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Merged
ALGW71 merged 5 commits into from
Apr 27, 2026
Merged

Return the logits #127

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374c09d
Rebase with main and solve merge conflicts.
ALGW71 Apr 27, 2026
eb0cb29
Add some comments to explain what is going on.
ALGW71 Feb 9, 2026
090820e
Rebase is complete.
ALGW71 Feb 9, 2026
aa9484c
Building in logic to one function to assess speed.
ALGW71 Mar 10, 2026
ddf8e22
Updated following Ben's suggestions.
ALGW71 Apr 27, 2026
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78 changes: 65 additions & 13 deletions notebook/examples.ipynb
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Original file line number Diff line number Diff line change
Expand Up @@ -2,35 +2,87 @@
"cells": [
{
"cell_type": "code",
"execution_count": 1,
"execution_count": 2,
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"Sequence 1 has lower than expected score for typical antibody sequences. Please inspect further for errors or misclassification.\n",
"Sequence 2 has lower than expected score for typical antibody sequences. Please inspect further for errors or misclassification.\n",
"\n",
"dict_keys(['Sequence 1', 'Sequence 2', 'Sequence 3', 'Sequence 4'])\n",
"\n",
"Sequence 1 : {'numbering': [((1, ' '), 'A'), ((2, ' '), 'Q'), ((3, ' '), 'S'), ((4, ' '), 'V'), ((5, ' '), 'T'), ((6, ' '), 'Q'), ((7, ' '), 'L'), ((8, ' '), 'G'), ((9, ' '), 'S'), ((10, ' '), 'H'), ((11, ' '), 'V'), ((12, ' '), 'S'), ((13, ' '), 'V'), ((14, ' '), 'S'), ((15, ' '), 'E'), ((16, ' '), 'G'), ((17, ' '), 'A'), ((18, ' '), 'L'), ((19, ' '), 'V'), ((20, ' '), 'L'), ((21, ' '), 'L'), ((22, ' '), 'R'), ((23, ' '), 'C'), ((24, ' '), 'N'), ((25, ' '), 'Y'), ((26, ' '), 'S'), ((27, ' '), 'S'), ((28, ' '), 'S'), ((29, ' '), 'V'), ((30, ' '), '-'), ((31, ' '), '-'), ((32, ' '), '-'), ((33, ' '), '-'), ((34, ' '), '-'), ((35, ' '), '-'), ((36, ' '), 'P'), ((37, ' '), 'P'), ((38, ' '), 'Y'), ((39, ' '), 'L'), ((40, ' '), 'F'), ((41, ' '), 'W'), ((42, ' '), 'Y'), ((43, ' '), 'V'), ((44, ' '), 'Q'), ((45, ' '), 'Y'), ((46, ' '), 'P'), ((47, ' '), 'N'), ((48, ' '), 'Q'), ((49, ' '), 'G'), ((50, ' '), 'L'), ((51, ' '), 'Q'), ((52, ' '), 'L'), ((53, ' '), 'L'), ((54, ' '), 'L'), ((55, ' '), 'K'), ((56, ' '), 'Y'), ((57, ' '), 'T'), ((58, ' '), 