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README.md
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license: mit
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# Caelis Neural Base 3 (CNB-3): A Foundational Protein Language Model
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[](https://huggingface.co/
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**Caelis Neural Base 3 (CNB-3)** is a ~950-million parameter autoregressive causal language model pre-trained exclusively on dense evolutionary sequence spaces. Engineered to act as a foundational **"Neural Base"** for biotechnology, CNB-3 functions as a versatile, general-purpose backbone for generating, completing, and optimizing functional proteins *de novo*.
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# Loading CaelisBioTokenizer-2 to train your own models!
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from transformers import AutoTokenizer
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tokenizer = AutoTokenizer.from_pretrained("
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print("Vocabulary size for your new protein model:", len(tokenizer))
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```
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import torch
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from transformers import AutoTokenizer, GPT2LMHeadModel
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repo_id = "
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tokenizer = AutoTokenizer.from_pretrained(repo_id)
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model = GPT2LMHeadModel.from_pretrained(repo_id)
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1. **Strict Length Hard-Capping**: Autoregressive decoding may output whitespace tokens due to native formatting. Always remove whitespaces (`"".join(seq.split())`) and slice the sequence dynamically to match your exact structural budget.
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2. **VRAM Budgeting**: Since ESMFold is resource-intensive, set the chunk size (`esm_folding_model.esm.trunk.set_chunk_size(64)`) to avoid CUDA Out of Memory (OOM) errors on consumer-grade or standard Colab GPUs during verification.
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3. **The Temperature Sweet-Spot**: Use a temperature of `0.7` to balance biochemical feasibility with sequence novelty. Lower values (`< 0.4`) generate highly conserved structures; higher values (`> 1.1`) increase structural entropy (greater risk of non-folding loop accumulation).
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# Caelis Neural Base 3 (CNB-3): A Foundational Protein Language Model
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[](https://huggingface.co/Inserloft/CaeisNeuralBase-3)
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**Caelis Neural Base 3 (CNB-3)** is a ~950-million parameter autoregressive causal language model pre-trained exclusively on dense evolutionary sequence spaces. Engineered to act as a foundational **"Neural Base"** for biotechnology, CNB-3 functions as a versatile, general-purpose backbone for generating, completing, and optimizing functional proteins *de novo*.
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# Loading CaelisBioTokenizer-2 to train your own models!
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from transformers import AutoTokenizer
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tokenizer = AutoTokenizer.from_pretrained("Inserloft/CaeisNeuralBase-3")
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print("Vocabulary size for your new protein model:", len(tokenizer))
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```
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import torch
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from transformers import AutoTokenizer, GPT2LMHeadModel
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repo_id = "Inserloft/CaeisNeuralBase-3"
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tokenizer = AutoTokenizer.from_pretrained(repo_id)
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model = GPT2LMHeadModel.from_pretrained(repo_id)
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1. **Strict Length Hard-Capping**: Autoregressive decoding may output whitespace tokens due to native formatting. Always remove whitespaces (`"".join(seq.split())`) and slice the sequence dynamically to match your exact structural budget.
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2. **VRAM Budgeting**: Since ESMFold is resource-intensive, set the chunk size (`esm_folding_model.esm.trunk.set_chunk_size(64)`) to avoid CUDA Out of Memory (OOM) errors on consumer-grade or standard Colab GPUs during verification.
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3. **The Temperature Sweet-Spot**: Use a temperature of `0.7` to balance biochemical feasibility with sequence novelty. Lower values (`< 0.4`) generate highly conserved structures; higher values (`> 1.1`) increase structural entropy (greater risk of non-folding loop accumulation).
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---
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## 📚 Resources & Community Support
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To facilitate the adoption and specialized fine-tuning of **Caelis Neural Base 3**, we provide the following interactive resources and endpoints:
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* **[Interactive Google Colab Notebook]**: Complete pipeline to generate custom sequences, fold structures local in GPU using ESMFold, analyze residue distributions, and export PDB structures.
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* **[Official Model Hub](https://huggingface.co/Inserloft/CaeisNeuralBase-3)**: Access the base model weights, standard configuration files, and community discussions.
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* **[Developer & Research Center](https://research.inserloft.com)**: Official research workspace and support for production-grade biopolymeric applications.
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