In [13]:
import pylearn2.utils
import pylearn2.config
import theano
import neukrill_net.dense_dataset
import neukrill_net.utils
import numpy as np
%matplotlib inline
import matplotlib.pyplot as plt
import holoviews as hl
%load_ext holoviews.ipython
import sklearn.metrics
The holoviews.ipython extension is already loaded. To reload it, use:
%reload_ext holoviews.ipython
In [5]:
cd ..
/afs/inf.ed.ac.uk/user/s13/s1320903/Neuroglycerin/neukrill-net-work
In [7]:
%env
Out[7]:
{'ASPELL_CONF': 'master british',
'BASH': '/bin/bash',
'BASH_FUNC__command_not_found()': '() { echo "bash: $1: command not found" 1>&2\n}',
'BASH_FUNC_colloq()': '() { more /usr/local/alert/misc/coll\n}',
'BASH_FUNC_command_not_found_handle()': '() { unset command_not_found_handle;\n if [[ "$IFS" != \' \t\n\' ]]; then\n _command_not_found $*;\n fi;\n function dbg () \n { \n [[ -n $CRICHTON_DEBUG ]] && echo $1 1>&2\n };\n SORT="/usr/bin/_SortBashRC";\n PATTERN=\'[0-9][0-9][0-9].*\';\n if [[ -n $CRICHTON_DEBUG ]]; then\n modules=$($SORT $CRICHTON_SYS/$PATTERN $CRICHTON_USR/$PATTERN);\n else\n modules=$($SORT $CRICHTON_SYS/$PATTERN $CRICHTON_USR/$PATTERN 2>&-);\n fi;\n dbg "- Found $(/bin/echo $modules | /usr/bin/wc -w 2>&-) modules.";\n for mod in ${modules} _command_not_found;\n do\n dbg "-- $(/bin/basename $mod 2>&-)";\n CRICHTON_SYS=$CRICHTON_SYS CRICHTON_USR=$CRICHTON_USR "$mod" $*;\n exit=$?;\n dbg "[exit $exit]";\n [[ $exit == 255 ]] && { \n _command_not_found $1;\n break\n };\n [[ $exit == 0 ]] && break;\n done;\n return 127\n}',
'BASH_FUNC_gnu()': '() { command gnu -u $LOGNAME $*\n}',
'BASH_FUNC_module()': '() { eval `/usr/bin/modulecmd bash $*`\n}',
'BASH_FUNC_purge()': '() { rm -f *~ .*~ \\#*\\# tmp*\n}',
'BASH_FUNC_resize()': '() { eval `command resize`\n}',
'BASH_FUNC_rvirsh()': '() { KVMHOST=$1;\n shift;\n if [ "$KVMHOST" ]; then\n if [ "$KVMHOST" = "." ]; then\n URI="qemu:///system";\n else\n URI="qemu+ssh://$KVMHOST/system";\n fi;\n else\n URI="qemu:///system";\n fi;\n virsh --connect $URI $@\n}',
'BASH_FUNC_setpath()': '() { if [ -f /usr/bin/pathfix ]; then\n pathfix_binary=/usr/bin/pathfix;\n else\n pathfix_binary=/usr/local/bin/pathfix;\n fi;\n new_PATH=`$pathfix_binary $@`;\n [ "$new_PATH" ] && PATH="$new_PATH";\n export PATH\n}',
'BASH_FUNC_setup()': '() { source /usr/local/share/setup/setup.sh $*\n}',
'CLICOLOR': '1',
'CRICHTON_SYS': '/etc/crichton.d',
'CRICHTON_USR': '/afs/inf.ed.ac.uk/user/s13/s1320903/.crichton.d',
'CUDA_ROOT': '/opt/cuda-5.0.35',
'CVS_RSH': 'ssh',
'EDITOR': '/usr/bin/emacs',
'ENVIRONMENT': 'fc5 ',
'ENV_ROOT': '/usr/share/defenv/bash',
'GIT_PAGER': 'cat',
'GNUSTEP_MAKEFILES': '/usr/lib64/GNUstep/Makefiles',
'G_BROKEN_FILENAMES': '1',
'HOME': '/afs/inf.ed.ac.uk/user/s13/s1320903',
'IDEA_JDK': '/usr/lib/jvm/java-sun',
'JPY_PARENT_PID': '74537',
'KDEDIRS': '/usr',
'KDE_IS_PRELINKED': '1',
'KRB5CCNAME': '/tmp/krb5cc_1024708_Fr20rB',
'LANG': 'en_GB.UTF-8',
'LD_LIBRARY_PATH': '/opt/cuda-5.0.35/lib:/opt/cuda-5.0.35/lib64',
'LESSOPEN': '|/usr/bin/lesspipe.sh %s',
'LOADEDMODULES': '',
'LOGNAME': 's1320903',
'LS_COLORS': 'rs=0:di=01;34:ln=01;36:mh=00:pi=40;33:so=01;35:do=01;35:bd=40;33;01:cd=40;33;01:or=40;31;01:mi=01;05;37;41:su=37;41:sg=30;43:ca=30;41:tw=30;42:ow=34;42:st=37;44:ex=01;32:*.tar=01;31:*.tgz=01;31:*.arj=01;31:*.taz=01;31:*.lzh=01;31:*.lzma=01;31:*.tlz=01;31:*.txz=01;31:*.zip=01;31:*.z=01;31:*.Z=01;31:*.dz=01;31:*.gz=01;31:*.lz=01;31:*.xz=01;31:*.bz2=01;31:*.tbz=01;31:*.tbz2=01;31:*.bz=01;31:*.tz=01;31:*.deb=01;31:*.rpm=01;31:*.jar=01;31:*.rar=01;31:*.ace=01;31:*.zoo=01;31:*.cpio=01;31:*.7z=01;31:*.rz=01;31:*.jpg=01;35:*.jpeg=01;35:*.gif=01;35:*.bmp=01;35:*.pbm=01;35:*.pgm=01;35:*.ppm=01;35:*.tga=01;35:*.xbm=01;35:*.xpm=01;35:*.tif=01;35:*.tiff=01;35:*.png=01;35:*.svg=01;35:*.svgz=01;35:*.mng=01;35:*.pcx=01;35:*.mov=01;35:*.mpg=01;35:*.mpeg=01;35:*.m2v=01;35:*.mkv=01;35:*.ogm=01;35:*.mp4=01;35:*.m4v=01;35:*.mp4v=01;35:*.vob=01;35:*.qt=01;35:*.nuv=01;35:*.wmv=01;35:*.asf=01;35:*.rm=01;35:*.rmvb=01;35:*.flc=01;35:*.avi=01;35:*.fli=01;35:*.flv=01;35:*.gl=01;35:*.dl=01;35:*.xcf=01;35:*.xwd=01;35:*.yuv=01;35:*.cgm=01;35:*.emf=01;35:*.axv=01;35:*.anx=01;35:*.ogv=01;35:*.ogx=01;35:*.aac=01;36:*.au=01;36:*.flac=01;36:*.mid=01;36:*.midi=01;36:*.mka=01;36:*.mp3=01;36:*.mpc=01;36:*.ogg=01;36:*.ra=01;36:*.wav=01;36:*.axa=01;36:*.oga=01;36:*.spx=01;36:*.xspf=01;36:',
'MAIL': '/var/mail/s1320903',
'MAPPATH': '/etc/amd:/etc',
'MODULEPATH': '/usr/share/Modules/modulefiles:/etc/modulefiles',
'MODULESHOME': '/usr/share/Modules',
'PAGER': 'cat',
'PATH': '/afs/inf.ed.ac.uk/user/s13/s1320903/Neuroglycerin/venv/bin:/afs/inf.ed.ac.uk/user/s13/s1320903/Neuroglycerin/venv/bin:/usr/lib64/qt-3.3/bin:/usr/lpp/mmfs/bin:/usr/local/bin/:/usr/local/sbin:/usr/bin:/bin:/opt/sicstus-4.0.1/bin',
'PWD': '/afs/inf.ed.ac.uk/user/s13/s1320903/Neuroglycerin/neukrill-net-work/notebooks',
'PYCHARM_JDK': '/usr/lib/jvm/java-sun',
'QTDIR': '/usr/lib64/qt-3.3',
'QTINC': '/usr/lib64/qt-3.3/include',
'QTLIB': '/usr/lib64/qt-3.3/lib',
'ROLES': ' ',
'SHELL': '/bin/bash',
'SHLVL': '3',
'SHORT_HOSTNAME': 'stonesoup',
'SSH_ASKPASS': '/usr/libexec/openssh/gnome-ssh-askpass',
'SSH_CLIENT': '129.215.91.176 37570 22',
'SSH_CONNECTION': '129.215.91.176 37570 129.215.33.107 22',
'SSH_TTY': '/dev/pts/21',
'STY': '73222.pts-21.stonesoup',
'SshAgent': '/usr/bin/ssh-agent',
'TERM': 'xterm-color',
'TERMCAP': 'SC|screen|VT 100/ANSI X3.64 virtual terminal:\\\n\t:DO=\\E[%dB:LE=\\E[%dD:RI=\\E[%dC:UP=\\E[%dA:bs:bt=\\E[Z:\\\n\t:cd=\\E[J:ce=\\E[K:cl=\\E[H\\E[J:cm=\\E[%i%d;%dH:ct=\\E[3g:\\\n\t:do=^J:nd=\\E[C:pt:rc=\\E8:rs=\\Ec:sc=\\E7:st=\\EH:up=\\EM:\\\n\t:le=^H:bl=^G:cr=^M:it#8:ho=\\E[H:nw=\\EE:ta=^I:is=\\E)0:\\\n\t:li#24:co#80:am:xn:xv:LP:sr=\\EM:al=\\E[L:AL=\\E[%dL:\\\n\t:cs=\\E[%i%d;%dr:dl=\\E[M:DL=\\E[%dM:dc=\\E[P:DC=\\E[%dP:\\\n\t:im=\\E[4h:ei=\\E[4l:mi:IC=\\E[%d@:ks=\\E[?1h\\E=:\\\n\t:ke=\\E[?1l\\E>:vi=\\E[?25l:ve=\\E[34h\\E[?25h:vs=\\E[34l:\\\n\t:ti=\\E[?1049h:te=\\E[?1049l:us=\\E[4m:ue=\\E[24m:so=\\E[3m:\\\n\t:se=\\E[23m:mb=\\E[5m:md=\\E[1m:mr=\\E[7m:me=\\E[m:ms:\\\n\t:Co#8:pa#64:AF=\\E[3%dm:AB=\\E[4%dm:op=\\E[39;49m:AX:\\\n\t:vb=\\Eg:G0:as=\\E(0:ae=\\E(B:\\\n\t:ac=\\140\\140aaffggjjkkllmmnnooppqqrrssttuuvvwwxxyyzz{{||}}~~..--++,,hhII00:\\\n\t:po=\\E[5i:pf=\\E[4i:k0=\\E[10~:k1=\\EOP:k2=\\EOQ:k3=\\EOR:\\\n\t:k4=\\EOS:k5=\\E[15~:k6=\\E[17~:k7=\\E[18~:k8=\\E[19~:\\\n\t:k9=\\E[20~:k;=\\E[21~:F1=\\E[23~:F2=\\E[24~:F3=\\E[1;2P:\\\n\t:F4=\\E[1;2Q:F5=\\E[1;2R:F6=\\E[1;2S:F7=\\E[15;2~:\\\n\t:F8=\\E[17;2~:F9=\\E[18;2~:FA=\\E[19;2~:kb=\x7f:K2=\\EOE:\\\n\t:kB=\\E[Z:kF=\\E[1;2B:kR=\\E[1;2A:*4=\\E[3;2~:*7=\\E[1;2F:\\\n\t:#2=\\E[1;2H:#3=\\E[2;2~:#4=\\E[1;2D:%c=\\E[6;2~:%e=\\E[5;2~:\\\n\t:%i=\\E[1;2C:kh=\\E[1~:@1=\\E[1~:kH=\\E[4~:@7=\\E[4~:\\\n\t:kN=\\E[6~:kP=\\E[5~:kI=\\E[2~:kD=\\E[3~:ku=\\EOA:kd=\\EOB:\\\n\t:kr=\\EOC:kl=\\EOD:km:',
'THEANO_FLAGS': 'device=gpu2,floatX=float32,base_compiledir=~/.theano/stonesoup2',
'USER': 's1320903',
'VIRTUAL_ENV': '/afs/inf.ed.ac.uk/user/s13/s1320903/Neuroglycerin/venv',
'WINDOW': '0',
'XPRINTER': 'xp_ps_spooldir_tmp_Xprintjobs',
'_': '/usr/bin/krenew'}
Alexnet-based with extra convlayer: (one of the best)
In [3]:
%run check_test_score.py -v run_settings/alexnet_based_extra_convlayer.json
Loading settings..
Loading model...
Loading data...
Applying normalisation: global
(24712,)
Finding batch size...
chosen batch size 3089 for 8 batches
Compiling forward prop...
Making predictions...
Batch 1 of 8
Batch 2 of 8
Batch 3 of 8
Batch 4 of 8
Batch 5 of 8
Batch 6 of 8
Batch 7 of 8
Batch 8 of 8
Collapsing predictions...
Log loss: 0.808119972321
/afs/inf.ed.ac.uk/user/s13/s1320903/Neuroglycerin/pylearn2/pylearn2/utils/iteration.py:783: UserWarning: dataset is using the old iterator interface which is deprecated and will become officially unsupported as of July 28, 2015. The dataset should implement a `get` method respecting the new interface.
warnings.warn("dataset is using the old iterator interface which "
Some 8aug models: (p5 is better but not very good)
In [6]:
%run check_test_score.py -v run_settings/8aug_extra_layers0p5.json
Loading settings..
Loading model...
Loading data...