'S'), ((59, ' '), '-'), ((60, ' '), '-'), ((61, ' '), '-'), ((62, ' '), '-'), ((63, ' '), '-'), ((64, ' '), 'A'), ((65, ' '), 'A'), ((66, ' '), 'T'), ((67, ' '), 'L'), ((68, ' '), 'V'), ((69, ' '), 'K'), ((70, ' '), 'G'), ((71, ' '), 'I'), ((72, ' '), 'N'), ((73, ' '), '-'), ((74, ' '), '-'), ((75, ' '), 'G'), ((76, ' '), 'F'), ((77, ' '), 'E'), ((78, ' '), 'A'), ((79, ' '), 'E'), ((80, ' '), 'F'), ((81, ' '), 'K'), ((82, ' '), 'K'), ((83, ' '), 'S'), ((84, ' '), 'E'), ((85, ' '), 'T'), ((86, ' '), 'S'), ((87, ' '), 'F'), ((88, ' '), 'H'), ((89, ' '), 'L'), ((90, ' '), 'T'), ((91, ' '), 'K'), ((92, ' '), 'P'), ((93, ' '), 'S'), ((94, ' '), 'A'), ((95, ' '), 'H'), ((96, ' '), 'M'), ((97, ' '), 'S'), ((98, ' '), 'D'), ((99, ' '), 'A'), ((100, ' '), 'A'), ((101, ' '), 'E'), ((102, ' '), 'Y'), ((103, ' '), 'F'), ((104, ' '), 'C'), ((105, ' '), 'A'), ((106, ' '), 'V'), ((107, ' '), 'S'), ((108, ' '), 'E'), ((109, ' '), 'Q'), ((110, ' '), '-'), ((111, ' '), '-'), ((112, ' '), '-'), ((113, ' '), 'D'), ((114, ' '), 'D'), ((115, ' '), 'K'), ((116, ' '), 'I'), ((117, ' '), 'I'), ((118, ' '), 'F'), ((119, ' '), 'G'), ((120, ' '), 'K'), ((121, ' '), 'G'), ((122, ' '), 'T'), ((123, ' '), 'R'), ((124, ' '), 'L'), ((125, ' '), 'H'), ((126, ' '), 'I'), ((127, ' '), 'L'), ((128, ' '), '-')], 'chain_type': 'K', 'score': 19.414453506469727, 'query_start': 0, 'query_end': 110, 'error': None, 'scheme': 'imgt'}\n",
"Sequence 2 : {'numbering': [((1, ' '), '-'), ((2, ' '), '-'), ((3, ' '), '-'), ((4, ' '), '-'), ((5, ' '), '-'), ((6, ' '), '-'), ((7, ' '), '-'), ((8, ' '), '-'), ((9, ' '), '-'), ((10, ' '), '-'), ((11, ' '), '-'), ((12, ' '), '-'), ((13, ' '), '-'), ((14, ' '), '-'), ((15, ' '), '-'), ((16, ' '), '-'), ((17, ' '), '-'), ((18, ' '), '-'), ((19, ' '), '-'), ((20, ' '), '-'), ((21, ' '), '-'), ((22, ' '), '-'), ((23, ' '), '-'), ((24, ' '), '-'), ((25, ' '), '-'), ((26, ' '), '-'), ((27, ' '), '-'), ((28, ' '), '-'), ((29, ' '), '-'), ((30, ' '), '-'), ((31, ' '), '-'), ((32, ' '), '-'), ((33, ' '), '-'), ((34, ' '), '-'), ((35, ' '), '-'), ((36, ' '), '-'), ((37, ' '), '-'), ((38, ' '), '-'), ((39, ' '), '-'), ((40, ' '), '-'), ((41, ' '), 'W'), ((42, ' '), 'Y'), ((43, ' '), 'R'), ((44, ' '), 'Q'), ((45, ' '), 'D'), ((46, ' '), 'P'), ((47, ' '), 'G'), ((48, ' '), 'L'), ((49, ' '), 'G'), ((50, ' '), 'L'), ((51, ' '), 'R'), ((52, ' '), 'L'), ((53, ' '), 'I'), ((54, ' '), 