multimolecule/pangolin on Ascend NPU
模型与任务
- 模型：
multimolecule/pangolin - Revision：
39f9ff44ed65f773099c363712934d13c277c8d0 - 适配路线：
splicing - 设备：
npu:0
环境依赖
{
"torch": "2.9.0+cpu",
"torch_npu_available": true,
"device_name": "Ascend910_9362",
"device_count": 2,
"torch_npu": "2.9.0.post1+gitee7ba04",
"transformers": "5.9.0",
"multimolecule": "unknown"
}安装：pip install -r requirements.txt
NPU 推理
默认执行：python inference.py
真实输入
{
"num_reference_sequences": 4,
"num_short_sequences": 2,
"num_variant_pairs": 4,
"sequence_length": 500,
"short_length": 30,
"construction": "deterministic random ACGU, motif GU/AG embedded, AU-rich, N-masked; SNV at central, donor disrupt, T vs U equivalence; plus short 30 nt from widget",
"alphabet": "ACGU (T->U via replace_T_with_U), N=pad/unk",
"replace_T_with_U": true,
"direction": "5'->3'",
"context": 10000,
"padding": "internal 5000 each side, valid conv crop to L",
"output_channels": "12 = 4 tissues * [score 2 + usage 1]",
"tissue_names": [
"heart",
"liver",
"brain",
"testis"
],
"reference_sequences": [
{
"name": "random_ACGU_500",
"length": 500,
"sha256": "98482eef4abb10139cbc75c7d71665f2e5b9e9d2c52c7f69018e148b378af165",
"preview": "UUAGUUGUGCCGCAGCGAAGUAGUGCUUGAAAUAUGCGAC"
},
{
"name": "motif_GU_AG_500",
"length": 500,
"sha256": "7631f32c7df548dad95fdf67acd07da8971b156c9c8737128ccb41f405c0d3a3",
"preview": "AGGACCCUAUGGCACGGUGGGCAAGCUCCCGCCCGGUACA"
},
{
"name": "AU_rich_500",
"length": 500,
"sha256": "8ff6870fca73be12c37607016e316a4f14889286bc5d6b72561af181aa50eb23",
"preview": "AUUAAUAUCAAAUUCUUAGUAUUUAUUAUAUAUAUUAACU"
},
{
"name": "N_masked_500",
"length": 500,
"sha256": "73692f245e721bce83610e1760efd4d469ef415e4604f8beafde479c17616c0b",
"preview": "CGCCUCAGCCGUUGACCGCAACACCGUGAAGCACGGGUAA"
}
],
"short_sequences": [
{
"name": "short_30_ref",
"length": 30,
"sha256": "b98f4f9f334cf254f1057f8ac540d68a0b02d90a845020cfecc8fcfd7fea590e",
"preview": "AUGCGAUCGAUCGAUCGAUCGAUCGAUCUA"
},
{
"name": "short_30_alt",
"length": 30,
"sha256": "ac0955f72078ed1699b87658ee878db1462e59fafc1ceff495b08b1d5455acb3",
"preview": "AUGCGAUCGAUCGAUUGAUCGAUCGAUCUA"
}
],
"variant_pairs": [
{
"name": "random_SNV_500",
"ref_sha256": "98482eef4abb10139cbc75c7d71665f2e5b9e9d2c52c7f69018e148b378af165",
"alt_sha256": "97c2cb9022f92fa88fdd9774e1505239519a6459781d14437b8d165630ecc656",
"preview_ref": "UUAGUUGUGCCGCAGCGAAGUAGUGCUUGAAAUAUGCGAC",
"preview_alt": "UUAGUUGUGCCGCAGCGAAGUAGUGCUUGAAAUAUGCGAC"
},
{
"name": "motif_donor_SNV",
"ref_sha256": "7631f32c7df548dad95fdf67acd07da8971b156c9c8737128ccb41f405c0d3a3",
"alt_sha256": "3e0e72dca80f4b93a04bab865da209965602ee5adcdcf7423c60b44b7745446f",
"preview_ref": "AGGACCCUAUGGCACGGUGGGCAAGCUCCCGCCCGGUACA",
"preview_alt": "AGGACCCUAUGGCACGGUGGGCAAGCUCCCGCCCGGUACA"
},
{
"name": "DNA_T_vs_RNA_U",
"ref_sha256": "73692f245e721bce83610e1760efd4d469ef415e4604f8beafde479c17616c0b",
