Closed yonromai closed 11 months ago
@dhimmel I added a new commit to address the changes that you asked for:
efo_label
Here are the first 10 lines of the updates output:
identifier precision proba_high proba_medium proba_low rs_classification efo_label prefix is_gwas_trait depth n_ancestors n_descendants intrinsic_ic intrinsic_ic_scaled intrinsic_ic_sanchez intrinsic_ic_sanchez_scaled n_parents n_roots n_children n_leaves xref__doid__count xref__gard__count xref__icd10__count xref__icd9__count xref__meddra__count xref__mesh__count xref__mondo__count xref__ncit__count xref__omim__count xref__omimps__count xref__orphanet__count xref__snomedct__count xref__umls__count pca_te_0 pca_te_1 pca_te_2 pca_te_3 pca_te_4 pca_te_5 pca_te_6 pca_te_7 pca_te_8 pca_te_9 pca_te_10 pca_te_11 pca_te_12 pca_te_13 pca_te_14 pca_te_15 pca_te_16 pca_te_17 pca_te_18 pca_te_19 pca_te_20 pca_te_21 pca_te_22 pca_te_23 pca_te_24 pca_te_25 pca_te_26 pca_te_27 pca_te_28 pca_te_29 pca_te_30 pca_te_31 pca_te_32 pca_te_33 pca_te_34 pca_te_35 pca_te_36 pca_te_37 pca_te_38 pca_te_39 pca_te_40 pca_te_41 pca_te_42 pca_te_43 pca_te_44 pca_te_45 pca_te_46 pca_te_47 pca_te_48 pca_te_49 pca_te_50 pca_te_51 pca_te_52 pca_te_53 pca_te_54 pca_te_55 pca_te_56 pca_te_57 pca_te_58 pca_te_59 pca_te_60 pca_te_61 pca_te_62 pca_te_63
DOID:0050890 low 0.00028 0.00063 0.99909 03-disease-area synucleinopathy doid False 3.0 7.0 8.0 8.055514335632324 0.7948248386383057 9.40687084197998 0.9541544318199158 2.0 2.0 2.0 4.0 0.0 0.0 0.0 0.0 0.0 1.0 1.0 0.0 0.0 0.0 0.0 0.0 1.0 -1.5259480476379395 -0.2341545969247818 -1.2303614616394043 -0.8325576186180115 -0.25777679681777954 1.145113229751587 1.3971177339553833 0.4552121162414551 -0.836563766002655 0.0354347750544548 -1.119293451309204 0.9378551244735718 0.18755923211574554 -0.7050077319145203 -0.3098467290401459 -0.1833728551864624 1.1776245832443237 -0.071957528591156 -0.4185025095939636 0.22024321556091309 0.5185545682907104 -0.6280837059020996 0.19802966713905334 0.07362869381904602 -0.2590044438838959 0.14766231179237366 0.004614487290382385 0.47755593061447144 -0.06752994656562805 0.24133142828941345 0.17379988729953766 -0.4488271474838257 0.28419846296310425 0.6668939590454102 0.17590837180614471 0.6661109328269958 0.2558993995189667 -0.05613671988248825 0.19678303599357605 0.09166446328163147 0.19197209179401398 -0.05938752368092537 0.1201208233833313 -0.2938452363014221 0.22624200582504272 -0.17448432743549347 -0.3885856866836548 -0.17940837144851685 -0.4560741186141968 0.052791789174079895 0.17347118258476257 0.022671625018119812 -0.40328696370124817 -0.10279969871044159 0.03752683103084564 -0.19509345293045044 0.3398292362689972 -0.023118361830711365 -0.1852674037218094 -0.10801161825656891 0.298456072807312 0.16781677305698395 -0.33339065313339233 -0.04248553514480591
