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Adding Figure 4 - Leave One Image Out Analysis #40

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Oct 26, 2023
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Adding Figure 4 - Leave One Image Out Analysis #40

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8182d52
add figure 4 and notebook LOIO
gwaybio Oct 3, 2023
f81d9e1
update LOIO viz for recalculated LOIO analysis
gwaybio Oct 26, 2023
9649139
add figure 4
gwaybio Oct 26, 2023
f73ed6e
update loio probabilties to include shuffled and retraining
gwaybio Oct 26, 2023
b3d0854
add notebook to summarize loio results
gwaybio Oct 26, 2023
c2b3780
add loio results files
gwaybio Oct 26, 2023
bafd35e
Merge branch 'main' into fig4
gwaybio Oct 26, 2023
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661 changes: 661 additions & 0 deletions 3.evaluate_model/LOIO_evaluation.ipynb
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1,978 changes: 1,978 additions & 0 deletions 3.evaluate_model/evaluations/LOIO_probas/LOIO_summary_ranks.tsv
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46 changes: 46 additions & 0 deletions 3.evaluate_model/evaluations/LOIO_probas/LOIO_summary_ranks_perphenotype.tsv
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Mitocheck_Phenotypic_Class Model_Feature_Type Average_Rank Average_P_Value Min_IQR_Rank Max_IQR_Rank Min_IQR_P_Value Max_IQR_P_Value Count
ADCCM CP 2.263157894736842 0.4347019627630367 1.0 3.0 0.03991696868571505 0.740536676233918 95
ADCCM CP_and_DP 2.2526315789473683 0.49607283313712114 1.0 3.0 0.0909810130982412 0.8251557330596422 95
ADCCM DP 2.705263157894737 0.44619382994810736 1.0 3.0 0.0689979354578983 0.8058845855176004 95
Anaphase CP 6.714285714285714 0.2702808420532919 1.0 12.0 9.443159329989546e-05 0.655247201756364 84
Anaphase CP_and_DP 6.607142857142857 0.27806836767635607 1.0 12.25 0.000515677417195775 0.694951039221164 84
Anaphase DP 6.333333333333333 0.2237394266771379 1.0 10.25 0.00079387356146395 0.39378208051519636 84
Apoptosis CP 4.336996336996337 0.37908020608469806 1.0 6.0 0.0047586553975621 0.823178672974805 273
Apoptosis CP_and_DP 3.7985347985347984 0.43995885791520467 1.0 5.0 0.0069235214610816 0.9549294221132149 273
Apoptosis DP 3.681318681318681 0.4073728878810171 1.0 5.0 0.0060269254147391 0.918020168529714 273
Binuclear CP 4.385869565217392 0.33291185588095096 1.0 4.25 0.003603286417450625 0.705928850706643 184
Binuclear CP_and_DP 4.413043478260869 0.3184585728324772 1.0 5.0 0.003076837824106675 0.6540498768682218 184
Binuclear DP 4.282608695652174 0.28014225563996403 1.0 5.0 0.00454867913841945 0.4711354310950646 184
Elongated CP 3.4363636363636365 0.6289932222652874 1.0 5.0 0.005028462031980675 0.9863411287518988 110
Elongated CP_and_DP 2.909090909090909 0.593133972686637 1.0 3.0 0.02978441802592275 0.9880589569437843 110
Elongated DP 2.9909090909090907 0.5261586855078849 1.0 4.0 0.015176264729504724 0.9865483951968639 110
Grape CP 2.5945945945945947 0.44734570223603537 1.0 3.0 0.09514407846833048 0.7314643440265027 74
Grape CP_and_DP 2.554054054054054 0.47662638451113837 1.0 2.0 0.0882226866418335 0.9035020322532835 74
Grape DP 3.0 0.4137585493081148 1.0 2.75 0.0525315466209757 0.7600723879725966 74
Hole CP 3.4298245614035086 0.4383052070601286 1.0 5.0 0.015550073220108051 0.8446672277401516 114
