Scholars@Duke
Shixin Xu

Shixin Xu

Assistant Professor of Mathematics at Duke Kunshan University
DKU Faculty

Selected Publications

Improving GBDT performance on imbalanced datasets: An empirical study of class-balanced loss functions

Journal Article Neurocomputing · June 14, 2025 Class imbalance poses a persistent challenge in machine learning, particularly for tabular data classification tasks. While Gradient Boosting Decision Trees (GBDT) models are widely regarded as state-of-the-art for these tasks, their effectiveness diminish ... Full text Cite

A multi-domain model for microcirculation in optic nerve: Blood flow and oxygen transport

Journal Article Physica D: Nonlinear Phenomena · November 1, 2024 Microcirculation of blood and transport of oxygen play important roles in the biological function of the optic nerve and its diseases. This work develops a multi-domain model for the optic nerve, that includes important biological structures and various ph ... Full text Cite

NCART: Neural Classification and Regression Tree for tabular data

Journal Article Pattern Recognition · October 1, 2024 Deep learning models have become popular in the analysis of tabular data, as they address the limitations of decision trees and enable valuable applications like semi-supervised learning, online learning, and transfer learning. However, these deep-learning ... Full text Cite

Micro-macro modeling of polymeric fluids and shear-induced microscopic behaviors with bond-breaking

Journal Article Physical Review Fluids · October 1, 2024 This paper explores the micro-macro modeling of polymeric fluids using the proposed microscopic elastic-plastic (EP) potential energy, in order to illustrate the effects of irreversible bond-breaking of microscopic polymer chains. Precisely, we first revis ... Full text Cite

VSG-GAN: A high-fidelity image synthesis method with semantic manipulation in retinal fundus image.

Journal Article Biophysical journal · September 2024 In recent years, advancements in retinal image analysis, driven by machine learning and deep learning techniques, have enhanced disease detection and diagnosis through automated feature extraction. However, challenges persist, including limited data set di ... Full text Cite

Study of impacts of two types of cellular aging on the yeast bud morphogenesis.

Journal Article PLoS computational biology · September 2024 Understanding the mechanisms of the cellular aging processes is crucial for attempting to extend organismal lifespan and for studying age-related degenerative diseases. Yeast cells divide through budding, providing a classical biological model for studying ... Full text Cite

Cellular communication among smooth muscle cells: The role of membrane potential via connexins.

Journal Article Journal of theoretical biology · January 2024 Communication via action potentials among neurons has been extensively studied. However, effective communication without action potentials is ubiquitous in biological systems, yet it has received much less attention in comparison. Multi-cellular communicat ... Full text Open Access Cite

Interaction of Ionic Solution with Permeable Membranes: a Variational Approach

Journal Article Journal of Mathematical Study · January 1, 2024 The movement of ionic solutions is an essential part of biology and technology. Fluidics, from nano-to microfluidics, is a burgeoning area of technology which is all about the movement of ionic solutions, on various scales. Many cells, tissues, and organs ... Full text Cite

Coupled chemical reactions: Effects of electric field, diffusion, and boundary control.

Journal Article Physical review. E · December 2023 Chemical reactions involve the movement of charges, and this paper presents a mathematical model for describing chemical reactions in electrolytes. The model is developed using an energy variational method that aligns with classical thermodynamics principl ... Full text Cite

Mathematical Model for Chemical Reactions in Electrolytes Applied to Cytochrome c Oxidase: An Electro-Osmotic Approach

Journal Article Computation · December 1, 2023 This study introduces a mathematical model for electrolytic chemical reactions, employing an energy variation approach grounded in classical thermodynamics. Our model combines electrostatics and chemical reactions within well-defined energetic and dissipat ... Full text Cite

HOMOGENIZATION THEORY OF ION TRANSPORTATION IN MULTICELLULAR TISSUE

Journal Article Discrete and Continuous Dynamical Systems - Series B · November 1, 2023 The transport of ions in biological tissues plays a crucial role in studying many biological and pathological problems. Certain multi-cellular structures, such as smooth muscles on vessel walls, can be considered as periodic bi-domain structures consisting ... Full text Open Access Cite

