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Given a tree U on a genome set G, a leaf removal consists of removing a given leaf from U, along with its parental node x, and if x is not the root joining the parent of x and the remaining child by a new edge.
If the GO term assigned to the transcript had depth greater than five, the corresponding parental node with depth five was reassigned and redundancy was removed.
This is in contrast to various network constructions where the various proteolytic fragments are collapsed into an APP parental node, possibly reflecting the UNIPROTKB identifier (P05067) being the same for each peptide.
Similarly, we calculate "messages" passed downstream to child j of node i: (14) m ↓ i j (x i j ) = ∫ d x i g (x i j, t i j | x i, t i ) m ↓ i (x i ) ∏ k ≠ j m ↑ i k (x i ) The integrand is the product of the downstream message from the parental node and the upstream messages from all children of node i other than child j.
In all our experiments we assign weights in the following way: all drug-susceptible strains are assigned weight - α v (defined as above); each drug-resistant strain i is assigned a weight 1 n, where n is the number of drug-resistant strains in the subtree (containing strain i) determined by its highest parental node, such that the subtree does not contain any drug-susceptible strain in its leaves.
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The state of each node was assumed to be conditionally dependent on the states of that node's parents, and conditionally independent (given the states of parental nodes) from the remainder of the graph nodes.
It is argued by Fenton et al. (2013b) that because opportunity, motive and intent are causes or pre-conditions for the offender to commit the crime, they should be parental nodes in a BN model.
If one GO term node was counted, all its parental nodes were excluded.
We can also combine these by applying different strategies at different parental nodes.
The associated graphs allow for multiple parental nodes thereby modeling the synergistic effects of multiple events in promoting subsequent mutations.
Next, proteins were directly annotated to their respective GO nodes and then annotated to their connected parental nodes until the root biological process was reached.
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com