Add Plant DNABERT model for H3K27ac prediction

README.md

@@ -1,3 +1,63 @@
----
-license: cc-by-nc-sa-4.0
----
+---
+license: cc-by-nc-sa-4.0
+widget:
+- text: GCGACTCCGCCGCCCCGATCTCCCCGTCGTCCTACAGTGCTCTCCACATCGTAGGCGACCTGGTTGGACTCCTCGACGCCTTGTCCCTACCGCAGGTGTTTGTGGTGGGACAAGGCTGGGGAGCCCTGCTGGCGTGGAACCTCTGCATGTTCCGCCCCGAGCGGGTGCGCGCGCTGGTCAACATGAGCGTCGCCTTCATGCCGCGCAACCCCTCCGTGAAGCCACTTGAGTTGTTTCGGCGGCTCTACGGCGACGGATACTACCTCCTCCGGCTGCAGGAAC
+tags:
+- DNA
+- biology
+- genomics
+---
+# Plant foundation DNA large language models
+
+The plant DNA large language models (LLMs) contain a series of foundation models based on different model architectures, which are pre-trained on various plant reference genomes.  
+All the models have a comparable model size between 90 MB and 150 MB, BPE tokenizer is used for tokenization and 8000 tokens are included in the vocabulary.  
+
+
+**Developed by:** zhangtaolab
+
+### Model Sources
+
+- **Repository:** [Plant DNA LLMs](https://github.com/zhangtaolab/plant_DNA_LLMs)
+- **Manuscript:** [Versatile applications of foundation DNA language models in plant genomes]() 
+
+### Architecture
+
+The model is trained based on the Google BERT base model with modified tokenizer specific for DNA sequence.
+
+This model is fine-tuned for predicting H3K27me3 histone modification.
+
+
+### How to use
+
+Install the runtime library first:
+```bash
+pip install transformers
+```
+
+Here is a simple code for inference:
+```python
+from transformers import AutoModelForSequenceClassification, AutoTokenizer, pipeline
+
+model_name = 'plant-dnabert-H3K4me3'
+# load model and tokenizer
+model = AutoModelForSequenceClassification.from_pretrained(f'zhangtaolab/{model_name}', trust_remote_code=True)
+tokenizer = AutoTokenizer.from_pretrained(f'zhangtaolab/{model_name}', trust_remote_code=True)
+
+# inference
+sequences = ['TTCATCTCGTCCGACGCTTCAACCCGCACCGATCCTGCGCCACCCCTTCGCCGGCGGCTTCTCCCCTCCTCTTCCTCCGCCGCTGCATCGCCGTCCCAGGAACTTGGACACGTCGCCTCTCGCCGGCGACCATGTACCGCGCCCTCCGCTCTCTCAAGGTTTCCCCGTCTGCACCCCCCCAACCTTCTACGACGTGTGGCGTTGCGTGTCTCGATCCATTTGGGATGAATGCGCTGGAGTGTTAGA',
+             'ATCAATATTCCCAACAGGTTTTGAAGCAATGGATGAAACATCATCCTTCACGGAACTGGATTATGGGATTCGCCGGCTGGACCACGCTGTTGGGAATGTGCCGGAGCTGGGTCCTGTAGTGGATTACATCAAGGCGTTTACGGGGTTTCATGAATTTGCGGAGTTTACAGCT']
+pipe = pipeline('text-classification', model=model, tokenizer=tokenizer,
+                trust_remote_code=True, top_k=None)
+results = pipe(sequences)
+print(results)
+
+```
+
+
+### Training data
+We use BertForSequenceClassification to fine-tune the model.  
+Detailed training procedure can be found in our manuscript.
+
+
+#### Hardware
+Model was trained on a NVIDIA GTX1080Ti GPU (11 GB).

added_tokens.json

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+{
+  "[CLS]": 8000,
+  "[MASK]": 8004,
+  "[PAD]": 8003,
+  "[SEP]": 8001,
+  "[UNK]": 8002
+}

config.json

@@ -0,0 +1,34 @@
+{
+  "_name_or_path": "Plant_DNABERT_H3K4me3",
+  "architectures": [
+    "BertForSequenceClassification"
+  ],
+  "attention_probs_dropout_prob": 0.1,
+  "classifier_dropout": null,
+  "hidden_act": "gelu",
+  "hidden_dropout_prob": 0.1,
+  "hidden_size": 768,
+  "id2label": {
+    "0": "Not H3K4me3",
+    "1": "H3K4me3"
+  },
+  "initializer_range": 0.02,
+  "intermediate_size": 3072,
+  "label2id": {
+    "Not H3K4me3": 0,
+    "H3K4me3": 1
+  },
+  "layer_norm_eps": 1e-12,
+  "max_position_embeddings": 512,
+  "model_type": "bert",
+  "num_attention_heads": 12,
+  "num_hidden_layers": 12,
+  "pad_token_id": 8003,
+  "position_embedding_type": "absolute",
+  "problem_type": "single_label_classification",
+  "torch_dtype": "float32",
+  "transformers_version": "4.39.1",
+  "type_vocab_size": 2,
+  "use_cache": true,
+  "vocab_size": 8005
+}

model.safetensors

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special_tokens_map.json

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spm.model

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+size 367999

tokenizer_config.json

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+{
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+  "tokenizer_class": "DebertaV2Tokenizer",
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+  "truncation_strategy": "longest_first",
+  "unk_token": "[UNK]"
+}