M&M model VEM updates¶
In [1]:
dat = readRDS('/home/gaow/Documents/GTExV8/Thyroid.Lung.FMO2.filled.rds')
attach(dat)
In [2]:
%get X Y --from R
Y = Y.as_matrix()
Loading required package: feather
In [3]:
from libgaow.regression_data import MNMASH
import numpy as np
In [4]:
model = MNMASH(X=X,Y=Y)
In [5]:
model.set_prior({'identity': np.identity(2),
'single_1': np.array([[1,0],[0,0]]),
'single_2': np.array([[0,0], [0,1]]),
'all_in': np.ones((2,2))},
[0.5,1],
[0.9,0.01,0.01,0.01,0.01,0.01,0.01,0.02,0.02])
In [ ]:
model.fit(niter=2)
In [7]:
model.post_mean_mat
Out[7]:
array([[ -2.32382184e-19, -1.36836333e-19],
[ -3.04885813e-17, -6.02915572e-17],
[ -3.02330316e-18, -3.35486223e-17],
...,
[ 3.44738982e-19, 1.68615485e-18],
[ -2.70497565e-19, -1.08394346e-19],
[ 3.88702714e-19, 2.04068922e-18]])
In [9]:
import seaborn as sns
import matplotlib.pyplot as plt
plt.scatter([x+1 for x in range(len(model.post_mean_mat[:,0]))], model.post_mean_mat[:,0], cmap="viridis")
ax = plt.gca()
plt.show()
In [10]:
import seaborn as sns
import matplotlib.pyplot as plt
plt.scatter([x+1 for x in range(len(model.post_mean_mat[:,1]))], model.post_mean_mat[:,1], cmap="viridis")
ax = plt.gca()
plt.show()
Debug previews¶
In [11]:
model.mash.B
Out[11]:
array([[-0.02767384, -0.06585172],
[-0.08742572, 0.00192239],
[-0.03943936, -0.01741381],
...,
[ 0.01151077, -0.00210548],
[-0.03341688, 0.07328577],
[ 0.01482872, 0.0044251 ]])
In [34]:
model.mash.S
Out[34]:
array([[ nan, nan],
[ nan, nan],
[ nan, nan],
...,
[ nan, nan],
[ nan, nan],
[ nan, nan]])
In [8]:
print(model)
{ 'Xr0': array([[ 0.09902838, 0.04492896],
[ 0.09905334, 0.04493302],
[-0.1277729 , -0.15765855],
...,
[-0.12777212, -0.15765836],
[ 0.09902838, 0.04492896],
[ 0.09902716, 0.04492899]]),
'Y': array([[ 1.60689480e-01, 7.73609574e-01],
[ 4.33098395e-01, 7.81487761e-01],
[ -2.15164667e-01, -6.50111523e-01],
...,
[ 6.17574628e-01, 2.16840434e-18],
[ 3.03576608e-18, -5.08905465e-02],
[ -1.49299907e-01, 3.02853264e-01]]),
'alpha0': array([[ 5.45933365e-017, 1.32758321e-016, 1.89175534e-016, ...,
6.77746859e-017, 5.29789647e-017, 7.05860121e-017],
[ 2.69163809e-015, 1.71270360e-014, 9.11265900e-015, ...,
3.79612830e-015, 2.45367078e-015, 3.70535731e-015],
[ 2.22321669e-309, 1.55446248e-309, 8.98221633e-310, ...,
8.14181125e-310, 1.30153690e-308, 8.28879486e-310],
[ 1.02446086e-171, 6.92914413e-172, 4.20738967e-172, ...,
3.62439472e-172, 3.95327136e-171, 3.64987152e-172],
[ 3.17571377e-152, 2.13684984e-152, 1.31182971e-152, ...,
1.11232803e-152, 1.17154032e-151, 1.12196194e-152]]),
'elbo': [],
'iter_id': 2,
'mash': { 'B': array([[-0.02767384, -0.06585172],
[-0.08742572, 0.00192239],
[-0.03943936, -0.01741381],
...,
[ 0.01151077, -0.00210548],
[-0.03341688, 0.07328577],
[ 0.01482872, 0.0044251 ]]),
'S': array([[ 0.03802662, 0.03427535],
[ 0.0682581 , 0.0617366 ],
[ 0.05373473, 0.04855798],