"alt_sha256": "5b9ef700b62dc8467e987cafc2afe7141d9cebb20d453cb10787527ea60770ac",
"preview_ref": "CGCCUCAGCCGUUGACCGCAACACCGUGAAGCACGGGUAA",
"preview_alt": "CGCCTCAGCCGTTGACCGCAACACCGTGAAGCACGGGTAA"
},
{
"name": "short_SNV_30",
"ref_sha256": "b98f4f9f334cf254f1057f8ac540d68a0b02d90a845020cfecc8fcfd7fea590e",
"alt_sha256": "ac0955f72078ed1699b87658ee878db1462e59fafc1ceff495b08b1d5455acb3",
"preview_ref": "AUGCGAUCGAUCGAUCGAUCGAUCGAUCUA",
"preview_alt": "AUGCGAUCGAUCGAUUGAUCGAUCGAUCUA"
}
],
"tokenizer": "RnaTokenizer vocab A0 C1 G2 U3 N4 pad N, replace_T_with_U True",
"dtype": "float32"
}真实推理结果
{
"output_shape_probabilities": [
4,
500,
12
],
"output_shape_short": [
2,
30,
12
],
"output_shape_delta": [
4,
500,
12
],
"dtype": "float32",
"probabilities_range": [
0.0026711926329880953,
0.9608384966850281
],
"delta_range": [
-0.07470118999481201,
0.04542946815490723
],
"probabilities_per_sequence_central": [
{
"name": "random_ACGU_500",
"max_usage": 0.7979575395584106,
"mean_prob": 0.3389914631843567
},
{
"name": "motif_GU_AG_500",
"max_usage": 0.8024621605873108,
"mean_prob": 0.3376014530658722
},
{
"name": "AU_rich_500",
"max_usage": 0.06548089534044266,
"mean_prob": 0.3403639793395996
},
{
"name": "N_masked_500",
"max_usage": 0.7080919742584229,
"mean_prob": 0.3387630879878998
}
],
"short_sample": [
[
0.9472239017486572,
0.05277614668011665,
0.029712308198213577,
0.948218047618866,
0.05178201198577881,
0.011563194915652275,
0.9488821029663086,
0.051117975264787674,
0.020187366753816605,
0.9479959011077881,
0.05200408399105072,
0.014677181839942932
],
[
0.9484885931015015,
0.05151141434907913,
0.035874877125024796,
0.9478874206542969,
0.052112579345703125,
0.00830162689089775,
0.9470071792602539,
0.052992839366197586,
0.02044040895998478,
0.9483068585395813,
0.05169321596622467,
0.015555384568870068
],
[
0.9486720561981201,
0.051327936351299286,
0.031181953847408295,
0.9473021030426025,
0.05269792303442955,
0.010689133778214455,
0.9483687281608582,
0.05163126438856125,
0.01739984005689621,
0.9486778378486633,
0.05132222920656204,
0.012048284523189068
]
],
"delta_per_pair_central": [
{
"name": "random_SNV_500",
"delta_max": 0.07470118999481201,
"delta_mean": 0.0003778986865654588,
"central_sample": [
[
0.0003345608711242676,
-0.0003345683217048645,
-0.0008051246404647827
],
[
0.0011563897132873535,
-0.0011564567685127258,
0.0003238413482904434
],
[
-0.0004355311393737793,
0.00043555349111557007,
-0.0019150469452142715
],
[
0.000495612621307373,
-0.0004955939948558807,
-0.005242329090833664
],
[
-0.0002682209014892578,
0.0002682246267795563,
0.001288844272494316
]
]
},
{
"name": "motif_donor_SNV",
"delta_max": 0.04542946815490723,
"delta_mean": 0.000564686197321862,
"central_sample": [
[
0.001277148723602295,
-0.0012771114706993103,
-0.009008759632706642
],
[
0.010753452777862549,
-0.010753337293863297,
-0.003165280446410179
