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As the experiments clearly show, a crucial issue is the possibly high memory consumption during stage 1, which may cause SISMA to fail.
In terms of running time, clasp (with and without clustering) outperforms CHAINER in any tested setting at the expense of a three-fold increased memory consumption during execution.
Memory monitoring began before each algorithm was executed to establish a baseline, and the maximum memory consumption during algorithm execution was measured relative to this baseline.
Owing to its high memory consumption during prefix-sorted automaton construction, an external memory implementation is needed to index a collection of human genomes, which is not yet available.
The memory consumption during index creation is limited as follows: at each step of the index generation we have one raw reference block of size at most BS bytes in main memory plus (roughly) 4∗BS bytes for its compressed suffix tree.
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The memory consumption of Simrank during indexing is moderate and grows linearly with the number of sequences and depends on the k-mer size defined by the user.
This approach is efficient for high dimensional datasets, as memory consumption remains stable during minimization, in contrast to other implementations based on quadratically constrained quadratic programming (Bach et al., 2004) or semi-infinite linear programming (Lanckriet et al., 2004).
Memory usage measures the maximum memory consumption of an application during its runtime.
The genome coverage increased from 81.16% to 93.91%, and memory consumption was ~2/3 lower during the point of largest memory consumption.
Consequently, the overall execution time of the WW algorithm is substantially less than the MS algorithm, and the memory consumption is also significantly reduced during the phase of the computation that is most memory-intensive and most susceptible to combinatorial explosion.
The time and memory consumption of the MS, SLP, and WW algorithms during extreme pathway identification were quite different.
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com