{
  "analytic": "regulatory-genome",
  "kind": "declared_analytical_or_constructed_example",
  "experimental_model_result": false,
  "panels": [
    {
      "kind": "line",
      "x": [
        -6.0,
        -5.925,
        -5.85,
        -5.775,
        -5.7,
        -5.625,
        -5.55,
        -5.475,
        -5.4,
        -5.325,
        -5.25,
        -5.175,
        -5.1,
        -5.025,
        -4.95,
        -4.875,
        -4.8,
        -4.725,
        -4.65,
        -4.575,
        -4.5,
        -4.425,
        -4.35,
        -4.275,
        -4.2,
        -4.125,
        -4.05,
        -3.975,
        -3.9,
        -3.825,
        -3.75,
        -3.6750000000000003,
        -3.6,
        -3.525,
        -3.45,
        -3.375,
        -3.3000000000000003,
        -3.225,
        -3.15,
        -3.075,
        -3.0,
        -2.9250000000000003,
        -2.85,
        -2.775,
        -2.7,
        -2.625,
        -2.5500000000000003,
        -2.475,
        -2.4000000000000004,
        -2.325,
        -2.25,
        -2.1750000000000003,
        -2.1,
        -2.0250000000000004,
        -1.9500000000000002,
        -1.875,
        -1.7999999999999998,
        -1.7250000000000005,
        -1.6500000000000004,
        -1.5750000000000002,
        -1.5,
        -1.4249999999999998,
        -1.3500000000000005,
        -1.2750000000000004,
        -1.2000000000000002,
        -1.125,
        -1.0499999999999998,
        -0.9750000000000005,
        -0.9000000000000004,
        -0.8250000000000002,
        -0.75,
        -0.6749999999999998,
        -0.6000000000000005,
        -0.5250000000000004,
        -0.4500000000000002,
        -0.375,
        -0.2999999999999998,
        -0.22500000000000053,
        -0.15000000000000036,
        -0.07500000000000018,
        0.0,
        0.07500000000000018,
        0.14999999999999947,
        0.22499999999999964,
        0.2999999999999998,
        0.375,
        0.4500000000000002,
        0.5249999999999995,
        0.5999999999999996,
        0.6749999999999998,
        0.75,
        0.8250000000000002,
        0.8999999999999995,
        0.9749999999999996,
        1.0499999999999998,
        1.125,
        1.1999999999999993,
        1.2749999999999995,
        1.3499999999999996,
        1.4249999999999998,
        1.5,
        1.5749999999999993,
        1.6499999999999995,
        1.7249999999999996,
        1.7999999999999998,
        1.875,
        1.9499999999999993,
        2.0250000000000004,
        2.0999999999999996,
        2.174999999999999,
        2.25,
        2.3249999999999993,
        2.4000000000000004,
        2.4749999999999996,
        2.549999999999999,
        2.625,
        2.6999999999999993,
        2.7750000000000004,
        2.8499999999999996,
        2.924999999999999,
        3.0,
        3.0749999999999993,
        3.1500000000000004,
        3.2249999999999996,
        3.299999999999999,
        3.375,
        3.4499999999999993,
        3.5250000000000004,
        3.5999999999999996,
        3.674999999999999,
        3.75,
        3.8249999999999993,
        3.9000000000000004,
        3.9749999999999996,
        4.049999999999999,
        4.125,
        4.199999999999999,
        4.275,
        4.35,
        4.424999999999999,
        4.5,
        4.574999999999999,
        4.65,
        4.725,
        4.799999999999999,
        4.875,
        4.949999999999999,
        5.025,
        5.1,
        5.174999999999999,
        5.25,
        5.324999999999999,
        5.4,
        5.475,
        5.549999999999999,
        5.625,
        5.699999999999999,
        5.775,
        5.85,
        5.924999999999999,
        6.0
      ],
      "series": [
        {
          "label": "Baseline response",
          "y": [
            0.0024726231566347743,
            0.002664688150919165,
            0.0028716291557003997,
            0.0030945914351618036,
            0.0033348073074133443,
            0.00359360258142009,
            0.0038724034406710317,
            0.004172743799782958,
            0.004496273160941178,
            0.004844764997639799,
            0.005220125693558397,
            0.0056244040645522814,
            0.0060598014915841155,
            0.006528682691921699,
            0.007033587154995161,
            0.007577241267860811,
            0.008162571153159897,
            0.008792716239674923,
            0.009471043581946108,
            0.010201162940769636,
            0.01098694263059318,
            0.011832526132668766,
            0.012742349464111609,
            0.013721159282518911,
            0.014774031693273055,
            0.015906391711814714,
