Research
My research develops machine learning and large language model-based methods for biological discovery,
with emphasis on antibody–antigen interaction modeling, antibody design and optimization, and structure-aware
prediction of binding and neutralization. I also build data-efficient and interpretable AI frameworks for biomedical
applications, including antiviral drug screening and medical image analysis.
Full list on Google Scholar.
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Comparative structural analysis of protein complexes with SPICE
Faisal Bin Ashraf, Stefano Lonardi
Nucleic Acids Research, Web Server Issue, 2026
paper
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webapp
End-to-end web platform for comparative structural analysis of protein–protein complexes,
supporting interface characterization, energetic analysis, and variant-level comparison.
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AbAffinity: A Large Language Model for Predicting Antibody Binding Affinity against SARS-CoV-2
Faisal Bin Ashraf, Animesh Ray, Stefano Lonardi
AAAI, FMs4Bio Workshop, 2025
paper
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code
Ab-Affinity, a language model that can accurately predict the binding affinity of antibodies
against a target peptide, e.g., the SARS-CoV-2 spike protein. The model achieved a peak Pearson correlation
coefficient of 0.712 and successfully mapped therapeutic antibody thermostability without explicit training.
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ASPred: Identification of Antigen-Specific B-Cell Receptors from Single V(D)J Sequences Using Large Language Models
Karen Paco, Mariana Paco Mendivil, Zihao Zhang, ..., Faisal Bin Ashraf, ..., Stefano Lonardi, Fernando L. Barroso da Silva, Animesh Ray
Journal of Immunology, 2025 · NeurIPS LXAI Workshop, 2024
paper
LLM-based framework trained on antigen-BCR sequence pairs. Accurately predicts antigen-specific
B-cell receptors from full repertoires, generalizes to unseen antigens, and validates candidates
via molecular dynamics simulations.
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A Large Language Model Guides the Affinity Maturation of Antibodies Generated by Combinatorial Optimization Algorithms
Faisal Bin Ashraf, Karen Paco, Zihao Zhang, Christian J. Dávila Ojeda, Mariana P. Mendivil, Jordan A. Lay, Tristan Y. Yang, Fernando L. Barroso da Silva, Matthew H. Sazinsky, Animesh Ray, Stefano Lonardi
Preprint (bioRxiv) · AAAI FMs4Bio Workshop, 2025
preprint
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code
Ab-Affinity: hybrid LLM-driven antibody design framework integrating genetic algorithms and simulated
annealing to generate novel SARS-CoV-2-targeting antibodies. Achieves >160× binding affinity
improvements over experimental candidates while maintaining strong biophysical stability.
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YoNet: A Neural Network for Yoga Pose Classification
Faisal Bin Ashraf, Muhammad Usama Islam, Md Rayhan Kabir, Jasim Uddin
SN Computer Science, 2023
paper
Data-efficient deep learning architecture for yoga pose recognition capturing spatial and depth features.
Outperforms ResNet, Inception, and Xception; achieves 94.9% accuracy and 95.6% precision.
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