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protein-structure-nppe2
Yogesh-2003/protein-structure-nppe2
protein-structure-nppe2 is a machine learning model from Yogesh-2003. Use it for the machine learning task on the model card, and read the license before you ship it in a product. It is set up for pytorch. The card lists the license as apache-2.0.
BiRNN and BiLSTM models for predicting Q8 (8-state) and Q3 (3-state) protein secondary structures.
Access
Public
Updated Dec 16, 2025
Repo size
64.3 MB
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0
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Repo makeup
Click a slice to open those files.
.ckpt35.8 MB · 100%
At a glance
- Library
- pytorch
- License
- apache-2.0
- Access
- Public
- Created
- Dec 16, 2025
- Updated
- Dec 16, 2025
- SHA
- 0410e15f
Datasets
Model card
From the Hugging Face model README
Protein Secondary Structure Prediction Models
BiRNN and BiLSTM models for predicting Q8 (8-state) and Q3 (3-state) protein secondary structures.
Model Performance
| Model | Val F1 Q8 | Val F1 Q3 | Harmonic F1 |
|---|---|---|---|
| BiRNN | 0.547 | 0.700 | 0.6222 |
| BiLSTM | 0.570 | 0.718 | 0.6352 |
Model Architecture
BiRNN
- Embedding: 128-dim
- Bidirectional RNN: 2 layers, hidden_dim=256
- Dropout: 0.3
- Parameters: 601K
BiLSTM
- Embedding: 128-dim
- Bidirectional LSTM: 2 layers, hidden_dim=256
- Dropout: 0.3
- Parameters: 2.4M
Files
birnn_best.ckpt: BiRNN checkpointbilstm_best.ckpt: BiLSTM checkpoint
Usage
import torch import pytorch_lightning as pl from huggingface_hub import hf_hub_download
Download checkpoint checkpoint_path = hf_hub_download( repo_id="yogesh-2003/protein-structure-nppe2", filename="bilstm_best.ckpt" )
Load model (requires ProteinStructurePredictor and BiLSTM classes) model = ProteinStructurePredictor.load_from_checkpoint( checkpoint_path, model=BiLSTM() )
- Library
- pytorch
- License
- apache-2.0
- Created
- Dec 16, 2025
- Updated
- Dec 16, 2025