API Patterns

Models in msmbuilder inherit from base classes in scikit-learn, and follow a similar API. Like sklearn, each type of model is a python class. Models are “fit” to data, and can then “transform” data into a different representation. Unlike sklearn, the data here is a list (or dataset) of time-series arrays or trajectories.


Hyperparameters are passed in via the __init__ method and set as instance attributes.

from msmbuilder.decomposition import tICA
tica = tICA(gamma=0.05)


The estimation of model parameters is done in fit(). In msmbuilder, the fit() method always accepts a list or dataset() of 2-dimensional arrays as input data, where each array represents a single timeseries (trajectory) and has a shape of (length_of_trajectory, n_features). Some models can also accept a list of MD trajectories (Trajectory) as opposed to a list of arrays.

features = [np.load('traj-1-features.npy'), np.load('traj-2-featues.npy')]
assert features[0].ndim == 2 and features[1].ndim == 2

clusterer = KCenters(n_clusters=100)


This is different from sklearn. In sklearn, estimators take a single 2D array as input in fit(). Here we use a list of arrays or trajectories. However, for many models, it’s still quite easy to go between sklearn-style input and msmbuilder-style input, as shown in the following code block.

import msmbuilder.cluster
import sklearn.cluster

X_sklearn = np.random.normal(size=(100, 10))  # sklearn style input: (n_samples, n_features)
X_msmb = [X_sklearn]  # MSMBuilder style input: list of (n_samples, n_features)

clusterer_sklearn = sklearn.cluster.KMeans(n_clusters=5)

clusterer_msmb = msmbuilder.cluster.KMeans(n_clusters=5)

Some models like tICA only require a single pass over the data. In this case, use the partial_fit method, which can incrementally learn the model one trajectory at a time and be more memory-efficient.


Parameters of the model which are learned or estimated during fit() are always set as instance attributes that are named with a trailing underscore. This is merely a convention, and not a special Python syntax.

tica = tICA(gamma=0.05)

# timescales is an estimated quantity, so it ends in an underscore


Many models also implement a transform() method, which converts an input dataset to an alternative representation. For example, the transform method of featurizers takes as input a list of trajectories and returns a list of 2D feature arrays. Clustering takes a list of 2D feature arrays and returns a list of 1D sequences.


The models in msmbuilder are designed to work together as part of a sklearn.pipeline.Pipeline

from msmbuilder.cluster import KMeans
from msmbuilder.msm import MarkovStateModel
from sklearn.pipeline import Pipeline
pipeline = Pipeline([
    ('cluster', KMeans(n_clusters=100)),
    ('msm', MarkovStateModel())