Noncritical bug in deciding how often to repeat nontopology optimization

[lutteropp]

TODO: Compare current implementation with this pseudocode:

\section{Pseudcodes for Nontopology Optimization}

\begin{algorithm} \DontPrintSemicolon \KwIn{The current network $annNetwork$ with parameter vector $\vartheta$; the optimization type $type$.} \KwOut{The current network, with optimized non-topology parameters in $\vartheta$.} score_epsilon $\gets 0.01$; max_rounds_slow $\gets 2$; act_rounds_slow $\gets 0$; got_better_slow $\gets$ True; \While{got_better_slow \textbf{and} act_rounds_slow $<$ max_rounds_slow}{ score_slow_before $\gets$ scoreNetwork(annNetwork); got_better_slow $\gets$ False; do_brlen_opt $\gets$ True; do_model_opt $\gets$ True; do_reticulation_opt $\gets$ True; got_better $\gets$ True; \While{got_better}{ got_better $\gets$ False; score_before $\gets$ scoreNetwork(annNetwork); \If{do_model_opt}{ score_before_modelopt $\gets$ scoreNetwork(annNetwork); optimizeModel(annNetwork); score_after_modelopt $\gets$ scoreNetwork(annNetwork); \If{score_before_modelopt - score_after_modelopt $<$ score_epsilon} { do_model_opt $\gets$ False; } } \If{do_brlen_opt}{ score_before_brlenopt $\gets$ scoreNetwork(annNetwork); optimizeBranches(annNetwork); score_after_brlenopt $\gets$ scoreNetwork(annNetwork); \If{score_before_brlenopt - score_after_brlenopt $<$ score_epsilon} { do_brlen_opt $\gets$ False; } } \If{do_reticulation_opt}{ score_before_reticulation_opt $\gets$ scoreNetwork(annNetwork); optimizeReticulations(annNetwork); score_after_reticulation_opt $\gets$ scoreNetwork(annNetwork); \If{score_before_reticulation_opt - score_after_reticulation_opt $>$ score_epsilon} { do_reticulation_opt $\gets$ False; } } score_after $\gets$ scoreNetwork(annNetwork); \If{score_before - score_after $>$ score_epsilon} { \If{type $\neq$ QUICK} { got_better $\gets$ True; } } } score_slow_after $\gets$ scoreNetwork(annNetwork); \If{score_before - score_after $>$ score_epsilon \textbf{and} type = SLOW}{ got_better_slow $\gets$ True; } act_rounds_slow += 1; } \Return{annNetwork}; \caption{optimizeNonTopology: Optimize all non-topology parameters.} \label{alg:nontopology_opt} \end{algorithm}