'Y'), ((55, ' '), 'Y'), ((56, ' '), 'S'), ((57, ' '), 'F'), ((58, ' '), 'D'), ((59, ' '), 'V'), ((60, ' '), 'K'), ((61, ' '), 'D'), ((62, ' '), 'I'), ((63, ' '), 'N'), ((64, ' '), 'K'), ((65, ' '), 'G'), ((66, ' '), 'E'), ((67, ' '), 'I'), ((68, ' '), 'S'), ((69, ' '), 'D'), ((70, ' '), 'G'), ((71, ' '), 'Y'), ((72, ' '), 'S'), ((73, ' '), '-'), ((74, ' '), '-'), ((75, ' '), '-'), ((76, ' '), '-'), ((77, ' '), '-'), ((78, ' '), 'V'), ((79, ' '), 'S'), ((80, ' '), 'R'), ((81, ' '), 'Q'), ((82, ' '), '-'), ((83, ' '), 'A'), ((84, ' '), 'Q'), ((85, ' '), 'A'), ((86, ' '), 'K'), ((87, ' '), 'F'), ((88, ' '), 'S'), ((89, ' '), 'L'), ((90, ' '), 'S'), ((91, ' '), 'L'), ((92, ' '), 'E'), ((93, ' '), 'S'), ((94, ' '), 'A'), ((95, ' '), 'I'), ((96, ' '), 'P'), ((97, ' '), 'N'), ((98, ' '), 'Q'), ((99, ' '), 'T'), ((100, ' '), 'A'), ((101, ' '), 'L'), ((102, ' '), 'Y'), ((103, ' '), 'F'), ((104, ' '), 'C'), ((105, ' '), 'A'), ((106, ' '), 'T'), ((107, ' '), 'S'), ((108, ' '), 'D'), ((109, ' '), 'E'), ((110, ' '), '-'), ((111, ' '), '-'), ((112, ' '), '-'), ((113, ' '), 'S'), ((114, ' '), 'Y'), ((115, ' '), 'G'), ((116, ' '), 'Y'), ((117, ' '), 'T'), ((118, ' '), 'F'), ((119, ' '), 'G'), ((120, ' '), 'S'), ((121, ' '), 'G'), ((122, ' '), 'T'), ((123, ' '), 'R'), ((124, ' '), 'L'), ((125, ' '), 'T'), ((126, ' '), 'V'), ((127, ' '), 'V'), ((128, ' '), 'E')], 'chain_type': 'H', 'score': 19.768274307250977, 'query_start': 32, 'query_end': 110, 'error': None, 'scheme': 'imgt'}\n",
"Sequence 3 : {'numbering': [((1, ' '), 'E'), ((2, ' '), 'I'), ((3, ' '), 'V'), ((4, ' '), 'M'), ((5, ' '), 'T'), ((6, ' '), 'Q'), ((7, ' '), 'S'), ((8, ' '), 'P'), ((9, ' '), 'D'), ((10, ' '), 'T'), ((11, ' '), 'L'), ((12, ' '), 'S'), ((13, ' '), 'V'), ((14, ' '), 'S'), ((15, ' '), 'P'), ((16, ' '), 'G'), ((17, ' '), 'E'), ((18, ' '), 'R'), ((19, ' '), 'A'), ((20, ' '), 'T'), ((21, ' '), 'L'), ((22, ' '), 'S'), ((23, ' '), 'C'), ((24, ' '), 'R'), ((25, ' '), 'A'), ((26, ' '), 'S'), ((27, ' '), 'E'), ((28, ' '), 'S'), ((29, ' '), 'I'), ((30, ' '), '-'), ((31, ' '), '-'), ((32, ' '), '-'), ((33, ' '), '-'), ((34, ' '), '-'), ((35, ' '), '-'), ((36, ' '), 'S'), ((37, ' '), 'S'), ((38, ' '), 'N'), ((39, ' '), 'L'), ((40, ' '), 'A'), ((41, ' '), 'W'), ((42, ' '), 'Y'), ((43, ' '), 'Q'), ((44, ' '), 'Q'), ((45, ' '), 'K'), ((46, ' '), 'P'), ((47, ' '), 'G'), ((48, ' '), 