We show genetic improvement of programs (GIP) can scale by evolving increased performance in a widely-used and highly complex 50000 line system. GISMOE found code that is 70 times faster (on average) and yet is at least as good functionally. Indeed it even gives a small semantic gain

Harman, M

Langdon, WB

UCL Discovery

1Optimising Existing Software with Genetic ProgrammingSUPPLEMENTARY INFORMATIONWilliam B. Langdon and Mark HarmanDept. Computer Science, University College London, Gower Street,WC1E 6BT, UK2disabled bt2 search.cpp line 1931 IF (metricsStderr)disabled bt2 io.cpp line 612 IF (r != (ssize_t)(offsLen << 2))replaced bt2 io.cpp line 622 for1 uint32_t i = 0 with int i = 0replaced bt2 io.cpp line 622 for2 i < offsLenSampled with i < this->_nPatreplaced bt2 io.cpp line 622 for3 i++ with i += 3inserted initedRef_ = true; before aligner sw.cpp line 145 (static_cast<void> (0));replaced aln sink.cpp line 758 IF (readIsPair()) with (nunpair2 > 0)disabled aln sink.cpp line 919 IF (nunpair1 > 0)replaced sa rescomb.cpp line 50 for2 i < satup_->offs.size() with 0disabled sa rescomb.cpp line 51 IF (satup_->offs[i] == 0xffffffff)deleted sa rescomb.cpp line 52 needResolving++;disabled sa rescomb.cpp line 66 for2 i < refscan_.size()deleted sa rescomb.cpp line 68 nfound++;disabled sa rescomb.cpp line 69 for2 j < satup_->offs.size()disabled sa rescomb.cpp line 69 for3 j++replaced sa rescomb.cpp line 70 IF (satup_->offs[j] == refscan_[i]) with (refscan_.empty())deleted sa rescomb.cpp line 72 found_[i] = false;deleted sa rescomb.cpp line 73 nfound--;disabled sa rescomb.cpp line 112 IF (refscan_[i] == off)replaced aligner swsse ee u8.cpp line 707 vh = _mm_max_epu8(vh, vf); with vmax = vlo;inserted vlo = _mm_xor_si128(vlo, vlo); before aligner swsse ee u8.cpp line 711 pvHStore += 4;replaced aligner swsse ee u8.cpp line 746 ve = _mm_load_si128(pvEStore); with met.dpsucc++;deleted aligner swsse ee u8.cpp line 766 pvFStore += 4;replaced aligner swsse ee u8.cpp line 772 _mm_store_si128(pvHStore, vh); withvh = _mm_max_epu8(vh, vf);deleted aligner swsse ee u8.cpp line 773 pvHStore += 4;deleted aligner swsse ee u8.cpp line 776 vh = _mm_subs_epu8(vh, rdgapo);deleted aligner swsse ee u8.cpp line 777 vh = _mm_subs_epu8(vh, *pvScore);deleted aligner swsse ee u8.cpp line 778 ve = _mm_max_epu8(ve, vh);replaced aligner swsse ee u8.cpp line 779 _mm_store_si128(pvEStore, ve); withd.maxPen_ = d.maxBonus_ = 0;deleted aligner swsse ee u8.cpp line 781 pvScore += 2;replaced aligner swsse ee u8.cpp line 785 pvFStore -= colstride; with met.gathcell++;inserted btnstack_.clear(); before aligner swsse ee u8.cpp line 788 vh = _mm_load_si128(pvHStore);deleted aligner swsse ee u8.cpp line 789 pvEStore -= colstride;replaced aligner swsse ee u8.cpp line 796 vh = _mm_load_si128(pvHStore); with d.bias_ = 0;replaced aligner swsse ee u8.cpp line 801 vf = _mm_subs_epu8(vf, rfgape); with btnstack_.expand();deleted aligner swsse ee u8.cpp line 802 vf = _mm_subs_epu8(vf, *pvScore);inserted rfgape = ((__m128i)__builtin_ia32_pshuflw ((__v8hi)rfgape, 0)); beforealigner swsse ee u8.cpp line 806 cmp = _mm_movemask_epi8(vtmp);deleted aligner swsse ee u8.cpp line 807 nfixup++;disabled aligner swsse ee u8.cpp line 1283 IF (!btnstack_.empty())Fig. 1. Evolved Solution. Best of generation 200 evolved version changes 39 lines in six Bowtie2 source files.3BEST INDIVIDUAL IN GENERATION 135Due to space constraints it is not possible to include adescription of the best individual from generation 135 or itsoperation in the main text of our article. Therefore they aregiven here. See Figure 2.The best member of generation 135 consists of90 substitution, deletion or line insertions. Togetherthese modify seven source files (bt2 search.cpp,bt2 idx.cpp, bt2 io.cpp, aligner sw.cpp, aligner result.cpp,sa rescomb.cpp and aligner swsse ee u8.cpp). Which intotal take 7.25 seconds to re-compile.Taking as an example the least effected ofthese, aligner result.cpp, there are two modifications:<_aligner_result_52>+<_aligner_result_62>which inserts a copy of line 62 before line 52 and<_aligner_result_1152> which deletes line 1152.Line 62 iscPretrimSoft_ = true;whilst line 52 istrimSoft_ = false;Thus line 52 becomes cPretrimSoft_ = true;trimSoft_ = false;Notice since cPretrimSoft is not used between line 52and line 62, setting it to true twice has no effect (exceptto increase the number of lines used). Whilst line 1152 isleft = right + diff - 1;Line 1152 occurs at the end of a for loop where both rightand diff may be updated. (However right is usuallyleft+ 1 and diff is usually 1.) It appears that the usualeffect of line 1152 is to step over the part of the data whichhas been processed by the current iteration of the loop and sonot updating left has a safe effect of sometimes requiringwork already done to be repeated. (This does not prevent looptermination, which is controlled by a separate variable.)On its five training strands of DNA the best of generation135 executes a total of 3 977 157 instrumented source lines.(This is 0.4% of the number of lines executed by theunmodified code). On the first two DNA sequences it findsidentical answers (i.e. 0 and 1 matches respectively). On thethird example Bowtie2 finds two poor matches, mean quality26.02, i.e. on average almost 10 worse than a perfect match,whereas the generation 135 code reports zero matches. Onthe last two test cases it finds 3 matches (versus 30) and10 matches (versus 116). However the average quality ofmatches on the last two test sequences is higher (30.89 v.29.20 and 34.60 v. 