---
license: apache-2.0
---

# Model Card for Model ID

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This modelcard aims to be a base template for new models. It has been generated using [this raw template](https://github.com/huggingface/huggingface_hub/blob/main/src/huggingface_hub/templates/modelcard_template.md?plain=1).

## Model Details

### Model Description

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- **Developed by:** [More Information Needed]
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- **Shared by [optional]:** [More Information Needed]
- **Model type:** [More Information Needed]
- **Language(s) (NLP):** [More Information Needed]
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- **Finetuned from model [optional]:** [More Information Needed]

### Model Sources [optional]

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## Uses

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### Direct Use

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```python
from transformers import AutoModelForCausalLM, AutoTokenizer
import torch

tokenizer = AutoTokenizer.from_pretrained('InstructPLM/MPNN-ProGen2-xlarge-CATH42', trust_remote_code=True)
model = AutoModelForCausalLM.from_pretrained('InstructPLM/MPNN-ProGen2-xlarge-CATH42', trust_remote_code=True)

model.cuda().eval()
model.requires_grad_(False)

batch = tokenizer('Fast-PETase.pyd|1MQTNPYARGPNPTAASLEASAGPFTVRSFTVSRPSGYGAGTVYYPTNAGGTVGAIAIVPGYTARQSSIKWWGPRLASHGFVVITIDTNSTLDQPESRSSQQMAALRQVASLNGTSSSPIYGKVDTARMGVMGWSMGGGGSLISAANNPSLKAAAPQAPWHSSTNFSSVTVPTLIFACENDSIAPVNSSALPIYDSMSQNAKQFLEIKGGSHSCANSGNSNQALIGKKGVAWMKRFMDNDTRYSTFACENPNSTAVSDFRTANCS2',return_tensors='pt').to(device=model.device)

labels = batch.input_ids.masked_fill((1-batch.attention_mask).bool(), -100)
labels[:, :tokenizer.n_queries+1] = -100

batch["labels"] = labels


with torch.no_grad():
    with torch.cuda.amp.autocast(dtype=torch.float16):
        output = model(**batch)

print(output.loss.item())

batch = tokenizer('Fast-PETase.pyd|1',return_tensors='pt').to(device=model.device)


tokens_batch = model.generate(
    **batch,
    do_sample=True,
    temperature=0.8, 
    max_length=512+tokenizer.n_queries,
    min_new_tokens=5,
    top_p=0.9, 
    num_return_sequences=5, 
    pad_token_id=0, 
    repetition_penalty=1.0, 
    bad_words_ids=[[3]]
    )

texts = tokenizer.batch_decode(tokens_batch)

def truncate_seq(text):
    bos = text.find('1')
    eos = text.find('2')
    if eos > bos and bos >= 0:
        return text[bos+1:eos]
    else:
        return text[bos+1:]
print([truncate_seq(t) for t in texts])