'Q'), ((49, ' '), 'V'), ((50, ' '), 'P'), ((51, ' '), 'R'), ((52, ' '), 'L'), ((53, ' '), 'L'), ((54, ' '), 'I'), ((55, ' '), 'Y'), ((56, ' '), 'G'), ((57, ' '), 'A'), ((58, ' '), '-'), ((59, ' '), '-'), ((60, ' '), '-'), ((61, ' '), '-'), ((62, ' '), '-'), ((63, ' '), '-'), ((64, ' '), '-'), ((65, ' '), 'S'), ((66, ' '), 'T'), ((67, ' '), 'R'), ((68, ' '), 'A'), ((69, ' '), 'T'), ((70, ' '), 'G'), ((71, ' '), 'V'), ((72, ' '), 'P'), ((73, ' '), '-'), ((74, ' '), 'A'), ((75, ' '), 'R'), ((76, ' '), 'F'), ((77, ' '), 'T'), ((78, ' '), 'G'), ((79, ' '), 'S'), ((80, ' '), 'G'), ((81, ' '), '-'), ((82, ' '), '-'), ((83, ' '), 'S'), ((84, ' '), 'G'), ((85, ' '), 'T'), ((86, ' '), 'E'), ((87, ' '), 'F'), ((88, ' '), 'T'), ((89, ' '), 'L'), ((90, ' '), 'T'), ((91, ' '), 'I'), ((92, ' '), 'S'), ((93, ' '), 'S'), ((94, ' '), 'L'), ((95, ' '), 'Q'), ((96, ' '), 'S'), ((97, ' '), 'E'), ((98, ' '), 'D'), ((99, ' '), 'F'), ((100, ' '), 'A'), ((101, ' '), 'V'), ((102, ' '), 'Y'), ((103, ' '), 'Y'), ((104, ' '), 'C'), ((105, ' '), 'Q'), ((106, ' '), 'Q'), ((107, ' '), 'Y'), ((108, ' '), 'N'), ((109, ' '), 'N'), ((110, ' '), '-'), ((111, ' '), '-'), ((112, ' '), '-'), ((113, ' '), 'R'), ((114, ' '), 'L'), ((115, ' '), 'P'), ((116, ' '), 'Y'), ((117, ' '), 'T'), ((118, ' '), 'F'), ((119, ' '), 'G'), ((120, ' '), 'Q'), ((121, ' '), 'G'), ((122, ' '), 'T'), ((123, ' '), 'K'), ((124, ' '), 'L'), ((125, ' '), 'E'), ((126, ' '), 'I'), ((127, ' '), 'K'), ((128, ' '), '-')], 'chain_type': 'K', 'score': 30.13271713256836, 'query_start': 0, 'query_end': 107, 'error': None, 'scheme': 'imgt'}\n",
"Sequence 4 : {'numbering': [((1, ' '), 'E'), ((2, ' '), 'V'), ((3, ' '), 'Q'), ((4, ' '), 'L'), ((5, ' '), 'L'), ((6, ' '), 'E'), ((7, ' '), 'S'), ((8, ' '), 'G'), ((9, ' '), 'G'), ((10, ' '), '-'), ((11, ' '), 'G'), ((12, ' '), 'L'), ((13, ' '), 'V'), ((14, ' '), 'Q'), ((15, ' '), 'P'), ((16, ' '), 'G'), ((17, ' '), 'G'), ((18, ' '), 'S'), ((19, ' '), 'L'), ((20, ' '), 'R'), ((21, ' '), 'L'), ((22, ' '), 'S'), ((23, ' '), 'C'), ((24, ' '), 'A'), ((25, ' '), 'A'), ((26, ' '), 'S'), ((27, ' '), 'G'), ((28, ' '), 'F'), ((29, ' '), 'T'), ((30, ' '), 'F'), ((31, ' '), '-'), ((32, ' '), '-'), ((33, ' '), '-'), ((34, ' '), '-'), ((35, ' '), 'N'), ((36, ' '), 'H'), ((37, ' '), 'Y'), ((38, ' '), 'A'), ((39, ' '), 'M'), ((40, ' '), 'T'), ((41, ' '), 'W'), ((42, ' '), 