Appointment: Associate Professor

Research topics:

• To use computational tools from PDE, differential geometry, algebraic topology and statistical learning to study the biomolecular structure, flexibility, dynamics, and functions.
• Topological data analysis (TDA), topology based machine learning/deep learning models, and their applications in drug design.

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1 to 10 of 69 Results
Replication Data for: Weighted persistent homology for biomolecular data analysis
Nov 8, 2023
Meng, Zhenyu; Anand, D Vijay; Lu, Yunpeng; Wu, Jie; Xia, Kelin, 2023, "Replication Data for: Weighted persistent homology for biomolecular data analysis", https://doi.org/10.21979/N9/4II1CF, DR-NTU (Data), V1
In this paper, we systematically review weighted persistent homology (WPH) models and their applications in biomolecular data analysis. Essentially, the weight value, which reflects physical, chemical and biological properties, can be assigned to vertices (atom centers), edges (b...
WPH_code.rar
Nov 8, 2023 - Replication Data for: Weighted persistent homology for biomolecular data analysis
RAR Archive - 366.7 KB - MD5: cafb2955290898f9377fcea9eb8428a9
Data and codes to generate LWPH based features for A-, B-, and Z-types of DNA
Replication Data for: Fingerprint-Enhanced Graph Attention Network (FinGAT) Model for Antibiotic Discovery
Jun 23, 2023
Choo, Hou Yee; Wee, JunJie; Shen, Cong; Xia, Kelin, 2023, "Replication Data for: Fingerprint-Enhanced Graph Attention Network (FinGAT) Model for Antibiotic Discovery", https://doi.org/10.21979/N9/FGKV7S, DR-NTU (Data), V1
Artificial Intelligence (AI) techniques are of great potential to fundamentally change antibiotic discovery industries. Efficient and effective molecular featurization is key to all highly accurate learning models for antibiotic discovery. In this paper, we propose a fingerprint-...
FinGAT.rar
Jun 23, 2023 - Replication Data for: Fingerprint-Enhanced Graph Attention Network (FinGAT) Model for Antibiotic Discovery
RAR Archive - 1.6 MB - MD5: 6b43a647395d45a8ab13ab6b9695d9d9
Replication Data for: Persistent spectral simplicial complex-based machine learning for chromosomal structural analysis in cellular differentiation
Jun 23, 2023
Gong, Weikang; Wee, JunJie; Wu, Min-Chun; Sun, Xiaohan; Li, Chunhua; Xia, Kelin, 2023, "Replication Data for: Persistent spectral simplicial complex-based machine learning for chromosomal structural analysis in cellular differentiation", https://doi.org/10.21979/N9/SBFIZD, DR-NTU (Data), V1
The three-dimensional (3D) chromosomal structure plays an essential role in all DNA-templated processes, including gene transcription, DNA replication and other cellular processes. Although developing chromosome conformation capture (3C) methods, such as Hi-C, which can generate...
PerSpectSC-ML.rar
Jun 23, 2023 - Replication Data for: Persistent spectral simplicial complex-based machine learning for chromosomal structural analysis in cellular differentiation
RAR Archive - 424.4 KB - MD5: 3b3eb2438b59f23819f5a285673f3926
Replication Data for: Hodge theory-based biomolecular data analysis
Jun 23, 2023
Wei, Ronald Koh Joon; Wee, JunJie; Laurent, Valerie Evangelin; Xia, Kelin, 2023, "Replication Data for: Hodge theory-based biomolecular data analysis", https://doi.org/10.21979/N9/0TK4YR, DR-NTU (Data), V1
Hodge theory reveals the deep intrinsic relations of differential forms and provides a bridge between differential geometry, algebraic topology, and functional analysis. Here we use Hodge Laplacian and Hodge decomposition models to analyze biomolecular structures. Different from...
Hodge-Theory-main.rar
Jun 23, 2023 - Replication Data for: Hodge theory-based biomolecular data analysis
RAR Archive - 7.5 MB - MD5: 6e2cf9d3d584e810b17b0a0be1a5183f
Replication Data for: Persistent spectral based ensemble learning (PerSpect-EL) for protein-protein binding affinity prediction
Jun 23, 2023
Wee, JunJie; Xia, Kelin, 2023, "Replication Data for: Persistent spectral based ensemble learning (PerSpect-EL) for protein-protein binding affinity prediction", https://doi.org/10.21979/N9/MEDJN1, DR-NTU (Data), V1
Protein–protein interactions (PPIs) play a significant role in nearly all cellular and biological activities. Data-driven machine learning models have demonstrated great power in PPIs. However, the design of efficient molecular featurization poses a great challenge for all learni...
PerSpect-Ensemble-Learning.rar
Jun 23, 2023 - Replication Data for: Persistent spectral based ensemble learning (PerSpect-EL) for protein-protein binding affinity prediction
RAR Archive - 11.7 MB - MD5: 3201186202272ef8fb129c2780986f5a
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