/afs/inf.ed.ac.uk/user/s13/s1320903/Neuroglycerin/neukrill-net-tools/neukrill_net/utils.py:484: UserWarning: Could not write full YAML specification to scratch. Not required for reproducibility, but can be used with Pylearn2 on its own, so may be useful.
warnings.warn("Could not write full YAML specification to scratch."
class: 0 of 120: acantharia_protist
class: 1 of 120: acantharia_protist_big_center
class: 2 of 120: acantharia_protist_halo
class: 3 of 120: amphipods
class: 4 of 120: appendicularian_fritillaridae
class: 5 of 120: appendicularian_slight_curve
class: 6 of 120: appendicularian_s_shape
class: 7 of 120: appendicularian_straight
class: 8 of 120: artifacts
class: 9 of 120: artifacts_edge
class: 10 of 120: chaetognath_non_sagitta
class: 11 of 120: chaetognath_other
class: 12 of 120: chaetognath_sagitta
class: 13 of 120: chordate_type1
class: 14 of 120: copepod_calanoid
class: 15 of 120: copepod_calanoid_eggs
class: 16 of 120: copepod_calanoid_eucalanus
class: 17 of 120: copepod_calanoid_flatheads
class: 18 of 120: copepod_calanoid_frillyAntennae
class: 19 of 120: copepod_calanoid_large
class: 20 of 120: copepod_calanoid_large_side_antennatucked
class: 21 of 120: copepod_calanoid_octomoms
class: 22 of 120: copepod_calanoid_small_longantennae
class: 23 of 120: copepod_cyclopoid_copilia
class: 24 of 120: copepod_cyclopoid_oithona
class: 25 of 120: copepod_cyclopoid_oithona_eggs
class: 26 of 120: copepod_other
class: 27 of 120: crustacean_other
class: 28 of 120: ctenophore_cestid
class: 29 of 120: ctenophore_cydippid_no_tentacles
class: 30 of 120: ctenophore_cydippid_tentacles
class: 31 of 120: ctenophore_lobate
class: 32 of 120: decapods
class: 33 of 120: detritus_blob
class: 34 of 120: detritus_filamentous
class: 35 of 120: detritus_other
class: 36 of 120: diatom_chain_string
class: 37 of 120: diatom_chain_tube
class: 38 of 120: echinoderm_larva_pluteus_brittlestar
class: 39 of 120: echinoderm_larva_pluteus_early
class: 40 of 120: echinoderm_larva_pluteus_typeC
class: 41 of 120: echinoderm_larva_pluteus_urchin
class: 42 of 120: echinoderm_larva_seastar_bipinnaria
class: 43 of 120: echinoderm_larva_seastar_brachiolaria
class: 44 of 120: echinoderm_seacucumber_auricularia_larva
class: 45 of 120: echinopluteus
class: 46 of 120: ephyra
class: 47 of 120: euphausiids
class: 48 of 120: euphausiids_young
class: 49 of 120: fecal_pellet
class: 50 of 120: fish_larvae_deep_body
class: 51 of 120: fish_larvae_leptocephali
class: 52 of 120: fish_larvae_medium_body
class: 53 of 120: fish_larvae_myctophids
class: 54 of 120: fish_larvae_thin_body
class: 55 of 120: fish_larvae_very_thin_body
class: 56 of 120: heteropod
class: 57 of 120: hydromedusae_aglaura
class: 58 of 120: hydromedusae_bell_and_tentacles
class: 59 of 120: hydromedusae_h15
class: 60 of 120: hydromedusae_haliscera
class: 61 of 120: hydromedusae_haliscera_small_sideview
class: 62 of 120: hydromedusae_liriope
class: 63 of 120: hydromedusae_narco_dark
class: 64 of 120: hydromedusae_narcomedusae
class: 65 of 120: hydromedusae_narco_young
class: 66 of 120: hydromedusae_other
class: 67 of 120: hydromedusae_partial_dark
class: 68 of 120: hydromedusae_shapeA
class: 69 of 120: hydromedusae_shapeA_sideview_small
class: 70 of 120: hydromedusae_shapeB
class: 71 of 120: hydromedusae_sideview_big
class: 72 of 120: hydromedusae_solmaris
class: 73 of 120: hydromedusae_solmundella
class: 74 of 120: hydromedusae_typeD
class: 75 of 120: hydromedusae_typeD_bell_and_tentacles
class: 76 of 120: hydromedusae_typeE
class: 77 of 120: hydromedusae_typeF
class: 78 of 120: invertebrate_larvae_other_A
class: 79 of 120: invertebrate_larvae_other_B
class: 80 of 120: jellies_tentacles
class: 81 of 120: polychaete
class: 82 of 120: protist_dark_center
class: 83 of 120: protist_fuzzy_olive
class: 84 of 120: protist_noctiluca
class: 85 of 120: protist_other
class: 86 of 120: protist_star
class: 87 of 120: pteropod_butterfly
class: 88 of 120: pteropod_theco_dev_seq
class: 89 of 120: pteropod_triangle
class: 90 of 120: radiolarian_chain
class: 91 of 120: radiolarian_colony
class: 92 of 120: shrimp_caridean
class: 93 of 120: shrimp-like_other
class: 94 of 120: shrimp_sergestidae
class: 95 of 120: shrimp_zoea
class: 96 of 120: siphonophore_calycophoran_abylidae
class: 97 of 120: siphonophore_calycophoran_rocketship_adult
class: 98 of 120: siphonophore_calycophoran_rocketship_young
class: 99 of 120: siphonophore_calycophoran_sphaeronectes
class: 100 of 120: siphonophore_calycophoran_sphaeronectes_stem
class: 101 of 120: siphonophore_calycophoran_sphaeronectes_young
class: 102 of 120: siphonophore_other_parts
class: 103 of 120: siphonophore_partial
class: 104 of 120: siphonophore_physonect
class: 105 of 120: siphonophore_physonect_young
class: 106 of 120: stomatopod
class: 107 of 120: tornaria_acorn_worm_larvae
class: 108 of 120: trichodesmium_bowtie
class: 109 of 120: trichodesmium_multiple
class: 110 of 120: trichodesmium_puff
class: 111 of 120: trichodesmium_tuft
class: 112 of 120: trochophore_larvae
class: 113 of 120: tunicate_doliolid
class: 114 of 120: tunicate_doliolid_nurse
class: 115 of 120: tunicate_partial
class: 116 of 120: tunicate_salp
class: 117 of 120: tunicate_salp_chains
class: 118 of 120: unknown_blobs_and_smudges
class: 119 of 120: unknown_sticks
class: 120 of 120: unknown_unclassified
Finding batch size...
chosen batch size 3089 for 1 batches
Compiling forward prop...
Making predictions...
Batch 1 of 1
Log loss: 0.93184134636
In [7]:
%run check_test_score.py -v run_settings/8aug_extra_layers0p8.json
Loading settings..
Loading model...
Loading data...
class: 0 of 120: acantharia_protist
class: 1 of 120: acantharia_protist_big_center
class: 2 of 120: acantharia_protist_halo
class: 3 of 120: amphipods
class: 4 of 120: appendicularian_fritillaridae
class: 5 of 120: appendicularian_slight_curve
class: 6 of 120: appendicularian_s_shape
class: 7 of 120: appendicularian_straight
class: 8 of 120: artifacts
class: 9 of 120: artifacts_edge
class: 10 of 120: chaetognath_non_sagitta
class: 11 of 120: chaetognath_other
class: 12 of 120: chaetognath_sagitta
class: 13 of 120: chordate_type1
class: 14 of 120: copepod_calanoid
class: 15 of 120: copepod_calanoid_eggs
class: 16 of 120: copepod_calanoid_eucalanus
class: 17 of 120: copepod_calanoid_flatheads
class: 18 of 120: copepod_calanoid_frillyAntennae
class: 19 of 120: copepod_calanoid_large
class: 20 of 120: copepod_calanoid_large_side_antennatucked
class: 21 of 120: copepod_calanoid_octomoms
class: 22 of 120: copepod_calanoid_small_longantennae
class: 23 of 120: copepod_cyclopoid_copilia
class: 24 of 120: copepod_cyclopoid_oithona
class: 25 of 120: copepod_cyclopoid_oithona_eggs
class: 26 of 120: copepod_other
class: 27 of 120: crustacean_other
class: 28 of 120: ctenophore_cestid
class: 29 of 120: ctenophore_cydippid_no_tentacles
class: 30 of 120: ctenophore_cydippid_tentacles
class: 31 of 120: ctenophore_lobate
class: 32 of 120: decapods
class: 33 of 120: detritus_blob
class: 34 of 120: detritus_filamentous
class: 35 of 120: detritus_other
class: 36 of 120: diatom_chain_string
class: 37 of 120: diatom_chain_tube
class: 38 of 120: echinoderm_larva_pluteus_brittlestar
class: 39 of 120: echinoderm_larva_pluteus_early
class: 40 of 120: echinoderm_larva_pluteus_typeC
class: 41 of 120: echinoderm_larva_pluteus_urchin
class: 42 of 120: echinoderm_larva_seastar_bipinnaria
class: 43 of 120: echinoderm_larva_seastar_brachiolaria
class: 44 of 120: echinoderm_seacucumber_auricularia_larva
class: 45 of 120: echinopluteus
class: 46 of 120: ephyra
class: 47 of 120: euphausiids
class: 48 of 120: euphausiids_young
class: 49 of 120: fecal_pellet
class: 50 of 120: fish_larvae_deep_body
class: 51 of 120: fish_larvae_leptocephali
class: 52 of 120: fish_larvae_medium_body
class: 53 of 120: fish_larvae_myctophids
class: 54 of 120: fish_larvae_thin_body
class: 55 of 120: fish_larvae_very_thin_body
class: 56 of 120: heteropod
class: 57 of 120: hydromedusae_aglaura
class: 58 of 120: hydromedusae_bell_and_tentacles
class: 59 of 120: hydromedusae_h15
class: 60 of 120: hydromedusae_haliscera
class: 61 of 120: hydromedusae_haliscera_small_sideview
class: 62 of 120: hydromedusae_liriope
class: 63 of 120: hydromedusae_narco_dark
class: 64 of 120: hydromedusae_narcomedusae
class: 65 of 120: hydromedusae_narco_young
class: 66 of 120: hydromedusae_other
class: 67 of 120: hydromedusae_partial_dark
class: 68 of 120: hydromedusae_shapeA
class: 69 of 120: hydromedusae_shapeA_sideview_small
class: 70 of 120: hydromedusae_shapeB
class: 71 of 120: hydromedusae_sideview_big
class: 72 of 120: hydromedusae_solmaris
class: 73 of 120: hydromedusae_solmundella
class: 74 of 120: hydromedusae_typeD
class: 75 of 120: hydromedusae_typeD_bell_and_tentacles
class: 76 of 120: hydromedusae_typeE
class: 77 of 120: hydromedusae_typeF
class: 78 of 120: invertebrate_larvae_other_A
class: 79 of 120: invertebrate_larvae_other_B
class: 80 of 120: jellies_tentacles
class: 81 of 120: polychaete
class: 82 of 120: protist_dark_center
class: 83 of 120: protist_fuzzy_olive
class: 84 of 120: protist_noctiluca
class: 85 of 120: protist_other
class: 86 of 120: protist_star
class: 87 of 120: pteropod_butterfly
class: 88 of 120: pteropod_theco_dev_seq
class: 89 of 120: pteropod_triangle
class: 90 of 120: radiolarian_chain
class: 91 of 120: radiolarian_colony
class: 92 of 120: shrimp_caridean
class: 93 of 120: shrimp-like_other
class: 94 of 120: shrimp_sergestidae
class: 95 of 120: shrimp_zoea
class: 96 of 120: siphonophore_calycophoran_abylidae
class: 97 of 120: siphonophore_calycophoran_rocketship_adult
class: 98 of 120: siphonophore_calycophoran_rocketship_young
class: 99 of 120: siphonophore_calycophoran_sphaeronectes
class: 100 of 120: siphonophore_calycophoran_sphaeronectes_stem
class: 101 of 120: siphonophore_calycophoran_sphaeronectes_young
class: 102 of 120: siphonophore_other_parts
class: 103 of 120: siphonophore_partial
class: 104 of 120: siphonophore_physonect
class: 105 of 120: siphonophore_physonect_young
class: 106 of 120: stomatopod
class: 107 of 120: tornaria_acorn_worm_larvae
class: 108 of 120: trichodesmium_bowtie
class: 109 of 120: trichodesmium_multiple
class: 110 of 120: trichodesmium_puff
class: 111 of 120: trichodesmium_tuft
class: 112 of 120: trochophore_larvae
class: 113 of 120: tunicate_doliolid
class: 114 of 120: tunicate_doliolid_nurse
class: 115 of 120: tunicate_partial
class: 116 of 120: tunicate_salp
class: 117 of 120: tunicate_salp_chains
class: 118 of 120: unknown_blobs_and_smudges
class: 119 of 120: unknown_sticks
class: 120 of 120: unknown_unclassified
Finding batch size...
chosen batch size 3089 for 1 batches
Compiling forward prop...
Making predictions...
Batch 1 of 1
Log loss: 0.990288483844
In [10]:
%run check_test_score.py -v run_settings/8aug_extra_layers_more_hidden.json
Loading settings..
Loading model...