'V'), ((43, ' '), 'R'), ((44, ' '), 'Q'), ((45, ' '), 'A'), ((46, ' '), 'P'), ((47, ' '), 'G'), ((48, ' '), 'K'), ((49, ' '), 'G'), ((50, ' '), 'L'), ((51, ' '), 'E'), ((52, ' '), 'W'), ((53, ' '), 'V'), ((54, ' '), 'A'), ((55, ' '), 'S'), ((56, ' '), 'S'), ((57, ' '), 'S'), ((58, ' '), 'G'), ((59, ' '), 'S'), ((60, ' '), '-'), ((61, ' '), '-'), ((62, ' '), 'G'), ((63, ' '), 'R'), ((64, ' '), 'S'), ((65, ' '), 'T'), ((66, ' '), 'Y'), ((67, ' '), 'Y'), ((68, ' '), 'T'), ((69, ' '), 'D'), ((70, ' '), 'S'), ((71, ' '), 'V'), ((72, ' '), 'K'), ((73, ' '), '-'), ((74, ' '), 'G'), ((75, ' '), 'R'), ((76, ' '), 'F'), ((77, ' '), 'S'), ((78, ' '), 'V'), ((79, ' '), 'S'), ((80, ' '), 'R'), ((81, ' '), 'D'), ((82, ' '), 'N'), ((83, ' '), 'S'), ((84, ' '), 'K'), ((85, ' '), 'N'), ((86, ' '), 'T'), ((87, ' '), 'L'), ((88, ' '), 'Y'), ((89, ' '), 'L'), ((90, ' '), 'Q'), ((91, ' '), 'M'), ((92, ' '), 'N'), ((93, ' '), 'S'), ((94, ' '), 'L'), ((95, ' '), 'R'), ((96, ' '), 'A'), ((97, ' '), 'E'), ((98, ' '), 'D'), ((99, ' '), 'T'), ((100, ' '), 'A'), ((101, ' '), 'V'), ((102, ' '), 'Y'), ((103, ' '), 'Y'), ((104, ' '), 'C'), ((105, ' '), 'A'), ((106, ' '), 'K'), ((107, ' '), 'S'), ((108, ' '), 'S'), ((109, ' '), 'N'), ((110, ' '), 'Y'), ((111, ' '), 'Y'), ((111, 'A'), 'G'), ((111, 'B'), 'S'), ((111, 'C'), 'G'), ((111, 'D'), 'S'), ((112, 'E'), 'Y'), ((112, 'D'), 'S'), ((112, 'C'), 'P'), ((112, 'B'), 'D'), ((112, 'A'), 'D'), ((112, ' '), 'Y'), ((113, ' '), 'Y'), ((114, ' '), 'H'), ((115, ' '), 'M'), ((116, ' '), 'D'), ((117, ' '), 'V'), ((118, ' '), 'W'), ((119, ' '), 'G'), ((120, ' '), 'Q'), ((121, ' '), 'G'), ((122, ' '), 'T'), ((123, ' '), 'T'), ((124, ' '), 'V'), ((125, ' '), 'T'), ((126, ' '), 'V'), ((127, ' '), 'S'), ((128, ' '), 'G')], 'chain_type': 'H', 'score': 30.51480484008789, 'query_start': 0, 'query_end': 128, 'error': None, 'scheme': 'imgt'}\n"
"Sequence 1 : tensor([22.5838, 31.6898, 31.4527, 32.8396, 39.1968, 28.7265, 26.4854, 35.5877,\n",
" 25.7327, 37.6802, 32.4417, 32.2934, 28.1486, 30.5405, 28.4391, 27.4314,\n",
" 28.2475, 26.0391, 34.2470, 31.3821, 30.3729, 37.3745, 30.3654, 27.6779,\n",
" 33.9490, 36.4483, 28.2443, 38.9543, 36.2434, 37.1170, 34.2787, 38.3308,\n",
" 31.8065, 29.0670, 26.3710, 25.5805, 28.6327, 33.4610, 31.6199, 36.7579,\n",
" 29.8569, 25.2630, 27.2584, 33.1403, 34.2393, 37.9991, 40.0970, 36.4892,\n",