            0.017124033315727736,
            0.01843314000110983,
            0.01984030573407751,
            0.021352556161020567,
            0.022977369910025615,
            0.02472269978037561,
            0.026596993576865856,
            0.0286092143005461,
            0.030768859357148008,
            0.033085978388704126,
            0.03557118927263617,
            0.038235691765958146,
            0.041091278200465015,
            0.04415034055836462,
            0.04742587317756678,
            0.05093147025294352,
            0.05468131721594076,
            0.05869017499209118,
            0.06297335605699649,
            0.0675466911396291,
            0.07242648536151769,
            0.07762946255648838,
            0.08317269649392235,
            0.08907352773556322,
            0.09534946489910949,
            0.10201806918913038,
            0.10909682119561294,
            0.11660296916113934,
            0.12455335818741639,
            0.13296424019782926,
            0.14185106490048782,
            0.15122825250907412,
            0.1611089495765852,
            0.17150476997540084,
            0.18242552380635635,
            0.19387893782385993,
            0.20587037180094725,
            0.21840253609763444,
            0.23147521650098232,
            0.24508501313237172,
            0.25922510081784605,
            0.2738850187392208,
            0.28905049737499594,
            0.3047033306524346,
            0.320821300824607,
            0.33737816282991756,
            0.35434369377420444,
            0.3716838117046337,
            0.38936076605077796,
            0.40733340004593027,
            0.4255574831883411,
            0.44398610945537986,
            0.46257015465625034,
            0.48125878412146467,
            0.5,
            0.5187412158785353,
            0.5374298453437494,
            0.5560138905446199,
            0.5744425168116589,
            0.5926665999540697,
            0.610639233949222,
            0.6283161882953661,
            0.6456563062257954,
            0.6626218371700825,
            0.679178699175393,
            0.6952966693475654,
            0.7109495026250039,
            0.7261149812607791,
            0.7407748991821539,
            0.7549149868676283,
            0.7685247834990175,
            0.7815974639023654,
            0.7941296281990525,
            0.8061210621761402,
            0.8175744761936437,
            0.828495230024599,
            0.8388910504234147,
            0.8487717474909258,
            0.8581489350995123,
            0.8670357598021706,
            0.8754466418125836,
            0.8833970308388606,
            0.8909031788043871,
            0.8979819308108695,
            0.9046505351008906,
            0.9109264722644368,
            0.9168273035060777,
            0.9223705374435115,
            0.9275735146384823,
            0.9324533088603709,
            0.9370266439430035,
            0.9413098250079087,
            0.9453186827840592,
            0.9490685297470565,
            0.9525741268224334,
            0.9558496594416355,
            0.958908721799535,
            0.9617643082340419,
            0.9644288107273639,
            0.9669140216112958,
            0.969231140642852,
            0.9713907856994539,
            0.973403006423134,
            0.9752773002196243,
            0.9770226300899744,
            0.9786474438389795,
            0.9801596942659225,
            0.9815668599988902,
            0.9828759666842724,
            0.9840936082881853,
            0.9852259683067269,
            0.9862788407174811,
            0.9872576505358884,
            0.9881674738673312,
            0.9890130573694068,
            0.9897988370592303,
            0.9905289564180538,
            0.9912072837603251,
            0.9918374288468401,
            0.9924227587321393,
            0.9929664128450049,
            0.9934713173080783,
            0.9939401985084158,
            0.9943755959354477,
            0.9947798743064417,
            0.9951552350023601,
            0.9955037268390589,
            0.995827256200217,
            0.9961275965593289,
            0.9964063974185798,
            0.9966651926925867,
            0.9969054085648383,
            0.9971283708442995,
            0.9973353118490808,
            0.9975273768433653
          ]
        },
        {
          "label": "Change for +1 input",
          "y": [
            0.004220227767650081,
            0.004545671262099881,
            0.0048959409223146046,
            0.005272887164267789,
            0.005678491345434478,
            0.006114873900053976,
            0.0065843027912470395,
