README.md

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# nuTCRacker model (pre-trained)

<!-- Provide a quick summary of what the model is/does. -->

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
The model is a pre-trained model.This model can be used for finetuning a sequence classificatin model for a binary classification task of predicting 
paired TCR-petide-HLA-I binding based on amino acid sequence inputs. It is a transformer model that is built on DeBERTa architecture.
<!-- Provide a longer summary of what this model is. -->



- **Developed by:** Justin Barton and Trupti Gore
- **Funded by [optional]:** [More Information Needed]
- **Shared by [optional]:** [More Information Needed]
- **Model type:** DeBERTa Transformer
- **Language(s) (NLP):** Python
- **License:** [More Information Needed]
- **Finetuned from model [optional]:** [More Information Needed]

### Model Sources [optional]

<!-- Provide the basic links for the model. -->

- **Repository:** [More Information Needed]
- **Paper [optional]:** [More Information Needed]
- **Demo [optional]:** [More Information Needed]

## Uses

<!-- Address questions around how the model is intended to be used, including the foreseeable users of the model and those affected by the model. -->

### How to Use 
```
from transformers import (DebertaForSequenceClassification,DebertaTokenizerFast)
model = DebertaForSequenceClassification.from_pretrained(f'shepherdgroup/nuTCRacker', num_labels=2)
tokenizer=DebertaTokenizerFast.from_pretrained('shepherdgroup/nuTCRacker')
example="'[cdra1]SSVPPY[cdra2]YTSAATLV[cdra3]CAVSAGDYKLSF[cdrb1]KGHDR[cdrb2]SFDVKD[cdrb3]CATSDSVAGNQPQHF','[peptide]ATDALMTGF[mhc]YFAMYQENMAHTDANTLYIIYRDYTWVARVYRGY'"
encoded_example=tokenizer(example,return_tensors='pt')
output=model(**encoded_example)
output

```

<!-- This section is for the model use without fine-tuning or plugging into a larger ecosystem/app. -->

[More Information Needed]

### Downstream Use [optional]

<!-- This section is for the model use when fine-tuned for a task, or when plugged into a larger ecosystem/app -->

[More Information Needed]

### Out-of-Scope Use

<!-- This section addresses misuse, malicious use, and uses that the model will not work well for. -->

[More Information Needed]

## Bias, Risks, and Limitations

<!-- This section is meant to convey both technical and sociotechnical limitations. -->

[More Information Needed]

### Recommendations

<!-- This section is meant to convey recommendations with respect to the bias, risk, and technical limitations. -->

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.

[More Information Needed]

## Training Details

## Training hyperparameters
```
vocab_size=len(tokenizer),
    num_attention_heads=8,
    num_hidden_layers=16,
    hidden_size=512,
    intermediate_size=2048,
    hidden_act='gelu',
    hidden_dropout_prob=0.15,
    relative_attention=True,
    pos_att_type='c2p|p2c',
    max_relative_positions=-1,
    position_biased_input=False,
    attention_probs_dropout_prob=0.15,
    initializer_range=0.02,
    layer_norm_eps=1e-7,
    
````

### Training Data

<!-- This should link to a Dataset Card, perhaps with a short stub of information on what the training data is all about as well as documentation related to data pre-processing or additional filtering. -->

[More Information Needed]

### Training Procedure

<!-- This relates heavily to the Technical Specifications. Content here should link to that section when it is relevant to the training procedure. -->

#### Preprocessing [optional]

[More Information Needed]


#### Training Hyperparameters

- **Training regime:** [More Information Needed] <!--fp32, fp16 mixed precision, bf16 mixed precision, bf16 non-mixed precision, fp16 non-mixed precision, fp8 mixed precision -->

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

<!-- This section provides information about throughput, start/end time, checkpoint size if relevant, etc. -->

[More Information Needed]

## Evaluation

<!-- This section describes the evaluation protocols and provides the results. -->

### Testing Data, Factors & Metrics

#### Testing Data

<!-- This should link to a Dataset Card if possible. -->

[More Information Needed]

#### Factors

<!-- These are the things the evaluation is disaggregating by, e.g., subpopulations or domains. -->

[More Information Needed]

#### Metrics

<!-- These are the evaluation metrics being used, ideally with a description of why. -->

[More Information Needed]

### Results

[More Information Needed]

#### Summary



## Model Examination [optional]

<!-- Relevant interpretability work for the model goes here -->

[More Information Needed]

## Environmental Impact

<!-- Total emissions (in grams of CO2eq) and additional considerations, such as electricity usage, go here. Edit the suggested text below accordingly -->

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]
- **Hours used:** [More Information Needed]
- **Cloud Provider:** [More Information Needed]
- **Compute Region:** [More Information Needed]
- **Carbon Emitted:** [More Information Needed]

## Technical Specifications [optional]

### Model Architecture and Objective

[More Information Needed]

### Compute Infrastructure

[More Information Needed]

#### Hardware

[More Information Needed]

#### Software

[More Information Needed]

## Citation [optional]

<!-- If there is a paper or blog post introducing the model, the APA and Bibtex information for that should go in this section. -->

**BibTeX:**

[More Information Needed]

**APA:**

[More Information Needed]

## Glossary [optional]

<!-- If relevant, include terms and calculations in this section that can help readers understand the model or model card. -->

[More Information Needed]

## More Information [optional]

[More Information Needed]

## Model Card Authors [optional]

[More Information Needed]

## Model Card Contact

[More Information Needed]