DOID:10113 medium 0.00058 0.99845 0.00098 02-disease-root trypanosomiasis doid False 3.0 4.0 5.0 8.525518417358398 0.8411993384361267 9.299240112304688 0.9432372450828552 1.0 1.0 3.0 3.0 0.0 0.0 0.0 2.0 0.0 1.0 1.0 0.0 0.0 0.0 0.0 1.0 1.0 -4.292663097381592 -0.012410089373588562 1.8242411613464355 1.935802936553955 0.06222572177648544 0.20745515823364258 -1.3777449131011963 -0.17498718202114105 0.15651896595954895 -0.4573137164115906 0.010859286412596703 0.297838419675827 -0.43391120433807373 -0.6581568717956543 -0.13336409628391266 0.017675593495368958 0.05749864503741264 -0.5611717700958252 0.0094582699239254 0.27805519104003906 0.11908496916294098 -0.5299090147018433 -0.4223472476005554 0.17494449019432068 0.2497742772102356 0.13226579129695892 0.21576140820980072 0.3098200857639313 -0.1536838412284851 -0.3770142197608948 -0.0462801419198513 0.4301183521747589 0.37766098976135254 -0.19248944520950317 -0.01779669150710106 0.46696823835372925 -0.3602733016014099 -0.4248644709587097 -0.2502250075340271 -0.26503461599349976 -0.17517341673374176 -0.08410072326660156 -0.2338671088218689 0.3454975187778473 -0.24611784517765045 0.0016789063811302185 0.02755538374185562 -0.1982964724302292 -0.14963236451148987 0.2049160599708557 -0.02968670427799225 0.012656927108764648 0.09475623071193695 -0.44386792182922363 -0.125501811504364 -0.09200803190469742 0.04397750645875931 -0.09944383054971695 -0.14161255955696106 0.05635999143123627 -0.10539209842681885 0.02940986305475235 0.18866941332817078 -0.2048323154449463
DOID:10718 medium 0.00117 0.99883 0.00000 02-disease-root giardiasis doid False 3.0 8.0 1.0 10.134956359863281 1.0 9.741073608398438 0.9880530834197998 2.0 2.0 0.0 1.0 0.0 0.0 0.0 1.0 0.0 1.0 1.0 0.0 0.0 0.0 0.0 2.0 1.0 -2.1711859703063965 2.1476523876190186 0.3029290437698364 2.2319693565368652 0.3124423027038574 -1.3254098892211914 -0.5455265045166016 0.02479447051882744 -1.3186272382736206 0.6500306129455566 0.10565608739852905 0.30391302704811096 0.4161183536052704 -0.09474004805088043 0.05271919071674347 0.15169045329093933 0.5001036524772644 -0.558479905128479 1.0360777378082275 0.10004164278507233 0.5725386142730713 -0.3290843069553375 0.4182170033454895 0.33021101355552673 0.3531874418258667 0.7132461667060852 0.7660188674926758 -0.06766881793737411 -0.3275296688079834 -0.5805946588516235 -0.039685431867837906 -0.24081352353096008 0.30845287442207336 -0.024329818785190582 -0.29781514406204224 0.2931155264377594 -0.1278868317604065 -0.003562379628419876 0.32983118295669556 0.23495084047317505 -0.2014816403388977 -0.03824345022439957 0.26103734970092773 -0.23837420344352722 0.0867302343249321 0.11267700791358948 -0.2687276005744934 -0.03720066696405411 -0.11061225086450577 -0.1751476675271988 -0.1137891411781311 -0.05317603051662445 -0.09181027114391327 -0.005521506071090698 -0.27813923358917236 -0.03908546268939972 -0.10759022831916809 -0.14243505895137787 -0.007824696600437164 0.014894582331180573 -0.2522224187850952 0.17425143718719482 -0.3088277578353882 -0.4380866289138794
