InstaDeepAI/ntv3_base_model

Unified base model repository for NTv3 models.

This repository contains shared modeling code used by both:

• Pre-trained models (masked language models)
• Post-trained models (conditioned multi-species models with functional genomics heads)

Note: This repo should not be used standalone. It provides modeling code that is referenced by individual model checkpoints via trust_remote_code=True.

Contents

File	Purpose
configuration_ntv3_pretrained.py	Config class: Ntv3PreTrainedConfig
configuration_ntv3_posttrained.py	Config classes: DiscreteConditionedNTv3Config, NTv3PostTrainedConfig
modeling_ntv3_pretrained.py	Pre-trained model: NTv3PreTrained
modeling_ntv3_posttrained.py	Post-trained model: NTv3PostTrained with conditioned towers and heads
tokenization_ntv3.py	Tokenizer: NTv3Tokenizer (DNA)

Architecture

• U-Net style conv tower → Transformer stack → deconv tower → LM head
• Post-trained models add adaptive layer norms and multi-species prediction heads
• Tokenizer: character-level over A T C G N + specials (<unk> <pad> <mask> <cls> <eos> <bos>)