Loading data...
class: 0 of 120: acantharia_protist
class: 1 of 120: acantharia_protist_big_center
class: 2 of 120: acantharia_protist_halo
class: 3 of 120: amphipods
class: 4 of 120: appendicularian_fritillaridae
class: 5 of 120: appendicularian_slight_curve
class: 6 of 120: appendicularian_s_shape
class: 7 of 120: appendicularian_straight
class: 8 of 120: artifacts
class: 9 of 120: artifacts_edge
class: 10 of 120: chaetognath_non_sagitta
class: 11 of 120: chaetognath_other
class: 12 of 120: chaetognath_sagitta
class: 13 of 120: chordate_type1
class: 14 of 120: copepod_calanoid
class: 15 of 120: copepod_calanoid_eggs
class: 16 of 120: copepod_calanoid_eucalanus
class: 17 of 120: copepod_calanoid_flatheads
class: 18 of 120: copepod_calanoid_frillyAntennae
class: 19 of 120: copepod_calanoid_large
class: 20 of 120: copepod_calanoid_large_side_antennatucked
class: 21 of 120: copepod_calanoid_octomoms
class: 22 of 120: copepod_calanoid_small_longantennae
class: 23 of 120: copepod_cyclopoid_copilia
class: 24 of 120: copepod_cyclopoid_oithona
class: 25 of 120: copepod_cyclopoid_oithona_eggs
class: 26 of 120: copepod_other
class: 27 of 120: crustacean_other
class: 28 of 120: ctenophore_cestid
class: 29 of 120: ctenophore_cydippid_no_tentacles
class: 30 of 120: ctenophore_cydippid_tentacles
class: 31 of 120: ctenophore_lobate
class: 32 of 120: decapods
class: 33 of 120: detritus_blob
class: 34 of 120: detritus_filamentous
class: 35 of 120: detritus_other
class: 36 of 120: diatom_chain_string
class: 37 of 120: diatom_chain_tube
class: 38 of 120: echinoderm_larva_pluteus_brittlestar
class: 39 of 120: echinoderm_larva_pluteus_early
class: 40 of 120: echinoderm_larva_pluteus_typeC
class: 41 of 120: echinoderm_larva_pluteus_urchin
class: 42 of 120: echinoderm_larva_seastar_bipinnaria
class: 43 of 120: echinoderm_larva_seastar_brachiolaria
class: 44 of 120: echinoderm_seacucumber_auricularia_larva
class: 45 of 120: echinopluteus
class: 46 of 120: ephyra
class: 47 of 120: euphausiids
class: 48 of 120: euphausiids_young
class: 49 of 120: fecal_pellet
class: 50 of 120: fish_larvae_deep_body
class: 51 of 120: fish_larvae_leptocephali
class: 52 of 120: fish_larvae_medium_body
class: 53 of 120: fish_larvae_myctophids
class: 54 of 120: fish_larvae_thin_body
class: 55 of 120: fish_larvae_very_thin_body
class: 56 of 120: heteropod
class: 57 of 120: hydromedusae_aglaura
class: 58 of 120: hydromedusae_bell_and_tentacles
class: 59 of 120: hydromedusae_h15
class: 60 of 120: hydromedusae_haliscera
class: 61 of 120: hydromedusae_haliscera_small_sideview
class: 62 of 120: hydromedusae_liriope
class: 63 of 120: hydromedusae_narco_dark
class: 64 of 120: hydromedusae_narcomedusae
class: 65 of 120: hydromedusae_narco_young
class: 66 of 120: hydromedusae_other
class: 67 of 120: hydromedusae_partial_dark
class: 68 of 120: hydromedusae_shapeA
class: 69 of 120: hydromedusae_shapeA_sideview_small
class: 70 of 120: hydromedusae_shapeB
class: 71 of 120: hydromedusae_sideview_big
class: 72 of 120: hydromedusae_solmaris
class: 73 of 120: hydromedusae_solmundella
class: 74 of 120: hydromedusae_typeD
class: 75 of 120: hydromedusae_typeD_bell_and_tentacles
class: 76 of 120: hydromedusae_typeE
class: 77 of 120: hydromedusae_typeF
class: 78 of 120: invertebrate_larvae_other_A
class: 79 of 120: invertebrate_larvae_other_B
class: 80 of 120: jellies_tentacles
class: 81 of 120: polychaete
class: 82 of 120: protist_dark_center
class: 83 of 120: protist_fuzzy_olive
class: 84 of 120: protist_noctiluca
class: 85 of 120: protist_other
class: 86 of 120: protist_star
class: 87 of 120: pteropod_butterfly
class: 88 of 120: pteropod_theco_dev_seq
class: 89 of 120: pteropod_triangle
class: 90 of 120: radiolarian_chain
class: 91 of 120: radiolarian_colony
class: 92 of 120: shrimp_caridean
class: 93 of 120: shrimp-like_other
class: 94 of 120: shrimp_sergestidae
class: 95 of 120: shrimp_zoea
class: 96 of 120: siphonophore_calycophoran_abylidae
class: 97 of 120: siphonophore_calycophoran_rocketship_adult
class: 98 of 120: siphonophore_calycophoran_rocketship_young
class: 99 of 120: siphonophore_calycophoran_sphaeronectes
class: 100 of 120: siphonophore_calycophoran_sphaeronectes_stem
class: 101 of 120: siphonophore_calycophoran_sphaeronectes_young
class: 102 of 120: siphonophore_other_parts
class: 103 of 120: siphonophore_partial
class: 104 of 120: siphonophore_physonect
class: 105 of 120: siphonophore_physonect_young
class: 106 of 120: stomatopod
class: 107 of 120: tornaria_acorn_worm_larvae
class: 108 of 120: trichodesmium_bowtie
class: 109 of 120: trichodesmium_multiple
class: 110 of 120: trichodesmium_puff
class: 111 of 120: trichodesmium_tuft
class: 112 of 120: trochophore_larvae
class: 113 of 120: tunicate_doliolid
class: 114 of 120: tunicate_doliolid_nurse
class: 115 of 120: tunicate_partial
class: 116 of 120: tunicate_salp
class: 117 of 120: tunicate_salp_chains
class: 118 of 120: unknown_blobs_and_smudges
class: 119 of 120: unknown_sticks
class: 120 of 120: unknown_unclassified
Finding batch size...
INFO (theano.gof.compilelock): Waiting for existing lock by unknown process (I am process '51266')
INFO:theano.gof.compilelock:Waiting for existing lock by unknown process (I am process '51266')
INFO (theano.gof.compilelock): To manually release the lock, delete /afs/inf.ed.ac.uk/user/s13/s1320903/.theano/stonesoup1/compiledir_Linux-2.6-el6.x86_64-x86_64-with-redhat-6.5-Carbon-x86_64-2.7.8-64/lock_dir
INFO:theano.gof.compilelock:To manually release the lock, delete /afs/inf.ed.ac.uk/user/s13/s1320903/.theano/stonesoup1/compiledir_Linux-2.6-el6.x86_64-x86_64-with-redhat-6.5-Carbon-x86_64-2.7.8-64/lock_dir
chosen batch size 3089 for 1 batches
Compiling forward prop...
---------------------------------------------------------------------------
KeyboardInterrupt Traceback (most recent call last)
/afs/inf.ed.ac.uk/user/s13/s1320903/Neuroglycerin/neukrill-net-work/check_test_score.py in <module>()
145 'repeats predictions.', type=int, default=1)
146 args = parser.parse_args()
--> 147 check_score(args.run_settings, verbose=args.v, augment=args.augment)
/afs/inf.ed.ac.uk/user/s13/s1320903/Neuroglycerin/neukrill-net-work/check_test_score.py in check_score(run_settings_path, verbose, augment)
77 f = theano.function(X,Y)
78 else:
---> 79 f = theano.function([X],Y)
80
81 # compute probabilities
/afs/inf.ed.ac.uk/user/s13/s1320903/Neuroglycerin/Theano/theano/compile/function.pyc in function(inputs, outputs, mode, updates, givens, no_default_updates, accept_inplace, name, rebuild_strict, allow_input_downcast, profile, on_unused_input)
263 allow_input_downcast=allow_input_downcast,
264 on_unused_input=on_unused_input,
--> 265 profile=profile)
266 # We need to add the flag check_aliased inputs if we have any mutable or
267 # borrowed used defined inputs
/afs/inf.ed.ac.uk/user/s13/s1320903/Neuroglycerin/Theano/theano/compile/pfunc.pyc in pfunc(params, outputs, mode, updates, givens, no_default_updates, accept_inplace, name, rebuild_strict, allow_input_downcast, profile, on_unused_input)
509 return orig_function(inputs, cloned_outputs, mode,
510 accept_inplace=accept_inplace, name=name, profile=profile,
--> 511 on_unused_input=on_unused_input)
512
513
/afs/inf.ed.ac.uk/user/s13/s1320903/Neuroglycerin/Theano/theano/compile/function_module.pyc in orig_function(inputs, outputs, mode, accept_inplace, name, profile, on_unused_input)
1555 profile=profile,
1556 on_unused_input=on_unused_input).create(
-> 1557 defaults)
1558
1559 t2 = time.time()
/afs/inf.ed.ac.uk/user/s13/s1320903/Neuroglycerin/Theano/theano/compile/function_module.pyc in create(self, input_storage, trustme)
1413 theano.config.traceback.limit = 0
1414 _fn, _i, _o = self.linker.make_thunk(
-> 1415 input_storage=input_storage_lists)
1416 finally:
1417 theano.config.traceback.limit = limit_orig
/afs/inf.ed.ac.uk/user/s13/s1320903/Neuroglycerin/Theano/theano/gof/link.pyc in make_thunk(self, profiler, input_storage, output_storage)
523 return self.make_all(profiler=profiler,
524 input_storage=input_storage,
--> 525 output_storage=output_storage)[:3]
526
527 def make_all(self, profiler, input_storage, output_storage):
/afs/inf.ed.ac.uk/user/s13/s1320903/Neuroglycerin/Theano/theano/gof/vm.pyc in make_all(self, profiler, input_storage, output_storage)
895 storage_map,
896 compute_map,
--> 897 no_recycling))
898 if not hasattr(thunks[-1], 'lazy'):
899 # We don't want all ops maker to think about lazy Ops.
/afs/inf.ed.ac.uk/user/s13/s1320903/Neuroglycerin/Theano/theano/gof/op.pyc in make_thunk(self, node, storage_map, compute_map, no_recycling)
711 logger.debug('Trying CLinker.make_thunk')
712 outputs = cl.make_thunk(input_storage=node_input_storage,
--> 713 output_storage=node_output_storage)
714 fill_storage, node_input_filters, node_output_filters = outputs
715
/afs/inf.ed.ac.uk/user/s13/s1320903/Neuroglycerin/Theano/theano/gof/cc.pyc in make_thunk(self, input_storage, output_storage, keep_lock)
1070 cthunk, in_storage, out_storage, error_storage = self.__compile__(
1071 input_storage, output_storage,
-> 1072 keep_lock=keep_lock)
1073
1074 res = _CThunk(cthunk, init_tasks, tasks, error_storage)
/afs/inf.ed.ac.uk/user/s13/s1320903/Neuroglycerin/Theano/theano/gof/cc.pyc in __compile__(self, input_storage, output_storage, keep_lock)
1012 input_storage,
1013 output_storage,
-> 1014 keep_lock=keep_lock)
1015 return (thunk,
1016 [link.Container(input, storage) for input, storage in
/afs/inf.ed.ac.uk/user/s13/s1320903/Neuroglycerin/Theano/theano/gof/cc.pyc in cthunk_factory(self, error_storage, in_storage, out_storage, keep_lock)
1439 else:
1440 module = get_module_cache().module_from_key(
-> 1441 key=key, lnk=self, keep_lock=keep_lock)
1442
1443 vars = self.inputs + self.outputs + self.orphans
/afs/inf.ed.ac.uk/user/s13/s1320903/Neuroglycerin/Theano/theano/gof/cmodule.pyc in module_from_key(self, key, lnk, keep_lock)
1038 # Is the source code already in the cache?
1039 module_hash = get_module_hash(src_code, key)
-> 1040 module = self._get_from_hash(module_hash, key, keep_lock=keep_lock)
1041 if module is not None:
1042 return module
/afs/inf.ed.ac.uk/user/s13/s1320903/Neuroglycerin/Theano/theano/gof/cmodule.pyc in _get_from_hash(self, module_hash, key, keep_lock)
939 key_data = self.module_hash_to_key_data[module_hash]
940 module = self._get_from_key(None, key_data)
--> 941 with compilelock.lock_ctx(keep_lock=keep_lock):
942 try:
943 key_data.add_key(key, save_pkl=bool(key[0]))
/usr/lib/python2.7/contextlib.pyc in __enter__(self)
15 def __enter__(self):
16 try:
---> 17 return self.gen.next()
18 except StopIteration:
19 raise RuntimeError("generator didn't yield")
/afs/inf.ed.ac.uk/user/s13/s1320903/Neuroglycerin/Theano/theano/gof/compilelock.pyc in lock_ctx(lock_dir, keep_lock, **kw)
52 @contextmanager
53 def lock_ctx(lock_dir=None, keep_lock=False, **kw):
---> 54 get_lock(lock_dir=lock_dir, **kw)
55 yield
56 if not keep_lock:
/afs/inf.ed.ac.uk/user/s13/s1320903/Neuroglycerin/Theano/theano/gof/compilelock.pyc in get_lock(lock_dir, **kw)
89 # Only really try to acquire the lock if we do not have it already.
90 if get_lock.n_lock == 0:
---> 91 lock(get_lock.lock_dir, **kw)
92 atexit.register(Unlocker.unlock, get_lock.unlocker)
93 # Store time at which the lock was set.
/afs/inf.ed.ac.uk/user/s13/s1320903/Neuroglycerin/Theano/theano/gof/compilelock.pyc in lock(tmp_dir, timeout, min_wait, max_wait, verbosity)
270 no_display = True
271 nb_wait += 1
--> 272 time.sleep(random.uniform(min_wait, max_wait))
273
274 try:
KeyboardInterrupt:
Could not run 8aug_extra_layers_more_hidden.json for some reason. (Theano lock of some sort). The next one is not bad:
In [8]:
%run check_test_score.py -v run_settings/8aug_flat_lr.json
Loading settings..
Loading model...
Loading data...
Applying normalisation: global
(24712,)
Finding batch size...
chosen batch size 3089 for 8 batches
Compiling forward prop...
Making predictions...
Batch 1 of 8
Batch 2 of 8
Batch 3 of 8
Batch 4 of 8
Batch 5 of 8
Batch 6 of 8
Batch 7 of 8
Batch 8 of 8
Collapsing predictions...
Log loss: 0.827019384595
/afs/inf.ed.ac.uk/user/s13/s1320903/Neuroglycerin/pylearn2/pylearn2/utils/iteration.py:783: UserWarning: dataset is using the old iterator interface which is deprecated and will become officially unsupported as of July 28, 2015. The dataset should implement a `get` method respecting the new interface.
warnings.warn("dataset is using the old iterator interface which "
This one is slightly worse but still in ~0.83 range.
In [9]:
%run check_test_score.py -v run_settings/8aug_online_extra_convlayer.json
Loading settings..
Loading model...
