End of training

README.md

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+---
+base_model: zhihan1996/DNABERT-2-117M
+tags:
+- generated_from_trainer
+metrics:
+- precision
+- recall
+- accuracy
+model-index:
+- name: DNABERT-2-117M_ft_BioS2_1kbpHG19_DHSs_H3K27AC
+  results: []
+---
+
+<!-- This model card has been generated automatically according to the information the Trainer had access to. You
+should probably proofread and complete it, then remove this comment. -->
+
+# DNABERT-2-117M_ft_BioS2_1kbpHG19_DHSs_H3K27AC
+
+This model is a fine-tuned version of [zhihan1996/DNABERT-2-117M](https://huggingface.co/zhihan1996/DNABERT-2-117M) on the None dataset.
+It achieves the following results on the evaluation set:
+- Loss: 0.4620
+- F1 Score: 0.7974
+- Precision: 0.8134
+- Recall: 0.7819
+- Accuracy: 0.7933
+- Auc: 0.8741
+- Prc: 0.8601
+
+## Model description
+
+More information needed
+
+## Intended uses & limitations
+
+More information needed
+
+## Training and evaluation data
+
+More information needed
+
+## Training procedure
+
+### Training hyperparameters
+
+The following hyperparameters were used during training:
+- learning_rate: 1e-05
+- train_batch_size: 16
+- eval_batch_size: 16
+- seed: 42
+- optimizer: Adam with betas=(0.9,0.999) and epsilon=1e-08
+- lr_scheduler_type: linear
+- num_epochs: 20
+- mixed_precision_training: Native AMP
+
+### Training results
+
+| Training Loss | Epoch  | Step | Validation Loss | F1 Score | Precision | Recall | Accuracy | Auc    | Prc    |
+|:-------------:|:------:|:----:|:---------------:|:--------:|:---------:|:------:|:--------:|:------:|:------:|
+| 0.706         | 0.1680 | 500  | 0.6216          | 0.6107   | 0.7600    | 0.5105 | 0.6616   | 0.7690 | 0.7525 |
+| 0.614         | 0.3360 | 1000 | 0.5784          | 0.7600   | 0.6685    | 0.8805 | 0.7108   | 0.7836 | 0.7638 |
+| 0.5795        | 0.5040 | 1500 | 0.5409          | 0.7576   | 0.6964    | 0.8307 | 0.7236   | 0.7938 | 0.7723 |
+| 0.557         | 0.6720 | 2000 | 0.5898          | 0.7622   | 0.6293    | 0.9661 | 0.6864   | 0.8063 | 0.7838 |
+| 0.561         | 0.8401 | 2500 | 0.5143          | 0.7770   | 0.7298    | 0.8307 | 0.7520   | 0.8183 | 0.7953 |
+| 0.5313        | 1.0081 | 3000 | 0.4928          | 0.7958   | 0.7300    | 0.8746 | 0.7666   | 0.8334 | 0.8096 |
+| 0.5167        | 1.1761 | 3500 | 0.5086          | 0.7590   | 0.7963    | 0.7250 | 0.7605   | 0.8471 | 0.8266 |
+| 0.5052        | 1.3441 | 4000 | 0.4732          | 0.8021   | 0.7578    | 0.8520 | 0.7814   | 0.8533 | 0.8327 |
+| 0.4923        | 1.5121 | 4500 | 0.4741          | 0.7898   | 0.7864    | 0.7932 | 0.7804   | 0.8572 | 0.8386 |
+| 0.493         | 1.6801 | 5000 | 0.4683          | 0.7821   | 0.7995    | 0.7654 | 0.7782   | 0.8618 | 0.8431 |
+| 0.4834        | 1.8481 | 5500 | 0.4522          | 0.8100   | 0.7702    | 0.8543 | 0.7916   | 0.8638 | 0.8465 |
+| 0.4871        | 2.0161 | 6000 | 0.4527          | 0.8160   | 0.7475    | 0.8982 | 0.7893   | 0.8665 | 0.8500 |
+| 0.457         | 2.1841 | 6500 | 0.6625          | 0.7653   | 0.6231    | 0.9916 | 0.6838   | 0.8679 | 0.8530 |
+| 0.4685        | 2.3522 | 7000 | 0.5230          | 0.7281   | 0.8393    | 0.6430 | 0.7503   | 0.8681 | 0.8521 |
+| 0.4567        | 2.5202 | 7500 | 0.4433          | 0.8198   | 0.7557    | 0.8956 | 0.7952   | 0.8702 | 0.8533 |
+| 0.4506        | 2.6882 | 8000 | 0.4520          | 0.8208   | 0.7520    | 0.9034 | 0.7948   | 0.8721 | 0.8580 |
+| 0.4443        | 2.8562 | 8500 | 0.4590          | 0.8029   | 0.7963    | 0.8097 | 0.7933   | 0.8730 | 0.8581 |
+| 0.4433        | 3.0242 | 9000 | 0.5848          | 0.7530   | 0.8380    | 0.6837 | 0.7668   | 0.8738 | 0.8592 |
+| 0.4355        | 3.1922 | 9500 | 0.4620          | 0.7974   | 0.8134    | 0.7819 | 0.7933   | 0.8741 | 0.8601 |
+
+
+### Framework versions
+
+- Transformers 4.42.3
+- Pytorch 2.3.0+cu121
+- Datasets 2.18.0
+- Tokenizers 0.19.0

