Comments (2)
Cheers, you are right, I have never added an example regarding that! My bad! For the time being, you can check this notebook: https://github.com/markovmodel/pyemma-workshop/blob/master/notebooks/02-io-features-hands-on.ipynb
The relevant bit is this:
from deeptime.decomposition import TICA, vamp_score_cv
fig, axes = plt.subplots(1, 3, figsize=(12, 3), sharey=True)
labels = ['backbone\ntorsions', 'heavy Atom\ndistances']
tica_estimator = TICA(lagtime=lags[0], dim=dim)
for ax, lag in zip(axes.flat, lags):
tica_estimator.lagtime = lag
torsions_scores = vamp_score_cv(tica_estimator, trajs=bbtorsions, blocksplit=False, n=3)
scores = [torsions_scores.mean()]
errors = [torsions_scores.std()]
distances_scores = vamp_score_cv(tica_estimator, trajs=heavy_atom_distances, blocksplit=False, n=3)
scores += [distances_scores.mean()]
errors += [distances_scores.std()]
ax.bar(labels, scores, yerr=errors, color=['C0', 'C1', 'C2'])
ax.set_title(r'lag time $\tau$={}ps'.format(lag))
axes[0].set_ylabel('VAMP2 score')
fig.tight_layout()
You can provide an estimated MSM and/or bayesian MSM as well.
Reference: https://deeptime-ml.github.io/latest/api/generated/deeptime.decomposition.vamp_score_cv.html
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Hello!
Thanks for the reply. I was able to implement the suggestion.
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Related Issues (20)
- TICA fit-once transform-many HOT 6
- Automate generating bdist wheels HOT 1
- Allowing weights for VAMP dimensionality reduction HOT 6
- Error importing deeptime with scikit-learn 1.2.0 HOT 4
- About applying Deeptime to molecular dynamics simulation trajectories on protien HOT 3
- Handling parallel simulations HOT 1
- Implied timescales from deeptime.decomposition.TICA HOT 2
- [Bug] At least one of the given states is not contained in this model HOT 2
- VAMPnet gives highly fluctuating score results HOT 1
- Bayesian Markov models give different MFPT
- How to compute any actual quantity of the coarse-grained kinetics with employing the fuzzy memberships? HOT 7
- Installation without conda and pip HOT 3
- Which version of VAMPNets is there? HOT 1
- deeptime cannot be installed on Mac computers with Apple Silicon and Python 3.12.0. HOT 4
- Does one need identical features to compare between related systems? HOT 4
- Example/tutorial for dealing with MD trajectories HOT 1
- Applying TICA to ragged feature vectors HOT 2
- KoopmanWeightingEstimator partial_fit method throws ValueError HOT 2
- Regarding trajectory data HOT 2
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