Loading data...
class: 0 of 120: acantharia_protist
class: 1 of 120: acantharia_protist_big_center
class: 2 of 120: acantharia_protist_halo
class: 3 of 120: amphipods
class: 4 of 120: appendicularian_fritillaridae
class: 5 of 120: appendicularian_slight_curve
class: 6 of 120: appendicularian_s_shape
class: 7 of 120: appendicularian_straight
class: 8 of 120: artifacts
class: 9 of 120: artifacts_edge
class: 10 of 120: chaetognath_non_sagitta
class: 11 of 120: chaetognath_other
class: 12 of 120: chaetognath_sagitta
class: 13 of 120: chordate_type1
class: 14 of 120: copepod_calanoid
class: 15 of 120: copepod_calanoid_eggs
class: 16 of 120: copepod_calanoid_eucalanus
class: 17 of 120: copepod_calanoid_flatheads
class: 18 of 120: copepod_calanoid_frillyAntennae
class: 19 of 120: copepod_calanoid_large
class: 20 of 120: copepod_calanoid_large_side_antennatucked
class: 21 of 120: copepod_calanoid_octomoms
class: 22 of 120: copepod_calanoid_small_longantennae
class: 23 of 120: copepod_cyclopoid_copilia
class: 24 of 120: copepod_cyclopoid_oithona
class: 25 of 120: copepod_cyclopoid_oithona_eggs
class: 26 of 120: copepod_other
class: 27 of 120: crustacean_other
class: 28 of 120: ctenophore_cestid
class: 29 of 120: ctenophore_cydippid_no_tentacles
class: 30 of 120: ctenophore_cydippid_tentacles
class: 31 of 120: ctenophore_lobate
class: 32 of 120: decapods
class: 33 of 120: detritus_blob
class: 34 of 120: detritus_filamentous
class: 35 of 120: detritus_other
class: 36 of 120: diatom_chain_string
class: 37 of 120: diatom_chain_tube
class: 38 of 120: echinoderm_larva_pluteus_brittlestar
class: 39 of 120: echinoderm_larva_pluteus_early
class: 40 of 120: echinoderm_larva_pluteus_typeC
class: 41 of 120: echinoderm_larva_pluteus_urchin
class: 42 of 120: echinoderm_larva_seastar_bipinnaria
class: 43 of 120: echinoderm_larva_seastar_brachiolaria
class: 44 of 120: echinoderm_seacucumber_auricularia_larva
class: 45 of 120: echinopluteus
class: 46 of 120: ephyra
class: 47 of 120: euphausiids
class: 48 of 120: euphausiids_young
class: 49 of 120: fecal_pellet
class: 50 of 120: fish_larvae_deep_body
class: 51 of 120: fish_larvae_leptocephali
class: 52 of 120: fish_larvae_medium_body
class: 53 of 120: fish_larvae_myctophids
class: 54 of 120: fish_larvae_thin_body
class: 55 of 120: fish_larvae_very_thin_body
class: 56 of 120: heteropod
class: 57 of 120: hydromedusae_aglaura
class: 58 of 120: hydromedusae_bell_and_tentacles
class: 59 of 120: hydromedusae_h15
class: 60 of 120: hydromedusae_haliscera
class: 61 of 120: hydromedusae_haliscera_small_sideview
class: 62 of 120: hydromedusae_liriope
class: 63 of 120: hydromedusae_narco_dark
class: 64 of 120: hydromedusae_narcomedusae
class: 65 of 120: hydromedusae_narco_young
class: 66 of 120: hydromedusae_other
class: 67 of 120: hydromedusae_partial_dark
class: 68 of 120: hydromedusae_shapeA
class: 69 of 120: hydromedusae_shapeA_sideview_small
class: 70 of 120: hydromedusae_shapeB
class: 71 of 120: hydromedusae_sideview_big
class: 72 of 120: hydromedusae_solmaris
class: 73 of 120: hydromedusae_solmundella
class: 74 of 120: hydromedusae_typeD
class: 75 of 120: hydromedusae_typeD_bell_and_tentacles
class: 76 of 120: hydromedusae_typeE
class: 77 of 120: hydromedusae_typeF
class: 78 of 120: invertebrate_larvae_other_A
class: 79 of 120: invertebrate_larvae_other_B
class: 80 of 120: jellies_tentacles
class: 81 of 120: polychaete
class: 82 of 120: protist_dark_center
class: 83 of 120: protist_fuzzy_olive
class: 84 of 120: protist_noctiluca
class: 85 of 120: protist_other
class: 86 of 120: protist_star
class: 87 of 120: pteropod_butterfly
class: 88 of 120: pteropod_theco_dev_seq
class: 89 of 120: pteropod_triangle
class: 90 of 120: radiolarian_chain
class: 91 of 120: radiolarian_colony
class: 92 of 120: shrimp_caridean
class: 93 of 120: shrimp-like_other
class: 94 of 120: shrimp_sergestidae
class: 95 of 120: shrimp_zoea
class: 96 of 120: siphonophore_calycophoran_abylidae
class: 97 of 120: siphonophore_calycophoran_rocketship_adult
class: 98 of 120: siphonophore_calycophoran_rocketship_young
class: 99 of 120: siphonophore_calycophoran_sphaeronectes
class: 100 of 120: siphonophore_calycophoran_sphaeronectes_stem
class: 101 of 120: siphonophore_calycophoran_sphaeronectes_young
class: 102 of 120: siphonophore_other_parts
class: 103 of 120: siphonophore_partial
class: 104 of 120: siphonophore_physonect
class: 105 of 120: siphonophore_physonect_young
class: 106 of 120: stomatopod
class: 107 of 120: tornaria_acorn_worm_larvae
class: 108 of 120: trichodesmium_bowtie
class: 109 of 120: trichodesmium_multiple
class: 110 of 120: trichodesmium_puff
class: 111 of 120: trichodesmium_tuft
class: 112 of 120: trochophore_larvae
class: 113 of 120: tunicate_doliolid
class: 114 of 120: tunicate_doliolid_nurse
class: 115 of 120: tunicate_partial
class: 116 of 120: tunicate_salp
class: 117 of 120: tunicate_salp_chains
class: 118 of 120: unknown_blobs_and_smudges
class: 119 of 120: unknown_sticks
class: 120 of 120: unknown_unclassified
Finding batch size...
chosen batch size 3089 for 1 batches
Compiling forward prop...
Making predictions...
Batch 1 of 1
Log loss: 0.830256764327
Alexnet-based models with many augmentations:
In [11]:
%run check_test_score.py -v run_settings/alexnet_based_16aug.json
Loading settings..
Loading model...
Loading data...
Applying normalisation: global
(49424,)
Finding batch size...
chosen batch size 3089 for 16 batches
Compiling forward prop...
Making predictions...
Batch 1 of 16
Batch 2 of 16
Batch 3 of 16
Batch 4 of 16
Batch 5 of 16
Batch 6 of 16
Batch 7 of 16
Batch 8 of 16
Batch 9 of 16
Batch 10 of 16
Batch 11 of 16
Batch 12 of 16
Batch 13 of 16
Batch 14 of 16
Batch 15 of 16
Batch 16 of 16
Collapsing predictions...
Log loss: 0.742401588184
Alexnet_based_16aug is best so far. Potentially write a .csv from it.
In [12]:
%run check_test_score.py -v run_settings/alexnet_based2.json
Loading settings..
Loading model...
Loading data...
(3089,)
Finding batch size...
chosen batch size 3089 for 1 batches
Compiling forward prop...
Making predictions...
Batch 1 of 1
Log loss: 1.42355736088
Okay, 40aug is expectedly better.
In [13]:
%run check_test_score.py -v run_settings/alexnet_based_40aug.json
Loading settings..
Loading model...
Loading data...
Applying normalisation: global
(123560,)
Finding batch size...
chosen batch size 3089 for 40 batches
Compiling forward prop...
Making predictions...
Batch 1 of 40
Batch 2 of 40
Batch 3 of 40
Batch 4 of 40
Batch 5 of 40
Batch 6 of 40
Batch 7 of 40
Batch 8 of 40
Batch 9 of 40
Batch 10 of 40
Batch 11 of 40
Batch 12 of 40
Batch 13 of 40
Batch 14 of 40
Batch 15 of 40
Batch 16 of 40
Batch 17 of 40
Batch 18 of 40
Batch 19 of 40
Batch 20 of 40
Batch 21 of 40
Batch 22 of 40
Batch 23 of 40
Batch 24 of 40
Batch 25 of 40
Batch 26 of 40
Batch 27 of 40
Batch 28 of 40
Batch 29 of 40
Batch 30 of 40
Batch 31 of 40
Batch 32 of 40
Batch 33 of 40
Batch 34 of 40
Batch 35 of 40
Batch 36 of 40
Batch 37 of 40
Batch 38 of 40
Batch 39 of 40
Batch 40 of 40
Collapsing predictions...
Log loss: 0.739251263639
In [20]:
reload(neukrill_net.dense_dataset)
Out[20]:
<module 'neukrill_net.dense_dataset' from '/afs/inf.ed.ac.uk/user/s13/s1320903/Neuroglycerin/neukrill-net-tools/neukrill_net/dense_dataset.py'>
In [21]:
%run check_test_score.py -v run_settings/alexnet_based_extra_convlayer_with_superclasses.json
Loading settings..
Loading model...
Loading data...
Applying normalisation: global
(3089, 188)
Finding batch size...
chosen batch size 3089 for 1 batches
Compiling forward prop...
Making predictions...
Batch 1 of 1
Log loss: 1.57363224286
In [22]:
%run check_test_score.py -v run_settings/alexnet_based_extra_convlayer_with_superclasses_aug.json
Loading settings..
Loading model...
Loading data...
Applying normalisation: global
(24712, 188)
Finding batch size...
chosen batch size 3089 for 8 batches
Compiling forward prop...
Making predictions...
Batch 1 of 8
Batch 2 of 8
Batch 3 of 8
Batch 4 of 8
Batch 5 of 8
Batch 6 of 8
Batch 7 of 8
Batch 8 of 8
Collapsing predictions...
Log loss: 1.98284825155
A bad one:
In [23]:
%run check_test_score.py -v run_settings/alexnet_based_listdataset.json
Loading settings..
Loading model...
Loading data...
class: 0 of 120: acantharia_protist
class: 1 of 120: acantharia_protist_big_center
class: 2 of 120: acantharia_protist_halo
class: 3 of 120: amphipods
class: 4 of 120: appendicularian_fritillaridae
class: 5 of 120: appendicularian_slight_curve
class: 6 of 120: appendicularian_s_shape
class: 7 of 120: appendicularian_straight
class: 8 of 120: artifacts
class: 9 of 120: artifacts_edge
class: 10 of 120: chaetognath_non_sagitta
class: 11 of 120: chaetognath_other
class: 12 of 120: chaetognath_sagitta
class: 13 of 120: chordate_type1
class: 14 of 120: copepod_calanoid
class: 15 of 120: copepod_calanoid_eggs
class: 16 of 120: copepod_calanoid_eucalanus
class: 17 of 120: copepod_calanoid_flatheads
class: 18 of 120: copepod_calanoid_frillyAntennae
class: 19 of 120: copepod_calanoid_large
class: 20 of 120: copepod_calanoid_large_side_antennatucked
class: 21 of 120: copepod_calanoid_octomoms
class: 22 of 120: copepod_calanoid_small_longantennae
class: 23 of 120: copepod_cyclopoid_copilia
class: 24 of 120: copepod_cyclopoid_oithona
class: 25 of 120: copepod_cyclopoid_oithona_eggs
class: 26 of 120: copepod_other
class: 27 of 120: crustacean_other
class: 28 of 120: ctenophore_cestid
class: 29 of 120: ctenophore_cydippid_no_tentacles
class: 30 of 120: ctenophore_cydippid_tentacles
class: 31 of 120: ctenophore_lobate
class: 32 of 120: decapods
class: 33 of 120: detritus_blob
class: 34 of 120: detritus_filamentous
class: 35 of 120: detritus_other
class: 36 of 120: diatom_chain_string
class: 37 of 120: diatom_chain_tube
class: 38 of 120: echinoderm_larva_pluteus_brittlestar
class: 39 of 120: echinoderm_larva_pluteus_early
class: 40 of 120: echinoderm_larva_pluteus_typeC
class: 41 of 120: echinoderm_larva_pluteus_urchin
class: 42 of 120: echinoderm_larva_seastar_bipinnaria
class: 43 of 120: echinoderm_larva_seastar_brachiolaria
class: 44 of 120: echinoderm_seacucumber_auricularia_larva
class: 45 of 120: echinopluteus
class: 46 of 120: ephyra
class: 47 of 120: euphausiids
class: 48 of 120: euphausiids_young
class: 49 of 120: fecal_pellet
class: 50 of 120: fish_larvae_deep_body
class: 51 of 120: fish_larvae_leptocephali
class: 52 of 120: fish_larvae_medium_body
class: 53 of 120: fish_larvae_myctophids
class: 54 of 120: fish_larvae_thin_body
class: 55 of 120: fish_larvae_very_thin_body
class: 56 of 120: heteropod
class: 57 of 120: hydromedusae_aglaura
class: 58 of 120: hydromedusae_bell_and_tentacles
class: 59 of 120: hydromedusae_h15
class: 60 of 120: hydromedusae_haliscera
class: 61 of 120: hydromedusae_haliscera_small_sideview
class: 62 of 120: hydromedusae_liriope
class: 63 of 120: hydromedusae_narco_dark
class: 64 of 120: hydromedusae_narcomedusae
class: 65 of 120: hydromedusae_narco_young
class: 66 of 120: hydromedusae_other
class: 67 of 120: hydromedusae_partial_dark
class: 68 of 120: hydromedusae_shapeA
class: 69 of 120: hydromedusae_shapeA_sideview_small
class: 70 of 120: hydromedusae_shapeB
class: 71 of 120: hydromedusae_sideview_big
class: 72 of 120: hydromedusae_solmaris
class: 73 of 120: hydromedusae_solmundella
class: 74 of 120: hydromedusae_typeD
class: 75 of 120: hydromedusae_typeD_bell_and_tentacles
class: 76 of 120: hydromedusae_typeE
class: 77 of 120: hydromedusae_typeF
class: 78 of 120: invertebrate_larvae_other_A
class: 79 of 120: invertebrate_larvae_other_B
class: 80 of 120: jellies_tentacles
class: 81 of 120: polychaete
class: 82 of 120: protist_dark_center
class: 83 of 120: protist_fuzzy_olive
class: 84 of 120: protist_noctiluca
class: 85 of 120: protist_other
class: 86 of 120: protist_star
class: 87 of 120: pteropod_butterfly
class: 88 of 120: pteropod_theco_dev_seq
class: 89 of 120: pteropod_triangle
class: 90 of 120: radiolarian_chain
class: 91 of 120: radiolarian_colony
class: 92 of 120: shrimp_caridean
class: 93 of 120: shrimp-like_other
class: 94 of 120: shrimp_sergestidae
class: 95 of 120: shrimp_zoea
class: 96 of 120: siphonophore_calycophoran_abylidae
class: 97 of 120: siphonophore_calycophoran_rocketship_adult
class: 98 of 120: siphonophore_calycophoran_rocketship_young
class: 99 of 120: siphonophore_calycophoran_sphaeronectes
class: 100 of 120: siphonophore_calycophoran_sphaeronectes_stem
class: 101 of 120: siphonophore_calycophoran_sphaeronectes_young
class: 102 of 120: siphonophore_other_parts
class: 103 of 120: siphonophore_partial
class: 104 of 120: siphonophore_physonect
class: 105 of 120: siphonophore_physonect_young
class: 106 of 120: stomatopod
class: 107 of 120: tornaria_acorn_worm_larvae
class: 108 of 120: trichodesmium_bowtie
class: 109 of 120: trichodesmium_multiple
class: 110 of 120: trichodesmium_puff
class: 111 of 120: trichodesmium_tuft
class: 112 of 120: trochophore_larvae
class: 113 of 120: tunicate_doliolid
class: 114 of 120: tunicate_doliolid_nurse
class: 115 of 120: tunicate_partial
class: 116 of 120: tunicate_salp
class: 117 of 120: tunicate_salp_chains
class: 118 of 120: unknown_blobs_and_smudges
class: 119 of 120: unknown_sticks
class: 120 of 120: unknown_unclassified
Finding batch size...
chosen batch size 3089 for 1 batches
Compiling forward prop...