TRBoost: a generic gradient boosting machine based on trust-region method

Journal Article Applied Intelligence · November 1, 2023 Gradient Boosting Machines (GBMs) have achieved remarkable success in effectively solving a wide range of problems by leveraging Taylor expansions in functional space. Second-order Taylor-based GBMs, such as XGBoost rooted in Newton’s method, consistently ... Full text Open Access Cite

Assessing the nonlinear association of environmental factors with antibiotic resistance genes (ARGs) in the Yangtze River Mouth, China.

Journal Article Scientific reports · November 2023 The emergence of antibacterial resistance (ABR) is an urgent and complex public health challenge worldwide. Antibiotic resistant genes (ARGs) are considered as a new pollutant by the WHO because of their wide distribution and emerging prevalence. The role ... Full text Open Access Cite

Enhancing Organic Dye Removal with Biopolymeric Ferric Sulfate-Modified Diatomite: Characterization, Adsorption Performance, and Mechanism Insights

Journal Article Science of Advanced Materials · November 1, 2023 Diatomite (DE) is a widely used adsorption material in wastewater treatment due to its cost-effectiveness, high porosity, and stability. To improve its adsorption properties, we synthesized biopolymeric ferric sulfate (BPFS) through biocatalytic ox ... Full text Cite

Diffuse interface model for cell interaction and aggregation with Lennard-Jones type potential

Journal Article Computer Methods in Applied Mechanics and Engineering · October 1, 2023 This study introduces a phase-field model designed to simulate the interaction and aggregation of multicellular systems under flow conditions within a bounded spatial domain. The model incorporates a multi-dimensional Lennard-Jones potential to account for ... Full text Open Access Cite

A bubble model for the gating of Kv channels

Journal Article IMA Journal of Applied Mathematics (Institute of Mathematics and Its Applications) · October 1, 2023 Voltage-gated Kv channels play fundamental roles in many biological processes, such as the generation of the action potential. The gating mechanism of Kv channels is characterized experimentally by single-channel recordings and ensemble properties of the c ... Full text Cite

Droplet dynamics: A phase-field model of mobile charges, polarization, and its leaky dielectric approximation

Journal Article Physics of Fluids · August 1, 2023 This paper presents a Poisson-Nernst-Planck-Navier-Stokes-Cahn-Hillard (PNP-NS-CH) model for an electrically charged droplet suspended in a viscous fluid under an external electric field. Our model incorporates spatial variations in electric permittivity a ... Full text Open Access Cite

Mimicking effects of cholesterol in lipid bilayer membranes by self-assembled amphiphilic block copolymers.

Journal Article Soft matter · July 2023 The effect of cholesterol on biological membranes is important in biochemistry. In this study, a polymer system is used to simulate the consequences of varying cholesterol content in membranes. The system consists of an AB-diblock copolymer, a hydrophilic ... Full text Open Access Cite

Analysis of clinical predictors of kidney diseases in type 2 diabetes patients based on machine learning.

Journal Article International urology and nephrology · March 2023 BackgroundThe heterogeneity of Type 2 Diabetes Mellitus (T2DM) complicated with renal diseases has not been fully understood in clinical practice. The purpose of the study was to propose potential predictive factors to identify diabetic kidney dis ... Full text Open Access Cite

Multi-objective learning and explanation for stroke risk assessment in Shanxi province.

