ArticleComputers in biology and medicine2023
Topological deep learning based deep mutational scanning.
Article in Computers in biology and medicine, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers.
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Who cites it
16 citing papers in PubMed.
- Article
- Machine Learning-Driven Simulations of the SARS-CoV-2 Fitness Landscape from Deep Mutational Scanning Experiments.Journal of chemical information and modeling · 2026Article
- Topological data analysis and topological deep learning beyond persistent homology: a review.Artificial intelligence review · 2026Article
- Interpretability and Representability of Commutative Algebra, Algebraic Topology, and Topological Spectral Theory for Real-World Data.Advanced intelligent discovery · 2025Article
- A Review of Topological Data Analysis and Topological Deep Learning in Molecular Sciences.Journal of chemical information and modeling · 2025Review
- Article
- Deep-learning structure elucidation from single-mutant deep mutational scanning.Nature communications · 2025Article
- Novel Antimicrobials from Computational Modelling and Drug Repositioning: PotentialMolecules (Basel, Switzerland) · 2025Review
- Decoding the functional impact of the cancer genome through protein-protein interactions.Nature reviews. Cancer · 2025Review
- Persistent Topological Laplacians-A Survey.Mathematics (Basel, Switzerland) · 2025Article
- Rapid response to fast viral evolution using AlphaFold 3-assisted topological deep learning.Virus evolution · 2025Article
- Determining key residues of engineered scFv antibody variants with improved MMP-9 binding using deep sequencing and machine learning.Computational and structural biotechnology journal · 2024Article
- Rapid response to fast viral evolution using AlphaFold 3-assisted topological deep learning.ArXiv · 2024Article
- Preventing future zoonosis: SARS-CoV-2 mutations enhance human-animal cross-transmission.Computers in biology and medicine · 2024Article
- Evaluation of AlphaFold 3's Protein-Protein Complexes for Predicting Binding Free Energy Changes upon Mutation.Journal of chemical information and modeling · 2024Article
- Position: Topological Deep Learning is the New Frontier for Relational Learning.Proceedings of machine learning research · 2024Article
Corrections and comments
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Authors and funding
5 authors.
Funding
Abstract
High-throughput deep mutational scanning (DMS) experiments have significantly impacted protein engineering, drug discovery, immunology, cancer biology, and evolutionary biology by enabling the systematic understanding of protein functions. However, the mutational space associated with proteins is astronomically large, making it overwhelming for current experimental capabilities. Therefore, alternative methods for DMS are imperative. We propose a topological deep learning (TDL) paradigm to facilitate in silico DMS. We utilize a new topological data analysis (TDA) technique based on the persistent spectral theory, also known as persistent Laplacian, to capture both topological invariants and the homotopic shape evolution of data. To validate our TDL-DMS model, we use SARS-CoV-2 datasets and show excellent accuracy and reliability for binding interface mutations. This finding is significant for SARS-CoV-2 variant forecasting and designing effective antibodies and vaccines. Our proposed model is expected to have a significant impact on drug discovery, vaccine design, precision medicine, and protein engineering.
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Registered trials
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