" 33.8836, 32.4874, 43.7763, 41.4126, 32.6784, 31.7495, 31.3672, 32.6218,\n",
" 34.0671, 26.6324, 30.1969, 23.7971, 29.4850, 29.5168, 29.9851, 31.4282,\n",
" 41.5857, 39.5168, 40.3152, 42.7991, 28.4216, 36.4930, 38.7311, 31.8494,\n",
" 30.0495, 35.8927, 38.6342, 32.0970, 33.6287, 32.7060, 32.9633, 40.2834,\n",
" 41.9010, 34.4784, 38.7741, 37.4402, 35.1924, 29.9138, 31.8103, 36.2601,\n",
" 33.1773, 27.1542, 33.3743, 33.0630, 44.4626, 31.2103, 32.4261, 30.3873,\n",
" 27.2959, 27.1992, 24.7456, 29.5603, 30.5400, 31.2875, 37.3359, 34.2773,\n",
" 29.0145, 26.5760, 25.4447, 28.7686, 25.8767, 24.9761, 25.0015, 17.5661,\n",
" 19.2424])\n",
"Sequence 2 : tensor([ 5.7148, 30.2179, 24.1872, 29.5509, 25.4001, 24.0097, 31.8529, 26.2123,\n",
" 25.0069, 19.8789, 27.6443, 28.4427, 30.4647, 25.9553, 31.3079, 32.4349,\n",
" 34.4294, 32.1585, 31.0647, 30.9016, 38.4637, 35.6251, 33.9866, 27.3903,\n",
" 34.0115, 37.0032, 37.7743, 36.1086, 26.6505, 29.8539, 29.1923, 27.6697,\n",
" 28.9249, 30.2062, 30.5036, 33.3199, 30.0542, 24.8211, 33.9624, 31.3401,\n",
" 33.3160, 34.2448, 29.5792, 34.1259, 34.4462, 27.1545, 40.5046, 39.4822,\n",
" 35.2835, 37.3627, 35.4036, 29.9326, 31.0929, 29.2970, 27.7120, 27.2299,\n",
" 28.4275, 30.9210, 34.0998, 31.3759, 31.2178, 34.9842, 33.3230, 36.9066,\n",
" 37.0539, 39.6846, 32.8623, 36.8928, 28.6145, 33.6384, 37.8850, 36.3539,\n",
" 36.8074, 36.1996, 26.8989, 33.8357, 42.3234, 38.9542, 36.2264, 42.3248,\n",
" 36.0258, 37.7112, 33.8739, 31.3762, 38.7569, 37.2933, 31.6094, 36.9466,\n",
" 34.7402, 39.0402, 30.6942, 32.1447, 29.9778, 26.7233, 25.6392, 24.6415,\n",
" 27.6697, 30.5254, 34.0342, 42.6502, 28.6823, 29.6582, 21.8303, 23.5069,\n",
" 27.7824, 30.2912, 25.5421, 19.1691, 19.7682])\n",
"Sequence 3 : tensor([12.9239, 25.0816, 28.3883, 28.4557, 31.5377, 27.5145, 27.1580, 27.2675,\n",
" 26.4965, 27.6224, 27.2985, 28.0900, 27.8811, 25.1745, 26.4641, 24.9921,\n",
" 25.5914, 25.4983, 24.5084, 27.7500, 26.1022, 28.9263, 26.2085, 27.4731,\n",
" 26.5021, 29.3956, 24.0369, 30.7517, 31.7431, 46.3120, 35.2302, 33.1150,\n",
" 26.6296, 32.4256, 29.6190, 26.2629, 26.6716, 28.7378, 27.5827, 32.7611,\n",
" 28.4548, 30.0210, 26.8251, 30.6011, 31.9220, 27.5251, 30.1503, 29.1241,\n",
" 30.5095, 28.2456, 37.8106, 34.9157, 33.4896, 29.1894, 30.3304, 26.1981,\n",
" 33.6441, 28.3460, 27.0327, 27.2014, 25.3401, 34.2528, 31.5774, 36.4322,\n",