...,
[ 0.05520583, 0.04987416],
[ 0.02957212, 0.02659511],
[ 0.05496787, 0.04966 ]]),
'U': { 'all_in.1': array([[ 0.25, 0.25],
[ 0.25, 0.25]]),
'all_in.2': array([[ 1., 1.],
[ 1., 1.]]),
'identity.1': array([[ 0.25, 0. ],
[ 0. , 0.25]]),
'identity.2': array([[ 1., 0.],
[ 0., 1.]]),
'null': array([[ 0., 0.],
[ 0., 0.]]),
'single_1.1': array([[ 0.25, 0. ],
[ 0. , 0. ]]),
'single_1.2': array([[ 1., 0.],
[ 0., 0.]]),
'single_2.1': array([[ 0. , 0. ],
[ 0. , 0.25]]),
'single_2.2': array([[ 0., 0.],
[ 0., 1.]])},
'V': array([[ 1. , 0.09728834],
[ 0.09728834, 1. ]]),
'X': array([[ 0.66232029, -0.08595989, -0.12194938, ..., -0.1364837 ,
0.44764338, -0.13791952],
[-0.33767971, -0.08595989, -0.12194938, ..., -0.1364837 ,
0.44764338, -0.13791952],
[-0.33767971, 0.91404011, -0.12194938, ..., -0.1364837 ,
0.44764338, -0.13791952],
...,
[-0.33767971, -0.08595989, -0.12194938, ..., -0.1364837 ,
-0.55235662, -0.13791952],
[-0.33767971, -0.08595989, -0.12194938, ..., -0.1364837 ,
0.44764338, -0.13791952],
[-0.33767971, -0.08595989, -0.12194938, ..., -0.1364837 ,
0.44764338, -0.13791952]]),
'Y': array([[ 0.06164614, 0.74777545],
[ 0.33403009, 0.75564958],
[-0.08740673, -0.47335813],
...,
[ 0.74533178, 0.1767532 ],
[-0.09904334, -0.07672467],
[-0.24834202, 0.27701911]]),
'Z': None,
'_is_common_cov': False,
'grid': [0.5, 1],
'l10bf': array([-0.7934147 , -0.96548204, -1.17737859, ..., -1.24902317,
-0.22649881, -1.24527793]),
'lik': { 'alt_loglik': array([ 0.98951102, 0.58062815, 1.09356474, ..., 1.16212554,
0.00991958, 1.16469863]),
'lfactor': array([ 2.81641587, 2.80373271, 3.80457912, ..., 4.03810768,
1.72474613, 4.03205702]),
'loglik': 10468.735437149146,
'marginal_loglik': array([ 2.72877639, 2.71033068, 3.70657695, ..., 3.93898994,
0.48996451, 3.93299318]),
'null_loglik': array([ 2.81641587, 2.80373271, 3.80457912, ..., 4.03810768,
0.53145236, 4.03205702]),
'relative_likelihood': array([[ 1. , 0.03750137, 0.00948399, ..., 0.19162327,
0.28587933, 0.14360527],
[ 1. , 0.03736103, 0.00956503, ..., 0.06208076,
0.12988375, 0.06530318],
[ 1. , 0.01397801, 0.00353161, ..., 0.05031885,
0.09742175, 0.04886843],
...,
[ 1. , 0.01109823, 0.00279809, ..., 0.04967414,
0.07767785, 0.0389271 ],
[ 0.30322088, 0.11164543, 0.02825018, ..., 0.50488899,
0.02786012, 0.01395332],
[ 1. , 0.01116438, 0.002815 , ..., 0.0494625 ,
0.07907928, 0.03963256]])},
'neg_prob_mat': array([[ 0.00823421, 0.00888351, 0.00433873, ..., 0.00189991,
0.00910786, 0.00182953],
[ 0.01476349, 0.00653534, 0.00484051, ..., 0.00063262,
0.04420548, 0.00050521]]),
'pi': array([ 0.9 , 0.01, 0.01, 0.01, 0.01, 0.01, 0.01, 0.02, 0.02]),
'post_mean2_mat': array([[ 2.39306787e-05, 1.23016555e-04, 2.56463989e-05, ...,
1.49876851e-05, 2.43208233e-05, 1.54335211e-05],
[ 8.64108730e-06, 9.43156561e-04, 3.07749605e-03, ...,
1.57969677e-04, 3.49071155e-05, 2.80215605e-04]]),