Hole CP_and_DP 2.7982456140350878 0.5456467470338106 1.0 4.0 0.02020463698325215 0.963050786377094 114
Hole DP 2.8508771929824563 0.45903914090157566 1.0 3.75 0.01444412203251165 0.9147749949920367 114
Interphase CP 4.880952380952381 0.35559516847565065 1.0 9.0 0.00028785238266282505 0.7982211047755633 420
Interphase CP_and_DP 5.223809523809524 0.3347457779765925 1.0 9.0 0.000863450492317075 0.7697075801186866 420
Interphase DP 4.623809523809523 0.3022407716788329 1.0 7.0 0.0021610979454459753 0.6431836067063876 420
Large CP 4.89873417721519 0.38480693692180296 1.0 8.0 0.00048123289820835 0.9303257353610606 79
Large CP_and_DP 4.822784810126582 0.33809666098714797 1.0 10.0 0.00089089155538495 0.8729742300486549 79
Large DP 5.0 0.3022558545358185 1.0 8.5 0.0016260897687653 0.7354550750683917 79
Metaphase CP 6.405405405405405 0.22491133421213946 2.0 10.75 0.000441831538696375 0.2945057329455094 74
Metaphase CP_and_DP 5.702702702702703 0.213856526207341 2.0 9.0 0.000969167780196625 0.2837208708876884 74
Metaphase DP 6.202702702702703 0.17842430767654563 2.0 9.0 0.00018661474645435 0.2121008504957944 74
MetaphaseAlignment CP 4.034285714285715 0.23311377379985954 2.0 6.0 0.00494538875450655 0.39169100593375145 175
MetaphaseAlignment CP_and_DP 3.6857142857142855 0.2910131693625261 1.0 5.0 0.0071285257109505 0.543634787402455 175
MetaphaseAlignment DP 4.04 0.2871567200509503 1.0 6.0 0.00475482845623885 0.5705315054624422 175
OutOfFocus CP 1.0855263157894737 0.9213723877927004 1.0 1.0 0.9818148010948586 0.9994443675844802 304
OutOfFocus CP_and_DP 1.0723684210526316 0.9178946634052295 1.0 1.0 0.9911872952846779 0.9998780736921491 304
OutOfFocus DP 1.069078947368421 0.9122444420456656 1.0 1.0 0.9959642637554971 0.9999715531136062 304
Polylobed CP 4.299727520435967 0.42535528453100907 1.0 7.0 0.00334714845487565 0.8509016012826602 367
Polylobed CP_and_DP 4.051771117166212 0.4557177734980324 1.0 6.0 0.0041955785070945 0.9138692187655341 367
Polylobed DP 3.5122615803814714 0.44572571608946354 1.0 4.0 0.007519107256989 0.896638760569409 367
Prometaphase CP 2.698550724637681 0.48212680335926106 1.0 3.0 0.0272687145576027 0.8433786530219477 345
Prometaphase CP_and_DP 2.7217391304347824 0.5417368493515994 1.0 3.0 0.034880373461323 0.9458115261914412 345
Prometaphase DP 2.6579710144927535 0.5224782324942703 1.0 3.0 0.0511073824641628 0.9570905081997236 345
SmallIrregular CP 3.817073170731707 0.36689618404964947 1.0 5.0 0.00681976406149445 0.7459970173518845 164
SmallIrregular CP_and_DP 3.018292682926829 0.42705401539324706 1.0 4.0 0.013056300540621851 0.7864578713213417 164
SmallIrregular DP 2.951219512195122 0.39303450325457745 1.0 3.0 0.03749621871591815 0.7328419054307281 164
91 changes: 91 additions & 0 deletions 3.evaluate_model/evaluations/LOIO_probas/LOIO_summary_ranks_perphenotype_withshuffled.tsv
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Model_type Mitocheck_Phenotypic_Class Model_Feature_Type Average_Rank Average_P_Value Min_IQR_Rank Max_IQR_Rank Min_IQR_P_Value Max_IQR_P_Value Count
final ADCCM CP 2.2736842105263158 0.4046483699313022 1.0 3.0 0.042985513492177954 0.6782837512509758 95
final ADCCM CP_and_DP 2.294736842105263 0.47074703003671103 1.0 3.0 0.09017276876883056 0.7930137006793192 95
