End of training
Browse files- README.md +77 -0
- config.json +37 -0
- pytorch_model.bin +3 -0
- special_tokens_map.json +51 -0
- tokenizer_config.json +70 -0
README.md
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---
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license: bsd-3-clause
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base_model: LongSafari/hyenadna-medium-160k-seqlen-hf
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tags:
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- generated_from_trainer
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metrics:
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- precision
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- recall
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- accuracy
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model-index:
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- name: hyenadna-medium-160k-seqlen-hf_ft_BioS45_1kbpHG19_DHSs_H3K27AC
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results: []
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---
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<!-- This model card has been generated automatically according to the information the Trainer had access to. You
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should probably proofread and complete it, then remove this comment. -->
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# hyenadna-medium-160k-seqlen-hf_ft_BioS45_1kbpHG19_DHSs_H3K27AC
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This model is a fine-tuned version of [LongSafari/hyenadna-medium-160k-seqlen-hf](https://huggingface.co/LongSafari/hyenadna-medium-160k-seqlen-hf) on the None dataset.
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It achieves the following results on the evaluation set:
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- Loss: 0.5104
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- F1 Score: 0.8100
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- Precision: 0.8002
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- Recall: 0.8202
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- Accuracy: 0.7993
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- Auc: 0.8765
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- Prc: 0.8748
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## Model description
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More information needed
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## Intended uses & limitations
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More information needed
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## Training and evaluation data
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More information needed
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## Training procedure
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### Training hyperparameters
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The following hyperparameters were used during training:
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- learning_rate: 1e-05
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- train_batch_size: 16
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- eval_batch_size: 16
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- seed: 42
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- optimizer: Adam with betas=(0.9,0.999) and epsilon=1e-08
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- lr_scheduler_type: linear
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- num_epochs: 20
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- mixed_precision_training: Native AMP
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### Training results
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| Training Loss | Epoch | Step | Validation Loss | F1 Score | Precision | Recall | Accuracy | Auc | Prc |
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|:-------------:|:------:|:----:|:---------------:|:--------:|:---------:|:------:|:--------:|:------:|:------:|
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| 0.5145 | 0.4205 | 500 | 0.4663 | 0.7945 | 0.8003 | 0.7887 | 0.7871 | 0.8575 | 0.8420 |
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| 0.4678 | 0.8410 | 1000 | 0.4667 | 0.8075 | 0.7334 | 0.8984 | 0.7766 | 0.8691 | 0.8628 |
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| 0.4586 | 1.2616 | 1500 | 0.4759 | 0.8157 | 0.7463 | 0.8992 | 0.7880 | 0.8674 | 0.8598 |
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| 0.4467 | 1.6821 | 2000 | 0.4349 | 0.8134 | 0.7961 | 0.8315 | 0.8010 | 0.8798 | 0.8751 |
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| 0.4298 | 2.1026 | 2500 | 0.4558 | 0.8170 | 0.7480 | 0.9 | 0.7897 | 0.8749 | 0.8679 |
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| 0.4068 | 2.5231 | 3000 | 0.4374 | 0.7982 | 0.8139 | 0.7831 | 0.7934 | 0.8830 | 0.8793 |
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| 0.4299 | 2.9437 | 3500 | 0.4358 | 0.8117 | 0.8033 | 0.8202 | 0.8014 | 0.8816 | 0.8787 |
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| 0.3994 | 3.3642 | 4000 | 0.4543 | 0.8120 | 0.8287 | 0.7960 | 0.8077 | 0.8815 | 0.8781 |
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| 0.3742 | 3.7847 | 4500 | 0.4463 | 0.8139 | 0.7948 | 0.8339 | 0.8010 | 0.8796 | 0.8733 |
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| 0.345 | 4.2052 | 5000 | 0.5104 | 0.8100 | 0.8002 | 0.8202 | 0.7993 | 0.8765 | 0.8748 |
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### Framework versions
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- Transformers 4.42.3
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- Pytorch 2.3.0+cu121
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- Datasets 2.18.0
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- Tokenizers 0.19.0
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config.json
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{
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"_name_or_path": "LongSafari/hyenadna-medium-160k-seqlen-hf",
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"activation_freq": 10,
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"architectures": [
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"HyenaDNAForSequenceClassification"
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],
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"auto_map": {
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"AutoConfig": "LongSafari/hyenadna-medium-160k-seqlen-hf--configuration_hyena.HyenaConfig",
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"AutoModel": "LongSafari/hyenadna-medium-160k-seqlen-hf--modeling_hyena.HyenaDNAModel",
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"AutoModelForCausalLM": "LongSafari/hyenadna-medium-160k-seqlen-hf--modeling_hyena.HyenaDNAForCausalLM",
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"AutoModelForSequenceClassification": "LongSafari/hyenadna-medium-160k-seqlen-hf--modeling_hyena.HyenaDNAForSequenceClassification"
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},
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"d_inner": 1024,
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"d_model": 256,
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"emb_dim": 5,
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"embed_dropout": 0.1,
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"filter_order": 64,
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"hyena_dropout": 0.0,
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"hyena_filter_dropout": 0.0,
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"hyena_order": 2,
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"initializer_range": 0.02,
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"layer_norm_epsilon": 1e-05,
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"max_seq_len": 160002,
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"model_type": "hyenadna",
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"n_layer": 8,
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"num_inner_mlps": 2,
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"pad_token_id": 4,
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"pad_vocab_size_multiple": 8,
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"problem_type": "single_label_classification",
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"short_filter_order": 3,
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"tie_word_embeddings": false,
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"torch_dtype": "float32",
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"train_freq": true,
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"transformers_version": "4.42.3",
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"use_bias": true,
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"vocab_size": 12