'post_mean_mat': array([[ -2.69293411e-04, -8.70337466e-04, -2.23409015e-04, ...,
5.52310537e-05, -3.89965362e-04, 6.94710584e-05],
[ -2.77021149e-04, -1.49338126e-03, -1.97428939e-03, ...,
4.29748021e-04, 1.91703541e-04, 5.80250853e-04]]),
'posterior_weights': array([[ 9.82435061e-01, 9.88112735e-01, 9.92668662e-01, ...,
9.93776666e-01, 9.38124442e-01, 9.93723104e-01],
[ 4.09362898e-04, 4.10187843e-04, 1.54172533e-04, ...,
1.22546287e-04, 3.83795424e-03, 1.23270019e-04],
[ 1.03526701e-04, 1.05014732e-04, 3.89524091e-05, ...,
3.08964546e-05, 9.71136134e-04, 3.10814382e-05],
...,
[ 2.09174906e-03, 6.81586522e-04, 5.54999372e-04, ...,
5.48500018e-04, 1.73562040e-02, 5.46133621e-04],
[ 6.24128611e-03, 2.85199523e-03, 2.14905606e-03, ...,
1.71543181e-03, 1.91545468e-03, 1.74628680e-03],
[ 3.13517457e-03, 1.43393109e-03, 1.07800347e-03, ...,
8.59663162e-04, 9.59326433e-04, 8.75195238e-04]]),
'trace_XXt': array([ 1285.74755823, 1645.74964547, 1474.99961843, 2431.86362943,
1573.93731825, 1985.63229086, 1722.71676782, 1196.84535627,
1559.24047364, 1812.54137461, 1500.25358956, 1529.93503045,
1641.61359624, 2421.81707409, 2502.98070591, 1466.36477889,
1311.17800224, 1837.40058792, 1280.98808451, 2296.5313088 ,
1823.03440129, 1445.79597251, 1276.6574532 , 2569.52069451,
1801.6875249 , 1918.92567644, 1119.48568772, 1474.59360472,
3182.36441038, 1408.49110789, 1633.08604459, 2947.11992813,
1780.1795657 , 1302.39633762, 2558.04266555, 2003.74278014,
1271.42831883, 1673.44238122, 1837.38071938, 1431.0667699 ,
2339.45352904, 1165.52710149, 1406.25637819, 1868.34089425,
1404.48221363, 1751.18786087, 2792.14230641, 1807.84155469,
2041.3750185 , 1994.74518213, 1107.19345517, 1695.42506499,
1164.7488248 , 1282.14399214, 2047.79815298, 1663.86864624,
1750.3086855 , 1816.51723114, 2170.27397904, 1232.73886654,
1929.79120324, 1880.64275364, 1600.76903406, 1314.8514994 ,
1632.18177111, 1778.8608687 , 1616.97077214, 2360.83005899,
1141.70381475, 2271.79282434, 1090.42953396, 1880.75447003,
2577.19383685, 1224.56201251, 2598.37454117, 1721.93015083,
2054.48789652, 2235.24321359, 1680.05146321, 1976.93371624,
1199.14600521, 1194.28547062, 1587.27532756, 1984.10486544,
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1579.77919589, 1244.69126434, 2102.29297498, 1446.81480073,
1575.27606396, 1471.53731059, 2077.5616407 , 1876.14991829,
1354.7084005 , 3180.6329562 , 2168.20829481, 1577.53896897,
1882.14825524, 1543.68836035, 2520.48587556, 2048.56379258,
1827.51752575, 2329.135439 , 2120.98914721, 2010.35685292,
1505.68978621, 1832.84672355, 2472.16332511, 1251.68095142,
1876.3534272 , 1488.53413204, 1894.88258687, 1523.21255155,
1780.98148671, 2049.15798936, 1074.5042261 , 2860.31880214,
1108.15890472, 1621.11428101, 1867.24206569, 1351.29065262,
980.16687775, 1736.09243627, 2028.68498729, 1717.28924331,
