annot_examples_added

aggregator_train_val/annot_files/labels.csv

@@ -0,0 +1,6 @@
+slide,family,age,location,max_cal_v12,prob_vector
+5E876B19-B3C5-42F0-9034-E171C9185A61,"Astrocytoma, IDH-mutant",34,Supratentorial,0.996568093,"[2.5556832837798506e-05, 0.00013934308023829195, 5.5599170975942274e-05, 0.996568093393978, 5.2541151675303404e-05, 2.023953159609098e-05, 4.069654638588267e-05, 0.00018460425261517945, 3.079167439002157e-05, 0.00183594640457765, 1.6897465058339038e-05, 2.669379984381747e-05, 0.0001105442772898893, 8.60906559849895e-06, 9.79088659242557e-06, 2.357291932781188e-05, 5.13079466495326e-06, 2.5303645804395707e-05, 7.06319252909343e-05, 5.04039745383133e-06, 1.43518305984953e-05, 1.34723287889747e-05, 9.9115144855786e-06, 6.52861061886433e-06, 1.8236393936707e-06, 1.9684487380903278e-05, 1.31252283934792e-05, 3.36034096251763e-06, 5.116590243002e-06, 1.611762266487298e-05, 1.13909354759939e-05, 6.42695418915583e-06, 1.0555378924072e-05, 5.91103870857324e-06, 8.509376175677711e-06, 5.35162916257592e-06, 2.61826129317681e-06, 2.852203182878987e-05, 6.28603740889761e-06, 1.38079371673126e-05, 2.18059205363144e-05, 4.42286256517939e-06, 1.09777539399029e-05, 6.5830777633995705e-06, 3.11278435723859e-06, 5.59343374323886e-06, 4.58001787819239e-06, 6.03283107514966e-06, 2.94972413630955e-06, 3.11793488723198e-06, 6.87427618612349e-06, 3.25637576669851e-06, 0.000126574031810493, 4.43569916882956e-06, 8.51255011591618e-06, 5.35293113698592e-06, 3.93918990954147e-06, 6.36075510461857e-06, 5.11831281819511e-06, 4.03936032814556e-06, 1.081837504514675e-05, 8.97422425306287e-06, 7.406328328675179e-06, 2.32985674883738e-06, 1.24987934731501e-05, 3.41127825988852e-06, 2.48597913364053e-06, 6.54577432450574e-06, 8.08875088739732e-06, 4.31786913674824e-06, 3.28874420521158e-06, 1.57545414661028e-05, 1.96231884902425e-06, 6.71477504624373e-06, 2.56173735363322e-06, 1.4246455797309e-05, 5.95171636706482e-05, 2.56421465104903e-06, 4.24136998477744e-06, 5.84899468807362e-06, 3.92842785072378e-06, 5.26052139510617e-06, 3.4991101352857e-06, 8.48899112824813e-06, 6.98277905897002e-06, 3.39361820773429e-06, 7.98624462936369e-06, 5.80280197658308e-06, 8.65356569635002e-06, 2.79254348187846e-06, 6.26989830185394e-06, 3.27493696513102e-06, 1.72278192279395e-06, 1.14871549982609e-06, 8.29539467584282e-06, 8.48236389327987e-07, 1.48528012175168e-06, 3.84566131071318e-06, 2.24401303082228e-06, 3.74366054878356e-06, 2.16651965675745e-06, 1.5482054821839e-06, 3.20977029939401e-06, 0.0, 0.0, 4.38636516709445e-06, 2.42035391165275e-06, 1.08852445652413e-05]"
+AFFB3AE9-F32E-428C-9F7B-83E9B1C056E9,"glioblastoma, IDH-wildtype",63,Supratentorial,0.998164997,"[0.9981649968490053, 0.00012431504387703076, 0.0001011134590161816, 5.71395310894277e-05, 2.388548751559467e-05, 1.8178139806462832e-05, 3.089386109020005e-05, 8.604571558525305e-05, 0.0001463263965983862, 5.28188009098043e-06, 1.891428997177343e-05, 3.239590210717313e-05, 9.840404568326773e-05, 9.28700830821929e-06, 1.245408379667088e-05, 9.22764307939207e-05, 5.59057404506014e-05, 2.2767988205252756e-05, 4.6670459747313054e-05, 9.76323564193656e-06, 7.53823028950527e-06, 1.12997511618003e-05, 1.41361695889565e-05, 4.6138805427482e-06, 1.71677080861649e-06, 2.6197416295001258e-05, 1.22870061028996e-05, 7.01484186658908e-06, 9.55697753906082e-06, 4.183542090798692e-05, 5.91273536132362e-05, 7.97032460582475e-06, 3.2655067146937e-06, 8.60724003261967e-06, 