            0.0070892022575827374,
            0.007632161823333059,
            0.008215945531813193,
            0.008843501349687078,
            0.009517970676710088,
            0.01024269787985683,
            0.011021239752902673,
            0.011857374782043888,
            0.012755112074797941,
            0.01371869978297058,
            0.014752632820665504,
            0.015861659644925613,
            0.017050787829446436,
            0.018325288120763138,
            0.019690696621332576,
            0.021152814695066552,
            0.022717706138321265,
            0.0243916911034913,
            0.026181336203804122,
            0.02809344016755976,
            0.030135014349146273,
            0.03231325734434023,
            0.034635522900801095,
            0.03710928026398201,
            0.039742066057214046,
            0.042541426766480955,
            0.04551485089011707,
            0.04866968982683035,
            0.05201306661831612,
            0.05555177174221995,
            0.059292145274834396,
            0.0632399449185363,
            0.06740019962453175,
            0.07177704884455077,
            0.07637356782242814,
            0.08119157979315351,
            0.08623145649573169,
            0.09149190902653818,
            0.09696977175693405,
            0.10265978280252208,
            0.10855436534502015,
            0.11464341494749584,
            0.12091409883803929,
            0.12735067392619936,
            0.13393433101340357,
            0.1406430732092694,
            0.14745163691171215,
            0.15433146378972049,
            0.1612507319651595,
            0.16817445397189978,
            0.17506464803640437,
            0.18188058774991597,
            0.18857913328686496,
            0.19511514499178906,
            0.20144197746213074,
            0.20751204928172257,
            0.21327748042411743,
            0.21869078618653973,
            0.22370561349387205,
            0.2282775026979436,
            0.23236465576028953,
            0.23592869010394396,
            0.23893535658464415,
            0.24135520006119104,
            0.24316414199074216,
            0.24434396633824745,
            0.2448826928166854,
            0.24477482496002279,
            0.24402146462012392,
            0.24263028897982508,
            0.24061539086805073,
            0.23799698781772255,
            0.23480100969424517,
            0.2310585786300049,
            0.22680539824786738,
            0.2220810716053616,
            0.21692836885211852,
            0.2113924662308997,
            0.20552017778555154,
            0.19935920003546503,
            0.19295738804578333,
            0.18636207890812906,
            0.1796194758109475,
            0.1727741027929176,
            0.16586833710512738,
            0.15894202301199822,
            0.15203216796960284,
            0.14517271953805522,
            0.13839441918672046,
            0.13172472738129726,
            0.12518781301581094,
            0.11880459936067611,
            0.11259285821028675,
            0.1065673437851129,
            0.10073995811926029,
            0.0951199400853665,
            0.08971407081443972,
            0.08452688900161898,
            0.07956091039800506,
            0.07481684662885957,
            0.07029381931263912,
            0.06598956625452679,
            0.061900637231084854,
            0.05802257755498008,
            0.0543500982022056,
            0.05087723179547188,
            0.04759747416720028,
            0.0445039115774446,
            0.041589333941832174,
            0.038846334639327296,
            0.036267397627028686,
            0.03384497269726039,
            0.03157153977869598,
            0.029439663215475087,
            0.027442036962976313,
            0.025571521622056115,
            0.023821174200437056,
            0.02218427144497126,
            0.020654327535518324,
            0.01922510687322576,
            0.01789063263561297,
            0.016645191709961704,
            0.015483336556646687,
            0.014399884496313686,
            0.013389914859978758,
            0.012448764389795586,
            0.011572021230627172,
            0.01075551780891204,
            0.00999532285557092,
            0.009287732793822556,
            0.00862926268061781,
            0.008016636861716164,
            0.00744677947505612,
            0.00691680491469715,
            0.006424008348029364,
            0.00596585636187974,
            0.005539977798347251,
            0.0051441548284515415,
            0.004776314300739659,
            0.004434519392671921,
            0.004116961584699985,