1753.61364016, 1287.96865884, 1854.74781003, 1666.40548762,
1772.65125925, 2046.64984723, 1551.85241594, 1495.22523802,
1856.67669612, 1679.03499347, 1784.42829523, 1165.74943211,
1335.89073313, 2030.78624698, 1449.63182155, 1797.26083305,
1870.59500025, 1659.29782134, 1336.86171951, 1880.54451749,
1489.69862907, 1687.88816593, 1778.22288543, 2979.13384148,
2219.60290816, 1542.66566184, 1849.72757782, 1354.08709788,
2425.79175125, 1809.26903606, 1917.89524961, 2582.26759531,
1490.52294777, 2259.98591129, 1710.86798463, 1397.69194794,
2126.20256525, 1798.07416528, 1228.0244146 , 1905.99427739,
1830.89934154, 1971.81605122, 1600.53784614, 1901.06211847,
2401.94992547, 1692.5492925 , 1536.97089501, 1950.93857886,
1771.6805314 , 1851.75209132, 1673.21627294, 1599.00456835,
2086.64891509, 2226.90433371, 1726.1777312 , 1429.99201969,
1908.82334272, 1667.57200967, 1702.6385838 , 1581.50122461,
2222.89076898, 1961.02175227, 1503.74992144, 1618.93206865,
1935.34352829, 1852.37492737, 1228.83133337, 1986.04026193,
1624.10064149, 2166.02944942, 2215.22786373, 2589.35496902,
1548.29904467, 2263.3811615 , 1652.95356814, 1480.98945128,
1955.42271738, 1760.44219279, 1383.8748652 , 1516.14480627,
1757.98039188, 1894.58291006, 1716.44178485, 1461.71367391,
1262.59870108, 1709.54977117, 1450.98949016, 1618.65626898,
2259.0100011 , 2139.12764895, 2451.27137701, 1287.91714163,
2071.45640174, 1721.90445093, 1257.27131608, 1434.54156191,
2134.77702028, 1698.03396031, 2687.41501611, 1582.43774926,
1421.3214198 , 2253.2854731 , 2953.40175672, 1888.40775033,
1402.75303916, 2170.40856114, 1288.41248976, 1792.24535534,
1619.2213481 , 1165.29208635, 1961.2511168 , 2576.69992737,
2383.62252091, 1586.27950291, 1288.62594599, 1651.12593724,
1865.91343249, 2632.74903021, 1466.92435296, 1661.76311691,
1614.29350153, 1247.95394424, 1499.80288593, 1818.90200185,
1616.17424872, 1872.49310273, 2029.87896568, 2218.82876974,
1090.56365103, 2131.75165388, 1981.89858884, 2337.28027807,
1708.39361387, 1710.2821638 , 1891.70007959, 1712.11355999,
1868.93488502, 1246.53354702, 1457.25226147, 2175.55219982,
1940.68228718, 1530.17149549, 1800.3476233 , 1815.01461078,
1319.9532181 , 1455.00614774, 1780.135671 , 2222.69679251,
2310.16023406, 1581.92564572, 1127.96808531, 1446.59031784,
1750.48757584, 1267.12427304, 1365.74965487, 1576.72264069,
2037.00051009, 1741.00179606, 2089.34171006, 1221.35096033,
3007.68112368, 2174.50319163, 1421.38332119, 1471.84749033,
2270.88298121, 2105.95088206, 1222.01742853, 1297.67548758,
996.47853645, 1803.19306973, 1428.9528776 , 2051.2396076 ,
1500.33635009, 2367.34069654, 1261.72969904, 1631.88117872,
2153.35033111, 1061.44667036, 1278.55436911, 2222.98977316,
1656.56439865, 1138.87174109, 2749.99265946, 1282.23922794,
2089.0355149 , 2137.17633761, 1340.68909187, 1786.81207285,
1337.70993155, 1427.52148213, 1476.73860896, 1449.50748773,
