Xia Kelin

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 10 of 10 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...
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-...
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...
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...
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...
Replication Data for: Forman Persistent Ricci Curvature (FPRC) in Protein-Ligand Binding Affinity Predictions Jun 23, 2023 Wee, JunJie; Xia, Kelin, 2023, "Replication Data for: Forman Persistent Ricci Curvature (FPRC) in Protein-Ligand Binding Affinity Predictions", https://doi.org/10.21979/N9/ZTA5MN, 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...
Replication Data for: Multiscale virtual particle based elastic network model (MVP-ENM) for normal mode analysis of large-sized biomolecules 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", https://doi.org/10.21979/N9/FIFOZS, 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...
Replication Data for: Weighted persistent homology for osmolyte molecular aggregation and hydrogen-bonding network analysis 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", https://doi.org/10.21979/N9/IXD1QX, 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...
Replication Data for: Hypergraph based persistent cohomology (HPC) for molecular representations in drug design Apr 6, 2021 Xia, Kelin, 2021, "Replication Data for: Hypergraph based persistent cohomology (HPC) for molecular representations in drug design", https://doi.org/10.21979/N9/16CFBW, 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...
Replication Data for: Ollivier Persistent Ricci Curvature-Based Machine Learning for the Protein–Ligand Binding Affinity Prediction Apr 2, 2021 Xia, Kelin, 2021, "Replication Data for: Ollivier Persistent Ricci Curvature-Based Machine Learning for the Protein–Ligand Binding Affinity Prediction", https://doi.org/10.21979/N9/JHXLSG, 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...

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...

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-...

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...

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...

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...

Replication Data for: Forman Persistent Ricci Curvature (FPRC) in Protein-Ligand Binding Affinity Predictions

Jun 23, 2023

Wee, JunJie; Xia, Kelin, 2023, "Replication Data for: Forman Persistent Ricci Curvature (FPRC) in Protein-Ligand Binding Affinity Predictions", https://doi.org/10.21979/N9/ZTA5MN, 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...

Replication Data for: Multiscale virtual particle based elastic network model (MVP-ENM) for normal mode analysis of large-sized biomolecules

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", https://doi.org/10.21979/N9/FIFOZS, 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...

Replication Data for: Weighted persistent homology for osmolyte molecular aggregation and hydrogen-bonding network analysis

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", https://doi.org/10.21979/N9/IXD1QX, 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...

Replication Data for: Hypergraph based persistent cohomology (HPC) for molecular representations in drug design

Apr 6, 2021

Xia, Kelin, 2021, "Replication Data for: Hypergraph based persistent cohomology (HPC) for molecular representations in drug design", https://doi.org/10.21979/N9/16CFBW, 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...

Replication Data for: Ollivier Persistent Ricci Curvature-Based Machine Learning for the Protein–Ligand Binding Affinity Prediction

Apr 2, 2021

Xia, Kelin, 2021, "Replication Data for: Ollivier Persistent Ricci Curvature-Based Machine Learning for the Protein–Ligand Binding Affinity Prediction", https://doi.org/10.21979/N9/JHXLSG, 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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