Journal Article Scientific reports · December 2022 Stroke is the leading cause of death in China (Zhou et al. in The Lancet, 2019). A dataset from Shanxi Province is analyzed to predict the risk of patients at four states (low/medium/high/attack) and to estimate transition probabilities between various sta ... Full text Open Access Cite

A phase field model for mass transport with semi-permeable interfaces

Journal Article Journal of Computational Physics · September 1, 2022 In this paper, a thermaldynamical consistent model for mass transfer across permeable moving interfaces is proposed by using the energy variation method. We consider a restricted diffusion problem where the flux across the interface depends on its conducta ... Full text Open Access Cite

A phase field model for compressible immiscible fluids with a new equation of state

Journal Article International Journal of Multiphase Flow · April 1, 2022 In this paper, we propose a new compressible phase field model of two different immiscible fluid components, in which the density of each phase is variable. In order to establish the compressible phase field model, a new P-V-T equation of state is introduc ... Full text Open Access Cite

AN ENERGY STABLE C0 FINITE ELEMENT SCHEME FOR A PHASE-FIELD MODEL OF VESICLE MOTION AND DEFORMATION

Journal Article SIAM Journal on Scientific Computing · January 1, 2022 A thermodynamically consistent phase-field model is introduced for simulating motion and shape transformation of vesicles under flow conditions. In particular, a general slip boundary condition is used to describe the interaction between vesicles and the w ... Full text Open Access Cite

Neural-PDE: a RNN based neural network for solving time dependent PDEs

Journal Article Communications in Information and Systems · January 1, 2022 Partial differential equations (PDEs) play a crucial role in studying a vast number of problems in science and engineering. Numerically solving nonlinear and/or high-dimensional PDEs is frequently a challenging task. Inspired by the traditional finite diff ... Full text Open Access Cite

A Level Set Method for the Simulation of Moving Contact Lines in Three Dimensions

Journal Article Communications in Computational Physics · January 1, 2022 We propose an efficient numerical method for the simulation of the two-phase flows with moving contact lines in three dimensions. The mathematical model consists of the incompressible Navier-Stokes equations for the two immiscible fluids with the standard ... Full text Open Access Cite

A tridomain model for potassium clearance in optic nerve of Necturus.

Journal Article Biophysical journal · August 2021 Complex fluids flow in complex ways in complex structures. Transport of water and various organic and inorganic molecules in the central nervous system are important in a wide range of biological and medical processes. However, the exact driving mechanisms ... Full text Open Access Cite

Predicting the risk of rupture for vertebral aneurysm based on geometric features of blood vessels.

Journal Article Royal Society open science · August 2021 A significant proportion of the adult population worldwide suffers from cerebral aneurysms. If left untreated, aneurysms may rupture and lead to fatal massive internal bleeding. On the other hand, treatment of aneurysms also involve significant risks. It i ... Full text Open Access Cite

Numerical method for parameter inference of systems of nonlinear ordinary differential equations with partial observations.

Journal Article Royal Society open science · July 2021 Parameter inference of dynamical systems is a challenging task faced by many researchers and practitioners across various fields. In many applications, it is common that only limited variables are observable. In this paper, we propose a method for paramete ... Full text Open Access Cite

Optic nerve microcirculation: Fluid flow and electrodiffusion

Journal Article Physics of Fluids · April 1, 2021 Complex fluids flow in complex ways in complex structures. Transport of water and various organic and inorganic molecules in the central nervous system (CNS) are important in a wide range of biological and medical processes [C. Nicholson and S. Hrabětová, ... Full text Open Access Cite

HOMOGENIZATION OF A DISCRETE NETWORK MODEL FOR CHEMICAL VAPOR INFILTRATION PROCESS*

Journal Article Communications in Mathematical Sciences · January 1, 2021 Chemical vapor infiltration (CVI) is an important engineering process for manufacturing composite materials. Reaction-diffusion of the reactant gas and the structure change are two mutual in uence processes. Some works have been done on the multi-scale mod ... Full text Open Access Cite

Analysis of main risk factors causing stroke in Shanxi Province based on machine learning models

Journal Article Informatics in Medicine Unlocked · January 1, 2021 Background: In China, stroke has been the first leading cause of death in recent years. It is a major cause of long-term physical and cognitive impairment, which bring great pressure on the National Public Health System. On the other hand, China is a big c ... Full text Open Access Cite

Modelling the linkage between influenza infection and cardiovascular events via thrombosis.

