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We exploit the semi-periodic nature of the videos to build an accurate background model for each model.
We want to build a background model for each frame such that the only 'foreground' would be the real fish.
We exploit this specific feature of these videos to build a background model for each frame using the similar frames that exist in the whole video.
To convert a PWM P, into a numerical feature, we first compute r, the maximum log likelihood ratio score between P and the background model for each possible position in the query sequence.
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Markov-chain background models for each species, based on both strands of the upstream non-coding regions of the genome, e.g. 2nt_upstream-noorf_Homo_sapiens_EnsEMBL-ovlp-2str for human.
In order to identify the HCGs within each network, we used a background model for the evaluation of the negative and positive coordination in each network, assuming no coordination, and considered genes to be HCGs if their observed coordination was higher by more then six standard deviations from the coordination that was estimated by our background model (for detail see Methods section).
A pseudo count of 0 was used for each contextual PWM and the background model for the LLR score was a 0-th order Markov chain learned from the host intergenic sequences.
These bimodal distributions, with two peaks not significantly different from each other in their sizes, serve as a good background model for our analysis.
It also shows how to set a background model for fitting with the cstat statistic.
These commands are equivalent ways of deleting the background model for the default background associated with the default source dataset.
When called with no arguments, get_bkg_source_plot returns the the data and preferences defining a plot of the unconvolved background model for the default background.
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Since I tried Ludwig back in 2017, I have been constantly using it in both editing and translation. Ever since, I suggest it to my translators at ProSciEditing.

Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com