# Ref. Seq 
#       'MQTNPYARGPNPTAASLEASAGPFTVRSFTVSRPSGYGAGTVYYPTNAGGTVGAIAIVPGYTARQSSIKWWGPRLASHGFVVITIDTNSTLDQPESRSSQQMAALRQVASLNGTSSSPIYGKVDTARMGVMGWSMGGGGSLISAANNPSLKAAAPQAPWHSSTNFSSVTVPTLIFACENDSIAPVNSSALPIYDSMSQNAKQFLEIKGGSHSCANSGNSNQALIGKKGVAWMKRFMDNDTRYSTFACENPNSTAVSDFRTANCS'
# Designed seq:
#       'METNPFHRGPDPTCASLEAGAGPFNVQSFRVDRPLGFGAGTVFYPTDAGGQVPAIAIAPGFTQTQSSVMWYGPRLASHGFVVIVIDTISTFDNPDSRSAQLLAALDQVANLNSNASSPIYGKVDTTRQAVMGHSMGGGGSLISAMNNPSLKAAAPMAPWHVSTNFSAVQVPTFIIGAENDTIAPVASHSIPFYNSIPSSLPKAYMELAGASHLAPNSSNPTIAKYSISWLKRFVDNDTRYEQFLCPAPTSTALISEYRDTCPY', 
#       'EETNPYSKGPDPTAASLEASAGPFTVQSFSVARPLGFGAGTVYYPTDAGGKVGAIAVVPGYTDTQGSIRWWGPRLASHGFVVMTIDTISSYDQPDSRSAQLMAALDQLANLNSTSSSPIYNKVDTTRQAVMGHSMGGGGSLISAMNNPNLKAAIPMAPWHSSTNFSSVKVPTMILGAERDTVAPVSSHAEPFYNSLPSSTPKAYLELKGASHFFPNTTNTPTFAKSVLAWLKRFVDNDTRYEQFLCPGPTSTDLTDYRNTCPY', 
#       'SETNPYIKGPDPTAASLEASAGAFTVQSFTVSRPTGFGAGTVYYPTDAGGRVGAIAIVPGYTATQSSIKWWGPRLASHGFVVMTIDTNSTYDQPDSRANQLMAALDQLTNLNSTRSSPIYGKVDTTRQGVMGHSMGGGGSLIAAQDNPNLKAAIPLAPWHSSSNFSSVTVPTLIIGAQNDTVAPVSSHSIPFYTSLPSSLDKAYLELNGASHFAPNSSNTTIAKYSISWLKRFIDNDTRYEQFLCPPPSGSALISEYRNTCPY', 
#       'EETWPYHRGPDPTAASLEASAGPFTVQSFTVARPLGFGAGTVYYPTDAGGRVGAVAVVPGYTQTQSAIRWWGPRLASHGFVVMTIDTISTFDQPDSRSAQLLAALDQLAVLNSTRSSPIYNKVDTTRQGVMGHSMGGGGSLISAMNNPSLKAAVPLAPWHASTNFSNVQVPTLIIGASDDTTASVTTHSIPFYNSIPSSVPKAYLELQGQSHFCPNTSNTTIAKYSISWLKRFIDNDTRYDQFLCPPPNGSAISDYRSTCPH', 
#       'METNPFIRGPNPTAASLEASAGPFQVSSFSVARPVGFGAGTVYYPTDAGGQVPAIAIAPGFTQTQASVKWYGPRLASHGFVVIVIDTNSTLDNPDSRSAQLLAALDQVSTLNSSSSSPIYGKVDTTRQGVMGHSMGGGGSLISAQNNPALKAAIPLAPWHVSTDFSGVTVPTLIIGAENDTVAPVGTHAEPFYNSIPSSTPKAYLELNNASHFAPNTSNTTIAKYSIAWLKRFVDNDTRYDQFLCPAPNGNAIQDYRDTCPH'
#
```

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### Downstream Use [optional]

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### Out-of-Scope Use

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## Bias, Risks, and Limitations

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### Recommendations

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Users (both direct and downstream) should be made aware of the risks, biases and limitations of the model. More information needed for further recommendations.

## How to Get Started with the Model

Use the code below to get started with the model.

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## Training Details

### Training Data

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### Training Procedure

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#### Preprocessing [optional]

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#### Training Hyperparameters

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#### Speeds, Sizes, Times [optional]

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## Evaluation

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### Testing Data, Factors & Metrics

#### Testing Data

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#### Factors

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#### Metrics

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### Results

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#### Summary



## Model Examination [optional]

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## Environmental Impact

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Carbon emissions can be estimated using the [Machine Learning Impact calculator](https://mlco2.github.io/impact#compute) presented in [Lacoste et al. (2019)](https://arxiv.org/abs/1910.09700).

- **Hardware Type:** [More Information Needed]
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## Technical Specifications [optional]

### Model Architecture and Objective

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### Compute Infrastructure

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#### Hardware

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#### Software

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## Citation [optional]

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**APA:**

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## Glossary [optional]

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## Model Card Authors [optional]

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