README.md

---
license: apache-2.0
tags:
- generated_from_trainer
metrics:
- accuracy
model-index:
- name: output_v3
  results: []
widget:
  - text: >-
      <|endoftext|>MAADGYLPDWLEDNLSEGIREWWALKPGAPQPKANQQHQDNARGLVLPGYKYLGPGNGL
---

<!-- 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. -->

# output_v3

This model is a fine-tuned version of [avuhong/ParvoGPT2](https://huggingface.co./avuhong/ParvoGPT2) on an unknown dataset.
It achieves the following results on the evaluation set:
- Loss: 0.4775
- Accuracy: 0.9290

## Model description

This model is a GPT2-like model for generating capsid amino acid sequences. It was trained exclusively on capsid aa_seqs of Piccovirales members.

## Intended uses & limitations

As a typical GPT model, it can be used to generate new sequences or used to evaluate the perplexity of given sequences.

### Generate novel sequences for viral capsid proteins

```python
from transformers import pipeline
protgpt2 = pipeline('text-generation', model="avuhong/PiccoviralesGPT")
sequences = protgpt2("<|endoftext|>", max_length=750, do_sample=True, top_k=950, repetition_penalty=1.2, num_return_sequences=10, eos_token_id=0)
```

### Calculate the perplexity of a protein sequence

```python
def calculatePerplexity(sequence, model, tokenizer):
    input_ids = torch.tensor(tokenizer.encode(sequence)).unsqueeze(0) 
    input_ids = input_ids.to(device)
    with torch.no_grad():
        outputs = model(input_ids, labels=input_ids)
    loss, logits = outputs[:2]
    return math.exp(loss)

def split_sequence(sequence):
    chunks = []
    max_i = 0
    for i in range(0, len(sequence), 60):
        chunk = sequence[i:i+60]
        
        if i == 0:
            chunk = '<|endoftext|>' + chunk
        chunks.append(chunk)
        max_i = i
    
    chunks = '\n'.join(chunks)
    
    if max_i+61==len(sequence):
        chunks = chunks+"\n<|endoftext|>"
    else:
        chunks = chunks+"<|endoftext|>"
    return chunks

seq = "MAADGYLPDWLEDNLSEGIREWWALKPGAPQPKANQQHQDNARGLVLPGYKYLGPGNGLDKGEPVNAADAAALEHDKAYDQQLKAGDNPYLKYNHADAEFQERLKEDTSFGGNLGRAVFQAKKRLLEPLGLVEEAAKTAPGKKRPVEQSPQEPDSSAGIGKSGAQPAKKRLNFGQTGDTESVPDPQPIGEPPAAPSGVGSLTMASGGGAPVADNNEGADGVGSSSGNWHCDSQWLGDRVITTSTRTWALPTYNNHLYKQISNSTSGGSSNDNAYFGYSTPWGYFDFNRFHCHFSPRDWQRLINNNWGFRPKRLNFKLFNIQVKEVTDNNGVKTIANNLTSTVQVFTDSDYQLPYVLGSAHEGCLPPFPADVFMIPQYGYLTLNDGSQAVGRSSFYCLEYFPSQMLRTGNNFQFSYEFENVPFHSSYAHSQSLDRLMNPLIDQYLYYLSKTINGSGQNQQTLKFSVAGPSNMAVQGRNYIPGPSYRQQRVSTTVTQNNNSEFAWPGASSWALNGRNSLMNPGPAMASHKEGEDRFFPLSGSLIFGKQGTGRDNVDADKVMITNEEEIKTTNPVATESYGQVATNHQSAQAQAQTGWVQNQGILPGMVWQDRDVYLQGPIWAKIPHTDGNFHPSPLMGGFGMKHPPPQILIKNTPVPADPPTAFNKDKLNSFITQYSTGQVSVEIEWELQKENSKRWNPEIQYTSNYYKSNNVEFAVNTEGVYSEPRPIGTRYLTRNL"
seq = split_sequence(seq)
print(f"{calculatePerplexity(seq, model, tokenizer):.2f}")
```

## Training and evaluation data

Traning script is included in bash file in this repository.

## Training procedure

### Training hyperparameters

The following hyperparameters were used during training:
- learning_rate: 5e-05
- train_batch_size: 1
- eval_batch_size: 1
- seed: 42
- distributed_type: multi-GPU
- num_devices: 2
- gradient_accumulation_steps: 4
- total_train_batch_size: 8
- total_eval_batch_size: 2
- optimizer: Adam with betas=(0.9,0.999) and epsilon=1e-08
- lr_scheduler_type: linear
- num_epochs: 32.0
- mixed_precision_training: Native AMP

### Training results

| Training Loss | Epoch | Step | Validation Loss | Accuracy |
|:-------------:|:-----:|:----:|:---------------:|:--------:|
| No log        | 1.0   | 220  | 1.1623          | 0.8225   |
| No log        | 2.0   | 440  | 0.9566          | 0.8539   |
| 1.1942        | 3.0   | 660  | 0.8456          | 0.8709   |
| 1.1942        | 4.0   | 880  | 0.7719          | 0.8801   |
| 0.7805        | 5.0   | 1100 | 0.7224          | 0.8872   |
| 0.7805        | 6.0   | 1320 | 0.6895          | 0.8928   |
| 0.6257        | 7.0   | 1540 | 0.6574          | 0.8972   |
| 0.6257        | 8.0   | 1760 | 0.6289          | 0.9014   |
| 0.6257        | 9.0   | 1980 | 0.6054          | 0.9045   |
| 0.5385        | 10.0  | 2200 | 0.5881          | 0.9077   |
| 0.5385        | 11.0  | 2420 | 0.5709          | 0.9102   |
| 0.4778        | 12.0  | 2640 | 0.5591          | 0.9121   |
| 0.4778        | 13.0  | 2860 | 0.5497          | 0.9143   |
| 0.427         | 14.0  | 3080 | 0.5385          | 0.9161   |
| 0.427         | 15.0  | 3300 | 0.5258          | 0.9180   |
| 0.394         | 16.0  | 3520 | 0.5170          | 0.9195   |
| 0.394         | 17.0  | 3740 | 0.5157          | 0.9212   |
| 0.394         | 18.0  | 3960 | 0.5038          | 0.9221   |
| 0.363         | 19.0  | 4180 | 0.4977          | 0.9234   |
| 0.363         | 20.0  | 4400 | 0.4976          | 0.9236   |
| 0.3392        | 21.0  | 4620 | 0.4924          | 0.9247   |
| 0.3392        | 22.0  | 4840 | 0.4888          | 0.9255   |
| 0.33          | 23.0  | 5060 | 0.4890          | 0.9262   |
| 0.33          | 24.0  | 5280 | 0.4856          | 0.9268   |
| 0.3058        | 25.0  | 5500 | 0.4803          | 0.9275   |
| 0.3058        | 26.0  | 5720 | 0.4785          | 0.9277   |
| 0.3058        | 27.0  | 5940 | 0.4813          | 0.9281   |
| 0.2973        | 28.0  | 6160 | 0.4799          | 0.9282   |
| 0.2973        | 29.0  | 6380 | 0.4773          | 0.9285   |
| 0.2931        | 30.0  | 6600 | 0.4778          | 0.9286   |
| 0.2931        | 31.0  | 6820 | 0.4756          | 0.9290   |
| 0.2879        | 32.0  | 7040 | 0.4775          | 0.9290   |


### Framework versions

- Transformers 4.26.1
- Pytorch 1.13.1+cu117
- Datasets 2.9.0
- Tokenizers 0.13.2