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  1. .gitattributes +9 -0
  2. demo_coding_vs_intergenomic_seqs/split/dev.csv +0 -0
  3. demo_coding_vs_intergenomic_seqs/split/test.csv +0 -0
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+ e:
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+ f0ugcbwht0bzsznis5d33rdup7dudruj:
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+ args:
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+ - --model_name_or_path
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+ - /home/n5huang/dna_token/pretrain/models/model_cpu_test_1/checkpoint-100000
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+ - --tokenizer_path
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+ - /home/n5huang/dna_token/tokenizer_evaluation/baseline_bpe/tokenizer.json
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+ - --trust_remote_code
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+ - "True"
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+ - --data_path
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+ - /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/NT-benchmarks/nucleotide_transformer_downstream_tasks_revised/enhancers/split
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+ - --kmer
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+ - "-1"
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+ - --run_name
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+ - hg38_BPE_base__baseline_bpe_tokenizer_3e-5_enhancers_seed42
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+ - --model_max_length
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+ - "100"
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+ - --per_device_train_batch_size
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+ - "128"
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+ - --per_device_eval_batch_size
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+ - "128"
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+ - --gradient_accumulation_steps
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+ - "1"
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+ - --learning_rate
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+ - "3e-5"
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+ - --num_train_epochs
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+ - "4"
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+ - --fp16
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+ - --save_steps
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+ - "200"
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+ - --output_dir
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+ - /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/enhancers
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+ - --evaluation_strategy
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+ - steps
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+ - --eval_steps
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+ - "200"
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+ - --warmup_steps
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+ - "30"
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+ - --logging_steps
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+ - "100000"
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+ - --log_level
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+ - info
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+ - --seed
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+ - "42"
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+ - --find_unused_parameters
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+ - "False"
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+ - --project_name
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+ - genomic_bench_tune_hg38_1024
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+ cpu_count: 128
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+ cpu_count_logical: 255
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+ cudaVersion: "12.2"
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+ disk:
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+ /:
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+ total: "1876350566400"
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+ used: "546900058112"
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+ email: mtapiapacheco@ucsd.edu
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+ executable: /home/n5huang/miniconda3/envs/nt_ft/bin/python
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+ git:
62
+ commit: 5dc8fdf47bc12e22d02cfdaea49a6cbeb2fdf4d6
63
+ remote: https://huggingface.co/JessieZhou25/Finetune-GenomicBenchmarks
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+ gpu: NVIDIA A100 80GB PCIe
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+ gpu_count: 8
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+ gpu_nvidia:
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+ - architecture: Ampere
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+ cudaCores: 6912
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+ memoryTotal: "85899345920"
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+ name: NVIDIA A100 80GB PCIe
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+ uuid: GPU-dc4eaee8-f907-9592-417e-e0dbe37f86a3
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+ uuid: GPU-a18369da-b15a-c8af-72f1-7f6272e479af
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+ - architecture: Ampere
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+ name: NVIDIA A100 80GB PCIe
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+ uuid: GPU-fb2ffc63-6c8a-5e90-0466-bd865bdd8b10
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+ name: NVIDIA A100 80GB PCIe
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+ uuid: GPU-d097eb04-aaca-ea9a-2730-e29dca4737a0
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+ host: sn4622116170
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+ memory:
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+ total: "4316310355968"
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+ os: Linux-5.15.0-72-generic-x86_64-with-glibc2.35
111
+ program: /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py
112
+ python: CPython 3.10.19
113
+ root: /data/n5huang/dna_token/Finetune-GenomicBenchmarks/ft_data
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+ startedAt: "2026-03-05T04:01:22.935924Z"
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+ WARNING:root:Perform single sequence classification...
2
+ WARNING:root:Perform single sequence classification...
3
+ WARNING:root:Perform single sequence classification...
4
+ Traceback (most recent call last):
5
+ File "/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py", line 455, in <module>
6
+ train()
7
+ File "/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py", line 406, in train
8
+ model = transformers.AutoModelForSequenceClassification.from_pretrained(
9
+ File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/models/auto/auto_factory.py", line 374, in from_pretrained
10
+ return model_class.from_pretrained(
11
+ File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/modeling_utils.py", line 4137, in from_pretrained
12
+ loading_info, disk_offload_index = cls._load_pretrained_model(model, state_dict, checkpoint_files, load_config)
13
+ File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/modeling_utils.py", line 4252, in _load_pretrained_model
14
+ merged_state_dict.update(load_state_dict(ckpt_file))
15
+ File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/modeling_utils.py", line 319, in load_state_dict
16
+ check_torch_load_is_safe()
17
+ File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/utils/import_utils.py", line 1270, in check_torch_load_is_safe
18
+ raise ValueError(
19
+ ValueError: Due to a serious vulnerability issue in `torch.load`, even with `weights_only=True`, we now require users to upgrade torch to at least v2.6 in order to use the function. This version restriction does not apply when loading files with safetensors.