Making predictions...
Batch 1 of 1
Log loss: 4.15057611444
An alright one:
In [24]:
%run check_test_score.py -v run_settings/alexnet_based_norm_global_8aug.json
Loading settings..
Loading model...
Loading data...
Applying normalisation: global
(24712,)
Finding batch size...
chosen batch size 3089 for 8 batches
Compiling forward prop...
Making predictions...
Batch 1 of 8
Batch 2 of 8
Batch 3 of 8
Batch 4 of 8
Batch 5 of 8
Batch 6 of 8
Batch 7 of 8
Batch 8 of 8
Collapsing predictions...
Log loss: 0.812747089013
In [25]:
%run check_test_score.py -v run_settings/alexnet_based_norm_global_8aug_pmlp1.json
Loading settings..
Loading model...
Loading data...
Applying normalisation: global
(24712,)
Finding batch size...
chosen batch size 3089 for 8 batches
Compiling forward prop...
Making predictions...
Batch 1 of 8
Batch 2 of 8
Batch 3 of 8
Batch 4 of 8
Batch 5 of 8
Batch 6 of 8
Batch 7 of 8
Batch 8 of 8
Collapsing predictions...
Log loss: 0.827511591327
Exception that will overwrite the file?
In [ ]:
%run check_test_score.py -v run_settings/alexnet_based_onlineaug.json
Not checking seeded:
In [28]:
%run check_test_score.py -v run_settings/alexnet_based_seeded.json
Loading settings..
Loading model...
Loading data...
(3089,)
Finding batch size...
chosen batch size 3089 for 1 batches
Compiling forward prop...
Making predictions...
Batch 1 of 1
Log loss: 2.35784087833
Not checking shapefix:
In [29]:
%run check_test_score.py -v run_settings/alexnet_based_shapefix.json
Loading settings..
Loading model...
Loading data...
Applying normalisation: global
(3089,)
Finding batch size...
chosen batch size 3089 for 1 batches
Compiling forward prop...
Making predictions...
Batch 1 of 1
Log loss: 1.58270344272
Dropout ones don't do well:
In [30]:
%run check_test_score.py -v run_settings/alexnet_extra_layer_dropouts.json
Loading settings..
Loading model...
Loading data...
Applying normalisation: global
(24712,)
Finding batch size...
chosen batch size 3089 for 8 batches
Compiling forward prop...
Making predictions...
Batch 1 of 8
Batch 2 of 8
Batch 3 of 8
Batch 4 of 8
Batch 5 of 8
Batch 6 of 8
Batch 7 of 8
Batch 8 of 8
Collapsing predictions...
Log loss: 1.04312886577
Learning rate differences:
In [31]:
%run check_test_score.py -v run_settings/alexnet_extra_layer_learning_rate.json
Loading settings..
Loading model...
Loading data...
Applying normalisation: global
(24712,)
Finding batch size...
chosen batch size 3089 for 8 batches
Compiling forward prop...
Making predictions...
Batch 1 of 8
Batch 2 of 8
Batch 3 of 8
Batch 4 of 8
Batch 5 of 8
Batch 6 of 8
Batch 7 of 8
Batch 8 of 8
Collapsing predictions...
Log loss: 0.815480132488
In [33]:
%run check_test_score.py -v run_settings/alexnet_learning_rate2.json
Loading settings..
Loading model...
Loading data...
Applying normalisation: global
(3089,)
Finding batch size...
chosen batch size 3089 for 1 batches
Compiling forward prop...
Making predictions...
Batch 1 of 1
Log loss: 1.24318076943
In [34]:
%run check_test_score.py -v run_settings/alexnet_learning_rate3.json
Loading settings..
Loading model...
Loading data...
Applying normalisation: global
(3089,)
Finding batch size...
chosen batch size 3089 for 1 batches
Compiling forward prop...
Making predictions...
Batch 1 of 1
Log loss: 1.2668249113
Scott's hopeful models: (problem with testing parallel models?)
In [41]:
%run check_test_score.py -v run_settings/continue_hopeful.json
Loading settings..
Loading model...
Loading data...
class: 0 of 120: acantharia_protist
class: 1 of 120: acantharia_protist_big_center
class: 2 of 120: acantharia_protist_halo
class: 3 of 120: amphipods
class: 4 of 120: appendicularian_fritillaridae
class: 5 of 120: appendicularian_slight_curve
class: 6 of 120: appendicularian_s_shape
class: 7 of 120: appendicularian_straight
class: 8 of 120: artifacts
class: 9 of 120: artifacts_edge
class: 10 of 120: chaetognath_non_sagitta
class: 11 of 120: chaetognath_other
class: 12 of 120: chaetognath_sagitta
class: 13 of 120: chordate_type1
class: 14 of 120: copepod_calanoid
class: 15 of 120: copepod_calanoid_eggs
class: 16 of 120: copepod_calanoid_eucalanus
class: 17 of 120: copepod_calanoid_flatheads
class: 18 of 120: copepod_calanoid_frillyAntennae
class: 19 of 120: copepod_calanoid_large
class: 20 of 120: copepod_calanoid_large_side_antennatucked
class: 21 of 120: copepod_calanoid_octomoms
class: 22 of 120: copepod_calanoid_small_longantennae
class: 23 of 120: copepod_cyclopoid_copilia
class: 24 of 120: copepod_cyclopoid_oithona
class: 25 of 120: copepod_cyclopoid_oithona_eggs
class: 26 of 120: copepod_other
class: 27 of 120: crustacean_other
class: 28 of 120: ctenophore_cestid
class: 29 of 120: ctenophore_cydippid_no_tentacles
class: 30 of 120: ctenophore_cydippid_tentacles
class: 31 of 120: ctenophore_lobate
class: 32 of 120: decapods
class: 33 of 120: detritus_blob
class: 34 of 120: detritus_filamentous
class: 35 of 120: detritus_other
class: 36 of 120: diatom_chain_string
class: 37 of 120: diatom_chain_tube
class: 38 of 120: echinoderm_larva_pluteus_brittlestar
class: 39 of 120: echinoderm_larva_pluteus_early
class: 40 of 120: echinoderm_larva_pluteus_typeC
class: 41 of 120: echinoderm_larva_pluteus_urchin
class: 42 of 120: echinoderm_larva_seastar_bipinnaria
class: 43 of 120: echinoderm_larva_seastar_brachiolaria
class: 44 of 120: echinoderm_seacucumber_auricularia_larva
class: 45 of 120: echinopluteus
class: 46 of 120: ephyra
class: 47 of 120: euphausiids
class: 48 of 120: euphausiids_young
class: 49 of 120: fecal_pellet
class: 50 of 120: fish_larvae_deep_body
class: 51 of 120: fish_larvae_leptocephali
class: 52 of 120: fish_larvae_medium_body
class: 53 of 120: fish_larvae_myctophids
class: 54 of 120: fish_larvae_thin_body
class: 55 of 120: fish_larvae_very_thin_body
class: 56 of 120: heteropod
class: 57 of 120: hydromedusae_aglaura
class: 58 of 120: hydromedusae_bell_and_tentacles
class: 59 of 120: hydromedusae_h15
class: 60 of 120: hydromedusae_haliscera
class: 61 of 120: hydromedusae_haliscera_small_sideview
class: 62 of 120: hydromedusae_liriope
class: 63 of 120: hydromedusae_narco_dark
class: 64 of 120: hydromedusae_narcomedusae
class: 65 of 120: hydromedusae_narco_young
class: 66 of 120: hydromedusae_other
class: 67 of 120: hydromedusae_partial_dark
class: 68 of 120: hydromedusae_shapeA
class: 69 of 120: hydromedusae_shapeA_sideview_small
class: 70 of 120: hydromedusae_shapeB
class: 71 of 120: hydromedusae_sideview_big
class: 72 of 120: hydromedusae_solmaris
class: 73 of 120: hydromedusae_solmundella
class: 74 of 120: hydromedusae_typeD
class: 75 of 120: hydromedusae_typeD_bell_and_tentacles
class: 76 of 120: hydromedusae_typeE
class: 77 of 120: hydromedusae_typeF
class: 78 of 120: invertebrate_larvae_other_A
class: 79 of 120: invertebrate_larvae_other_B
class: 80 of 120: jellies_tentacles
class: 81 of 120: polychaete
class: 82 of 120: protist_dark_center
class: 83 of 120: protist_fuzzy_olive
class: 84 of 120: protist_noctiluca
class: 85 of 120: protist_other
class: 86 of 120: protist_star
class: 87 of 120: pteropod_butterfly
class: 88 of 120: pteropod_theco_dev_seq
class: 89 of 120: pteropod_triangle
class: 90 of 120: radiolarian_chain
class: 91 of 120: radiolarian_colony
class: 92 of 120: shrimp_caridean
class: 93 of 120: shrimp-like_other
class: 94 of 120: shrimp_sergestidae
class: 95 of 120: shrimp_zoea
class: 96 of 120: siphonophore_calycophoran_abylidae
class: 97 of 120: siphonophore_calycophoran_rocketship_adult
class: 98 of 120: siphonophore_calycophoran_rocketship_young
class: 99 of 120: siphonophore_calycophoran_sphaeronectes
class: 100 of 120: siphonophore_calycophoran_sphaeronectes_stem
class: 101 of 120: siphonophore_calycophoran_sphaeronectes_young
class: 102 of 120: siphonophore_other_parts
class: 103 of 120: siphonophore_partial
class: 104 of 120: siphonophore_physonect
class: 105 of 120: siphonophore_physonect_young
class: 106 of 120: stomatopod
class: 107 of 120: tornaria_acorn_worm_larvae
class: 108 of 120: trichodesmium_bowtie
class: 109 of 120: trichodesmium_multiple
class: 110 of 120: trichodesmium_puff
class: 111 of 120: trichodesmium_tuft
class: 112 of 120: trochophore_larvae
class: 113 of 120: tunicate_doliolid
class: 114 of 120: tunicate_doliolid_nurse
class: 115 of 120: tunicate_partial
class: 116 of 120: tunicate_salp
class: 117 of 120: tunicate_salp_chains
class: 118 of 120: unknown_blobs_and_smudges
class: 119 of 120: unknown_sticks
class: 120 of 120: unknown_unclassified
Finding batch size...
chosen batch size 3089 for 1 batches
Compiling forward prop...
Making predictions...
---------------------------------------------------------------------------
TimeoutError Traceback (most recent call last)
/afs/inf.ed.ac.uk/user/s13/s1320903/Neuroglycerin/neukrill-net-work/check_test_score.py in <module>()
145 'repeats predictions.', type=int, default=1)
146 args = parser.parse_args()
--> 147 check_score(args.run_settings, verbose=args.v, augment=args.augment)
/afs/inf.ed.ac.uk/user/s13/s1320903/Neuroglycerin/neukrill-net-work/check_test_score.py in check_score(run_settings_path, verbose, augment)
92 iterator = dataset.iterator(batch_size=batch_size,num_batches=n_batches,
93 mode='even_sequential', data_specs=data_specs)
---> 94 for batch in iterator:
95 if verbose:
96 print(" Batch {0} of {1}".format(i+1,n_batches*augment))
/afs/inf.ed.ac.uk/user/s13/s1320903/Neuroglycerin/neukrill-net-tools/neukrill_net/parallel_dataset.py in next(self)
35 Xbatch1,Xbatch2 = [np.array(batch).reshape(
36 self.batch_size, self.final_shape[0], self.final_shape[1], 1)
---> 37 for batch in zip(*self.result.get(timeout=10.0))]
38 elif len(self.final_shape) == 3:
39 Xbatch1,Xbatch2 = [np.array(batch)
/usr/lib/python2.7/multiprocessing/pool.pyc in get(self, timeout)
552 self.wait(timeout)
553 if not self._ready:
--> 554 raise TimeoutError
555 if self._success:
556 return self._value
TimeoutError:
In [42]:
%run check_test_score.py -v run_settings/continue_hopeful_v2.json
Loading settings..
Loading model...
Loading data...
