lucagplm 1.1.3

LucaGPLM - The LUCA general purpose language model.

LucaGPLM

LucaGPLM - The LUCA general purpose language model.

Installation

You can install the package from source using pip:

pip install .

Usage

Basic Model Usage

from lucagplm import LucaGPLMModel, LucaGPLMTokenizer

# Load model
model = LucaGPLMModel.from_pretrained("Yuanfei/lucavirus-large-step3.8M")
tokenizer = LucaGPLMTokenizer.from_pretrained("Yuanfei/lucavirus-large-step3.8M")

# Example usage
seq = "ATCG"
inputs = tokenizer(seq, seq_type="gene",return_tensors="pt")
outputs = model(**inputs)

seq = "NSQTA"
inputs = tokenizer(seq, seq_type="prot",return_tensors="pt")
outputs = model(**inputs)

print(outputs.last_hidden_state.shape)

Pretraining Model Usage

The package also includes a pretraining model with multiple pretraining heads for different tasks:

from lucagplm import LucaGPLMForPretraining, LucaGPLMTokenizer

# Load pretraining model
model = LucaGPLMForPretraining.from_pretrained("path/to/pretraining/model")
tokenizer = LucaGPLMTokenizer.from_pretrained("path/to/pretraining/model")

# Example usage with pretraining tasks
seq = "ATCGATCGATCG"
inputs = tokenizer(seq, seq_type="gene", return_tensors="pt")

# Forward pass with pretraining heads
outputs = model(**inputs)

# Access logits for different pretraining tasks
print("Available task logits:", list(outputs['logits'].keys()))

# Token-level tasks (e.g., masked language modeling)
if 'token_level' in outputs['logits']:
    for task_name, logits in outputs['logits']['token_level'].items():
        print(f"Token-level task '{task_name}' logits shape:", logits.shape)

# Span-level tasks
if 'span_level' in outputs['logits']:
    for task_name, logits in outputs['logits']['span_level'].items():
        print(f"Span-level task '{task_name}' logits shape:", logits.shape)

# Sequence-level tasks
if 'seq_level' in outputs['logits']:
    for task_name, logits in outputs['logits']['seq_level'].items():
        print(f"Sequence-level task '{task_name}' logits shape:", logits.shape)

Converting Old Models

The package includes a utility script to convert old LucaOneVirus checkpoints to the new LucaGPLM format:

Using the command-line tool:

# Convert without pretraining heads
lucagplm-convert --old-checkpoint /path/to/old/checkpoint --output-dir /path/to/new/model

# Convert with pretraining heads
lucagplm-convert --old-checkpoint /path/to/old/checkpoint --output-dir /path/to/new/model --with-pretraining-heads

Using the Python API:

from lucagplm.convert_model import convert_old_weights

# Convert without pretraining heads
convert_old_weights(
    old_checkpoint_path="/path/to/old/checkpoint",
    output_dir="/path/to/new/model",
    with_pretraining_heads=False
)

# Convert with pretraining heads
convert_old_weights(
    old_checkpoint_path="/path/to/old/checkpoint",
    output_dir="/path/to/new/model",
    with_pretraining_heads=True
)

Pretraining Tasks

The LucaGPLMForPretraining model includes multiple pretraining tasks organized into three levels:

1. Token-level tasks: Tasks that operate on individual tokens

   • mlm: Masked Language Modeling
   • erc: Entity Recognition and Classification
   • pos: Part-of-Speech tagging

2. Span-level tasks: Tasks that operate on spans of tokens

   • ner: Named Entity Recognition
   • sbo: Span Boundary Optimization
   • spr: Span Prediction and Recovery

3. Sequence-level tasks: Tasks that operate on entire sequences

   • cls: Sequence Classification
   • sim: Sequence Similarity
   • gen: Sequence Generation

Each task has its own prediction head (classifier) that can be fine-tuned for specific downstream applications.