2170.02782887, 1795.70239075, 2021.10542433, 1895.34146167,
1275.08074997, 1392.34628739, 1668.01708356, 1695.83133968,
1547.01733046, 1779.83853728, 1881.51380317, 1432.97144617,
1083.84896859, 2042.70842077, 1586.96708022, 1724.01518957,
2393.66448239, 2139.16015292, 1919.46022539, 1692.96477627,
1568.84406209, 1170.97478071, 2231.14919726, 1607.58877398,
1976.50408074, 1329.54698861, 1165.24089492, 1719.27936168,
1870.65543025, 2082.54956485, 1767.28140209, 2027.79550976,
1581.95668379, 1576.22729322, 1912.12977045, 1727.14181351,
1906.29896751, 1460.25776999, 1968.33739437, 1479.79013701,
1723.85799538, 1878.84347833, 1823.93810996, 1964.67051034,
1577.16042339, 2027.21205143, 1960.49829546, 1745.82275172,
2273.94379945, 1308.35760164, 2704.607246 , 1999.26006729,
2060.21937435, 1573.34086242, 2130.9254276 , 1688.98635608,
1280.25528863, 1552.37643851, 1509.65780429, 1756.43548393,
1680.75004299, 2089.32546131, 1808.86458918, 2221.90486917,
1284.85037995, 1326.08884812, 2104.63675071, 1623.78935009,
1383.69761097, 1662.24233841, 2319.37917338, 2051.823454 ,
1763.78030232, 1062.82273609, 1139.07298837, 2264.87750034,
1651.56673381, 2133.39398325, 1659.35256755, 1453.10988452,
1316.05963324, 1895.11444276, 1655.37104284, 2175.32235811,
1515.22606298, 2757.8617471 , 1781.83697221, 1502.61395545,
2213.59209845, 1602.10979231, 2546.42552565, 2110.9557598 ,
2046.0810098 , 1702.66509563, 1934.18421471, 1715.99037373,
1262.6850038 , 1724.67395604, 1498.5637194 , 1510.37342723,
1641.14021919, 3077.64927317, 1279.61084888, 1820.26179225,
1792.42239711, 1925.99235023, 1363.1074914 , 1608.75135895,
2219.79118552, 1933.26759567, 1379.44146001, 2125.13115317,
1735.40373488, 1466.06994584, 1937.00462103, 1517.00077582,
1753.47643184, 1271.33010334, 2087.11467041, 1783.02891271,
1847.1938205 , 1853.36220511, 1708.66793599, 1628.52849681,
1813.06977372, 1925.78442635, 1582.76486923, 1768.01516728,
1227.24964394, 1285.43945145, 2008.04997476, 1913.79687334,
1716.83565044, 1385.33903232, 1294.80934815, 1692.15155153,
1937.85777001, 1893.67208591, 1873.16586457, 2438.94654087,
1778.47693373, 2283.05938635, 1780.14912259, 2092.53721615,
2022.44759638, 1607.02846195, 2136.85996526, 2228.82487455,
1490.3321924 , 1231.41771403, 1060.08760193, 2505.80933758,
2174.95580707, 1711.78849927, 2959.46689646, 1878.14831438,
2272.88900263, 2137.5432506 , 1409.98548167, 2819.0300547 ,
1673.89422018, 1542.50156279, 1653.33924711, 1698.1670182 ,
1668.88503967, 1761.69523583, 1498.27940222, 1349.33674986,
1893.27703749, 1827.21332248, 1126.03308085, 2093.59587377,
1336.20438621, 1600.90097887, 1265.8223054 , 1685.78861116,
1684.23437005, 1433.34944604, 1545.17620487, 1824.62130741,
1901.70624434, 1577.77314478, 1277.63595909, 2083.278325 ,
2040.30254126, 1060.43430105, 1488.48889656, 1453.48652563,
1144.7684432 , 1740.4405586 , 1917.61920168, 2077.70171515,
