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notebooks/01-data-io-and-featurization.ipynb

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"name": "python",
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"nbconvert_exporter": "python",
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"pygments_lexer": "ipython3",
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"version": "3.6.5"
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"version": "3.6.6"
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notebooks/02-dimension-reduction-and-discretization.ipynb

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"because in the initial phase you want to explore the phase space as much as possible.\n",
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"The downside of placing states in areas of low density is that we will have poor statistics on these states. \n",
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"\n",
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"Another advantage of regular space clustering is that it is very fast in comparison to $k$-means:\n",
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"Another advantage of regular space clustering is that it is fast in comparison to $k$-means:\n",
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"regspace clustering runs in linear time while $k$-means is superpolynomial in time.\n",
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"\n",
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"⚠️ For very large datasets we also offer a mini batch version of $k$-means which has the same semantics as the original method but trains the centers on subsets of your data.\n",
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"⚠️ For large datasets we also offer a mini batch version of $k$-means which has the same semantics as the original method but trains the centers on subsets of your data.\n",
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"This tutorial does not cover this case, but you should keep in mind that $k$-means requires your low dimensional space to fit into your main memory.\n",
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"The main result of a discretization for Markov modeling, however,\n",
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"cell_type": "markdown",
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"metadata": {},
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"In this very simple example, we clearly see a significant correlation between the $y$ component of the input data and the first independent component.\n",
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"In this simple example, we clearly see a significant correlation between the $y$ component of the input data and the first independent component.\n",
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"## Case 2: low-dimensional molecular dynamics data (alanine dipeptide)\n",
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"cell_type": "markdown",
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"metadata": {},
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"This is not very helpful as it only shows that some of our $x, y, z$-coordinates correlate with the TICA components.\n",
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"This is not helpful as it only shows that some of our $x, y, z$-coordinates correlate with the TICA components.\n",
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"Since we rather expect the slow processes to happen in backbone torsion space, this comes to no surprise. \n",
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"\n",
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"To understand what the TICs really mean, let us do a more systematic approach and scan through some angular features.\n",
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"name": "python",
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"nbconvert_exporter": "python",
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"pygments_lexer": "ipython3",
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"version": "3.6.5"
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"version": "3.6.6"
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"base_numbering": 1,

notebooks/03-msm-estimation-and-validation.ipynb

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"name": "python",
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"version": "3.6.5"
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"version": "3.6.6"
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"toc": {
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"base_numbering": 1,

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