Zhong Li

• Curtin Singapore

Background/Objectives: RNA research is critical for understanding gene regulation, disease mechanisms, and therapeutic development. Constructing effective RNA benchmark models for accurate downstream analysis has become a significant research challenge. The objective of this study is to propose a robust benchmark model, DRFormer, for RNA sequence d...

Traditional Chinese Medicine (TCM) prescriptions are derived from the distinctive thought process and clinical experiences of Chinese medical theory. With the advent of artificial intelligence (AI), there is an enhanced ability to formulate these prescriptions by analyzing symptom data. However, the inherent sparseness of herb-symptom association d...

Introduction The evolution of SARS-CoV-2 has precipitated the emergence of new mutant strains, some exhibiting enhanced transmissibility and immune evasion capabilities, thus escalating the infection risk and diminishing vaccine efficacy. Given the continuous impact of SARS-CoV-2 mutations on global public health, the economy, and society, a profou...

PI3K (phosphatidylinositol 3-kinase) is an intracellular phosphatidylinositol kinase composed of a regulatory subunit, p85, and a catalytic subunit, p110. Based on the different structures of the p110 catalytic subunit, PI3K can be divided into four isoforms: PI3Kα, PI3Kβ, PI3Kγ, and PI3Kδ. As molecularly targeted drugs, PI3K inhibitors have demons...

Deep learning methods have significantly advanced medical image segmentation, yet their success hinges on large volumes of manually annotated data, which require specialized expertise for accurate labeling. Additionally, these methods often demand substantial computational resources, particularly for three-dimensional medical imaging tasks. Consequ...

Combination therapy aims to synergistically enhance efficacy or reduce toxic side effects and has widely been used in clinical practice. However, with the rapid increase in the types of drug combinations, identifying the synergistic relationships between drugs remains a highly challenging task. This paper proposes a novel deep learning model MMFSyn...

In the process of pharmaceutical crystallization, the automatic detection of crystal shapes in images is important since controlling the morphology of the crystals improves the quality of pharmaceutical crystals. In this paper, a novel image detection method called RECDet is proposed. It leverages an automatically adapted binary image to bypass bac...

Background Proteins play a pivotal role in the diverse array of biological processes, making the precise prediction of protein–protein interaction (PPI) sites critical to numerous disciplines including biology, medicine and pharmacy. While deep learning methods have progressively been implemented for the prediction of PPI sites within proteins, the...

Motivation: Protein-protein interaction (PPI) networks and transcriptional regulatory networks are critical in regulating cells and their signaling. A thorough understanding of PPIs can provide more insights into cellular physiology at normal and disease states. Although numerous methods have been proposed to predict PPIs, it is still challenging...

This paper presents a cocrystal prediction model based on molecular point cloud information and a graph attention network (GAT). We firstly expand our experimental dataset for the training purpose. This...

Background With single-cell RNA sequencing (scRNA-seq) methods, gene expression patterns at the single-cell resolution can be revealed. But as impacted by current technical defects, dropout events in scRNA-seq lead to missing data and noise in the gene-cell expression matrix and adversely affect downstream analyses. Accordingly, the true gene expre...

Background: With single-cell RNA sequencing (scRNA-seq) methods, gene expression patterns at the single-cell resolution can be revealed. But as impacted by current technical defects, dropout events in scRNA-seq lead to missing data and noise in the gene-cell expression matrix and adversely affect downstream analyses. Accordingly, the true gene expr...

Recently, an increasing number of studies have demonstrated that miRNAs are involved in human diseases, indicating that miRNAs might be a potential pathogenic factor for various diseases. Therefore, figuring out the relationship between miRNAs and diseases plays a critical role in not only the development of new drugs, but also the formulation of i...

Local self-similarity of 3D model is a fundamental problem in the shape analysis. The construction of a local shape descriptor is very important to the final result of self-similarity analysis. To solve this problem, a self-similarity analysis method based on the tensor fusion feature descriptor is proposed. Firstly, the shape diame-ter function (S...

Purpose: Our aim is to conduct analysis and comparison of some methods commonly used to measure the volume of hematoma, for example, slice method, voxelization method, and 3D-Slicer software method (projection method). Method: In order to validate the accuracy of the slice method, voxelization method, and 3D-Slicer method, these three methods we...