],
[
0.00020200014114379883,
-0.00020194798707962036,
-0.006747644394636154
],
[
0.00021314620971679688,
-0.00021316856145858765,
-0.005954652093350887
],
[
0.0005840063095092773,
-0.0005841553211212158,
-0.0012862542644143105
]
]
},
{
"name": "DNA_T_vs_RNA_U",
"delta_max": 0.0,
"delta_mean": 0.0,
"central_sample": [
[
0.0,
0.0,
0.0
],
[
0.0,
0.0,
0.0
],
[
0.0,
0.0,
0.0
],
[
0.0,
0.0,
0.0
],
[
0.0,
0.0,
0.0
]
]
},
{
"name": "short_SNV_30",
"delta_max": 0.01678704470396042,
"delta_mean": 0.0005158275598660111,
"central_sample": [
[
0.0012259483337402344,
-0.0012258999049663544,
0.0001253373920917511
],
[
0.0009818673133850098,
-0.0009819790720939636,
0.00015214458107948303
],
[
0.0012229681015014648,
-0.0012228935956954956,
-5.934759974479675e-05
],
[
0.0012123584747314453,
-0.0012124553322792053,
-0.0009995624423027039
],
[
0.0016332268714904785,
-0.0016332454979419708,
-0.00040858983993530273
]
]
}
],
"device_proof": "first_param:npu:0, logits:npu:0, short:npu:0, delta:npu:0, input:npu:0",
"probabilities_sample": [
[
0.9476736783981323,
0.052326351404190063,
0.026391422376036644
],
[
0.9476853609085083,
0.05231470614671707,
0.022920886054635048
],
[
0.9500923156738281,
0.04990772157907486,
0.02561817318201065
],
[
0.9501460194587708,
0.04985402897000313,
0.030140889808535576
]
],
"delta_sample_pair0": [
[
0.0003345608711242676,
-0.0003345683217048645,
-0.0008051246404647827
],
[
0.0011563897132873535,
-0.0011564567685127258,
0.0003238413482904434
],
[
-0.0004355311393737793,
0.00043555349111557007,
-0.0019150469452142715
],
[
0.000495612621307373,
-0.0004955939948558807,
-0.005242329090833664
],
[
-0.0002682209014892578,
0.0002682246267795563,
0.001288844272494316
]
],
"per_tissue_softmax_check": true
}CPU-NPU 一致性
{
"atol": 0.0005,
"rtol": 0.001,
"max_abs_diff_prob": 0.00022774934768676758,
"mean_abs_diff_prob": 1.8122060282621533e-05,
"max_abs_diff_short": 0.00014290958642959595,
"mean_abs_diff_short": 2.1248208213364705e-05,
"max_abs_diff_delta": 0.00011473894119262695,
"mean_abs_diff_delta": 1.948858334799297e-05,
"passed": true,
"passed_prob": true,
"passed_short": true,
"passed_delta": true,
"pearson_prob": 0.9999999985389169,
"pearson_delta": 0.9998687579590108,
"shape_prob": [
2,
500,
12
],
"shape_short": [
2,
30,
12
],
"shape_delta": [
2,
500,
12
]
}性能
{
"first_run_ms": 3939.7183670662344,
"first_var_run_ms": 7559.639531187713,
"second_run_ms": 3780.374507419765,
"short_run_ms": 2132.776544895023,
"avg_ms": 3851.483988855034,
"min_ms": 3778.3678262494504,
"max_ms": 4126.697968225926,
"p50_ms": 3783.962103072554,
"p90_ms": 3991.247631702572,
"throughput_seq_per_s": 1.0385607240156582,
"throughput_bases_per_s": 519.2803620078291,
"batch_size": 4,
"sequence_length": 500,
"dtype": "float32"
}自验证截图
三张图片均由 xterm.js 根据本次真实日志生成。
已知限制
- 仅对本次记录的模型 revision、输入契约、dtype 与 Ascend 环境完成验证。
标签
#NPU #Ascend #Ascend910