DOID:13406 high 0.99981 0.00019 0.00000 01-disease-subtype pulmonary sarcoidosis doid False 6.0 15.0 1.0 10.134956359863281 1.0 9.794317245483398 0.9934537410736084 2.0 2.0 0.0 1.0 0.0 0.0 0.0 1.0 0.0 1.0 1.0 1.0 0.0 0.0 0.0 2.0 1.0 -3.053466320037842 1.9353625774383545 0.7435942888259888 1.2261756658554077 0.3459858298301697 -1.3341552019119263 -0.28965288400650024 -1.294089674949646 -0.9193390607833862 0.2850755453109741 0.5618708729743958 -0.6974412798881531 0.3673611581325531 -0.10952895134687424 0.5655360221862793 0.571872889995575 -0.04232296347618103 -0.2792437672615051 -0.04745875298976898 -0.5458601713180542 -0.09988430142402649 -0.5230472683906555 0.4379386007785797 0.06626390665769577 0.039266280829906464 -0.017388835549354553 -0.15713253617286682 0.0509331040084362 -0.2276216298341751 0.3091808557510376 0.04430576413869858 0.06439712643623352 0.19343256950378418 0.09192248433828354 0.052678607404232025 0.3791302442550659 -0.2742898166179657 -0.06509727239608765 0.15427455306053162 0.23731906712055206 -0.11749233305454254 0.17581462860107422 -0.10765983909368515 -0.13087287545204163 0.02043258398771286 -0.08507407456636429 -0.11625076085329056 -0.2965066730976105 -0.3207240104675293 -0.00482650101184845 0.1927568018436432 0.10474809259176254 -0.04025161266326904 -0.0002699242904782295 0.031086549162864685 0.16730231046676636 0.03486368805170059 0.03765247017145157 0.03559812903404236 0.07144510000944138 0.11908143758773804 -0.14880043268203735 -0.12750791013240814 -0.1889151930809021
DOID:1947 medium 0.00023 0.99966 0.00010 02-disease-root trichomoniasis doid False 3.0 4.0 2.0 9.441808700561523 0.931608259677887 9.635712623596191 0.9773662090301514 1.0 1.0 1.0 1.0 0.0 0.0 0.0 3.0 0.0 1.0 1.0 1.0 0.0 0.0 0.0 2.0 1.0 -4.358615875244141 0.6257417798042297 0.5706757307052612 0.24123653769493103 -0.042641766369342804 0.45498359203338623 1.082244634628296 -0.1843864917755127 -0.4928770959377289 -0.9325709342956543 -0.17557352781295776 0.586540699005127 -0.601270854473114 0.2704795002937317 -0.05116390436887741 0.2683708667755127 0.7495367527008057 -0.23735424876213074 0.19494563341140747 0.04613890498876572 0.3087756931781769 -0.16967998445034027 -0.3209839165210724 0.09971511363983154 -0.03665013611316681 0.6205025315284729 0.4157359004020691 -0.01912776380777359 -0.07497791945934296 -0.8846695423126221 -0.21718677878379822 0.17011749744415283 -0.05097880959510803 -0.25961947441101074 -0.1203642189502716 0.32943180203437805 -0.3577299118041992 -0.31262314319610596 -0.1708638072013855 -0.08372326195240021 0.07257656753063202 -0.08842091262340546 -0.09863071143627167 -0.3582797646522522 -0.3948209285736084 0.2187349796295166 -0.13157141208648682 -0.03057733178138733 -0.27927345037460327 0.23326550424098969 -0.08040181547403336 -0.12052103877067566 -0.2778048813343048 -0.027752041816711426 -0.15173453092575073 0.1490785926580429 -0.2247905433177948 -0.1218884214758873 -0.14009954035282135 0.027499020099639893 -0.19819411635398865 -0.07656015455722809 0.0010087201371788979 -0.28624898195266724
DOID:7551 medium 0.00105 0.99895 0.00000 02-disease-root gonorrhea doid False 3.0 10.0 1.0 10.134956359863281 1.0 9.763545989990234 0.9903325438499451 2.0 2.0 0.0 1.0 0.0 1.0 0.0 4.0 0.0 1.0 1.0 1.0 0.0 0.0 1.0 3.0 2.0 7.652980804443359 4.843362808227539 1.2024866342544556 3.034327268600464 1.6186671257019043 -1.6181623935699463 -0.6018027663230896 0.13195493817329407 -1.0106589794158936 -0.8107593655586243 -0.4734506905078888 0.7407383918762207 0.32743096351623535 0.243345245718956 -1.2468758821487427 -0.9833461046218872 0.23341131210327148 0.14591965079307556 