class: 0 of 120: acantharia_protist
class: 1 of 120: acantharia_protist_big_center
class: 2 of 120: acantharia_protist_halo
class: 3 of 120: amphipods
class: 4 of 120: appendicularian_fritillaridae
class: 5 of 120: appendicularian_slight_curve
class: 6 of 120: appendicularian_s_shape
class: 7 of 120: appendicularian_straight
class: 8 of 120: artifacts
class: 9 of 120: artifacts_edge
class: 10 of 120: chaetognath_non_sagitta
class: 11 of 120: chaetognath_other
class: 12 of 120: chaetognath_sagitta
class: 13 of 120: chordate_type1
class: 14 of 120: copepod_calanoid
class: 15 of 120: copepod_calanoid_eggs
class: 16 of 120: copepod_calanoid_eucalanus
class: 17 of 120: copepod_calanoid_flatheads
class: 18 of 120: copepod_calanoid_frillyAntennae
class: 19 of 120: copepod_calanoid_large
class: 20 of 120: copepod_calanoid_large_side_antennatucked
class: 21 of 120: copepod_calanoid_octomoms
class: 22 of 120: copepod_calanoid_small_longantennae
class: 23 of 120: copepod_cyclopoid_copilia
class: 24 of 120: copepod_cyclopoid_oithona
class: 25 of 120: copepod_cyclopoid_oithona_eggs
class: 26 of 120: copepod_other
class: 27 of 120: crustacean_other
class: 28 of 120: ctenophore_cestid
class: 29 of 120: ctenophore_cydippid_no_tentacles
class: 30 of 120: ctenophore_cydippid_tentacles
class: 31 of 120: ctenophore_lobate
class: 32 of 120: decapods
class: 33 of 120: detritus_blob
class: 34 of 120: detritus_filamentous
class: 35 of 120: detritus_other
class: 36 of 120: diatom_chain_string
class: 37 of 120: diatom_chain_tube
class: 38 of 120: echinoderm_larva_pluteus_brittlestar
class: 39 of 120: echinoderm_larva_pluteus_early
class: 40 of 120: echinoderm_larva_pluteus_typeC
class: 41 of 120: echinoderm_larva_pluteus_urchin
class: 42 of 120: echinoderm_larva_seastar_bipinnaria
class: 43 of 120: echinoderm_larva_seastar_brachiolaria
class: 44 of 120: echinoderm_seacucumber_auricularia_larva
class: 45 of 120: echinopluteus
class: 46 of 120: ephyra
class: 47 of 120: euphausiids
class: 48 of 120: euphausiids_young
class: 49 of 120: fecal_pellet
class: 50 of 120: fish_larvae_deep_body
class: 51 of 120: fish_larvae_leptocephali
class: 52 of 120: fish_larvae_medium_body
class: 53 of 120: fish_larvae_myctophids
class: 54 of 120: fish_larvae_thin_body
class: 55 of 120: fish_larvae_very_thin_body
class: 56 of 120: heteropod
class: 57 of 120: hydromedusae_aglaura
class: 58 of 120: hydromedusae_bell_and_tentacles
class: 59 of 120: hydromedusae_h15
class: 60 of 120: hydromedusae_haliscera
class: 61 of 120: hydromedusae_haliscera_small_sideview
class: 62 of 120: hydromedusae_liriope
class: 63 of 120: hydromedusae_narco_dark
class: 64 of 120: hydromedusae_narcomedusae
class: 65 of 120: hydromedusae_narco_young
class: 66 of 120: hydromedusae_other
class: 67 of 120: hydromedusae_partial_dark
class: 68 of 120: hydromedusae_shapeA
class: 69 of 120: hydromedusae_shapeA_sideview_small
class: 70 of 120: hydromedusae_shapeB
class: 71 of 120: hydromedusae_sideview_big
class: 72 of 120: hydromedusae_solmaris
class: 73 of 120: hydromedusae_solmundella
class: 74 of 120: hydromedusae_typeD
class: 75 of 120: hydromedusae_typeD_bell_and_tentacles
class: 76 of 120: hydromedusae_typeE
class: 77 of 120: hydromedusae_typeF
class: 78 of 120: invertebrate_larvae_other_A
class: 79 of 120: invertebrate_larvae_other_B
class: 80 of 120: jellies_tentacles
class: 81 of 120: polychaete
class: 82 of 120: protist_dark_center
class: 83 of 120: protist_fuzzy_olive
class: 84 of 120: protist_noctiluca
class: 85 of 120: protist_other
class: 86 of 120: protist_star
class: 87 of 120: pteropod_butterfly
class: 88 of 120: pteropod_theco_dev_seq
class: 89 of 120: pteropod_triangle
class: 90 of 120: radiolarian_chain
class: 91 of 120: radiolarian_colony
class: 92 of 120: shrimp_caridean
class: 93 of 120: shrimp-like_other
class: 94 of 120: shrimp_sergestidae
class: 95 of 120: shrimp_zoea
class: 96 of 120: siphonophore_calycophoran_abylidae
class: 97 of 120: siphonophore_calycophoran_rocketship_adult
class: 98 of 120: siphonophore_calycophoran_rocketship_young
class: 99 of 120: siphonophore_calycophoran_sphaeronectes
class: 100 of 120: siphonophore_calycophoran_sphaeronectes_stem
class: 101 of 120: siphonophore_calycophoran_sphaeronectes_young
class: 102 of 120: siphonophore_other_parts
class: 103 of 120: siphonophore_partial
class: 104 of 120: siphonophore_physonect
class: 105 of 120: siphonophore_physonect_young
class: 106 of 120: stomatopod
class: 107 of 120: tornaria_acorn_worm_larvae
class: 108 of 120: trichodesmium_bowtie
class: 109 of 120: trichodesmium_multiple
class: 110 of 120: trichodesmium_puff
class: 111 of 120: trichodesmium_tuft
class: 112 of 120: trochophore_larvae
class: 113 of 120: tunicate_doliolid
class: 114 of 120: tunicate_doliolid_nurse
class: 115 of 120: tunicate_partial
class: 116 of 120: tunicate_salp
class: 117 of 120: tunicate_salp_chains
class: 118 of 120: unknown_blobs_and_smudges
class: 119 of 120: unknown_sticks
class: 120 of 120: unknown_unclassified
Finding batch size...
chosen batch size 3089 for 1 batches
Compiling forward prop...
Making predictions...
---------------------------------------------------------------------------
TimeoutError Traceback (most recent call last)
/afs/inf.ed.ac.uk/user/s13/s1320903/Neuroglycerin/neukrill-net-work/check_test_score.py in <module>()
145 'repeats predictions.', type=int, default=1)
146 args = parser.parse_args()
--> 147 check_score(args.run_settings, verbose=args.v, augment=args.augment)
/afs/inf.ed.ac.uk/user/s13/s1320903/Neuroglycerin/neukrill-net-work/check_test_score.py in check_score(run_settings_path, verbose, augment)
92 iterator = dataset.iterator(batch_size=batch_size,num_batches=n_batches,
93 mode='even_sequential', data_specs=data_specs)
---> 94 for batch in iterator:
95 if verbose:
96 print(" Batch {0} of {1}".format(i+1,n_batches*augment))
/afs/inf.ed.ac.uk/user/s13/s1320903/Neuroglycerin/neukrill-net-tools/neukrill_net/parallel_dataset.py in next(self)
35 Xbatch1,Xbatch2 = [np.array(batch).reshape(
36 self.batch_size, self.final_shape[0], self.final_shape[1], 1)
---> 37 for batch in zip(*self.result.get(timeout=10.0))]
38 elif len(self.final_shape) == 3:
39 Xbatch1,Xbatch2 = [np.array(batch)
/usr/lib/python2.7/multiprocessing/pool.pyc in get(self, timeout)
552 self.wait(timeout)
553 if not self._ready:
--> 554 raise TimeoutError
555 if self._success:
556 return self._value
TimeoutError:
In [43]:
%run check_test_score.py -v run_settings/experiment_setting_colnorms_aug.json
Loading settings..
Loading model...
Loading data...
class: 0 of 120: acantharia_protist
class: 1 of 120: acantharia_protist_big_center
class: 2 of 120: acantharia_protist_halo
class: 3 of 120: amphipods
class: 4 of 120: appendicularian_fritillaridae
class: 5 of 120: appendicularian_slight_curve
class: 6 of 120: appendicularian_s_shape
class: 7 of 120: appendicularian_straight
class: 8 of 120: artifacts
class: 9 of 120: artifacts_edge
class: 10 of 120: chaetognath_non_sagitta
class: 11 of 120: chaetognath_other
class: 12 of 120: chaetognath_sagitta
class: 13 of 120: chordate_type1
class: 14 of 120: copepod_calanoid
class: 15 of 120: copepod_calanoid_eggs
class: 16 of 120: copepod_calanoid_eucalanus
class: 17 of 120: copepod_calanoid_flatheads
class: 18 of 120: copepod_calanoid_frillyAntennae
class: 19 of 120: copepod_calanoid_large
class: 20 of 120: copepod_calanoid_large_side_antennatucked
class: 21 of 120: copepod_calanoid_octomoms
class: 22 of 120: copepod_calanoid_small_longantennae
class: 23 of 120: copepod_cyclopoid_copilia
class: 24 of 120: copepod_cyclopoid_oithona
class: 25 of 120: copepod_cyclopoid_oithona_eggs
class: 26 of 120: copepod_other
class: 27 of 120: crustacean_other
class: 28 of 120: ctenophore_cestid
class: 29 of 120: ctenophore_cydippid_no_tentacles
class: 30 of 120: ctenophore_cydippid_tentacles
class: 31 of 120: ctenophore_lobate
class: 32 of 120: decapods
class: 33 of 120: detritus_blob
class: 34 of 120: detritus_filamentous
class: 35 of 120: detritus_other
class: 36 of 120: diatom_chain_string
class: 37 of 120: diatom_chain_tube
class: 38 of 120: echinoderm_larva_pluteus_brittlestar
class: 39 of 120: echinoderm_larva_pluteus_early
class: 40 of 120: echinoderm_larva_pluteus_typeC
class: 41 of 120: echinoderm_larva_pluteus_urchin
class: 42 of 120: echinoderm_larva_seastar_bipinnaria
class: 43 of 120: echinoderm_larva_seastar_brachiolaria
class: 44 of 120: echinoderm_seacucumber_auricularia_larva
class: 45 of 120: echinopluteus
class: 46 of 120: ephyra
class: 47 of 120: euphausiids
class: 48 of 120: euphausiids_young
class: 49 of 120: fecal_pellet
class: 50 of 120: fish_larvae_deep_body
class: 51 of 120: fish_larvae_leptocephali
class: 52 of 120: fish_larvae_medium_body
class: 53 of 120: fish_larvae_myctophids
class: 54 of 120: fish_larvae_thin_body
class: 55 of 120: fish_larvae_very_thin_body
class: 56 of 120: heteropod
class: 57 of 120: hydromedusae_aglaura
class: 58 of 120: hydromedusae_bell_and_tentacles
class: 59 of 120: hydromedusae_h15
class: 60 of 120: hydromedusae_haliscera
class: 61 of 120: hydromedusae_haliscera_small_sideview
class: 62 of 120: hydromedusae_liriope
class: 63 of 120: hydromedusae_narco_dark
class: 64 of 120: hydromedusae_narcomedusae
class: 65 of 120: hydromedusae_narco_young
class: 66 of 120: hydromedusae_other
class: 67 of 120: hydromedusae_partial_dark
class: 68 of 120: hydromedusae_shapeA
class: 69 of 120: hydromedusae_shapeA_sideview_small
class: 70 of 120: hydromedusae_shapeB
class: 71 of 120: hydromedusae_sideview_big
class: 72 of 120: hydromedusae_solmaris
class: 73 of 120: hydromedusae_solmundella
class: 74 of 120: hydromedusae_typeD
class: 75 of 120: hydromedusae_typeD_bell_and_tentacles
class: 76 of 120: hydromedusae_typeE
class: 77 of 120: hydromedusae_typeF
class: 78 of 120: invertebrate_larvae_other_A
class: 79 of 120: invertebrate_larvae_other_B
class: 80 of 120: jellies_tentacles
class: 81 of 120: polychaete
class: 82 of 120: protist_dark_center
class: 83 of 120: protist_fuzzy_olive
class: 84 of 120: protist_noctiluca
class: 85 of 120: protist_other
class: 86 of 120: protist_star
class: 87 of 120: pteropod_butterfly
class: 88 of 120: pteropod_theco_dev_seq
class: 89 of 120: pteropod_triangle
class: 90 of 120: radiolarian_chain
class: 91 of 120: radiolarian_colony
class: 92 of 120: shrimp_caridean
class: 93 of 120: shrimp-like_other
class: 94 of 120: shrimp_sergestidae
class: 95 of 120: shrimp_zoea
class: 96 of 120: siphonophore_calycophoran_abylidae
class: 97 of 120: siphonophore_calycophoran_rocketship_adult
class: 98 of 120: siphonophore_calycophoran_rocketship_young
class: 99 of 120: siphonophore_calycophoran_sphaeronectes
class: 100 of 120: siphonophore_calycophoran_sphaeronectes_stem
class: 101 of 120: siphonophore_calycophoran_sphaeronectes_young
class: 102 of 120: siphonophore_other_parts
class: 103 of 120: siphonophore_partial
class: 104 of 120: siphonophore_physonect
class: 105 of 120: siphonophore_physonect_young
class: 106 of 120: stomatopod
class: 107 of 120: tornaria_acorn_worm_larvae
class: 108 of 120: trichodesmium_bowtie
class: 109 of 120: trichodesmium_multiple
class: 110 of 120: trichodesmium_puff
class: 111 of 120: trichodesmium_tuft
class: 112 of 120: trochophore_larvae
class: 113 of 120: tunicate_doliolid
class: 114 of 120: tunicate_doliolid_nurse
class: 115 of 120: tunicate_partial
class: 116 of 120: tunicate_salp
class: 117 of 120: tunicate_salp_chains
class: 118 of 120: unknown_blobs_and_smudges
class: 119 of 120: unknown_sticks
class: 120 of 120: unknown_unclassified
Finding batch size...
chosen batch size 3089 for 1 batches
Compiling forward prop...
Making predictions...
Batch 1 of 1
Log loss: 1.36543821403
In [45]:
%run check_test_score.py -v run_settings/experiment_setting_colnorms_higher_aug.json
Loading settings..
Loading model...
Loading data...
