Protein2Text: Resampling Mechanism to Translate Protein Sequences into Human-Interpretable Text

[NAACL 2025]

• Base Model: meta-llama/Meta-Llama-3.1-8B-Instruct
• Base Protein Encoder: facebook/esm2_t33_650M_UR50D
• Library: PEFT

Model Details

Model Description

The Protein2Text model is a multimodal transformer-based model designed to generate human-interpretable text from protein sequences. It combines a protein sequence encoder (ESM2) and a large language model (LLaMA 3.1-8B Instruct), leveraging resampling mechanisms to improve text generation. The model was trained and fine-tuned on the Protein2Text-QA dataset, which contains question-answer (QA) pairs generated from biomedical literature.

• Developed by: TumorAI Lab
• Model Type: Multimodal Instruction-Tuned Transformer
• Language(s) (NLP): English (Biomedical Domain)
• License: Apache 2.0
• Finetuned from model: meta-llama/Meta-Llama-3.1-8B-Instruct

Model Sources

• Repository: GitHub Repository
• Paper: [More Information Needed]
• Demo: [More Information Needed]

Uses

Direct Use

• Generating textual descriptions of protein functions from protein sequences.
• Biomedical research and explainable AI applications in genomics and proteomics.

Downstream Use

• Can be fine-tuned for specific protein annotation tasks.
• Can be adapted for biomedical question-answering related to proteins.

Out-of-Scope Use

• Not designed for general NLP tasks outside of biomedical research.
• Should not be used for clinical decision-making without expert validation.

Bias, Risks, and Limitations

• The model relies on automatically generated QA pairs, which may introduce hallucinated or inaccurate information.
• Some rare proteins may not have sufficient training data, leading to unreliable outputs.
• Always verify outputs with domain experts.
• Further fine-tuning may be required for specific biomedical applications.

Training Details

Training Data

The model was fine-tuned on the Protein2Text-QA dataset, which includes:

• Protein-related abstracts retrieved from PubMed Central (PMC).
• QA pairs generated using LLaMA3, conditioned on specific protein mentions.

Training Procedure

Preprocessing

• Abstract cleaning: Removal of redundant sections (e.g., "Methods", "Conclusion").
• QA filtering: Removing phrases like "no information found".

Training Hyperparameters

Evaluation

Metrics

• BLEU-2, BLEU-4 (for text quality).
• ROUGE-1, ROUGE-2, ROUGE-L (for relevance).
• METEOR (for fluency).

Model Examination

• Hardware Used: 2 × NVIDIA H100 PCIe 82GB
• Training Hours: 12-15 hours

Citation

BibTeX:

@inproceedings{jararweh2025protein2text,
  title={Protein2Text: Resampling Mechanism to Translate Protein Sequences into Human-Interpretable Text},
  author={Jararweh, Ala and Macaulay, Oladimeji and Arredondo, David and Hu, Yue and Tafoya, Luis E and Virupakshappa, Kushal and Sahu, Avinash},
  booktitle={Proceedings of the 2025 Conference of the Nations of the Americas Chapter of the Association for Computational Linguistics: Human Language Technologies (Volume 3: Industry Track)},
  pages={918--937},
  year={2025}
}