33.88).4<IF_aligner_sw_1193> <IF_bt2_search_1954> <_bt2_idx_1334> <_aligner_sw_252><IF_aligner_sw_1201><IF_aligner_sw_1193> <IF_aligner_sw_251><IF_aligner_sw_101><IF_aligner_swsse_ee_u8_1351> <_aligner_swsse_ee_u8_746>+<_aligner_swsse_ee_u8_745><IF_bt2_search_1995> <_aligner_swsse_ee_u8_805><_aligner_swsse_ee_u8_717><_aligner_swsse_ee_u8_342><_aligner_swsse_ee_u8_756><_aligner_swsse_ee_u8_359> <_aligner_swsse_ee_u8_806><_bt2_search_1985><_bt2_search_1662> <_aligner_swsse_ee_u8_739><_aligner_swsse_ee_u8_745> <_aligner_swsse_ee_u8_762><_aligner_swsse_ee_u8_807><_aligner_swsse_ee_u8_773> <_aligner_result_52>+<_aligner_result_62><_aligner_swsse_ee_u8_360><_aligner_swsse_ee_u8_733> <_aligner_swsse_ee_u8_1338><for1_sa_rescomb_69><for1_sa_rescomb_50> <_aligner_swsse_ee_u8_755><IF_bt2_search_1636> <for3_sa_rescomb_66> <_bt2_search_1426> <for2_sa_rescomb_66><for3_aligner_sw_402> <_aligner_swsse_ee_u8_776><_aligner_swsse_ee_u8_343><_aligner_swsse_ee_u8_804> <_aligner_swsse_ee_u8_765><IF_bt2_idx_1399><IF_bt2_idx_1403> <_sa_rescomb_52><_sa_rescomb_64><_aligner_swsse_ee_u8_807><_aligner_swsse_ee_u8_361><for2_sa_rescomb_69><for2_sa_rescomb_50> <_sa_rescomb_67>+<_sa_rescomb_44><_bt2_idx_1343> <IF_aligner_sw_300><IF_aligner_sw_2040><IF_aligner_swsse_ee_u8_1235><IF_aligner_swsse_ee_u8_1101><_aligner_swsse_ee_u8_766> <_aligner_swsse_ee_u8_743><for3_sa_rescomb_69><for3_sa_rescomb_50> <_aligner_swsse_ee_u8_740><_aligner_swsse_ee_u8_394> <_aligner_swsse_ee_u8_779> <_bt2_io_623><_bt2_io_517><_aligner_swsse_ee_u8_726><_aligner_swsse_ee_u8_957> <_aligner_swsse_ee_u8_780><_aligner_swsse_ee_u8_796><for1_bt2_io_622><for1_bt2_io_421> <for2_sa_rescomb_50><for2_sa_rescomb_66><_aligner_swsse_ee_u8_769><_aligner_swsse_ee_u8_680><_bt2_search_1985>+<_bt2_search_1843> <for2_bt2_io_622><for2_bt2_io_448><_sa_rescomb_68>+<_sa_rescomb_73> <_bt2_idx_138> <_aligner_swsse_ee_u8_778><for3_bt2_io_622><for3_bt2_io_321> <_sa_rescomb_73>+<_sa_rescomb_64><_aligner_swsse_ee_u8_797><_aligner_swsse_ee_u8_393><IF_aligner_swsse_ee_u8_784> <_sa_rescomb_72> <IF_aligner_swsse_ee_u8_1283><IF_sa_rescomb_70> <_aligner_swsse_ee_u8_1074><_aligner_swsse_ee_u8_727>+<_aligner_swsse_ee_u8_947><_aligner_swsse_ee_u8_801>+<_aligner_swsse_ee_u8_363><_aligner_swsse_ee_u8_802> <_aligner_swsse_ee_u8_772><_aligner_swsse_ee_u8_803><_aligner_swsse_ee_u8_365><_sa_rescomb_71>+<_sa_rescomb_43> <for2_aligner_sw_233><for2_aligner_sw_1188><_aligner_result_1152> <for3_sa_rescomb_50><for3_sa_rescomb_69><_aligner_swsse_ee_u8_795>+<_aligner_swsse_ee_u8_364><for3_sa_rescomb_111><for3_sa_rescomb_69><_aligner_swsse_ee_u8_695><_aligner_swsse_ee_u8_1074> <IF_sa_rescomb_51><_aligner_swsse_ee_u8_777><_aligner_swsse_ee_u8_755>+<_aligner_swsse_ee_u8_740><_aligner_swsse_ee_u8_781><_aligner_swsse_ee_u8_955><for2_sa_rescomb_111><for2_sa_rescomb_50> <for1_sa_rescomb_50><for1_sa_rescomb_69><for1_sa_rescomb_66><for1_sa_rescomb_69> <IF_sa_rescomb_112> <_bt2_idx_920><for1_sa_rescomb_111><for1_sa_rescomb_69> <_bt2_search_3095><_bt2_search_278><_aligner_swsse_ee_u8_793><_aligner_swsse_ee_u8_958>Fig. 2. Best member in generation 135

Optimising Existing Software with Genetic Programming

http://discovery.ucl.ac.uk/1413298/2/bowtie2_supplementary%281%29.pdf

Optimising Existing Software with Genetic Programming

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