class: 0 of 120: acantharia_protist
class: 1 of 120: acantharia_protist_big_center
class: 2 of 120: acantharia_protist_halo
class: 3 of 120: amphipods
class: 4 of 120: appendicularian_fritillaridae
class: 5 of 120: appendicularian_slight_curve
class: 6 of 120: appendicularian_s_shape
class: 7 of 120: appendicularian_straight
class: 8 of 120: artifacts
class: 9 of 120: artifacts_edge
class: 10 of 120: chaetognath_non_sagitta
class: 11 of 120: chaetognath_other
class: 12 of 120: chaetognath_sagitta
class: 13 of 120: chordate_type1
class: 14 of 120: copepod_calanoid
class: 15 of 120: copepod_calanoid_eggs
class: 16 of 120: copepod_calanoid_eucalanus
class: 17 of 120: copepod_calanoid_flatheads
class: 18 of 120: copepod_calanoid_frillyAntennae
class: 19 of 120: copepod_calanoid_large
class: 20 of 120: copepod_calanoid_large_side_antennatucked
class: 21 of 120: copepod_calanoid_octomoms
class: 22 of 120: copepod_calanoid_small_longantennae
class: 23 of 120: copepod_cyclopoid_copilia
class: 24 of 120: copepod_cyclopoid_oithona
class: 25 of 120: copepod_cyclopoid_oithona_eggs
class: 26 of 120: copepod_other
class: 27 of 120: crustacean_other
class: 28 of 120: ctenophore_cestid
class: 29 of 120: ctenophore_cydippid_no_tentacles
class: 30 of 120: ctenophore_cydippid_tentacles
class: 31 of 120: ctenophore_lobate
class: 32 of 120: decapods
class: 33 of 120: detritus_blob
class: 34 of 120: detritus_filamentous
class: 35 of 120: detritus_other
class: 36 of 120: diatom_chain_string
class: 37 of 120: diatom_chain_tube
class: 38 of 120: echinoderm_larva_pluteus_brittlestar
class: 39 of 120: echinoderm_larva_pluteus_early
class: 40 of 120: echinoderm_larva_pluteus_typeC
class: 41 of 120: echinoderm_larva_pluteus_urchin
class: 42 of 120: echinoderm_larva_seastar_bipinnaria
class: 43 of 120: echinoderm_larva_seastar_brachiolaria
class: 44 of 120: echinoderm_seacucumber_auricularia_larva
class: 45 of 120: echinopluteus
class: 46 of 120: ephyra
class: 47 of 120: euphausiids
class: 48 of 120: euphausiids_young
class: 49 of 120: fecal_pellet
class: 50 of 120: fish_larvae_deep_body
class: 51 of 120: fish_larvae_leptocephali
class: 52 of 120: fish_larvae_medium_body
class: 53 of 120: fish_larvae_myctophids
class: 54 of 120: fish_larvae_thin_body
class: 55 of 120: fish_larvae_very_thin_body
class: 56 of 120: heteropod
class: 57 of 120: hydromedusae_aglaura
class: 58 of 120: hydromedusae_bell_and_tentacles
class: 59 of 120: hydromedusae_h15
class: 60 of 120: hydromedusae_haliscera
class: 61 of 120: hydromedusae_haliscera_small_sideview
class: 62 of 120: hydromedusae_liriope
class: 63 of 120: hydromedusae_narco_dark
class: 64 of 120: hydromedusae_narcomedusae
class: 65 of 120: hydromedusae_narco_young
class: 66 of 120: hydromedusae_other
class: 67 of 120: hydromedusae_partial_dark
class: 68 of 120: hydromedusae_shapeA
class: 69 of 120: hydromedusae_shapeA_sideview_small
class: 70 of 120: hydromedusae_shapeB
class: 71 of 120: hydromedusae_sideview_big
class: 72 of 120: hydromedusae_solmaris
class: 73 of 120: hydromedusae_solmundella
class: 74 of 120: hydromedusae_typeD
class: 75 of 120: hydromedusae_typeD_bell_and_tentacles
class: 76 of 120: hydromedusae_typeE
class: 77 of 120: hydromedusae_typeF
class: 78 of 120: invertebrate_larvae_other_A
class: 79 of 120: invertebrate_larvae_other_B
class: 80 of 120: jellies_tentacles
class: 81 of 120: polychaete
class: 82 of 120: protist_dark_center
class: 83 of 120: protist_fuzzy_olive
class: 84 of 120: protist_noctiluca
class: 85 of 120: protist_other
class: 86 of 120: protist_star
class: 87 of 120: pteropod_butterfly
class: 88 of 120: pteropod_theco_dev_seq
class: 89 of 120: pteropod_triangle
class: 90 of 120: radiolarian_chain
class: 91 of 120: radiolarian_colony
class: 92 of 120: shrimp_caridean
class: 93 of 120: shrimp-like_other
class: 94 of 120: shrimp_sergestidae
class: 95 of 120: shrimp_zoea
class: 96 of 120: siphonophore_calycophoran_abylidae
class: 97 of 120: siphonophore_calycophoran_rocketship_adult
class: 98 of 120: siphonophore_calycophoran_rocketship_young
class: 99 of 120: siphonophore_calycophoran_sphaeronectes
class: 100 of 120: siphonophore_calycophoran_sphaeronectes_stem
class: 101 of 120: siphonophore_calycophoran_sphaeronectes_young
class: 102 of 120: siphonophore_other_parts
class: 103 of 120: siphonophore_partial
class: 104 of 120: siphonophore_physonect
class: 105 of 120: siphonophore_physonect_young
class: 106 of 120: stomatopod
class: 107 of 120: tornaria_acorn_worm_larvae
class: 108 of 120: trichodesmium_bowtie
class: 109 of 120: trichodesmium_multiple
class: 110 of 120: trichodesmium_puff
class: 111 of 120: trichodesmium_tuft
class: 112 of 120: trochophore_larvae
class: 113 of 120: tunicate_doliolid
class: 114 of 120: tunicate_doliolid_nurse
class: 115 of 120: tunicate_partial
class: 116 of 120: tunicate_salp
class: 117 of 120: tunicate_salp_chains
class: 118 of 120: unknown_blobs_and_smudges
class: 119 of 120: unknown_sticks
class: 120 of 120: unknown_unclassified
Finding batch size...
chosen batch size 3089 for 1 batches
Compiling forward prop...
Making predictions...
Batch 1 of 1
Log loss: 0.935334935387
In [47]:
%run check_test_score.py -v run_settings/replicate_8aug.json
Loading settings..
Loading model...
Loading data...
class: 0 of 120: acantharia_protist
class: 1 of 120: acantharia_protist_big_center
class: 2 of 120: acantharia_protist_halo
class: 3 of 120: amphipods
class: 4 of 120: appendicularian_fritillaridae
class: 5 of 120: appendicularian_slight_curve
class: 6 of 120: appendicularian_s_shape
class: 7 of 120: appendicularian_straight
class: 8 of 120: artifacts
class: 9 of 120: artifacts_edge
class: 10 of 120: chaetognath_non_sagitta
class: 11 of 120: chaetognath_other
class: 12 of 120: chaetognath_sagitta
class: 13 of 120: chordate_type1
class: 14 of 120: copepod_calanoid
class: 15 of 120: copepod_calanoid_eggs
class: 16 of 120: copepod_calanoid_eucalanus
class: 17 of 120: copepod_calanoid_flatheads
class: 18 of 120: copepod_calanoid_frillyAntennae
class: 19 of 120: copepod_calanoid_large
class: 20 of 120: copepod_calanoid_large_side_antennatucked
class: 21 of 120: copepod_calanoid_octomoms
class: 22 of 120: copepod_calanoid_small_longantennae
class: 23 of 120: copepod_cyclopoid_copilia
class: 24 of 120: copepod_cyclopoid_oithona
class: 25 of 120: copepod_cyclopoid_oithona_eggs
class: 26 of 120: copepod_other
class: 27 of 120: crustacean_other
class: 28 of 120: ctenophore_cestid
class: 29 of 120: ctenophore_cydippid_no_tentacles
class: 30 of 120: ctenophore_cydippid_tentacles
class: 31 of 120: ctenophore_lobate
class: 32 of 120: decapods
class: 33 of 120: detritus_blob
class: 34 of 120: detritus_filamentous
class: 35 of 120: detritus_other
class: 36 of 120: diatom_chain_string
class: 37 of 120: diatom_chain_tube
class: 38 of 120: echinoderm_larva_pluteus_brittlestar
class: 39 of 120: echinoderm_larva_pluteus_early
class: 40 of 120: echinoderm_larva_pluteus_typeC
class: 41 of 120: echinoderm_larva_pluteus_urchin
class: 42 of 120: echinoderm_larva_seastar_bipinnaria
class: 43 of 120: echinoderm_larva_seastar_brachiolaria
class: 44 of 120: echinoderm_seacucumber_auricularia_larva
class: 45 of 120: echinopluteus
class: 46 of 120: ephyra
class: 47 of 120: euphausiids
class: 48 of 120: euphausiids_young
class: 49 of 120: fecal_pellet
class: 50 of 120: fish_larvae_deep_body
class: 51 of 120: fish_larvae_leptocephali
class: 52 of 120: fish_larvae_medium_body
class: 53 of 120: fish_larvae_myctophids
class: 54 of 120: fish_larvae_thin_body
class: 55 of 120: fish_larvae_very_thin_body
class: 56 of 120: heteropod
class: 57 of 120: hydromedusae_aglaura
class: 58 of 120: hydromedusae_bell_and_tentacles
class: 59 of 120: hydromedusae_h15
class: 60 of 120: hydromedusae_haliscera
class: 61 of 120: hydromedusae_haliscera_small_sideview
class: 62 of 120: hydromedusae_liriope
class: 63 of 120: hydromedusae_narco_dark
class: 64 of 120: hydromedusae_narcomedusae
class: 65 of 120: hydromedusae_narco_young
class: 66 of 120: hydromedusae_other
class: 67 of 120: hydromedusae_partial_dark
class: 68 of 120: hydromedusae_shapeA
class: 69 of 120: hydromedusae_shapeA_sideview_small
class: 70 of 120: hydromedusae_shapeB
class: 71 of 120: hydromedusae_sideview_big
class: 72 of 120: hydromedusae_solmaris
class: 73 of 120: hydromedusae_solmundella
class: 74 of 120: hydromedusae_typeD
class: 75 of 120: hydromedusae_typeD_bell_and_tentacles
class: 76 of 120: hydromedusae_typeE
class: 77 of 120: hydromedusae_typeF
class: 78 of 120: invertebrate_larvae_other_A
class: 79 of 120: invertebrate_larvae_other_B
class: 80 of 120: jellies_tentacles
class: 81 of 120: polychaete
class: 82 of 120: protist_dark_center
class: 83 of 120: protist_fuzzy_olive
class: 84 of 120: protist_noctiluca
class: 85 of 120: protist_other
class: 86 of 120: protist_star
class: 87 of 120: pteropod_butterfly
class: 88 of 120: pteropod_theco_dev_seq
class: 89 of 120: pteropod_triangle
class: 90 of 120: radiolarian_chain
class: 91 of 120: radiolarian_colony
class: 92 of 120: shrimp_caridean
class: 93 of 120: shrimp-like_other
class: 94 of 120: shrimp_sergestidae
class: 95 of 120: shrimp_zoea
class: 96 of 120: siphonophore_calycophoran_abylidae
class: 97 of 120: siphonophore_calycophoran_rocketship_adult
class: 98 of 120: siphonophore_calycophoran_rocketship_young
class: 99 of 120: siphonophore_calycophoran_sphaeronectes
class: 100 of 120: siphonophore_calycophoran_sphaeronectes_stem
class: 101 of 120: siphonophore_calycophoran_sphaeronectes_young
class: 102 of 120: siphonophore_other_parts
class: 103 of 120: siphonophore_partial
class: 104 of 120: siphonophore_physonect
class: 105 of 120: siphonophore_physonect_young
class: 106 of 120: stomatopod
class: 107 of 120: tornaria_acorn_worm_larvae
class: 108 of 120: trichodesmium_bowtie
class: 109 of 120: trichodesmium_multiple
class: 110 of 120: trichodesmium_puff
class: 111 of 120: trichodesmium_tuft
class: 112 of 120: trochophore_larvae
class: 113 of 120: tunicate_doliolid
class: 114 of 120: tunicate_doliolid_nurse
class: 115 of 120: tunicate_partial
class: 116 of 120: tunicate_salp
class: 117 of 120: tunicate_salp_chains
class: 118 of 120: unknown_blobs_and_smudges
class: 119 of 120: unknown_sticks
class: 120 of 120: unknown_unclassified
Finding batch size...
chosen batch size 3089 for 1 batches
Compiling forward prop...
Making predictions...
Batch 1 of 1
Log loss: 0.886893997188
In [48]:
%run check_test_score.py -v run_settings/replicate_8aug_repeat.json
Loading settings..
Loading model...
Loading data...
class: 0 of 120: acantharia_protist
class: 1 of 120: acantharia_protist_big_center
class: 2 of 120: acantharia_protist_halo
class: 3 of 120: amphipods
class: 4 of 120: appendicularian_fritillaridae
class: 5 of 120: appendicularian_slight_curve
class: 6 of 120: appendicularian_s_shape
class: 7 of 120: appendicularian_straight
class: 8 of 120: artifacts
class: 9 of 120: artifacts_edge
class: 10 of 120: chaetognath_non_sagitta
class: 11 of 120: chaetognath_other
class: 12 of 120: chaetognath_sagitta
class: 13 of 120: chordate_type1
class: 14 of 120: copepod_calanoid
class: 15 of 120: copepod_calanoid_eggs
class: 16 of 120: copepod_calanoid_eucalanus
class: 17 of 120: copepod_calanoid_flatheads
class: 18 of 120: copepod_calanoid_frillyAntennae
class: 19 of 120: copepod_calanoid_large
class: 20 of 120: copepod_calanoid_large_side_antennatucked
class: 21 of 120: copepod_calanoid_octomoms
class: 22 of 120: copepod_calanoid_small_longantennae
class: 23 of 120: copepod_cyclopoid_copilia
class: 24 of 120: copepod_cyclopoid_oithona
class: 25 of 120: copepod_cyclopoid_oithona_eggs
class: 26 of 120: copepod_other
class: 27 of 120: crustacean_other
class: 28 of 120: ctenophore_cestid
class: 29 of 120: ctenophore_cydippid_no_tentacles
class: 30 of 120: ctenophore_cydippid_tentacles
class: 31 of 120: ctenophore_lobate
class: 32 of 120: decapods
class: 33 of 120: detritus_blob
class: 34 of 120: detritus_filamentous
class: 35 of 120: detritus_other
class: 36 of 120: diatom_chain_string
class: 37 of 120: diatom_chain_tube
class: 38 of 120: echinoderm_larva_pluteus_brittlestar
class: 39 of 120: echinoderm_larva_pluteus_early
class: 40 of 120: echinoderm_larva_pluteus_typeC
class: 41 of 120: echinoderm_larva_pluteus_urchin
class: 42 of 120: echinoderm_larva_seastar_bipinnaria
class: 43 of 120: echinoderm_larva_seastar_brachiolaria
class: 44 of 120: echinoderm_seacucumber_auricularia_larva
class: 45 of 120: echinopluteus
class: 46 of 120: ephyra
class: 47 of 120: euphausiids
class: 48 of 120: euphausiids_young
class: 49 of 120: fecal_pellet
class: 50 of 120: fish_larvae_deep_body
class: 51 of 120: fish_larvae_leptocephali
class: 52 of 120: fish_larvae_medium_body
class: 53 of 120: fish_larvae_myctophids
class: 54 of 120: fish_larvae_thin_body
class: 55 of 120: fish_larvae_very_thin_body
class: 56 of 120: heteropod
class: 57 of 120: hydromedusae_aglaura
class: 58 of 120: hydromedusae_bell_and_tentacles
class: 59 of 120: hydromedusae_h15
class: 60 of 120: hydromedusae_haliscera
class: 61 of 120: hydromedusae_haliscera_small_sideview
class: 62 of 120: hydromedusae_liriope
class: 63 of 120: hydromedusae_narco_dark
class: 64 of 120: hydromedusae_narcomedusae
class: 65 of 120: hydromedusae_narco_young
class: 66 of 120: hydromedusae_other
class: 67 of 120: hydromedusae_partial_dark
class: 68 of 120: hydromedusae_shapeA
class: 69 of 120: hydromedusae_shapeA_sideview_small
class: 70 of 120: hydromedusae_shapeB
class: 71 of 120: hydromedusae_sideview_big
class: 72 of 120: hydromedusae_solmaris
class: 73 of 120: hydromedusae_solmundella
class: 74 of 120: hydromedusae_typeD
class: 75 of 120: hydromedusae_typeD_bell_and_tentacles
class: 76 of 120: hydromedusae_typeE
class: 77 of 120: hydromedusae_typeF
class: 78 of 120: invertebrate_larvae_other_A
class: 79 of 120: invertebrate_larvae_other_B
class: 80 of 120: jellies_tentacles
class: 81 of 120: polychaete
class: 82 of 120: protist_dark_center
class: 83 of 120: protist_fuzzy_olive
class: 84 of 120: protist_noctiluca
class: 85 of 120: protist_other
class: 86 of 120: protist_star
class: 87 of 120: pteropod_butterfly
class: 88 of 120: pteropod_theco_dev_seq
class: 89 of 120: pteropod_triangle
class: 90 of 120: radiolarian_chain
class: 91 of 120: radiolarian_colony
class: 92 of 120: shrimp_caridean
class: 93 of 120: shrimp-like_other
class: 94 of 120: shrimp_sergestidae
class: 95 of 120: shrimp_zoea
class: 96 of 120: siphonophore_calycophoran_abylidae
class: 97 of 120: siphonophore_calycophoran_rocketship_adult
class: 98 of 120: siphonophore_calycophoran_rocketship_young
class: 99 of 120: siphonophore_calycophoran_sphaeronectes
class: 100 of 120: siphonophore_calycophoran_sphaeronectes_stem
class: 101 of 120: siphonophore_calycophoran_sphaeronectes_young
class: 102 of 120: siphonophore_other_parts
class: 103 of 120: siphonophore_partial
class: 104 of 120: siphonophore_physonect
class: 105 of 120: siphonophore_physonect_young
class: 106 of 120: stomatopod
class: 107 of 120: tornaria_acorn_worm_larvae
class: 108 of 120: trichodesmium_bowtie
class: 109 of 120: trichodesmium_multiple
class: 110 of 120: trichodesmium_puff
class: 111 of 120: trichodesmium_tuft
class: 112 of 120: trochophore_larvae
class: 113 of 120: tunicate_doliolid
class: 114 of 120: tunicate_doliolid_nurse
class: 115 of 120: tunicate_partial
class: 116 of 120: tunicate_salp
class: 117 of 120: tunicate_salp_chains
class: 118 of 120: unknown_blobs_and_smudges
class: 119 of 120: unknown_sticks
class: 120 of 120: unknown_unclassified
Finding batch size...