0.9679398536682129 0.4644564092159271 -0.5032130479812622 -0.8251446485519409 0.5328627228736877 0.8762052059173584 0.35654217004776 0.8831218481063843 0.9349535703659058 0.5793136954307556 -0.12494811415672302 -1.0961215496063232 -0.5771422982215881 0.3646371066570282 -0.9633585810661316 -0.22651579976081848 -0.17963209748268127 0.0863700583577156 -0.33167973160743713 -0.6272316575050354 0.3866034746170044 0.5838128328323364 -0.7333778142929077 -0.2068389654159546 0.0029905885457992554 -0.5885534286499023 -0.6146354079246521 0.2973923683166504 0.30839040875434875 -0.19612199068069458 0.5697736144065857 -0.1719053089618683 0.04697195440530777 0.6568117737770081 -0.43808215856552124 0.19207635521888733 -0.006294466555118561 -0.44620275497436523 -0.4011954367160797 0.32881081104278564 0.3663390278816223 0.2286163866519928 0.05143958330154419 0.3333771526813507 -0.08463650941848755 -0.16844049096107483
EFO:0000094 high 0.99944 0.00056 0.00000 01-disease-subtype B-cell acute lymphoblastic leukemia efo True 3.0 28.0 2.0 9.441808700561523 0.931608259677887 9.82376480102539 0.9964406490325928 2.0 4.0 1.0 1.0 2.0 0.0 0.0 0.0 0.0 0.0 1.0 1.0 0.0 0.0 0.0 1.0 0.0 11.128454208374023 1.0209791660308838 -0.8652997016906738 1.689063549041748 -0.1835705041885376 0.7448073029518127 2.5177831649780273 0.6460842490196228 -0.03240668773651123 0.2827354073524475 0.0801127552986145 -0.8458119034767151 -0.02401795983314514 -2.1516900062561035 1.5172958374023438 -1.6414721012115479 0.41878771781921387 -0.5412120819091797 -1.051668643951416 -0.44271165132522583 -0.2999247908592224 -0.7069023847579956 -0.2726597785949707 -0.8692215085029602 0.6464934349060059 0.6723757982254028 -0.48477596044540405 0.4093879461288452 1.0532820224761963 0.19099655747413635 -0.355294406414032 -0.001095995306968689 -0.07091590762138367 0.007893219590187073 -0.05441289395093918 0.582928478717804 0.3379111886024475 -0.07260769605636597 -0.7162529230117798 1.0698399543762207 -0.014526605606079102 0.2582075893878937 -0.3666952848434448 -0.1856209933757782 -0.4324628412723541 -0.1706363558769226 0.39273953437805176 0.035026952624320984 0.5012767910957336 -0.1212281882762909 -0.1197638288140297 -0.24914872646331787 0.08537015318870544 0.0732237696647644 -0.3219563364982605 0.09170031547546387 -0.07978761196136475 -0.054105792194604874 -0.20619694888591766 0.02372048795223236 -0.17961224913597107 -0.15795671939849854 -0.2573228180408478 -0.20552240312099457
EFO:0000095 medium 0.00088 0.99912 0.00000 02-disease-root chronic lymphocytic leukemia efo True 4.0 31.0 2.0 9.441808700561523 0.931608259677887 9.827107429504395 0.9967796802520752 4.0 4.0 1.0 1.0 1.0 1.0 2.0 1.0 1.0 1.0 1.0 1.0 1.0 0.0 1.0 0.0 2.0 4.58543062210083 5.451262474060059 -0.709334135055542 0.0013892650604248047 -0.2116018384695053 -0.9329459071159363 -0.39983832836151123 -1.362183928489685 -0.5016438364982605 -0.8915143609046936 -2.2134506702423096 -0.5105847120285034 0.3028690218925476 0.7573581337928772 -0.21298396587371826 -0.6568986773490906 0.12795089185237885 -0.32726234197616577 -0.5017027854919434 -0.6387689113616943 -0.808106005191803 0.035661935806274414 -0.6334644556045532 -0.341848760843277 0.20179647207260132 -0.2649608850479126 0.0025481805205345154 0.20200304687023163 0.37214332818984985 -0.177973672747612 -0.4732191562652588 -0.4914882779121399 -0.1005815863609314 0.23284175992012024 -1.1204171180725098 0.509072482585907 -0.19007283449172974 -0.2253798097372055 -0.23807118833065033 -0.2579413056373596 -0.18090595304965973 0.09062853455543518 -0.13168823719024658 0.32868361473083496 -0.10866905748844147 -0.5691341757774353 0.4499610960483551 -0.3624628484249115 0.5611351728439331 -0.1262049376964569 0.14938515424728394 -0.35689884424209595 0.13040611147880554 -0.17435169219970703 -0.24893386662006378 -0.07152017951011658 -0.007178366184234619 0.09548397362232208 0.045310989022254944 0.11406274139881134 0.19890078902244568 -0.08418260514736176 -0.042736977338790894 0.08541814982891083
EFO:0000096 medium 0.00054 0.99822 0.00125 02-disease-root neoplasm of mature B-cells efo True 3.0 18.0 39.0 6.4713945388793945 0.638522207736969 8.878026962280273 0.9005128741264343 1.0 4.0 8.0 30.0 1.0 0.0 0.0 1.0 0.0 0.0 1.0 2.0 0.0 0.0 0.0 1.0 1.0 4.738305568695068 5.625391006469727 0.3204062581062317 -0.6047797203063965 1.7348039150238037 -0.6747610569000244 0.44827455282211304 0.5333905816078186 0.5934811234474182 -0.33994847536087036 -2.7748541831970215 0.0016219764947891235 -0.0977252647280693 0.80450040102005 0.01199561357498169 -0.1832766830921173 1.4177908897399902 -0.9073195457458496 -1.289145588874817 -0.5556608438491821 -0.9741578102111816 -0.2685505449771881 -0.504262387752533 -0.6959699988365173 0.065402090549469 -0.6395871043205261 -0.5538464784622192 -0.2695954740047455 0.5331799387931824 -0.5416421890258789 -0.8517335057258606 -0.05361565947532654 0.8653509616851807 0.5677962899208069 -0.27996766567230225 0.6408759355545044 -0.1262664794921875 -0.21582552790641785 -0.10029469430446625 0.5043128132820129 -0.03579314053058624 0.15132993459701538 -0.17875544726848602 0.11429625004529953 -0.16657105088233948 -0.15872012078762054 0.4313417971134186 0.04224897921085358 0.22212675213813782 0.2161094844341278 -0.051062680780887604 -0.36110615730285645 0.3048466742038727 -0.17278432846069336 -0.3914314806461334 -0.41992291808128357 -0.01219351589679718 -0.21843977272510529 -0.02015511691570282 0.23409664630889893 0.23764610290527344 0.2660714089870453 0.31361186504364014 -0.37614133954048157
Note: I'll squash the commit to erase history prior to merging
Here are the first 10 lines of the updates output
Interesting, some floats still look verbose. Not a huge deal if we can't get float_format to work.
I'll squash the commit to erase history prior to merging
Squash merging should be sufficient I think, no need to do locally. Branch gets deleted after the merge.
Interesting, some floats still look verbose. Not a huge deal if we can't get float_format to work.
Right, good catch. It's surprising how some floats got formatted but not all. I'll take a look at it would save a little on file size.
Squash merging should be sufficient I think
:+1:
Right, good catch. It's surprising how some floats got formatted but not all. I'll take a look at it would save a little on file size.
