Llama-Affinity: A Predictive Antibody Antigen Binding Model Integrating Antibody Sequences with Llama3 Backbone Architecture
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arXiv
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| Format: | Preprint |
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2025
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| _version_ | 1866912422765264896 |
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| author | Hossain, Delower Saghapour, Ehsan Song, Kevin Chen, Jake Y. |
| author_facet | Hossain, Delower Saghapour, Ehsan Song, Kevin Chen, Jake Y. |
| contents | Antibody-facilitated immune responses are central to the body's defense against pathogens, viruses, and other foreign invaders. The ability of antibodies to specifically bind and neutralize antigens is vital for maintaining immunity. Over the past few decades, bioengineering advancements have significantly accelerated therapeutic antibody development. These antibody-derived drugs have shown remarkable efficacy, particularly in treating cancer, SARS-CoV-2, autoimmune disorders, and infectious diseases. Traditionally, experimental methods for affinity measurement have been time-consuming and expensive. With the advent of artificial intelligence, in silico medicine has been revolutionized; recent developments in machine learning, particularly the use of large language models (LLMs) for representing antibodies, have opened up new avenues for AI-based design and improved affinity prediction. Herein, we present an advanced antibody-antigen binding affinity prediction model (LlamaAffinity), leveraging an open-source Llama 3 backbone and antibody sequence data sourced from the Observed Antibody Space (OAS) database. The proposed approach shows significant improvement over existing state-of-the-art (SOTA) methods (AntiFormer, AntiBERTa, AntiBERTy) across multiple evaluation metrics. Specifically, the model achieved an accuracy of 0.9640, an F1-score of 0.9643, a precision of 0.9702, a recall of 0.9586, and an AUC-ROC of 0.9936. Moreover, this strategy unveiled higher computational efficiency, with a five-fold average cumulative training time of only 0.46 hours, significantly lower than in previous studies. |
| format | Preprint |
| id |
arxiv_https___arxiv_org_abs_2506_09052 |
| institution | arXiv |
| publishDate | 2025 |
| record_format | arxiv |
| spellingShingle | Llama-Affinity: A Predictive Antibody Antigen Binding Model Integrating Antibody Sequences with Llama3 Backbone Architecture Hossain, Delower Saghapour, Ehsan Song, Kevin Chen, Jake Y. Machine Learning Artificial Intelligence Quantitative Methods Antibody-facilitated immune responses are central to the body's defense against pathogens, viruses, and other foreign invaders. The ability of antibodies to specifically bind and neutralize antigens is vital for maintaining immunity. Over the past few decades, bioengineering advancements have significantly accelerated therapeutic antibody development. These antibody-derived drugs have shown remarkable efficacy, particularly in treating cancer, SARS-CoV-2, autoimmune disorders, and infectious diseases. Traditionally, experimental methods for affinity measurement have been time-consuming and expensive. With the advent of artificial intelligence, in silico medicine has been revolutionized; recent developments in machine learning, particularly the use of large language models (LLMs) for representing antibodies, have opened up new avenues for AI-based design and improved affinity prediction. Herein, we present an advanced antibody-antigen binding affinity prediction model (LlamaAffinity), leveraging an open-source Llama 3 backbone and antibody sequence data sourced from the Observed Antibody Space (OAS) database. The proposed approach shows significant improvement over existing state-of-the-art (SOTA) methods (AntiFormer, AntiBERTa, AntiBERTy) across multiple evaluation metrics. Specifically, the model achieved an accuracy of 0.9640, an F1-score of 0.9643, a precision of 0.9702, a recall of 0.9586, and an AUC-ROC of 0.9936. Moreover, this strategy unveiled higher computational efficiency, with a five-fold average cumulative training time of only 0.46 hours, significantly lower than in previous studies. |
| title | Llama-Affinity: A Predictive Antibody Antigen Binding Model Integrating Antibody Sequences with Llama3 Backbone Architecture |
| topic | Machine Learning Artificial Intelligence Quantitative Methods |
| url | https://arxiv.org/abs/2506.09052 |