Residue-residue contact prediction has become an increasingly important tool for modeling the three-dimensional structure of a protein when no homologous structure is available. Ultradeep residual neural network (ResNet) has become the most popular method for making contact predictions because it captures the contextual information between residues...

The type III secretion system (T3SS) is a special protein delivery system in Gram-negative bacteria which delivers T3SS-secreted effectors (T3SEs) to host cells causing pathological changes. Numerous experiments have verified that T3SEs play important roles in many biological activities and in host-pathogen interactions. Accurate identification of...

The 3D structure of a protein is closely related to its function, and the similarity analysis between their structures can help reveal the function of proteins. However, there exist two problems arising from the analysis of 3D structures of proteins. The proteins with a similar sequence may have different structures, while the proteins with a simil...

Curve skeleton is an important shape descriptor with many potential applications in computer graphics, visualization and machine intelligence. We present a curve skeleton expression based on the set of the cross‐section centroids from a point cloud model and propose a corresponding extraction approach. We first provide the substitution of a distanc...

Complexes formed by proteins binding to RNAs are essential in biological processes, and can also be useful for identifying causal disease variants, gene expression regulation and translation. Protein-RNA interactions identified in vivo can be affected by experimental condition, noise, and some bias, while in vitro experiments yield clearer signals....

The prediction of protein secondary structure continues to be an active area of research in bioinformatics. In this paper, a Bi-LSTM based ensemble model is developed for the prediction of protein secondary structure. The ensemble model with dual loss function consists of five sub-models, which are finally joined by a Bi-LSTM layer. In contrast to...

The analysis of protein similarity is a matter of concern in the bioinformatics field, since studying the protein similarity can help understand the protein structure-function relationship. To this aim, several methods have been proposed, but currently, protein similarity results are still not satisfactory. Here we presented a novel method for eval...

The prediction of the protein secondary structure is a crucial point in bioinformatics and related fields. In the last years, machine learning methods have become a valuable tool, achieving satisfactory results. However, the prediction accuracy needs to be further ameliorated. This paper proposes a new method based on an improved fuzzy support vect...

The coding pattern of protein can greatly affect the prediction accuracy of protein secondary structure. In this paper, a novel hybrid coding method based on the physicochemical properties of amino acids and tendency factors is proposed for the prediction of protein secondary structure. The principal component analysis (PCA) is first applied to the...

Background Clustering is a common technique used by molecular biologists to group homologous sequences and study evolution. There remain issues such as how to cluster molecular sequences accurately and in particular how to evaluate the certainty of clustering results. Results We presented a model-based clustering method to analyze molecular sequen...

Proteins play a special role in bioinformatics. The surface shape of a protein, which is an important characteristic of the protein, defines a geometric and biochemical domain where the protein interacts with other proteins. The similarity analysis among protein models has become an important topic of protein analysis, by which it can reveal the st...

In order to solve the computing speed and efficiency problem of existing dynamic clothing simulation, this paper presents a dynamic garment simulation based on a hybrid bounding volume hierarchy. It firstly uses MCASG graph theory to do the primary segmentation for a given three-dimensional human body model. And then it applies K-means cluster to d...

In this article, an effective compact difference scheme is proposed to solve two-dimensional neutral delay parabolic differential equations (NDPDEs). Concrete and detailed derivation of the scheme is given. The unique solvability and unconditional stability are obtained. Several numerical experiments indicate that the scheme has second-order accura...

A new graphical representation of protein sequences is introduced in this paper. Nine main physicochemical properties of amino acids were used to obtain a 2D discrete point set for protein sequences by applying principal component analysis. The fractal method was then employed to interpolate discrete points in constructing a graphical representatio...

We present a novel line drawing approach for 3D models by introducing their skeleton information into the rendering process. Based on the silhouettes of the input,3D models, we first extract feature lines in geometric regions by utilizing their curvature, torsion and view-dependent information. Then, the skeletons of the models are extracted by our...

In order to compare the similarity between two protein models, a shape analysis algorithm based on skeleton extraction is presented in this paper. It firstly extracts the skeleton of a given protein surface by an improved Multi-resolution Reeb Graph (MRG) method. A number of points on the model surface are then collected to compute the local diamet...