config.json

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+{
+  "_name_or_path": "zhihan1996/DNABERT-2-117M",
+  "alibi_starting_size": 512,
+  "architectures": [
+    "BertForSequenceClassification"
+  ],
+  "attention_probs_dropout_prob": 0.0,
+  "auto_map": {
+    "AutoConfig": "zhihan1996/DNABERT-2-117M--configuration_bert.BertConfig",
+    "AutoModel": "zhihan1996/DNABERT-2-117M--bert_layers.BertModel",
+    "AutoModelForMaskedLM": "zhihan1996/DNABERT-2-117M--bert_layers.BertForMaskedLM",
+    "AutoModelForSequenceClassification": "zhihan1996/DNABERT-2-117M--bert_layers.BertForSequenceClassification"
+  },
+  "classifier_dropout": null,
+  "gradient_checkpointing": false,
+  "hidden_act": "gelu",
+  "hidden_dropout_prob": 0.1,
+  "hidden_size": 768,
+  "initializer_range": 0.02,
+  "intermediate_size": 3072,
+  "layer_norm_eps": 1e-12,
+  "max_position_embeddings": 512,
+  "model_type": "bert",
+  "num_attention_heads": 12,
+  "num_hidden_layers": 12,
+  "pad_token_id": 0,
+  "position_embedding_type": "absolute",
+  "problem_type": "single_label_classification",
+  "torch_dtype": "float32",
+  "transformers_version": "4.42.3",
+  "type_vocab_size": 2,
+  "use_cache": true,
+  "vocab_size": 4096
+}

model.safetensors

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special_tokens_map.json

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+{
+  "cls_token": {
+    "content": "[CLS]",
+    "lstrip": false,
+    "normalized": false,
+    "rstrip": false,
+    "single_word": false
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+    "single_word": false
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+  "pad_token": {
+    "content": "[PAD]",
+    "lstrip": false,
+    "normalized": false,
+    "rstrip": false,
+    "single_word": false
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+  "sep_token": {
+    "content": "[SEP]",
+    "lstrip": false,
+    "normalized": false,
+    "rstrip": false,
+    "single_word": false
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+  "unk_token": {
+    "content": "[UNK]",
+    "lstrip": false,
+    "normalized": false,
+    "rstrip": false,
+    "single_word": false
+  }
+}

tokenizer_config.json

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+{
+  "added_tokens_decoder": {
+    "0": {
+      "content": "[UNK]",
+      "lstrip": false,
+      "normalized": false,
+      "rstrip": false,
+      "single_word": false,
+      "special": true
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+      "single_word": false,
+      "special": true
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+      "lstrip": false,
+      "normalized": false,
+      "rstrip": false,
+      "single_word": false,
+      "special": true
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+    "3": {
+      "content": "[PAD]",
+      "lstrip": false,
+      "normalized": false,
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+      "single_word": false,
+      "special": true
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+      "lstrip": false,
+      "normalized": false,
+      "rstrip": false,
+      "single_word": false,
+      "special": true
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+  },
+  "clean_up_tokenization_spaces": true,
+  "cls_token": "[CLS]",
+  "mask_token": "[MASK]",
+  "model_max_length": 1000000000000000019884624838656,
+  "pad_token": "[PAD]",
+  "sep_token": "[SEP]",
+  "tokenizer_class": "PreTrainedTokenizerFast",
+  "unk_token": "[UNK]"
+}

training_args.bin

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