20
+ See the vulnerability report here https://nvd.nist.gov/vuln/detail/CVE-2025-32434
21
+ Traceback (most recent call last):
22
+ File "/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py", line 455, in <module>
23
+ train()
24
+ File "/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py", line 406, in train
25
+ model = transformers.AutoModelForSequenceClassification.from_pretrained(
26
+ File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/models/auto/auto_factory.py", line 374, in from_pretrained
27
+ return model_class.from_pretrained(
28
+ File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/modeling_utils.py", line 4137, in from_pretrained
29
+ loading_info, disk_offload_index = cls._load_pretrained_model(model, state_dict, checkpoint_files, load_config)
30
+ File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/modeling_utils.py", line 4252, in _load_pretrained_model
31
+ merged_state_dict.update(load_state_dict(ckpt_file))
32
+ File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/modeling_utils.py", line 319, in load_state_dict
33
+ check_torch_load_is_safe()
34
+ File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/utils/import_utils.py", line 1270, in check_torch_load_is_safe
35
+ raise ValueError(
36
+ ValueError: Due to a serious vulnerability issue in `torch.load`, even with `weights_only=True`, we now require users to upgrade torch to at least v2.6 in order to use the function. This version restriction does not apply when loading files with safetensors.
37
+ See the vulnerability report here https://nvd.nist.gov/vuln/detail/CVE-2025-32434
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1
+ hf-xet==1.3.2
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7
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9
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12
+ GitPython==3.1.46
13
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14
+ pycparser==2.23
15
+ triton==3.1.0
16
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17
+ numpy==2.2.6
18
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19
+ gitdb==4.0.12
20
+ rich==14.3.3
21
+ PyYAML==6.0.3
22
+ pytz==2026.1.post1
23
+ packaging==25.0
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+ transformers==5.3.0
25
+ networkx==3.4.2
26
+ platformdirs==4.9.2
27
+ ittapi==1.2.1
28
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29
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31
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32
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33
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34
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36
+ pip==26.0.1
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+ six==1.17.0
38
+ frozenlist==1.8.0
39
+ filelock==3.20.3
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42
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44
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46
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47
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53
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54
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55
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56
+ safetensors==0.7.0
57
+ tokenizers==0.22.2
58
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59
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60
+ aiosignal==1.4.0
61
+ multidict==6.7.1
62
+ typing-inspection==0.4.2
63
+ accelerate==1.13.0
64
+ torch==2.5.1
65
+ brotlicffi==1.2.0.0
66
+ gmpy2==2.2.2
67
+ datasets==4.6.1
68
+ anyio==4.12.1
69
+ annotated-types==0.7.0
70
+ tqdm==4.67.3
71
+ mkl-service==2.4.0
72
+ sentry-sdk==2.54.0
73
+ torchvision==0.20.1
74
+ shellingham==1.5.4
75
+ torchaudio==2.5.1
76
+ sympy==1.13.1
77
+ h11==0.16.0
78
+ pillow==12.1.1
79
+ protobuf==6.33.5
80
+ click==8.3.1
81
+ MarkupSafe==3.0.2
82
+ urllib3==2.6.3
83
+ propcache==0.4.1
84
+ regex==2026.2.28
85
+ xxhash==3.6.0
86
+ setuptools==80.10.2
87
+ scikit-learn==1.7.2
88
+ huggingface_hub==1.5.0
89
+ joblib==1.5.3
90
+ aiohappyeyeballs==2.6.1
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+ "--run_name",
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+ - --model_name_or_path
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+ - /home/n5huang/dna_token/tokenizer_evaluation/baseline_bpe/tokenizer.json
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+ - "True"
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+ - /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/enhancers_types
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52
+ cpu_count: 128
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+ total: "1876350566400"
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+ email: mtapiapacheco@ucsd.edu
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+ executable: /home/n5huang/miniconda3/envs/nt_ft/bin/python
61
+ git:
62
+ commit: 5dc8fdf47bc12e22d02cfdaea49a6cbeb2fdf4d6
63
+ remote: https://huggingface.co/JessieZhou25/Finetune-GenomicBenchmarks
64
+ gpu: NVIDIA A100 80GB PCIe
65
+ gpu_count: 8
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+ gpu_nvidia:
67
+ - architecture: Ampere
68
+ cudaCores: 6912
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+ memoryTotal: "85899345920"
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+ program: /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py
112
+ python: CPython 3.10.19
113
+ root: /data/n5huang/dna_token/Finetune-GenomicBenchmarks/ft_data
114
+ startedAt: "2026-03-05T04:01:36.144515Z"
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wandb/run-20260305_040136-qpc17ycl/files/output.log ADDED
@@ -0,0 +1,37 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ WARNING:root:Perform single sequence classification...
