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243 | 243 | "the first four dimensions contain all relevant information of the slow dynamics.\n", |
244 | 244 | "\n", |
245 | 245 | "Based on this result, we try a TICA projection with lag time 0.5 ns (5 steps).\n", |
246 | | - "Please note that this is a modeler's choice based on the best heuristics that is currently available to our knowledge. \n", |
| 246 | + "Please note that this is a modeler's choice based on the best heuristic that is currently available to our knowledge. \n", |
247 | 247 | "It might be necessary to re-adjust the TICA lag time after the MSM estimation. \n", |
248 | 248 | "\n", |
249 | 249 | "\n", |
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350 | 350 | "⚠️ It is a priori unclear what the optimal number of cluster centers $k$ is.\n", |
351 | 351 | "It largely depends on the distribution of our data and on the number of dimensions we use.\n", |
352 | 352 | "\n", |
353 | | - "In the following, we will estimate unvalidated Markov models using different numbers of cluster centers and use the VAMP-2 score (using cross validation) as a heuristics.\n", |
| 353 | + "In the following, we will estimate unvalidated Markov models using different numbers of cluster centers and use the VAMP-2 score (using cross validation) as a heuristic.\n", |
354 | 354 | "This approach requires us to guess the MSM lag time, which we set to the TICA lag time of $5$ steps (or $0.5$ ns).\n", |
355 | 355 | "Since the clustering algorithm is stochastic,\n", |
356 | 356 | "we conduct multiple rounds of discretization at each number of cluster centers." |
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394 | 394 | "We will use this number for further analysis.\n", |
395 | 395 | "\n", |
396 | 396 | "As already stated above, the score has been generated using MSMs that were not validated,\n", |
397 | | - "meaning that the above plot is really just a heuristics.\n", |
| 397 | + "meaning that the above plot is really just a heuristic.\n", |
398 | 398 | "Besides having an optimal score, we want to obtain a model that describes physically interesting states.\n", |
399 | 399 | "Thus, the number of states $k$ is often re-adjusted after model inspection." |
400 | 400 | ] |
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531 | 531 | "The highest $k$ can be adjusted using the `mlags` keyword argument of `msm.cktest()`.\n", |
532 | 532 | "\n", |
533 | 533 | "Since we can only inspect the result for a small number of (macro-) states,\n", |
534 | | - "we use the implied timescales plot as a heuristics to estimate a number of metastable states to test for. \n", |
| 534 | + "we use the implied timescales plot as a heuristic to estimate a number of metastable states to test for. \n", |
535 | 535 | "We can resolve $4$ slow processes up to lag times of $2.5$ ns.\n", |
536 | 536 | "Since the Chapman-Kolmogorov test involves estimations at higher lag times,\n", |
537 | 537 | "we will attempt to capture those processes choosing $5$ metastable states." |
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