final ADCCM DP 2.736842105263158 0.4156538802911994 1.0 3.0 0.08435602160606989 0.6980218215079088 95
final Anaphase CP 6.7023809523809526 0.2646484268617994 1.0 12.0 0.000183778711277075 0.6439284691773464 84
final Anaphase CP_and_DP 6.761904761904762 0.27157107475587894 1.0 13.0 0.00093461316276555 0.6768319834629739 84
final Anaphase DP 6.285714285714286 0.21076303726335333 2.0 11.0 0.0010245366630419 0.2856395696634698 84
final Apoptosis CP 4.333333333333333 0.37710400165439223 1.0 6.0 0.0055062860369288 0.8109288028725148 273
final Apoptosis CP_and_DP 3.750915750915751 0.4332619641146736 1.0 5.0 0.0100730674119546 0.9418695805419468 273
final Apoptosis DP 3.641025641025641 0.3991913532505883 1.0 5.0 0.0119218780691075 0.8756362142429823 273
final Binuclear CP 4.380434782608695 0.32823641352217797 1.0 5.0 0.0043029122539749 0.6892865214402515 184
final Binuclear CP_and_DP 4.391304347826087 0.3171988186533409 1.0 5.0 0.004444848211955775 0.5892817229380966 184
final Binuclear DP 4.184782608695652 0.27228657390089095 1.0 5.0 0.00827070694930385 0.4685993719275702 184
final Elongated CP 3.3727272727272726 0.6263896480890214 1.0 5.0 0.0077809462193372 0.9841555157857194 110
final Elongated CP_and_DP 2.9454545454545453 0.5878778875192842 1.0 3.0 0.026869247708928873 0.9827661325364139 110
final Elongated DP 3.036363636363636 0.5147494740755217 1.0 4.75 0.01978528632176645 0.96242801240062 110
final Grape CP 2.6621621621621623 0.44111921991084874 1.0 3.0 0.11100837376774138 0.7176606977366309 74
final Grape CP_and_DP 2.608108108108108 0.4633581306664853 1.0 2.0 0.0876451976736364 0.8785604157810208 74
final Grape DP 3.054054054054054 0.40511896061091907 1.0 3.0 0.04645616816954205 0.7095967839309061 74
final Hole CP 3.4649122807017543 0.4307379815658381 1.0 5.0 0.0163133301732615 0.8315202013673747 114
final Hole CP_and_DP 2.824561403508772 0.5415309101492877 1.0 4.0 0.028297382163239574 0.9589030931528443 114
final Hole DP 2.763157894736842 0.43940256400769995 1.0 3.0 0.032107540971926175 0.8298160647527348 114
final Interphase CP 4.8880952380952385 0.3528256028300763 1.0 9.0 0.00039181085171055 0.7838048676708562 420
final Interphase CP_and_DP 5.15952380952381 0.33480563865895674 1.0 9.0 0.001395532020837675 0.7411927792594089 420
final Interphase DP 4.166666666666667 0.2902540101932557 1.0 6.0 0.0056852006443786005 0.5554222392885083 420
final Large CP 4.8734177215189876 0.38236271853048825 1.0 8.0 0.00048703238187425 0.9245702862203045 79
final Large CP_and_DP 4.89873417721519 0.33336264616266537 1.0 10.0 0.00151395845934605 0.8151098530138964 79
final Large DP 5.025316455696203 0.28329939594142545 1.0 8.5 0.00371519652196935 0.6849758273525526 79
final Metaphase CP 6.3108108108108105 0.21971737588603696 1.25 10.0 0.000615675499966875 0.30559227965439006 74
final Metaphase CP_and_DP 5.527027027027027 0.2143194106332183 2.0 8.0 0.0013526845760871249 0.28363697399849597 74
final Metaphase DP 6.202702702702703 0.16258843473569742 2.0 10.0 0.00049741901489025 0.19480348380609663 74
final MetaphaseAlignment CP 4.017142857142857 0.23101774855589988 2.0 6.0 0.00642208972818285 0.3931204267296831 175
final MetaphaseAlignment CP_and_DP 3.737142857142857 0.28743346712936346 1.0 5.0 0.01098857590386745 0.5563434761098529 175