Fixed ^ in the last push (using convert_dtypes
, nice find @dhimmel )
Top 10 lines now:
identifier precision proba_high proba_medium proba_low rs_classification efo_label prefix is_gwas_trait depth n_ancestors n_descendants intrinsic_ic intrinsic_ic_scaled intrinsic_ic_sanchez intrinsic_ic_sanchez_scaled n_parents n_roots n_children n_leaves xref__doid__count xref__gard__count xref__icd10__count xref__icd9__count xref__meddra__count xref__mesh__count xref__mondo__count xref__ncit__count xref__omim__count xref__omimps__count xref__orphanet__count xref__snomedct__count xref__umls__count pca_te_0 pca_te_1 pca_te_2 pca_te_3 pca_te_4 pca_te_5 pca_te_6 pca_te_7 pca_te_8 pca_te_9 pca_te_10 pca_te_11 pca_te_12 pca_te_13 pca_te_14 pca_te_15 pca_te_16 pca_te_17 pca_te_18 pca_te_19 pca_te_20 pca_te_21 pca_te_22 pca_te_23 pca_te_24 pca_te_25 pca_te_26 pca_te_27 pca_te_28 pca_te_29 pca_te_30 pca_te_31 pca_te_32 pca_te_33 pca_te_34 pca_te_35 pca_te_36 pca_te_37 pca_te_38 pca_te_39 pca_te_40 pca_te_41 pca_te_42 pca_te_43 pca_te_44 pca_te_45 pca_te_46 pca_te_47 pca_te_48 pca_te_49 pca_te_50 pca_te_51 pca_te_52 pca_te_53 pca_te_54 pca_te_55 pca_te_56 pca_te_57 pca_te_58 pca_te_59 pca_te_60 pca_te_61 pca_te_62 pca_te_63
DOID:0050890 low 0.00093254 0.00035292 0.99871 03-disease-area synucleinopathy doid False 3 7 8 8.0555 0.79482 9.4069 0.95415 2 2 2 4 0 0 0 0 0 1 1 0 0 0 0 0 1 -1.5259 -0.23416 -1.2304 -0.83256 -0.25777 1.1451 1.3971 0.45521 -0.83657 0.035402 -1.1193 0.93785 0.18754 -0.70501 -0.30986 -0.18339 1.1776 -0.071934 -0.4185 0.22026 0.51855 -0.62808 0.19805 0.073615 -0.25903 0.14761 0.004626 0.47755 -0.067554 0.24133 0.1738 -0.44884 0.28417 0.66689 0.17593 0.66609 0.25595 -0.056128 0.19684 0.091684 0.19224 -0.059334 0.12009 -0.29377 0.22616 -0.17504 -0.38881 -0.17914 -0.45509 0.052302 0.16953 0.020416 -0.40884 -0.10488 0.038316 -0.19511 0.34087 0.0041448 -0.2176 -0.10685 0.3011 0.19759 -0.33105 -0.10116
DOID:10113 medium 0.00056487 0.99829 0.001141 02-disease-root trypanosomiasis doid False 3 4 5 8.5255 0.8412 9.2992 0.94324 1 1 3 3 0 0 0 2 0 1 1 0 0 0 0 1 1 -4.2927 -0.012409 1.8242 1.9358 0.06221 0.20745 -1.3777 -0.17499 0.15652 -0.45731 0.010871 0.29784 -0.43393 -0.65814 -0.13337 0.017674 0.057508 -0.56117 0.0094563 0.27806 0.11908 -0.52992 -0.42233 0.17494 0.24975 0.13232 0.21576 0.30981 -0.1537 -0.37701 -0.046296 0.4301 0.37768 -0.19247 -0.017783 0.46699 -0.36022 -0.42488 -0.25018 -0.26505 -0.17507 -0.083977 -0.23389 0.34542 -0.24645 0.0016976 0.028001 -0.19759 -0.15024 0.20434 -0.032703 0.014206 0.093413 -0.44536 -0.12246 -0.087519 0.053074 -0.08962 -0.15297 0.045897 -0.093867 0.039216 0.21087 -0.15763