9.51899446380614e-06, 5.44788559387148e-06, 3.25112447044336e-06, 2.54488182518227e-05, 9.32369852765951e-06, 3.24441250463015e-05, 1.23909231957052e-05, 3.38106694316719e-05, 9.09398373378159e-06, 8.36627969156497e-06, 4.45412094928069e-06, 3.88531064275312e-06, 4.28529477162143e-06, 3.07955928886424e-06, 2.63393063041435e-06, 2.68591238793144e-06, 1.59145995635169e-05, 2.46009880313905e-06, 2.08850017417291e-05, 4.06223902275672e-06, 5.70544434037403e-06, 2.32230038455714e-06, 3.69324054770149e-06, 7.1171187115498e-06, 4.85000869822685e-06, 5.27484701979582e-06, 1.454414945126354e-05, 7.97888402799049e-06, 9.43715032979858e-06, 2.09247724490648e-06, 7.80985914431724e-06, 5.81770784131891e-06, 3.04302420372681e-06, 0.000134521311857497, 7.14078072471588e-06, 3.54115287608329e-06, 3.30544387996517e-06, 8.39551908278502e-06, 1.95209602335529e-06, 5.06141604288412e-06, 2.69865428578959e-06, 2.20841697505522e-06, 4.39794339381756e-06, 6.4799893326872e-06, 3.95495429965371e-06, 6.25566595154146e-06, 3.76294118910702e-06, 4.84882406829415e-06, 3.2347408475526e-06, 9.63019026610793e-06, 1.38359562192056e-05, 4.05891591760703e-06, 1.23347778431044e-05, 1.87801647180425e-05, 7.00326806826102e-06, 2.50452169887026e-06, 1.72925268761162e-05, 4.84581738716237e-06, 2.06346298478946e-06, 1.40904071602818e-06, 7.37266541874917e-06, 9.54563305737481e-07, 1.47808579135567e-06, 3.28024213304909e-06, 5.3602738156417e-06, 2.87906934008151e-06, 2.00088854345467e-06, 1.49432713696719e-06, 3.9344201112402e-06, 0.0, 0.0, 2.65134985249374e-06, 2.52533828767519e-06, 5.23906213244277e-06]"
+A25CE88C-329D-4FB5-8A53-D7D5B98A6F7B,"glioblastoma, IDH-wildtype",74,unknown,0.993111935,"[0.9931119347167814, 7.517830657058763e-05, 4.4712437949118866e-05, 8.82076474682495e-06, 8.54249100736162e-06, 1.4285074579173915e-05, 1.0844105276229137e-05, 1.308404956506582e-05, 2.0066503587453304e-05, 1.0829519582363e-06, 1.068194947293435e-05, 1.096077076387673e-05, 1.721686138764813e-05, 3.85463920074218e-06, 4.90481468268927e-06, 1.459740713626436e-05, 0.00621491524535023, 1.1529789655164581e-05, 1.404160386578696e-05, 1.50774421385314e-05, 5.46317571848202e-06, 1.19299460934313e-05, 4.56168949106649e-06, 1.50475778146032e-06, 5.92356657209229e-07, 6.05568171810201e-06, 5.18098573512241e-06, 1.37718239466633e-05, 9.20518771338205e-06, 1.845234373843985e-05, 4.11652750721766e-05, 3.947505508175203e-06, 9.83173528110773e-07, 6.58673306104774e-06, 2.4479294257484186e-06, 1.9028200749711559e-06, 2.30300826899799e-06, 1.0853737010935355e-05, 6.30018503069615e-06, 3.24904793393212e-06, 4.95879389591132e-06, 7.62617394772356e-05, 2.55795320698956e-06, 2.981296342946314e-06, 1.45971939726385e-06, 1.40296161732273e-06, 2.50337255229271e-06, 1.39910980737684e-06, 3.09349851106928e-06, 1.15915774634623e-06, 4.18773175759075e-06, 1.73856582439329e-06, 6.94028423413622e-06, 1.596560172640693e-06, 2.2739132557354e-06, 9.56406429753889e-07, 1.2825914887391492e-06, 3.06959982516172e-06, 1.54488903580601e-06, 4.05413319194319e-06, 5.3407496570327865e-06, 3.22225861444041e-06, 2.8270877920093997e-06, 7.27082171254155e-07, 1.70177496261408e-06, 2.21299804641788e-06, 2.36399030178445e-06, 2.22302281173248e-06, 3.12098833986654e-06, 1.19243476174474e-06, 1.02971106258087e-06, 3.55861856457833e-06, 6.68146410033017e-07, 1.71888454371137e-06, 1.06035205279807e-06, 6.943080231910519e-07, 8.54804096494607e-07, 1.00979029870086e-06, 