final MetaphaseAlignment DP 3.9828571428571427 0.2855604895271028 1.0 6.0 0.0106127447218113 0.5267488308207264 175
final OutOfFocus CP 1.0888157894736843 0.9204384192837964 1.0 1.0 0.9782214882613491 0.9991394324171032 304
final OutOfFocus CP_and_DP 1.0855263157894737 0.907406476588655 1.0 1.0 0.988256299597478 0.999794780568327 304
final OutOfFocus DP 1.0460526315789473 0.9198335965364282 1.0 1.0 0.9897118437456291 0.9998379308339417 304
final Polylobed CP 4.332425068119891 0.4237668623762527 1.0 7.0 0.0039539166153696 0.8455980616089478 367
final Polylobed CP_and_DP 4.0 0.4536309833012622 1.0 6.0 0.0053376556286726 0.8986637777562956 367
final Polylobed DP 3.4959128065395095 0.44059020490041356 1.0 5.0 0.01023597555975695 0.8741900813836523 367
final Prometaphase CP 2.7246376811594204 0.4762152012419447 1.0 3.0 0.0276585509233951 0.832890051960929 345
final Prometaphase CP_and_DP 2.684057971014493 0.533353632822085 1.0 3.0 0.0375590354415911 0.9292670046684858 345
final Prometaphase DP 2.6 0.5143103724469645 1.0 3.0 0.0561792265860687 0.9272341023751018 345
final SmallIrregular CP 3.8353658536585367 0.3621799248807112 1.0 5.0 0.0080302815750639 0.7274677491843592 164
final SmallIrregular CP_and_DP 3.0792682926829267 0.41459056313370574 1.0 4.0 0.01674649439386785 0.7656281401836026 164
final SmallIrregular DP 2.908536585365854 0.3715347374853791 1.0 4.0 0.06359083407646375 0.6513111948768355 164
shuffled ADCCM CP 11.91578947368421 0.01801480902272983 10.0 14.0 0.0061500201722871 0.0243023434707513 95
shuffled ADCCM CP_and_DP 10.83157894736842 0.03394587335249585 9.0 13.0 0.0104396150994682 0.036045443622017656 95
shuffled ADCCM DP 8.673684210526316 0.0380787055875299 5.5 12.0 0.0006377577271607 0.0431414857210886 95
shuffled Anaphase CP 11.011904761904763 0.029795253482773426 9.0 14.0 0.009916834300583401 0.04215862725476838 84
shuffled Anaphase CP_and_DP 9.119047619047619 0.036490982945659056 6.0 12.25 0.002707314536830275 0.046669490240089824 84
shuffled Anaphase DP 8.452380952380953 0.04053248504975413 6.0 11.0 0.001242485230918825 0.0464051466534498 84
shuffled Apoptosis CP 5.183150183150183 0.09440398694822721 3.0 7.0 0.0583053979278328 0.1232318829571747 273
shuffled Apoptosis CP_and_DP 6.091575091575091 0.09287546938124143 3.0 9.0 0.0059069116685541 0.1081578125443246 273
shuffled Apoptosis DP 6.91941391941392 0.069566878978984 3.0 10.0 0.0044468894395305 0.0714523096751163 273
shuffled Binuclear CP 7.978260869565218 0.05694546545174261 6.0 10.0 0.038200742259475104 0.06910906128418097 184
shuffled Binuclear CP_and_DP 7.239130434782608 0.06776732828700599 4.0 11.0 0.004893048609533875 0.06776423530245201 184
shuffled Binuclear DP 7.326086956521739 0.07872110252851934 4.0 10.0 0.004853894017771725 0.06378804096775145 184
shuffled Elongated CP 9.663636363636364 0.04628236766827726 8.0 12.0 0.02107524909799725 0.05427016690941745 110
shuffled Elongated CP_and_DP 10.036363636363637 0.013487803728890751 8.0 13.0 0.000321759142212825 0.009313128443300425 110
shuffled Elongated DP 8.445454545454545 0.04069323292810818 6.0 11.0 0.005688361089689475 0.05591995974427495 110
shuffled Grape CP 11.878378378378379 0.02043910926030465 10.25 14.0 0.00690445509858295 0.025769621295513898 74
shuffled Grape CP_and_DP 10.662162162162161 0.016227561022057795 8.0 14.0 0.00063497684399765 0.03200755371463145 74