            0.0038219529703078514,
            0.0035479189097005204,
            0.0032933910302308522,
            0.0030570005728473015,
            0.0028374720807666787,
            0.0026336174241066157,
            0.0024443301522485417,
            0.002268580164206946,
            0.0021054086861359567,
            0.0019539235442936898,
            0.001813294721234593,
            0.0016827501826612856,
            0.001561571962234054
          ]
        }
      ],
      "xlabel": "Constructed regulatory coordinate",
      "ylabel": "Normalized response / change",
      "logx": false,
      "logy": false
    },
    {
      "kind": "line",
      "x": [
        0.0,
        0.06,
        0.12,
        0.18,
        0.24,
        0.3,
        0.36,
        0.42,
        0.48,
        0.54,
        0.6,
        0.6599999999999999,
        0.72,
        0.78,
        0.84,
        0.8999999999999999,
        0.96,
        1.02,
        1.08,
        1.14,
        1.2,
        1.26,
        1.3199999999999998,
        1.38,
        1.44,
        1.5,
        1.56,
        1.6199999999999999,
        1.68,
        1.74,
        1.7999999999999998,
        1.8599999999999999,
        1.92,
        1.98,
        2.04,
        2.1,
        2.16,
        2.2199999999999998,
        2.28,
        2.34,
        2.4,
        2.46,
        2.52,
        2.58,
        2.6399999999999997,
        2.6999999999999997,
        2.76,
        2.82,
        2.88,
        2.94,
        3.0,
        3.06,
        3.12,
        3.1799999999999997,
        3.2399999999999998,
        3.3,
        3.36,
        3.42,
        3.48,
        3.54,
        3.5999999999999996,
        3.6599999999999997,
        3.7199999999999998,
        3.78,
        3.84,
        3.9,
        3.96,
        4.02,
        4.08,
        4.14,
        4.2,
        4.26,
        4.32,
        4.38,
        4.4399999999999995,
        4.5,
        4.56,
        4.62,
        4.68,
        4.74,
        4.8,
        4.859999999999999,
        4.92,
        4.9799999999999995,
        5.04,
        5.1,
        5.16,
        5.22,
        5.279999999999999,
        5.34,
        5.3999999999999995,
        5.46,
        5.52,
        5.58,
        5.64,
        5.7,
        5.76,
        5.819999999999999,
        5.88,
        5.9399999999999995,
        6.0,
        6.06,
        6.12,
        6.18,
        6.24,
        6.3,
        6.359999999999999,
        6.42,
        6.4799999999999995,
        6.54,
        6.6,
        6.66,
        6.72,
        6.779999999999999,
        6.84,
        6.8999999999999995,
        6.96,
        7.02,
        7.08,
        7.14,
        7.199999999999999,
        7.26,
        7.319999999999999,
        7.38,
        7.4399999999999995,
        7.5,
        7.56,
        7.62,
        7.68,
        7.739999999999999,
        7.8,
        7.859999999999999,
        7.92,
        7.9799999999999995,
        8.04,
        8.1,
        8.16,
        8.219999999999999,
        8.28,
        8.34,
        8.4,
        8.459999999999999,
        8.52,
        8.58,
        8.64,
        8.7,
        8.76,
        8.82,
        8.879999999999999,
        8.94,
        9.0
      ],
      "series": [
        {
          "label": "Ideal signal correlation",
          "y": [
            1.0,
            0.9712858623572642,
            0.9449111825230679,
            0.9205746178983235,
            0.8980265101338745,
            0.8770580193070292,
            0.8574929257125443,
            0.8391813582966892,
            0.8219949365267866,
            0.8058229640253802,
            0.7905694150420948,
            0.7761505257063328,
            0.7624928516630234,
            0.7495316889958615,
            0.7372097807744856,
            0.7254762501100117,
            0.7142857142857143,
            0.7035975447302919,
            0.6933752452815364,
            0.6835859270246633,
            0.674199862463242,
            0.6651901052377394,
            0.6565321642986128,
            0.6482037235521644,
            0.6401843996644799,
            0.6324555320336759,
            0.625,
            0.6178020632152155,
            0.6108472217815262,
            0.604122093330177,
            0.5976143046671968,
            0.5913123959890826,
            0.5852057359806528,
            0.5792844463634923,
            0.5735393346764045,
            0.5679618342470648,
            0.562543950463012,
            0.5572782125753528,
            0.5521576303742327,
            0.5471756551645828,
            0.5423261445466404,
            0.5376033305704704,
            0.5330017908890261,