1.30391853568125e-06, 2.56081202869425e-06, 1.45283481431618e-06, 1.48504131385979e-06, 1.2881099789813e-06, 3.4276675382043607e-06, 2.97898013995419e-06, 1.36051603532987e-06, 3.35185453790957e-06, 6.25292463414969e-06, 1.89737557366157e-06, 8.86595888217937e-07, 6.45189554553286e-06, 2.56592885884189e-06, 6.67807702804246e-07, 4.73948812558528e-07, 5.49483457788272e-06, 3.89166727190615e-07, 1.83020987678293e-06, 1.09365857645682e-06, 8.96644381939616e-07, 9.60655003011685e-07, 7.16954950945199e-07, 5.17491228058173e-07, 1.48427425898373e-06, 0.0, 0.0, 1.46949744308819e-06, 9.85478849033002e-07, 2.01635272246694e-06]"
+F1E00FC3-6ACB-4983-AD0A-E0ABB844FB4F,"glioblastoma, IDH-wildtype",48,unknown,0.948818309,"[0.9488183093711693, 0.003714895911025025, 0.004646787902424117, 0.000716952624380769, 0.000716943562166008, 0.0004977471121888719, 0.0006807658593721771, 0.001684057152627574, 0.0020061266827617365, 7.2854874454384e-05, 0.000263988611581167, 0.0006008574441129109, 0.001518545945969378, 0.00036075499105369, 0.0002902385351439719, 0.002465209063510481, 0.000222228785757911, 0.0008208246580662544, 0.001148851353762856, 0.000138944358094253, 0.000537250706500536, 0.000160025804452572, 0.000657406154669241, 0.000119871908520782, 4.13977126933373e-05, 0.000650582085517759, 0.000285707118108792, 0.000138006019593029, 0.00404022372105703, 0.0004344513430286384, 0.00158974377954747, 0.0002074688436841371, 8.55955756787254e-05, 0.000208408256222557, 0.0005078012781585207, 0.0001312076754256014, 5.78761988772819e-05, 0.0008437792094154811, 0.000348193001882332, 0.000366629268091261, 0.000243203923075041, 0.00246263511278357, 0.000185817606895196, 0.001290907450983666, 0.000116309961057172, 0.000100636676973579, 8.91125969104452e-05, 8.63236360441187e-05, 9.41145167637863e-05, 7.94571537880879e-05, 5.81733763754291e-05, 7.8179268771802e-05, 9.13440602049519e-05, 9.87288605187059e-05, 9.49025196152045e-05, 6.55772515158849e-05, 8.81226534765886e-05, 0.000857502327659405, 0.000258892875056665, 0.000192245314704108, 0.0002809674720616452, 0.000238459479165993, 0.0001653812429315157, 5.10156607532965e-05, 0.000213644213566131, 0.00117122893054798, 6.41964435092409e-05, 0.000729421300581113, 0.00021036393792677, 7.14954858772106e-05, 0.00018787515694263, 0.000173459630892309, 4.93920984432405e-05, 0.000123673234232647, 5.94716618053435e-05, 4.3505437797185194e-05, 0.000129285542016283, 0.000120466787718446, 0.000103147251245613, 0.000394286526959428, 0.000102340391720463, 0.000268276044470959, 0.000104620266056528, 0.0003591607113343029, 0.000406566209360438, 0.000109525577151411, 0.000801310501650497, 2.82348402232432e-05, 0.000243687006025025, 6.00015168632988e-05, 0.00032830330423886, 0.000141822181624967, 4.27723371936541e-05, 4.05658327112348e-05, 0.000150269018065394, 2.20538264503187e-05, 0.00207975319265287, 9.10978596210304e-05, 0.00011438734832855, 6.92142886762161e-05, 6.33500715304851e-05, 3.61201031645704e-05, 9.25476545422238e-05, 0.0, 0.0, 2.61959821595204e-05, 7.50486091163958e-05, 0.000132340226172121]"
