HoarfrostLab/LGv1_OptimalTempClassifier

LookingGlass Optimal Temperature Classifier

Identifies whether a DNA read originates from an enzyme with a psychrophilic (<15°C), mesophilic (20-40°C), or thermophilic (>50°C) optimal temperature with 70.1% accuracy.

This is a pure PyTorch implementation fine-tuned from the LookingGlass base model.

Links

• Paper: Deep learning of a bacterial and archaeal universal language of life enables transfer learning and illuminates microbial dark matter (Nature Communications, 2022)
• GitHub: ahoarfrost/LookingGlass
• Base Model: HoarfrostLab/lookingglass-v1

Citation

@article{hoarfrost2022deep,
  title={Deep learning of a bacterial and archaeal universal language of life
         enables transfer learning and illuminates microbial dark matter},
  author={Hoarfrost, Adrienne and Aptekmann, Ariel and Farfanuk, Gaetan and Bromberg, Yana},
  journal={Nature Communications},
  volume={13},
  number={1},
  pages={2606},
  year={2022},
  publisher={Nature Publishing Group}
}

Model

Architecture	LookingGlass encoder + classification head
Encoder	AWD-LSTM (3-layer, unidirectional)
Classes	3 classes: psychrophilic, mesophilic, thermophilic
Parameters	~17M

Installation

pip install torch
git clone https://huggingface.co/HoarfrostLab/LGv1_OptimalTempClassifier
cd LGv1_OptimalTempClassifier

Usage

from lookingglass_classifier import LookingGlassClassifier, LookingGlassTokenizer

model = LookingGlassClassifier.from_pretrained('.')
tokenizer = LookingGlassTokenizer()
model.eval()

inputs = tokenizer(["GATTACA", "ATCGATCGATCG"], return_tensors=True)

# Get predictions
predictions = model.predict(inputs['input_ids'])
print(predictions)  # tensor([class_idx, class_idx])

# Get probabilities
probs = model.predict_proba(inputs['input_ids'])
print(probs.shape)  # torch.Size([2, 3])

# Get raw logits
logits = model(inputs['input_ids'])
print(logits.shape)  # torch.Size([2, 3])

License

MIT License