq_dir, clustering_dir) 56 else: 57 print('Running the {}th cycle'.format(i+1)) ---> 58 cv = KFold(len(trajectories), n_folds=6, shuffle=True) #split the dataset into training set and test set 59 results = [] 60 print_results = [] #train score, test score

TypeError: init() got an unexpected keyword argument 'n_folds'

Any suggestions? thanks Sandor

[drdoppio]

sklearn.cross_validation is not working I have changed it to sklearn.model_selection

[ykhdrew]

Hi Sandor

Were you able to solve the issue? I tried with a newly-created conda environment with my script i.e. conda env create -n msmbuilder -f environment.yml and GMRQ.ipynb works fine on my end.

This tutorial was using a very old scikit learn and things might be quite different in newer version.

[drdoppio]

I was not able to resolve the problem with changing the n_folders to n_splits I still have the error:

Input In [1], in <cell line: 87>() 84 no_clusters=[700,800,900] 85 tica_lagtime=[2,4,6] ---> 87 GMRQ(no_of_features,no_of_components,no_clusters,tica_lagtime)

Input In [1], in GMRQ(no_of_features, no_of_components, no_clusters, tica_lagtime, parameter, gmrq_dir, clustering_dir) 56 else: 57 print('Running the {}th cycle'.format(i+1)) ---> 58 cv = KFold(len(trajectories), n_splits=6, shuffle=True) #split the dataset into training set and test set 59 results = [] 60 print_results = [] #train score, test score

TypeError: init() got multiple values for argument 'n_splits'

--

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Dr. Sandor Lovas, Professor Associate Editor, Frontiers in Chemical Biology

Department of Biomedical Sciences Creighton University, School of Medicine 2500 California Plaza Omaha, NE 68178, USA Phone: 402-280-5753 Fax: 402-280-2690

On Mon, 2023-06-05 at 17:13 -0700, Andrew Yik wrote:

Were you able to solve the issue? I tried with a newly-created conda environment with my script i.e. conda env create -n msmbuilder -f environment.yml and GMRQ.ipynb works fine on my end.

This tutorial was using a very old scikit learn and things might be quite different in newer version.

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[msinclair-py]

KFold no longer takes data at the first position as in this tutorial. The KFold line should read as: kf = KFold(n_splits=6, shuffle=True)

Then in the for loop: for fold, (train_index, test_index) in enumerate( kf.split( list( range( len( trajectories ) ) ) ) ):