+F58F3C16-B220-41FD-B299-A3B5F90CAAC7,"Oligodendroglioma, IDH-mutant and 1p/19q-codeleted",unknown,Supratentorial,0.999678673,"[3.194020706786801e-06, 2.090802668994929e-05, 8.556829152884675e-06, 0.00012889779709761553, 7.54215461808506e-06, 2.835195128487442e-06, 5.778888558095141e-06, 1.0731195721405269e-05, 3.4545505681936535e-06, 0.999678672666334, 2.473445673528856e-06, 4.090725048667184e-06, 1.914103164208538e-05, 1.20562372921449e-06, 1.32227290144791e-06, 2.013748502391925e-06, 7.07573306657567e-07, 3.357243407281681e-06, 1.142478143672357e-05, 6.66519599906742e-07, 2.92122526606132e-06, 1.81627646540108e-06, 1.43566817860718e-06, 8.94506819636471e-07, 2.34899273846482e-07, 2.036963509949583e-06, 1.94674638648452e-06, 4.61064155010852e-07, 7.57456460063525e-07, 1.880922668711374e-06, 1.61130383239652e-06, 8.38413758323882e-07, 1.73099403016127e-06, 7.8922283838866e-07, 9.79194822734194e-07, 6.90541802597844e-07, 3.57577804872764e-07, 3.456701792141551e-06, 8.42040865090058e-07, 1.22024760611714e-06, 2.5333653146325e-06, 5.58216503476981e-07, 1.65529767779485e-06, 9.02960788272236e-07, 4.01276270872827e-07, 7.52130559353307e-07, 6.22552226639108e-07, 8.8220083534117e-07, 4.32288734980908e-07, 4.2032205007103e-07, 5.43065206986824e-07, 4.85512462674312e-07, 5.88640159112539e-06, 5.87251446355083e-07, 8.87786403931573e-07, 8.01843710910767e-07, 5.100685691942571e-07, 8.72581650448411e-07, 6.86872460463808e-07, 5.43484553152611e-07, 1.4904369330728408e-06, 1.27180453204313e-06, 9.43734304646406e-07, 2.99706935257173e-07, 1.46180239332328e-06, 4.26465532601752e-07, 3.04164850364632e-07, 6.29506894976468e-07, 1.36263497805633e-06, 5.30510775218406e-07, 4.0777901058084e-07, 1.98128113826597e-06, 2.5076268262799e-07, 9.72170312574368e-07, 3.31455324982227e-07, 3.0742561885480683e-06, 3.5553935320985e-06, 3.4029261586249e-07, 5.20612600642486e-07, 7.37475551611718e-07, 5.18579031892027e-07, 6.21837991609019e-07, 4.38834353897796e-07, 1.054190576332253e-06, 9.02531039171486e-07, 4.40450436348095e-07, 1.00052564627081e-06, 6.41165955414979e-07, 8.20998249210552e-07, 3.73910518438519e-07, 7.77305924795757e-07, 4.00194653392151e-07, 2.2323012707131e-07, 1.4558347858829e-07, 1.11059290298021e-06, 1.09114667939642e-07, 1.89543706350994e-07, 5.13164832584725e-07, 2.13833031762902e-07, 4.71395011988641e-07, 2.72998050847701e-07, 1.99176595463e-07, 4.47270485146793e-07, 0.0, 0.0, 4.75832937460655e-07, 3.13156727198705e-07, 1.59059880427027e-06]"

aggregator_train_val/annot_files/split_example.yaml

@@ -0,0 +1,29 @@
+test:
+- EFD06C7B-D5F1-4341-A557-0D5C5B1F238D
+- 81BF21A2-B7F9-48A5-866B-1CF7721869D3
+- A94B23F8-E9D3-4026-ADFC-E51CA384F680
+- 708C4C70-0C7C-4CC9-AD48-0CF96AFBA92D
+- 789F5F05-1FA7-48A1-A63D-60894BEBAF42
+
+train:
+- 76A6DA4B-58BB-459B-91FE-B3D849B32C4D
+- 29320F4A-9913-4F1E-B14F-59CF7002C0E9
+- 0A3E8F3A-704C-4AA2-89B7-ADA28EB5EEF9
+- A1355CCD-6C62-45C7-8F8A-2CE823DAC8C0
+- E9633817-F804-4EB2-8206-5649BB511365
+- FB6AEB30-E765-449E-8F40-67FBB7679312
+- F5363CC4-50FC-44A5-BB2F-34A0C1E27E78
+- CDF53623-4CD4-468B-BEC8-60199AA687D8
+- 651E9FDB-0C43-4C19-AD4C-1382CBEFBF48
+- 8F33A677-B715-460C-A127-DBE761C95310
+- 49099240-1B9C-40E8-A677-0E5F1C56EA05
+- E8950565-D547-455E-A2C3-33E2E3621BAE
+- 96E85133-A4BF-4767-8365-4384D125E441
+- EE48D74A-1B11-476B-864E-ED2A245D5B9B
+- 587D1D78-0037-4BCB-8A52-8601C713C02C
+- 1D02E333-D047-4EB9-9483-CCE6EEB80AAF
+- B362764D-7C7D-40E8-801C-BB439683E52A
+- 0F39BF35-5117-44FA-B3AC-554533DD5687
+- 54F6885B-EEC1-4818-BC09-D4C6BDAB59EF
+- 3F3ABC5A-7545-4C51-9A4D-FF6CAA6B4AD8
+

aggregator_train_val/annot_files/tumor_label_mapping_example.yaml

@@ -0,0 +1,7 @@
+mapping:
+  glioblastoma, IDH-wildtype: 0
+  posterior fossa ependymoma group A: 1
+  supratentorial ependymoma, ZFTA fusion-positive: 2
+  Astrocytoma, IDH-mutant: 3
+
+