shuffled Grape DP 11.14864864864865 0.016131365303253386 9.0 14.0 0.000415092979677925 0.018759554891719224 74
shuffled Hole CP 10.342105263157896 0.03345073260189788 9.0 13.0 0.018350420600979724 0.04143496832090805 114
shuffled Hole CP_and_DP 9.526315789473685 0.027000667154455822 8.0 12.0 0.001620115694602725 0.03462351679139783 114
shuffled Hole DP 9.157894736842104 0.025403829134963828 7.0 12.0 0.0005975906705447 0.0367800934999437 114
shuffled Interphase CP 3.9904761904761905 0.12185842402226899 2.0 5.0 0.07577769123896122 0.15420668683458608 420
shuffled Interphase CP_and_DP 5.373809523809523 0.15584546997215173 2.0 8.0 0.0264223441829376 0.16631184063513535 420
shuffled Interphase DP 5.811904761904762 0.1638805347166295 2.0 9.0 0.007822367414750925 0.19387655449904215 420
shuffled Large CP 11.20253164556962 0.028549410709207215 10.0 14.0 0.010925640826997499 0.038751360121798945 79
shuffled Large CP_and_DP 8.455696202531646 0.04283739686097812 5.0 11.5 0.00414163050824435 0.0534913584066877 79
shuffled Large DP 8.734177215189874 0.02813164167020773 5.5 12.0 0.00043928097276 0.040813625052025154 79
shuffled Metaphase CP 11.675675675675675 0.02494736114900807 11.0 14.0 0.0064977891958143755 0.03497687792174847 74
shuffled Metaphase CP_and_DP 10.08108108108108 0.026246972636685562 8.0 13.0 0.001759103362976575 0.030604463525761474 74
shuffled Metaphase DP 9.513513513513514 0.025548139426537518 7.0 12.0 0.002324259547550675 0.030920616315688574 74
shuffled MetaphaseAlignment CP 7.354285714285714 0.05234074739590591 6.0 9.0 0.029589289838816202 0.06965646982779505 175
shuffled MetaphaseAlignment CP_and_DP 7.9314285714285715 0.0371751354550505 5.0 10.0 0.00599018200288535 0.047254847030928096 175
shuffled MetaphaseAlignment DP 7.988571428571428 0.03560342786074245 5.0 10.0 0.00416234609740955 0.047925077914691194 175
shuffled OutOfFocus CP 7.019736842105263 0.060989805089416115 5.0 8.0 0.0412088174661866 0.07787332210937627 304
shuffled OutOfFocus CP_and_DP 6.819078947368421 0.06599225931236292 3.0 10.0 0.009810445281074099 0.06546554213939165 304
shuffled OutOfFocus DP 8.394736842105264 0.0703731712515792 3.0 13.0 0.00027665014151152497 0.10135370311480048 304
shuffled Polylobed CP 4.016348773841962 0.12613869045479414 2.0 5.0 0.0784844896717357 0.1512608058459144 367
shuffled Polylobed CP_and_DP 6.106267029972752 0.12321896425221338 2.0 9.0 0.00759154922210415 0.13343035134559217 367
shuffled Polylobed DP 6.1035422343324255 0.12320122836884424 2.0 10.0 0.0073116328414517 0.13552884433060447 367
shuffled Prometaphase CP 4.284057971014493 0.1140931940157222 2.0 5.0 0.0717118038286185 0.1376924388498034 345
shuffled Prometaphase CP_and_DP 5.284057971014493 0.12082677751628353 2.0 7.0 0.0147600229571647 0.1572645094320973 345
shuffled Prometaphase DP 4.460869565217391 0.15848635121570268 2.0 6.0 0.0190109128082312 0.2053264676391812 345
shuffled SmallIrregular CP 8.170731707317072 0.04548787395632086 7.0 10.0 0.028097616522523676 0.05824467199689533 164
shuffled SmallIrregular CP_and_DP 7.9817073170731705 0.059508573434921455 5.0 11.0 0.00308836354223295 0.05330143728245445 164
shuffled SmallIrregular DP 8.853658536585366 0.0387966015480015 5.75 13.0 0.0019522874842537751 0.03782821754060953 164
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