DOID:10718 medium 0.0012826 0.99864 7.2945e-05 02-disease-root giardiasis doid False 3 8 1 10.135 1 9.7411 0.98805 2 2 0 1 0 0 0 1 0 1 1 0 0 0 0 2 1 -2.1712 2.1477 0.30292 2.232 0.31242 -1.3254 -0.54553 0.024786 -1.3186 0.65003 0.10564 0.30391 0.41612 -0.094753 0.052711 0.15168 0.50011 -0.55848 1.0361 0.10005 0.57254 -0.32908 0.41823 0.33019 0.35304 0.71332 0.76601 -0.067692 -0.32753 -0.5806 -0.039709 -0.24083 0.30844 -0.024331 -0.29778 0.2931 -0.12784 -0.0035215 0.32994 0.23504 -0.20127 -0.038089 0.26153 -0.2384 0.086324 0.11208 -0.26877 -0.037157 -0.11064 -0.17566 -0.11797 -0.054032 -0.092926 -0.0023528 -0.28574 -0.042844 -0.11242 -0.12217 -0.058572 0.003556 -0.23765 0.14262 -0.25846 -0.48124
DOID:13406 high 0.99984 0.00015597 1.0226e-07 01-disease-subtype pulmonary sarcoidosis doid False 6 15 1 10.135 1 9.7943 0.99345 2 2 0 1 0 0 0 1 0 1 1 1 0 0 0 2 1 -3.0535 1.9354 0.74359 1.2262 0.34597 -1.3342 -0.28965 -1.2941 -0.91933 0.28509 0.56187 -0.69744 0.36737 -0.10955 0.56553 0.57187 -0.042317 -0.27924 -0.047463 -0.54586 -0.099872 -0.52304 0.43795 0.066247 0.039269 -0.017382 -0.15713 0.05092 -0.22763 0.30918 0.044318 0.06438 0.19343 0.091892 0.052718 0.37916 -0.27421 -0.06512 0.15434 0.23744 -0.11737 0.17613 -0.10756 -0.13096 0.020084 -0.084787 -0.11527 -0.29659 -0.32255 -0.0092712 0.19102 0.10606 -0.03741 0.011247 0.021643 0.16582 0.029547 0.030767 0.053846 0.06838 0.121 -0.13137 -0.11696 -0.18361
DOID:1947 medium 7.7861e-05 0.99985 7.066e-05 02-disease-root trichomoniasis doid False 3 4 2 9.4418 0.93161 9.6357 0.97737 1 1 1 1 0 0 0 3 0 1 1 1 0 0 0 2 1 -4.3586 0.62574 0.57067 0.24124 -0.042643 0.45498 1.0822 -0.18438 -0.49288 -0.93258 -0.17555 0.58654 -0.60126 0.27049 -0.05115 0.26838 0.74954 -0.23734 0.19494 0.046145 0.30878 -0.16969 -0.32098 0.099715 -0.036773 0.6205 0.41573 -0.01913 -0.074971 -0.88467 -0.21722 0.17013 -0.050962 -0.2596 -0.12037 0.32947 -0.3577 -0.31258 -0.17085 -0.083796 0.072687 -0.088522 -0.098938 -0.35801 -0.39478 0.21852 -0.13262 -0.030014 -0.27808 0.23588 -0.082757 -0.12044 -0.28082 -0.040695 -0.14838 0.15446 -0.21649 -0.11045 -0.16968 0.023799 -0.16846 -0.082827 0.066082 -0.25304
DOID:7551 medium 0.0012944 0.99871 5.4699e-09 02-disease-root gonorrhea doid False 3 10 1 10.135 1 9.7635 0.99033 2 2 0 1 0 1 0 4 0 1 1 1 0 0 1 3 2 7.653 4.8434 1.2025 3.0343 1.6186 -1.6182 -0.60181 0.13195 -1.0107 -0.81077 -0.47342 0.74074 0.32741 0.24337 -1.2469 -0.98335 0.23341 0.14592 0.96794 0.46444 -0.50321 -0.82514 0.5329 0.87618 0.35637 0.8832 0.93496 0.5793 -0.12497 -1.0961 -0.57719 0.3647 -0.96333 -0.22651 -0.17969 0.086365 -0.33169 -0.62713 0.3866 0.58373 -0.73356 -0.20722 0.0028579 -0.58841 -0.6139 0.29656 0.30643 -0.19723 0.5725 -0.16997 0.05256 0.65295 -0.4405 0.18417 0.0015717 -0.45146 -0.40878 0.32704 0.38567 0.21539 0.050819 0.33751 0.017643 -0.19848