Journal Article Scientific reports · August 2020 There is a heavy burden associated with influenza including all-cause hospitalization as well as severe cardiovascular and cardiorespiratory events. Influenza associated cardiac events have been linked to multiple biological pathways in a human host. To st ... Full text Open Access Cite

A mathematical model for persistent post-CSD vasoconstriction.

Journal Article PLoS computational biology · July 2020 Cortical spreading depression (CSD) is the propagation of a relatively slow wave in cortical brain tissue that is linked to a number of pathological conditions such as stroke and migraine. Most of the existing literature investigates the dynamics of short ... Full text Open Access Cite

An energy stable C0 finite element scheme for a quasi-incompressible phase-field model of moving contact line with variable density

Journal Article Journal of Computational Physics · March 15, 2020 In this paper, we focus on modeling and simulation of two-phase flow problems with moving contact lines and variable density. A thermodynamically consistent phase-field model with general Navier boundary condition is developed based on the concept of quasi ... Full text Open Access Cite

Effect of heating temperature on oxidation behavior of low density steels with medium manganese content

Journal Article Metallurgical Research & Technology · 2020 The high temperature oxidation behavior of Fe–C (0.22%)–Mn (5.3%)–Al (2.5–3.2%)–Si (2.2%) low density steel was studied in the atmosphere of (2%O2 + Ar) by high temperature oxidation simulation tests. The samples were kept at 9 ... Full text Cite

Behavior of different numerical schemes for random genetic drift

Journal Article BIT Numerical Mathematics · September 1, 2019 In the problem of random genetic drift, the probability density of one gene is governed by a degenerated convection-dominated diffusion equation. Dirac singularities will always be developed at boundary points as time evolves, which is known as the fixatio ... Full text Open Access Cite

A Bidomain Model for Lens Microcirculation.

Journal Article Biophysical journal · March 2019 There exists a large body of research on the lens of the mammalian eye over the past several decades. The objective of this work is to provide a link between the most recent computational models and some of the pioneering work in the 1970s and 80s. We intr ... Full text Open Access Cite

Multi-Scale Models of Deformation of Blood Clots

Conference Biophysical Journal · February 2019 Full text Cite

Numerical method for multi-alleles genetic drift problem

Journal Article SIAM Journal on Numerical Analysis · January 1, 2019 Genetic drift describes random fluctuations in the number of genes variants in a population. One of the most popular models is the Wright-Fisher model. The diffusion limit of this model is a degenerate diffusion-convection equation. Due to the degeneration ... Full text Open Access Cite

Three-phase Model of Visco-elastic Incompressible Fluid Flow and its Computational Implementation.

Journal Article Communications in computational physics · January 2019 Energetic Variational Approach is used to derive a novel thermodynamically consistent three-phase model of a mixture of Newtonian and visco-elastic fluids. The model which automatically satisfies the energy dissipation law and is Galilean invariant, consis ... Full text Open Access Cite

Non-stokes drag coefficient in single-particle electrophoresis: New insights on a classical problem

Journal Article Chinese Physics B · January 1, 2019 We measured the intrinsic electrophoretic drag coefficient of a single charged particle by optically trapping the particle and applying an AC electric field, and found it to be markedly different from that of the Stokes drag. The drag coefficient, along wi ... Full text Open Access Cite

Vertebral artery fusiform aneurysm geometry in predicting rupture risk.

Journal Article Royal Society open science · October 2018 Cerebral aneurysms affect a significant portion of the adult population worldwide. Despite significant progress, the development of robust techniques to evaluate the risk of aneurysm rupture remains a critical challenge. We hypothesize that vertebral arter ... Full text Open Access Cite

Model predictions of deformation, embolization and permeability of partially obstructive blood clots under variable shear flow.