Computing the roots of polynomials is an important issue in various geometric problems. In this paper, we introduce a new family of iterative methods with sixth and seventh order convergence for nonlinear equations (or polynomials). The new method is obtained by combining a different fourth-order iterative method with Newton's method and using the...

A new graphical representation for protein sequences is introduced in this paper. We firstly construct a 3D space discrete point set for amino acids of protein sequences based on three physicochemical properties of amino acids. Then, we use a cubic Bezier spline curve to interpolate these discrete points to represent protein sequences. Different fr...

Purpose – The purpose of this paper is to present a novel method of 3D foot and shoe model matching based on oriented bounding box (OBB) and axis-aligned bounding box (AABB). Design/methodology/approach – The paper first calculates their OBBs of foot and shoe models; aligns three axial directions of their OBBs to be parallel to three axes of world...

Computing the roots of polynomials is an important issue in various geometric problems. In this paper, we introduce a new family of iterative methods with sixth and seventh order convergence for nonlinear equations (or polynomials). The new method is obtained by combining a different fourth-order iterative method with Newtons method and using the a...

Given a set of scattered Hermite data with noise, we use an extension of the weighted least squares method to find the solution based on the bivariate spline. This method can adjust some weights according to different noise sizes to get a better approximation. We show that our method produces a unique spline to fit the data. Also we give the error...

Skinning animation is one of the important contents in computer animation. This paper presents a skinning mesh algorithm improvement based on double weights for the bone bending and rotating movements. When the bone bends, we use the original weight; when the bone rotates, we set the new weight according to the Gaussian curvature in the influencing...

The clustering accuracy of K-means algorithm highly depends on the initial number of clusters and it takes a long time when dealing with the large sample data with high dimension. To solve these problems, this paper proposes a method to reduce the dimensionality for high dimensional data by multidimensional scaling transformation and designs a meas...

K-means is a typical clustering representation in data mining. It is simple and suitable for different kinds of data, but can't be applied to the non-spherical clusters, different size or different density clusters. And it can not deal with the nonlinear division efficiently too. In this paper, we present a new K-means algorithm based on the kernel...

This paper proposes an approaching method to compute the straightest path between two vertices on meshes. An initial cutting plane is first constructed using the normal information of the source and destination vertices. Then an optimal cutting plane is iteratively created by comparing with previous path distance. Our study shows that the final st...

In this paper, we present a extension of weighted least squares method to fit the Hermite scattered data with noise. This method is different from the method in [1] which can only deal with the Lagrange scattered data. We give some numerical experiments to show the performance of our method. In addition, suppose the number of noisy data is large en...

Based on the current undergraduate teaching characteristics and the actual teaching situation of numerical analysis curriculum, this paper gives a useful discussion and appropriate adjustments for this course’s teaching content and style, and it also proposes some new curriculum reform plans to improve the teaching effectiveness which can develop s...

This paper presents a method for moving least square curve and surface fitting with interpolation conditions. The method is firstly proposed for solving the problem of the curve fitting with interpolation conditions. It has more advantages including that the degree of fitting function is low and the fitting computation is convenient. Then, the meth...

To obtain the approximation of the shortest path between two points on mesh models, a new method for approximately computing the straightest path on mesh models is proposed in this paper. It utilizes the neighboring feature of the starting point and the end point to determine the initial cutting plane. Then, it calculates the intersection point on...

In Photometric stereo, the existence of specularities hampers to recover the normal map. To deal with this common reflective phenomenon, we introduce a novel representation for specular reflection with a set of specular basis functions with different roughness values. This representation is suitable for any intensively or weakly specular object, an...

The 3D clothing fitting on a body model is an important research topic in the garment computer aided design (GCAD). During the fitting process, the match between the clothing and body models is still a problem for researchers. In this paper, we provide a 3D clothing fitting method based on the feature point match. We firstly use a new cubic-order w...

In this paper, we extend Razdan and Bae's second-order local fitting method to construct an effective third-order fitting patch. Compared to other estimation algorithms, this weighted bicubic Bezier patch more accurately obtains the normal vector and curvature estimation of a triangular mesh model. Furthermore, we define the principal geodesic tors...