1359.67055475, 1640.13714215, 1451.73565304, 1360.74353502,
1391.6637903 , 1365.67859571, 1443.16902443, 2092.09429581,
1462.63779656, 2182.3830016 , 1584.4420074 , 1979.1612867 ,
1860.44440846, 1921.84302764, 2155.05430968, 1659.24191012,
1269.24115874, 2060.73424094, 2574.83795033, 2548.06939391,
1226.25746284, 1724.11828114, 1596.88899576, 1844.00553416,
2078.49144423, 1765.99744996, 2264.02407678, 1419.35515037,
1776.88373638, 1628.97284853, 1614.14839518, 1986.83732036,
1437.93798741, 1343.98164477, 1889.81143605, 1394.20297264,
1167.89362759, 1556.88361156, 1770.54756355, 1995.42516744,
1809.01616904, 1315.38453508, 2578.85084327, 1889.25872354,
1306.22177432, 2380.48915491, 1365.85761828, 2149.95563042,
1653.91441811, 1733.2956507 , 1459.78753131, 1486.84586102,
2003.37293015, 2084.77564708, 2638.89469655, 1585.24054182,
1624.85227054, 1569.23770603, 1360.57351921, 1365.24837917,
3175.51805951, 1710.51581824, 1600.45591997, 1337.66271675,
1474.16344088, 1560.7587983 , 1830.15966399, 1483.36454525,
1151.40304048, 1852.80650561, 1447.11177489, 2142.37680734,
1876.53387498, 1921.82739841, 1597.32795465, 1807.79066839,
1807.44686878, 1560.47093778, 1655.77326384, 1688.12285863,
1571.04021997, 2481.97460006, 1464.86960377, 1666.86310585,
1749.0044958 , 1509.74895576, 1676.93305953, 1442.89021285,
1360.04116783, 1715.31858826, 1312.80658248, 1475.06186649,
1344.95992985, 1430.20770055, 1104.8839583 , 2734.27226154,
1573.66317959, 1277.71758345, 1335.83007779, 1388.9561474 ,
1300.21639275, 2051.70360448, 2030.46555767, 1552.73702999,
1904.32138669, 2086.02641062, 1390.44217529, 1848.11667207,
1948.53071236, 1722.30306049, 1665.22319103, 1839.24052821,
3506.50015831, 2499.587074 , 2004.30138752, 2593.24765943,
1555.62340477, 3127.05792883, 2078.43826105, 1521.86226946,
1884.20897122, 1985.42702119, 1858.6670123 , 1489.39470748,
2012.23146471, 1752.293432 , 1931.76795821, 1207.12045482,
2050.21345444, 1903.98738195, 2017.90770096, 1592.90254654,
1135.37919832, 1751.99801803, 1891.66212847, 1581.44965142,
1758.30413559, 2013.54473369, 2644.57459095, 1501.71620824,
1435.28018764, 1397.56391215, 1507.66198833, 1345.80092816,
2106.59321081, 1457.03221165, 1719.15477915, 1197.31458789,
1830.48941053, 1594.11199994, 1431.08603553, 1621.10001645,
2063.26021581, 3146.42859182, 2578.17393432, 2218.42350389,
1494.07773519, 2429.83431774, 2069.09548515, 1829.38368409,
2160.14143159, 2056.7431172 , 1578.48562599, 2152.37262937,
2046.87922352, 2214.33113537, 2247.61466536, 1573.46427022,
1297.56212325, 2202.69071816, 3384.09956651, 1787.83456528,
1818.90310555, 1195.18379937, 1894.51793372, 2555.79038553,
2297.52516797, 1447.54704907, 2031.94968376, 1125.15426718,
1592.83454948, 1652.03605506, 1937.06272432, 1579.71531201,
1397.32763121, 1674.12473403]),
'x_centered': True,
'y_centered': True,