" 35.0746, 35.1558, 31.0661, 36.6514, 35.7466, 30.8785, 37.5318, 34.3933,\n",
" 40.8922, 31.1796, 28.3882, 35.5020, 39.9505, 38.7772, 39.6565, 39.7621,\n",
" 39.9021, 31.4047, 38.0572, 33.0229, 33.4130, 35.8297, 28.7221, 36.7525,\n",
" 29.8354, 33.2201, 25.4760, 27.4983, 29.2145, 26.0279, 23.3462, 26.4837,\n",
" 25.8504, 28.4705, 33.5156, 40.2963, 35.5027, 31.2086, 27.2284, 26.2414,\n",
" 27.1899, 26.6214, 21.9226, 18.5307, 21.7540])\n",
"Sequence 4 : tensor([13.7804, 23.9711, 28.4706, 29.3610, 28.8592, 27.8211, 26.9738, 31.3445,\n",
" 28.0319, 29.5990, 28.4382, 26.0240, 26.5408, 27.2972, 26.3980, 25.5782,\n",
" 28.1557, 29.1561, 28.4808, 30.0942, 30.7771, 28.3871, 32.3001, 25.5386,\n",
" 31.3489, 24.2413, 39.0182, 38.4196, 37.6164, 37.9333, 35.5819, 33.6417,\n",
" 34.4938, 28.1510, 31.5333, 28.2369, 28.2892, 28.3823, 30.5997, 32.1254,\n",
" 33.9772, 33.2400, 30.6017, 26.6109, 28.0319, 34.3041, 30.7074, 31.0401,\n",
" 32.8398, 29.3260, 27.8884, 36.6228, 28.8538, 32.8881, 29.4708, 30.3701,\n",
" 30.9103, 31.9164, 30.5789, 26.6090, 26.5611, 24.6113, 27.3579, 28.4574,\n",
" 27.9184, 30.7647, 26.5552, 32.3514, 30.8712, 32.5677, 30.2417, 28.9319,\n",
" 26.5740, 25.9156, 31.4575, 34.0288, 36.7491, 32.8318, 39.9403, 32.0150,\n",
" 38.8725, 31.8909, 32.5510, 28.2403, 45.1687, 40.5855, 42.3462, 41.7061,\n",
" 41.2951, 37.1519, 36.4636, 40.6107, 36.3662, 36.8156, 36.6676, 37.3680,\n",
" 30.5122, 35.5027, 25.7525, 29.6473, 26.9661, 30.0284, 28.2872, 25.8404,\n",
" 25.0895, 26.7326, 25.9506, 26.7012, 25.3409, 25.9425, 25.0675, 25.2981,\n",
" 25.2231, 28.4855, 25.6817, 25.6900, 26.3425, 26.1936, 27.1129, 33.5035,\n",
" 36.2804, 30.3952, 27.2605, 26.2464, 25.7583, 25.9494, 22.5090, 16.8636,\n",
" 16.3859])\n"
]
}
],
"source": [
"##### It can process a list of seqs #####\n",
"from anarcii import Anarcii\n",
"\n",
"model = Anarcii(seq_type=\"antibody\", batch_size=128, \n",
" cpu=False, \n",
" ncpu=8, \n",
"model = Anarcii(seq_type=\"unknown\", batch_size=128, \n",
" cpu=False, ncpu=14, \n",
" mode=\"accuracy\", verbose=False,\n",
" low_score_warn=True\n",
" )\n",
" return_logits=True)\n",
"\n",
"seq = [\n",
" #Alpha\n",
Expand All @@ -52,7 +104,7 @@
"print()\n",
"\n",
"for key, value in results.items():\n",
" print(key, \":\", value)\n"
" print(key, \":\", value[\"logits\"])\n"
]
},
{
Expand Down
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