Support larger graphs (N>40)

[gkirgizov]

Example of the problem is Tree Search. Or BAMT graphs (see discussion).

The problem is that Tree search is caught in local minima for graphs with N>20. Small graphs are found without problem in 50-100 iterations, while larger graphs (with N>=30 already almost for sure) can't be found. Optimization is stuck after 100-200 iterations with almost no hope. This situation must be investigated.

I have a hypothesis that current mutation set adds cycles and can't remove them. Also it would be nice to add specific set of constraints for GraphVerifier suited for trees.

Encountered while doing #60

Plan:

1. [ ] Profile GOLEM

Possibly issue #142 could provide additional information about where GOLEM is slower compared to other evolutionary frameworks.

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Updates:

• @ShikovEgor proposed to substitute NetworkX (hich is Pure Python) with something more performant).
• @SuperSashka brought our attention to the fact, that the objective of finding Same Graph can be ill-defined, and that's why evolutionary algorithm in principle can't resolve it. Yet we should conduct comparison with other papers with similar synthetic tasks for graph search.
• An investigation into architectural barriers of GOLEM must be considered.

[gkirgizov]

75 Didn't really helped, still the cycles that were added by add_edge mutation are preserved

[gkirgizov]

Maybe adding mutations specifically related to breaking cycles would help

[KarinaKarina6]

Такая проблема на байесовских сетях. На средних и больших БС не получается достичь хороших результатов. Ссылка на пример запуска: examples/bn/bn_score_shd.py