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The first starting point is given by the initial parameter vector.
Maximize T in (A.1) with respect to θ that is on the one-dimensional straight line determined by the initial parameter vector θ0 and the gradient vector u (Linear Search; e.g., Kowalik and Osborne, 1968).
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The Markov chain was initialized by randomly selecting the initial parameter value and each Markov chain was sampled every 100 cycles for 1,000,000 generations with a burn in of 100,000 cycles.
An HMM's performance usually is affected by the initial parameters and its structure.
Furthermore, the reference parameter set θ j 0 (equation 6) is exchanged in this case by θ j 1 (the initial parameter set representing phenotype B) in order to regularize the backward trajectory.
The analysis-by-synthesis procedure is performed in three steps that are designed to optimize the initial parameter set iteratively by applying a hill-climb search to reduce the overall mean square error in the log frequency domain.
After generating the initial parameter values by uniform distributions, we first identify the most likely path ("best path") by Viterbi algorithm [29].
K p were restricted to be positive by setting the lower boundaries of the initial parameter estimates.
When the fitting was poor, fits were redone by adjusting the initial parameters.
Our tests show that the initial parameters produced by the weighted vote method cause almost 50% of child nodes to fail the conditional independence test, but as the EM algorithm learns more likely parameter settings, fewer and fewer nodes fail the test.
The number of parameters set npt is fixed as the maximum of the domain of variation of the initial parameters divided by their uncertainty u in the process of fabrication [ 38 ]: npt = max { [ max (r 1 0 ) − min (r 1 0 ) ] / u (r 1 ) ; [max(e ) − min(e )] /u (e ); [ max (n 1 0 ) − min (n 1 0 ) ] / u (n 1 ) ; [max − min] /u }.
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com