chosen batch size 3089 for 1 batches
Compiling forward prop...
Making predictions...
Batch 1 of 1
Log loss: 3.01278362328
In [50]:
%run check_test_score.py -v run_settings/replicate_8aug_lrschedule.json
Loading settings..
---------------------------------------------------------------------------
IOError Traceback (most recent call last)
/afs/inf.ed.ac.uk/user/s13/s1320903/Neuroglycerin/neukrill-net-work/check_test_score.py in <module>()
145 'repeats predictions.', type=int, default=1)
146 args = parser.parse_args()
--> 147 check_score(args.run_settings, verbose=args.v, augment=args.augment)
/afs/inf.ed.ac.uk/user/s13/s1320903/Neuroglycerin/neukrill-net-work/check_test_score.py in check_score(run_settings_path, verbose, augment)
29 settings = neukrill_net.utils.Settings("settings.json")
30 run_settings = neukrill_net.utils.load_run_settings(run_settings_path,
---> 31 settings, force=True)
32
33 # load the model
/afs/inf.ed.ac.uk/user/s13/s1320903/Neuroglycerin/neukrill-net-tools/neukrill_net/utils.pyc in load_run_settings(run_settings_path, settings, settings_path, verbose, force)
392 * modeldir - directory in which to save models
393 * pickle abspath - abspath where _this_ run will save its pickle file
--> 394 """
395
396 with open(run_settings_path) as rf:
IOError: [Errno 2] No such file or directory: 'run_settings/replicate_8aug_lrschedule.json'
Find best hierarchical model:
In [6]:
%run check_test_score.py -v run_settings/alexnet_based_extra_convlayer_with_superclasses_testAug.json
Running run_settings/alexnet_based_extra_convlayer_with_superclasses_testAug.json predictions.
Loading settings..
Loading model...
Loading data...
Applying normalisation: global
Finding batch size...
chosen batch size 3089 for 2 batches per pass
Compiling forward prop...
Making predictions...
Batch 1 of 2
Batch 2 of 2
Collapsing predictions...
/afs/inf.ed.ac.uk/user/s13/s1320903/Neuroglycerin/pylearn2/pylearn2/utils/iteration.py:783: UserWarning: dataset is using the old iterator interface which is deprecated and will become officially unsupported as of July 28, 2015. The dataset should implement a `get` method respecting the new interface.
warnings.warn("dataset is using the old iterator interface which "
---------------------------------------------------------------------------
ValueError Traceback (most recent call last)
/afs/inf.ed.ac.uk/user/s13/s1320903/Neuroglycerin/neukrill-net-work/check_test_score.py in <module>()
174 y,labels = make_predictions(run_settings, verbose=args.v, augment=args.augment)
175 predictions.append(y)
--> 176 check_score(labels, args.run_settings, predictions, verbose=args.v)
/afs/inf.ed.ac.uk/user/s13/s1320903/Neuroglycerin/neukrill-net-work/check_test_score.py in check_score(labels, run_settings, y_arrays, verbose)
148 else:
149 # calculate score
--> 150 logloss = sklearn.metrics.log_loss(labels,y_arrays[0])
151 print("Log loss: {0}".format(logloss))
152 return logloss
/afs/inf.ed.ac.uk/user/s13/s1320903/Neuroglycerin/venv/lib/python2.7/site-packages/sklearn/metrics/metrics.pyc in log_loss(y_true, y_pred, eps, normalize)
1118
1119 # Check if dimensions are consistent.
-> 1120 T, Y = check_arrays(T, Y)
1121 if T.shape[1] != Y.shape[1]:
1122 raise ValueError("y_true and y_pred have different number of classes "
/afs/inf.ed.ac.uk/user/s13/s1320903/Neuroglycerin/venv/lib/python2.7/site-packages/sklearn/utils/validation.pyc in check_arrays(*arrays, **options)
252 if size != n_samples:
253 raise ValueError("Found array with dim %d. Expected %d"
--> 254 % (size, n_samples))
255
256 if not allow_lists or hasattr(array, "shape"):
ValueError: Found array with dim 3089. Expected 1545
In [10]:
%env THEANO_FLAGS = device=gpu0,floatX=float32,base_compiledir=~/.theano/stonesoup0
env: THEANO_FLAGS=device=gpu0,floatX=float32,base_compiledir=~/.theano/stonesoup0
In [14]:
%run check_test_score.py -v --augment 16 run_settings/experiment_highcolnorms_aug_lr.json
Running run_settings/experiment_highcolnorms_aug_lr.json predictions.
Loading settings..
Loading model...
Loading data...
class: 0 of 120: acantharia_protist
class: 1 of 120: acantharia_protist_big_center
class: 2 of 120: acantharia_protist_halo
class: 3 of 120: amphipods
class: 4 of 120: appendicularian_fritillaridae
class: 5 of 120: appendicularian_slight_curve
class: 6 of 120: appendicularian_s_shape
class: 7 of 120: appendicularian_straight
class: 8 of 120: artifacts
class: 9 of 120: artifacts_edge
class: 10 of 120: chaetognath_non_sagitta
class: 11 of 120: chaetognath_other
class: 12 of 120: chaetognath_sagitta
class: 13 of 120: chordate_type1
class: 14 of 120: copepod_calanoid
class: 15 of 120: copepod_calanoid_eggs
class: 16 of 120: copepod_calanoid_eucalanus
class: 17 of 120: copepod_calanoid_flatheads
class: 18 of 120: copepod_calanoid_frillyAntennae
class: 19 of 120: copepod_calanoid_large
class: 20 of 120: copepod_calanoid_large_side_antennatucked
class: 21 of 120: copepod_calanoid_octomoms
class: 22 of 120: copepod_calanoid_small_longantennae
class: 23 of 120: copepod_cyclopoid_copilia
class: 24 of 120: copepod_cyclopoid_oithona
class: 25 of 120: copepod_cyclopoid_oithona_eggs
class: 26 of 120: copepod_other
class: 27 of 120: crustacean_other
class: 28 of 120: ctenophore_cestid
class: 29 of 120: ctenophore_cydippid_no_tentacles
class: 30 of 120: ctenophore_cydippid_tentacles
class: 31 of 120: ctenophore_lobate
class: 32 of 120: decapods
class: 33 of 120: detritus_blob
class: 34 of 120: detritus_filamentous
class: 35 of 120: detritus_other
class: 36 of 120: diatom_chain_string
class: 37 of 120: diatom_chain_tube
class: 38 of 120: echinoderm_larva_pluteus_brittlestar
class: 39 of 120: echinoderm_larva_pluteus_early
class: 40 of 120: echinoderm_larva_pluteus_typeC
class: 41 of 120: echinoderm_larva_pluteus_urchin
class: 42 of 120: echinoderm_larva_seastar_bipinnaria
class: 43 of 120: echinoderm_larva_seastar_brachiolaria
class: 44 of 120: echinoderm_seacucumber_auricularia_larva
class: 45 of 120: echinopluteus
class: 46 of 120: ephyra
class: 47 of 120: euphausiids
class: 48 of 120: euphausiids_young
class: 49 of 120: fecal_pellet
class: 50 of 120: fish_larvae_deep_body
class: 51 of 120: fish_larvae_leptocephali
class: 52 of 120: fish_larvae_medium_body
class: 53 of 120: fish_larvae_myctophids
class: 54 of 120: fish_larvae_thin_body
class: 55 of 120: fish_larvae_very_thin_body
class: 56 of 120: heteropod
class: 57 of 120: hydromedusae_aglaura
class: 58 of 120: hydromedusae_bell_and_tentacles
class: 59 of 120: hydromedusae_h15
class: 60 of 120: hydromedusae_haliscera
class: 61 of 120: hydromedusae_haliscera_small_sideview
class: 62 of 120: hydromedusae_liriope
class: 63 of 120: hydromedusae_narco_dark
class: 64 of 120: hydromedusae_narcomedusae
class: 65 of 120: hydromedusae_narco_young
class: 66 of 120: hydromedusae_other
class: 67 of 120: hydromedusae_partial_dark
class: 68 of 120: hydromedusae_shapeA
class: 69 of 120: hydromedusae_shapeA_sideview_small
class: 70 of 120: hydromedusae_shapeB
class: 71 of 120: hydromedusae_sideview_big
class: 72 of 120: hydromedusae_solmaris
class: 73 of 120: hydromedusae_solmundella
class: 74 of 120: hydromedusae_typeD
class: 75 of 120: hydromedusae_typeD_bell_and_tentacles
class: 76 of 120: hydromedusae_typeE
class: 77 of 120: hydromedusae_typeF
class: 78 of 120: invertebrate_larvae_other_A
class: 79 of 120: invertebrate_larvae_other_B
class: 80 of 120: jellies_tentacles
class: 81 of 120: polychaete
class: 82 of 120: protist_dark_center
class: 83 of 120: protist_fuzzy_olive
class: 84 of 120: protist_noctiluca
class: 85 of 120: protist_other
class: 86 of 120: protist_star
class: 87 of 120: pteropod_butterfly
class: 88 of 120: pteropod_theco_dev_seq
class: 89 of 120: pteropod_triangle
class: 90 of 120: radiolarian_chain
class: 91 of 120: radiolarian_colony
class: 92 of 120: shrimp_caridean
class: 93 of 120: shrimp-like_other
class: 94 of 120: shrimp_sergestidae
class: 95 of 120: shrimp_zoea
class: 96 of 120: siphonophore_calycophoran_abylidae
class: 97 of 120: siphonophore_calycophoran_rocketship_adult
class: 98 of 120: siphonophore_calycophoran_rocketship_young
class: 99 of 120: siphonophore_calycophoran_sphaeronectes
class: 100 of 120: siphonophore_calycophoran_sphaeronectes_stem
class: 101 of 120: siphonophore_calycophoran_sphaeronectes_young
class: 102 of 120: siphonophore_other_parts
class: 103 of 120: siphonophore_partial
class: 104 of 120: siphonophore_physonect
class: 105 of 120: siphonophore_physonect_young
class: 106 of 120: stomatopod
class: 107 of 120: tornaria_acorn_worm_larvae
class: 108 of 120: trichodesmium_bowtie
class: 109 of 120: trichodesmium_multiple
class: 110 of 120: trichodesmium_puff
class: 111 of 120: trichodesmium_tuft
class: 112 of 120: trochophore_larvae
class: 113 of 120: tunicate_doliolid
class: 114 of 120: tunicate_doliolid_nurse
class: 115 of 120: tunicate_partial
class: 116 of 120: tunicate_salp
class: 117 of 120: tunicate_salp_chains
class: 118 of 120: unknown_blobs_and_smudges
class: 119 of 120: unknown_sticks
class: 120 of 120: unknown_unclassified
Finding batch size...
chosen batch size 3089 for 1 batches per pass
Compiling forward prop...
Making predictions...
---------------------------------------------------------------------------
TimeoutError Traceback (most recent call last)
/afs/inf.ed.ac.uk/user/s13/s1320903/Neuroglycerin/neukrill-net-work/check_test_score.py in <module>()
172 if args.v:
173 print("Running {0} predictions.".format(run_settings))
--> 174 y,labels = make_predictions(run_settings, verbose=args.v, augment=args.augment)
175 predictions.append(y)
176 check_score(labels, args.run_settings, predictions, verbose=args.v)
/afs/inf.ed.ac.uk/user/s13/s1320903/Neuroglycerin/neukrill-net-work/check_test_score.py in make_predictions(run_settings_path, verbose, augment)
90 iterator = dataset.iterator(batch_size=batch_size,num_batches=n_batches,
91 mode='even_sequential', data_specs=data_specs)
---> 92 for batch in iterator:
93 if verbose:
94 print(" Batch {0} of {1}".format(i+1,n_batches*augment))
/afs/inf.ed.ac.uk/user/s13/s1320903/Neuroglycerin/neukrill-net-tools/neukrill_net/image_directory_dataset.py in next(self)
82 # allocate array
83 if len(self.final_shape) == 2:
---> 84 Xbatch = np.array(self.result.get(timeout=10.0)).reshape(
85 self.batch_size, self.final_shape[0],
86 self.final_shape[1], 1)
/usr/lib/python2.7/multiprocessing/pool.pyc in get(self, timeout)
552 self.wait(timeout)
553 if not self._ready:
--> 554 raise TimeoutError
555 if self._success:
556 return self._value
TimeoutError:
In [ ]:
Content source: Neuroglycerin/neukrill-net-work
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