EFO:0000094 high 0.99922 0.00073459 4.0677e-05 01-disease-subtype B-cell acute lymphoblastic leukemia efo True 3 28 2 9.4418 0.93161 9.8238 0.99644 2 4 1 1 2 0 0 0 0 0 1 1 0 0 0 1 0 11.128 1.021 -0.8653 1.6891 -0.18358 0.7448 2.5178 0.64609 -0.032413 0.28274 0.080104 -0.84583 -0.024075 -2.1517 1.5172 -1.6415 0.4188 -0.5412 -1.0517 -0.44271 -0.29992 -0.7069 -0.27265 -0.86924 0.64635 0.67251 -0.48477 0.40944 1.0533 0.19102 -0.35529 -0.001094 -0.070926 0.0078777 -0.054386 0.58287 0.33798 -0.072675 -0.71621 1.0699 -0.014512 0.25846 -0.36599 -0.18599 -0.43291 -0.17089 0.39381 0.034798 0.50026 -0.12069 -0.12005 -0.25027 0.085056 0.077729 -0.33189 0.087196 -0.088243 -0.024413 -0.21181 0.041453 -0.16567 -0.18489 -0.24415 -0.24093
EFO:0000095 medium 0.00089337 0.99911 3.4966e-09 02-disease-root chronic lymphocytic leukemia efo True 4 31 2 9.4418 0.93161 9.8271 0.99678 4 4 1 1 1 1 2 1 1 1 1 1 1 0 1 0 2 4.5854 5.4513 -0.70934 0.0013847 -0.2116 -0.93294 -0.39983 -1.3622 -0.50164 -0.89158 -2.2134 -0.51059 0.30288 0.75736 -0.21298 -0.65689 0.12796 -0.32726 -0.50171 -0.63878 -0.80809 0.035644 -0.63347 -0.34184 0.20185 -0.26492 0.0025463 0.20202 0.37214 -0.17795 -0.47322 -0.49149 -0.10062 0.23284 -1.1204 0.50912 -0.19001 -0.22539 -0.23815 -0.25802 -0.18117 0.09039 -0.13205 0.32876 -0.10839 -0.56848 0.45003 -0.36222 0.56082 -0.12581 0.15213 -0.35511 0.13484 -0.18291 -0.24112 -0.067584 -0.0060349 0.078428 0.084495 0.12397 0.17471 -0.064032 -0.011173 0.11933
EFO:0000096 medium 0.00066393 0.99833 0.0010048 02-disease-root neoplasm of mature B-cells efo True 3 18 39 6.4714 0.63852 8.878 0.90051 1 4 8 30 1 0 0 1 0 0 1 2 0 0 0 1 1 4.7383 5.6254 0.3204 -0.60477 1.7348 -0.67476 0.44827 0.5334 0.59347 -0.34003 -2.7748 0.0016211 -0.097706 0.8045 0.012011 -0.18326 1.4178 -0.90728 -1.2892 -0.55566 -0.97415 -0.26856 -0.50427 -0.69597 0.065537 -0.63958 -0.55385 -0.26956 0.5332 -0.54162 -0.85174 -0.053674 0.86533 0.56777 -0.27995 0.64088 -0.12622 -0.21593 -0.10032 0.5044 -0.035795 0.1515 -0.17864 0.11424 -0.1668 -0.15824 0.43227 0.041674 0.22118 0.21532 -0.04722 -0.36042 0.30506 -0.17032 -0.39657 -0.42843 -0.024295 -0.22153 -0.024354 0.2483 0.21122 0.30704 0.28381 -0.38331
Also the file went from 25MB down to 10MB 💯 :
(nxontology-ml-py3.10) ~/d/nxontology-ml ❯❯❯ ls -lah data
drwxr-xr-x 9 romain staff 288B Sep 21 15:12 .
drwxr-xr-x 30 romain staff 960B Sep 21 15:15 ..
-rw-r--r-- 1 romain staff 1.5M Sep 21 14:38 efo_otar_slim_v3.43.0_rs_classification.tsv
-rw-r--r-- 1 romain staff 10M Sep 21 15:12 efo_otar_slim_v3.57.0_precisions.tsv
@dhimmel @eric-czech This PR adds logic to run the top performing model (Catboost with topological features + PCA64) trained on all the labeled data and run inference on the latest version of the ontology. Exports both precisions and features in tsv files.
Since the files are large, here are the first 10 lines of each:
Here are the export file sizes:
@dhimmel you confirm you'd like the feature file checked in?