'z_centered': False,
'zero_prob_mat': array([[ 0.98867805, 0.99014968, 0.99432948, ..., 0.99541813,
0.98985692, 0.99535752],
[ 0.98386766, 0.99316192, 0.994919 , ..., 0.99563 ,
0.94058365, 0.99558975]])},
'mu0': array([[[ -1.39197867e-04, -8.54325569e-05],
[ -4.26502931e-04, -1.10794709e-03],
[ -3.58714775e-04, -4.85011436e-03],
...,
[ 2.58961565e-04, 1.18478475e-03],
[ -6.49469076e-06, -2.53193515e-06],
[ 2.90978181e-04, 1.32773314e-03]],
[[ -8.35115644e-05, -4.91047758e-05],
[ -1.77683748e-03, -3.51166823e-03],
[ -3.24322802e-04, -3.58085377e-03],
...,
[ 8.61899065e-05, 4.23024806e-04],
[ -1.10101764e-04, -4.41217329e-05],
[ 9.93598440e-05, 5.25447257e-04]],
[[ -2.40596333e-04, -3.00815981e-04],
[ -9.63229461e-04, -2.37319068e-03],
[ -2.37511528e-04, -2.93260676e-03],
...,
[ 5.66656544e-05, 6.76872108e-04],
[ -4.77825176e-04, 6.01048442e-04],
[ 7.20482091e-05, 9.26485644e-04]],
[[ -2.69634190e-04, -2.80914307e-04],
[ -8.64482000e-04, -1.54874228e-03],
[ -2.21927582e-04, -2.03979944e-03],
...,
[ 5.50013709e-05, 4.48409466e-04],
[ -3.93143717e-04, 2.24807523e-04],
[ 6.94340890e-05, 6.05632166e-04]],
[[ -2.69293411e-04, -2.77021149e-04],
[ -8.70337466e-04, -1.49338126e-03],
[ -2.23409015e-04, -1.97428939e-03],
...,
[ 5.52310537e-05, 4.29748021e-04],
[ -3.89965362e-04, 1.91703541e-04],
[ 6.94710584e-05, 5.80250853e-04]]]),
'post_mean_mat': array([[ -2.32382184e-19, -1.36836333e-19],
[ -3.04885813e-17, -6.02915572e-17],
[ -3.02330316e-18, -3.35486223e-17],
...,
[ 3.44738982e-19, 1.68615485e-18],
[ -2.70497565e-19, -1.08394346e-19],
[ 3.88702714e-19, 2.04068922e-18]])}
In [7]:
model.mash.X @ (np.vstack(model.alpha0[4,:]) * model.mu0[4,:,:])
Out[7]:
array([[ 0.00141929, 0.00349287],
[-0.00089172, 0.00162742],
[-0.00116825, 0.00088264],
...,
[-0.00049898, 0.00130733],
[ 0.00147354, 0.0035191 ],
[-0.00060989, 0.00060893]])
In [13]:
(model.alpha0[2,:] == model.alpha0[4,:]).all()
Out[13]:
True
In [9]:
(model.mu0[4,:,:] == model.mu0[4,:,:]).all()
Out[9]:
True
In [11]:
(np.vstack(model.alpha0[4,:]) * model.mu0[4,:,:])
Out[11]:
array([[ -7.89963793e-09, -5.20032243e-09],
[ -9.65163534e-08, -2.28080366e-07],
[ -2.87999221e-08, -6.00510760e-07],
...,
[ 1.11552458e-08, 7.98473138e-08],
[ -4.28912388e-09, -2.21049054e-09],
[ 1.22126119e-08, 9.02205960e-08]])
In [7]:
lala = np.exp((model.mash.l10bf - np.max(model.mash.l10bf)) * np.log(10))
/home/gaow/Public/miniconda3/lib/python3.6/site-packages/ipykernel_launcher.py:1: RuntimeWarning: invalid value encountered in subtract """Entry point for launching an IPython kernel.
In [7]:
lik = model.mash.lik
np.min(lik['null_loglik'])
Out[7]:
-348.70485097407152
In [9]:
np.max(model.alpha0)
Out[9]:
0.99997864314616747
In [12]:
np.max(lik['alt_loglik'] - lik['null_loglik'])
Out[12]:
345.62420250283145
In [ ]:
Copyright © 2016-2020 Gao Wang et al at Stephens Lab, University of Chicago