Journal Article Journal of the Royal Society, Interface · November 2017 Thromboembolism, one of the leading causes of morbidity and mortality worldwide, is characterized by formation of obstructive intravascular clots (thrombi) and their mechanical breakage (embolization). A novel two-dimensional multi-phase computational mode ... Full text Open Access Cite

Strong Binding of Platelet Integrin αIIbβ3 to Fibrin Clots: Potential Target to Destabilize Thrombi.

Journal Article Scientific reports · October 2017 The formation of platelet thrombi is determined by the integrin αIIbβ3-mediated interactions of platelets with fibrinogen and fibrin. Blood clotting in vivo is catalyzed by thrombin, which simultaneously induces fibrinogen binding to αIIbβ3 and converts fi ... Full text Open Access Cite

Homogenization for chemical vapor infiltration process

Journal Article Communications in Mathematical Sciences · January 1, 2017 Multi-scale modeling and numerical simulations of the isothermal chemical vapor infiltration (CVI) process for the fabrication of carbon fiber reinforced silicon carbide (C/SiC) composites were presented in [Bai, Yue and Zeng, Commun. Comput. Phys., 7(3):5 ... Full text Open Access Cite

Reinitialization of the Level-Set Function in 3d Simulation of Moving Contact Lines

Journal Article Communications in Computational Physics · November 1, 2016 The level set method is one of the most successful methods for the simulation of multi-phase flows. To keep the level set function close the signed distance function, the level set function is constantly reinitialized by solving a Hamilton-Jacobi type of e ... Full text Open Access Cite

Homogenization: In mathematics or physics?

Journal Article Discrete and Continuous Dynamical Systems - Series S · October 1, 2016 In mathematics, homogenization theory considers the limitations of the sequences of the problems and their solutions when a parameter tends to zero. This parameter is regarded as the ratio of the characteristic size between the micro scale and macro scale. ... Full text Open Access Cite

STEP-NC based reverse engineering of in-process model of NC simulation

Journal Article The International Journal of Advanced Manufacturing Technology · October 2016 Full text Cite

Homogenization of thermal-hydro-mass transfer processes

Journal Article Discrete and Continuous Dynamical Systems - Series S · February 1, 2015 In the repository, multi-physics processes are induced due to the long-time heat-emitting from the nuclear waste, which is modeled as a nonlinear system with oscillating coefficients. In this paper we first derive the homogenized system for the thermal-hyd ... Full text Open Access Cite

Derivation of a continuum model and the energy law for moving contact lines with insoluble surfactants

Journal Article Physics of Fluids · June 5, 2014 A continuous model is derived for the dynamics of two immiscible fluids with moving contact lines and insoluble surfactants based on thermodynamic principles. The continuum model consists of the Navier-Stokes equations for the dynamics of the two fluids an ... Full text Open Access Cite

An energetic variational approach for ION transport

Journal Article Communications in Mathematical Sciences · March 6, 2014 The transport and distribution of charged particles are crucial in the study of many physical and biological problems. In this paper, we employ an Energy Variational Approach to derive the coupled Poisson-Nernst-Planck-Navier-Stokes system. All of the phys ... Full text Open Access Cite

Self-consistent approach to global charge neutrality in electrokinetics: A surface potential trap model

Journal Article Physical Review X · January 1, 2014 In this work, we treat the Poisson-Nernst-Planck (PNP) equations as the basis for a consistent framework of the electrokinetic effects. The static limit of the PNP equations is shown to be the charge-conserving Poisson-Boltzmann (CCPB) equation, with guara ... Full text Open Access Cite

Modeling and Simulating Asymmetrical Conductance Changes in Gramicidin Pores

Journal Article Computational and Mathematical Biophysics · January 1, 2014 Gramicidin A is a small and well characterized peptide that forms an ion channel in lipid membranes. An important feature of gramicidin A (gA) pore is that its conductance is affected by the electric charges near the its entrance. This property has led to ... Full text Open Access Cite

The Uncut Lawn Cognition Algorithm Based on Image Analysis

Conference 2014 11TH WORLD CONGRESS ON INTELLIGENT CONTROL AND AUTOMATION (WCICA) · 2014 Cite