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}
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pytorch_model.bin
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version https://git-lfs.github.com/spec/v1
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oid sha256:bd64eb41de44ed36dd42bc970162805342d3212a9b7b22c7e758deac0f87955a
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size 57008026
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special_tokens_map.json
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{
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"bos_token": {
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"content": "[BOS]",
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"lstrip": false,
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"normalized": false,
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"rstrip": false,
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"single_word": false
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},
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"cls_token": {
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"content": "[CLS]",
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"lstrip": false,
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"normalized": false,
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"rstrip": false,
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"single_word": false
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},
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"eos_token": {
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"content": "[SEP]",
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"lstrip": false,
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"normalized": false,
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"rstrip": false,
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"single_word": false
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},
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"mask_token": {
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"content": "[MASK]",
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"lstrip": false,
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"normalized": false,
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"rstrip": false,
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"single_word": false
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},
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"pad_token": {
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"content": "[PAD]",
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"lstrip": false,
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"normalized": false,
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"rstrip": false,
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"single_word": false
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},
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"sep_token": {
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"content": "[SEP]",
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"lstrip": false,
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"normalized": false,
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"rstrip": false,
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"single_word": false
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},
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"unk_token": {
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"content": "[UNK]",
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"lstrip": false,
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"normalized": false,
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"rstrip": false,
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"single_word": false
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}
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}
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tokenizer_config.json
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{
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"add_prefix_space": false,
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"added_tokens_decoder": {
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"0": {
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"content": "[CLS]",
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"lstrip": false,
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"normalized": false,
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"rstrip": false,
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"single_word": false,
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"special": true
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},
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"1": {
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"content": "[SEP]",
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"lstrip": false,
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"normalized": false,
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"rstrip": false,
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"single_word": false,
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"special": true
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},
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"2": {
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"content": "[BOS]",
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"lstrip": false,
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"normalized": false,
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"rstrip": false,
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"single_word": false,
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"special": true
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},
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"3": {
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"content": "[MASK]",
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"lstrip": false,
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"normalized": false,
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"rstrip": false,
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"single_word": false,
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"special": true
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},
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"4": {
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"content": "[PAD]",
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"lstrip": false,
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"normalized": false,
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"rstrip": false,
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"single_word": false,
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"special": true
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},
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"6": {
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"content": "[UNK]",
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"lstrip": false,
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"normalized": false,
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"rstrip": false,
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"single_word": false,
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"special": true
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}
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},
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"auto_map": {
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"AutoTokenizer": [
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"LongSafari/hyenadna-medium-160k-seqlen-hf--tokenization_hyena.HyenaDNATokenizer",
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null
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]
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},
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"bos_token": "[BOS]",
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"clean_up_tokenization_spaces": true,
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"cls_token": "[CLS]",
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"eos_token": "[SEP]",
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"mask_token": "[MASK]",
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"model_max_length": 160002,
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"pad_token": "[PAD]",
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"padding_side": "left",
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"sep_token": "[SEP]",
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"tokenizer_class": "HyenaDNATokenizer",
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"unk_token": "[UNK]"
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}
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