A method based on Visual Hull is proposed for simultaneously recovering an object's shape and its reflectance properties from multiple images. Here, the reflectance properties are described by the Ward BRDF model. Firstly, the shape represented by voxels is acquired by applying SFS (Shape from Silhouettes) method, and the triangular mesh of the sur...

We present a novel mesh denoising and smoothing method in this paper. Our approach starts by estimating the principal curvatures and mesh saliency value for each vertex. Then, we calculate the uniform principal curvature of each vertex based on the weighted average of local principal curvatures. After that, we use the weighted bi-quadratic Bézier s...

This paper presents a novel mesh denoising and smoothing method. We first estimate the principal curvatures and mesh saliency value of each vertex of the mesh, the uniform principal curvatures of a vertex is then calculated based on the weighted average of local mesh saliency values. The weighted bi-cubic Bezier surface is used to fit the neighborh...

This paper presents a new feature extraction method on the mesh model with some noise. Firstly, we compute Mesh saliency value of every vertex on the mesh model. Then we set it as the weighted factor and employ the weighted bi-quadratic Bézier surface to fit the vertex and its neighborhood by the least square method. So we obtain the smoothed princ...

Feature sensitive hole filling is important for many computer graphics and geometric modeling applications. In this paper, we address the problem of reconstructing the salient features when filling holes in mesh. It respects fine shape features and works well on various types of shapes, including natural mesh and mechanical parts. For representing...

Motivated by the conception of Lee et al. (2005)’s mesh saliency and Chen (2005)’s contextual discontinuities, a novel adaptive smoothing approach is proposed for noise removal and feature preservation. Mesh saliency is employed as a multiscale measure to detect contextual discontinuity for feature preserving and control of the smoothing speed. The...

A good saliency map captures the locally sharp features effectively. So a number of tasks in graphics can benefit from a computational model of mesh saliency. Motivated by the conception of Lee’s mesh saliency [12] and its successful application to mesh simplification and viewpoint selection, we modified Laplacian smoothing operator with mesh sali...

A novel reconstruction method from contours lines is provided. First, we use a simple method to get rid of redundant points on every contour, then we interpolate them by using cubic Bézier spline curve. For corresponding points of different contours, we interpolate them by the cubic Bézier spline curve too, so the whole surface can be reconstructed...

A reconstruction method from contours is provided based on bicubic Bezier spline surface. At first, we interpolate every contour by the cubic Bezier spline curve. For corresponding points of different contours, we interpolate them by the cubic Bezier spline curve too, so the whole object can be reconstructed by the bi-cubic Bezier spline surface. T...

In this paper, we use the undetermined coefficient method to find a desirable pair of cubic Bezier spirals and a desirable pair of quintic PH spirals to generate planar G2 transition curve between two separated circles. The G2 transition curve can be gotten by the rooting formula, which simplifies the computation, and the ratio of two radii has no...

This paper presents a collaborative virtual design environment based on the globally shared product model conforming to STEP Standard. The platform provides an integration environment and changes paradigms between I_DEAS, Smarteam (PDM software) and Conceptual Innovation Design System (CIDS). The platform is illustrated for sugarcane harvester desi...

The monotone curvature condition for rational quadratic B-spline curves is studied in this paper. At first, we present the necessary and sufficient conditions of monotone curvature for the uniform rational quadratic B-spline segment and we compare it to the curvature condition of rational quadratic Bezier curve. Then, we give the sufficient conditi...

In this paper, we present a digital repair method for archeological relics with some vacant areas. We first use the simple method to find the neighboring area which influences the shape of the vacant area. Then we construct the bi-cubic Bezier spline surface to interpolate given points in the influencing area. Re-sampling points on the bi-cubic Bez...

A generating algorithm for rational quadratic Bézier curves is provided. In the algorithm, we find the recurrence relation to get every pixel along the curve, using the bidirectional strategy for rendering and the forward and backward difference method for computing. The algorithm has a fast generating speed, and the curves keep a reasonable render...

A new approach is proposed to motion editing based on motion capture data, i.e., motion mapping. The key to our framework is the spacetime optimization method based on physical model. For reducing the complexity of optimization problem, we map the captured motion to a new character by using a simplified model. This model is a transformation tool an...