|
--- |
|
license: apache-2.0 |
|
--- |
|
|
|
# Model Card for Model ID |
|
|
|
<!-- 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 |
|
|
|
<!-- Provide a longer summary of what this model is. --> |
|
|
|
|
|
|
|
- **Developed by:** [More Information Needed] |
|
- **Funded by [optional]:** [More Information Needed] |
|
- **Shared by [optional]:** [More Information Needed] |
|
- **Model type:** [More Information Needed] |
|
- **Language(s) (NLP):** [More Information Needed] |
|
- **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. --> |
|
|
|
### Direct Use |
|
|
|
<!-- This section is for the model use without fine-tuning or plugging into a larger ecosystem/app. --> |
|
```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' |
|
# |
|
``` |
|
|
|
[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 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] |