            0.52851642258169,
            0.5241424183609591,
            0.5198752449100363,
            0.5157106231293968,
            0.5116445100966509,
            0.5076730825668095,
            0.5037927218598783,
            0.5,
            0.4962916669854651,
            0.4926646390821466,
            0.4891159880445185,
            0.4856429311786321,
            0.48224282217041214,
            0.47891314261057577,
            0.4756514941544941,
            0.47245559126153397,
            0.469323254463932,
            0.4662524041201569,
            0.46324105461207943,
            0.46028730894916176,
            0.45738935374634826,
            0.45454545454545453,
            0.45175395145262565,
            0.44901325506693723,
            0.4463218426774518,
            0.44367825470805694,
            0.4410810913912309,
            0.4385290096535146,
            0.4360207201969473,
            0.43355498476205995,
            0.4311306135592269,
            0.42874646285627216,
            0.42640143271122083,
            0.4240944648399854,
            0.4218245406095978,
            0.4195906791483446,
            0.4173919355648411,
            0.41522739926869984,
            0.4130961923860138,
            0.4109974682633933,
            0.4089304100547653,
            0.40689422938557973,
            0.404888165089458,
            0.4029114820126901,
            0.40096346988231274,
            0.3990434422338111,
            0.3971507353947688,
            0.3952847075210474,
            0.39344473768231686,
            0.39163022499397865,
            0.38984058779272523,
            0.3880752628531664,
            0.3863337046431279,
            0.3846153846153846,
            0.3829197905337418,
            0.3812464258315117,
            0.37959480900056175,
            0.3779644730092272,
            0.3763549647474907,
            0.37476584449793077,
            0.37319668543103796,
            0.37164707312358314,
            0.3701166050988026,
            0.3686048903872428,
            0.3671115491071762,
            0.36563621206356534,
            0.3641785203646149,
            0.36273812505500586,
            0.3613146867649621,
            0.35990787537434726,
            0.35851736969103737,
            0.35714285714285715,
            0.35578403348241,
            0.3544406025041679,
            0.35311227577322435,
            0.35179877236514595,
            0.3504998186163908,
            0.34921514788478913,
            0.3479445003196105,
            0.3466876226407682,
            0.34544426792673344,
            0.3442141954107571,
            0.34299717028501764,
            0.3417929635123316,
            0.34060135164508576,
            0.3394221166510653,
            0.33825504574586923,
            0.337099931231621,
            0.3359565703416979,
            0.3348247650912125,
            0.33370432213299994,
            0.3325950526188697,
            0.33149677206589795,
            0.3304093002275449,
            0.3293324609693921,
            0.3282660821493064,
            0.3272099955018442,
            0.3261640365267211,
            0.32512804438117754,
            0.3241018617760822,
            0.32308533487561925,
            0.3220783132004154,
            0.3210806495339678,
            0.32009219983223997,
            0.3191128231363014,
            0.3181423814878889,
            0.3171807398477756,
            0.31622776601683794
          ]
        }
      ],
      "xlabel": "Noise variance / signal variance",
      "ylabel": "Correlation ceiling",
      "logx": false,
      "logy": false
    }
  ],
  "title": "Background saturation and measurement noise alter effect interpretation",
  "assumptions": "Sigmoid constructed response, +1 input shift. Independent additive noise; ideal predictor equals latent signal. No DNA or genome-model outputs.",
  "worked": "基线z=0时增量0.231059，z=3时约0.029440；噪声方差等于信号方差时理想相关sqrt(1/2)≈0.707107。",
  "checks": {
    "delta_z0": 0.2310585786300049,
    "delta_z3": 0.029439663215475087,
    "ceiling_equal_noise": 0.7071067811865475
  },
  "generator_source_sha256": {
    "ops/datacenter/editorial_guides/science_figures.py": "01890ea429a67a880650c9b0602b1b66ed6ddeaa9704b7224897857a5f4803d7",
    "ops/datacenter/editorial_guides/deep_figures.py": "158969d9b1f5a4bd13906cf78dd71affc2692df9194593918059d861a6f59c85"
  },
  "source_ids": [
    "alphagenome",
    "enformer",
    "arxiv-2102.11107"
  ],
  "formula_source": "Article equations and this versioned script",
  "diagram_nodes": [
    "序列与轨道字典",
    "长程条件化预测",
    "参考 / 替代 / 组合",
    "基因座与组织留出",
    "外部干预与反证",
    "机制和条件的版本化"
  ]
}