Yogesh-2003/protein-structure-nppe2

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 checkpoint
• bilstm_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() )