Appointment: Assistant 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 9 of 9 Results
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",, 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-...
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",, 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...
Jun 23, 2023
Wei, Ronald Koh Joon; Wee, JunJie; Laurent, Valerie Evangelin; Xia, Kelin, 2023, "Replication Data for: Hodge theory-based biomolecular data analysis",, 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...
Jun 23, 2023
Wee, JunJie; Xia, Kelin, 2023, "Replication Data for: Persistent spectral based ensemble learning (PerSpect-EL) for protein-protein binding affinity prediction",, 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...
Jun 23, 2023
Wee, JunJie; Xia, Kelin, 2023, "Replication Data for: Forman Persistent Ricci Curvature (FPRC) in Protein-Ligand Binding Affinity Predictions",, DR-NTU (Data), V1
Artificial intelligence (AI) techniques have already been gradually applied to the entire drug design process, from target discovery, lead discovery, lead optimization and preclinical development to the final three phases of clinical trials. Currently, one of the central challeng...
Jun 12, 2023
Xia, Kelin, 2023, "Replication Data for: Multiscale virtual particle based elastic network model (MVP-ENM) for normal mode analysis of large-sized biomolecules",, DR-NTU (Data), V1
In this paper, a multiscale virtual particle based elastic network model (MVP-ENM) is proposed for the normal mode analysis of large-sized biomolecules. The multiscale virtual particle (MVP) model is proposed for the discretization of biomolecular density data. With this model, l...
Jun 12, 2023
Anand, D Vijay; Meng, Zhenyu; Xia, Kelin; Mu, Yuguang, 2023, "Replication Data for: Weighted persistent homology for osmolyte molecular aggregation and hydrogen-bonding network analysis",, DR-NTU (Data), V1
It has long been observed that trimethylamine N-oxide (TMAO) and urea demonstrate dramatically different properties in a protein folding process. Even with the enormous theoretical and experimental research work on these two osmolytes, various aspects of their underlying mechanis...
Apr 6, 2021
Xia, Kelin, 2021, "Replication Data for: Hypergraph based persistent cohomology (HPC) for molecular representations in drug design",, DR-NTU (Data), V2
Artificial intelligence (AI) based drug design has demonstrated great potential to fundamentally change the pharmaceutical industries. Currently, a key issue in AI-based drug design is efficient transferable molecular descriptors or fingerprints. Here, we present hypergraph-based...
Apr 2, 2021
Xia, Kelin, 2021, "Replication Data for: Ollivier Persistent Ricci Curvature-Based Machine Learning for the Protein–Ligand Binding Affinity Prediction",, DR-NTU (Data), V1
Efficient molecular featurization is one of the major issues for machine learning models in drug design. Here, we propose a persistent Ricci curvature (PRC), in particular, Ollivier PRC (OPRC), for the molecular featurization and feature engineering, for the first time. The filtr...
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