2
+ WARNING:root:Perform single sequence classification...
3
+ WARNING:root:Perform single sequence classification...
4
+ Traceback (most recent call last):
5
+ File "/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py", line 455, in <module>
6
+ train()
7
+ File "/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py", line 406, in train
8
+ model = transformers.AutoModelForSequenceClassification.from_pretrained(
9
+ File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/models/auto/auto_factory.py", line 374, in from_pretrained
10
+ return model_class.from_pretrained(
11
+ File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/modeling_utils.py", line 4137, in from_pretrained
12
+ loading_info, disk_offload_index = cls._load_pretrained_model(model, state_dict, checkpoint_files, load_config)
13
+ File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/modeling_utils.py", line 4252, in _load_pretrained_model
14
+ merged_state_dict.update(load_state_dict(ckpt_file))
15
+ File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/modeling_utils.py", line 319, in load_state_dict
16
+ check_torch_load_is_safe()
17
+ File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/utils/import_utils.py", line 1270, in check_torch_load_is_safe
18
+ raise ValueError(
19
+ ValueError: Due to a serious vulnerability issue in `torch.load`, even with `weights_only=True`, we now require users to upgrade torch to at least v2.6 in order to use the function. This version restriction does not apply when loading files with safetensors.
20
+ See the vulnerability report here https://nvd.nist.gov/vuln/detail/CVE-2025-32434
21
+ Traceback (most recent call last):
22
+ File "/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py", line 455, in <module>
23
+ train()
24
+ File "/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py", line 406, in train
25
+ model = transformers.AutoModelForSequenceClassification.from_pretrained(
26
+ File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/models/auto/auto_factory.py", line 374, in from_pretrained
27
+ return model_class.from_pretrained(
28
+ File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/modeling_utils.py", line 4137, in from_pretrained
29
+ loading_info, disk_offload_index = cls._load_pretrained_model(model, state_dict, checkpoint_files, load_config)
30
+ File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/modeling_utils.py", line 4252, in _load_pretrained_model
31
+ merged_state_dict.update(load_state_dict(ckpt_file))
32
+ File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/modeling_utils.py", line 319, in load_state_dict
33
+ check_torch_load_is_safe()
34
+ File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/utils/import_utils.py", line 1270, in check_torch_load_is_safe
35
+ raise ValueError(
36
+ ValueError: Due to a serious vulnerability issue in `torch.load`, even with `weights_only=True`, we now require users to upgrade torch to at least v2.6 in order to use the function. This version restriction does not apply when loading files with safetensors.
37
+ See the vulnerability report here https://nvd.nist.gov/vuln/detail/CVE-2025-32434
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1
+ hf-xet==1.3.2
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3
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5
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6
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7
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11
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26
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27
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28
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29
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31
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32
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33
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34
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35
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36
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37
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38
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39
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40
+ annotated-doc==0.0.4
41
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42
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43
+ typing_extensions==4.15.0
44
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45
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46
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54
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56
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+ tokenizers==0.22.2
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60
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61
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62
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63
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64
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65
+ brotlicffi==1.2.0.0
66
+ gmpy2==2.2.2
67
+ datasets==4.6.1
68
+ anyio==4.12.1
69
+ annotated-types==0.7.0
70
+ tqdm==4.67.3
71
+ mkl-service==2.4.0
72
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73
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74
+ shellingham==1.5.4
75
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76
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77
+ h11==0.16.0
78
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79
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80
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81
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82
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83
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84
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85
+ xxhash==3.6.0
86
+ setuptools==80.10.2
87
+ scikit-learn==1.7.2
88
+ huggingface_hub==1.5.0
89
+ joblib==1.5.3
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+ aiohappyeyeballs==2.6.1
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+ "args": [
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+ "--model_name_or_path",
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+ "/home/n5huang/dna_token/pretrain/models/model_cpu_test_1/checkpoint-100000",
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+ "--tokenizer_path",
9
+ "/home/n5huang/dna_token/tokenizer_evaluation/baseline_bpe/tokenizer.json",
10
+ "--trust_remote_code",
11
+ "True",
12
+ "--data_path",
13
+ "/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/NT-benchmarks/nucleotide_transformer_downstream_tasks_revised/enhancers_types/split",
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+ "--kmer",
15
+ "-1",
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+ "--run_name",
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+ "hg38_BPE_base__baseline_bpe_tokenizer_3e-5_enhancers_types_seed42",
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+ "100",
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+ "/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/enhancers_types",
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+ "--evaluation_strategy",
36
+ "steps",
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+ "--eval_steps",
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+ "200",
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+ "--warmup_steps",
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+ "30",
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+ "--logging_steps",
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+ "100000",
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+ "--log_level",
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+ "info",
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+ "--seed",
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+ "42",
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+ "False",
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