Hoai Van Tran

Hoai Van Tran
Ho Chi Minh City University of Technology (HCMUT) | HCMUT · Faculty of Computer Science and Engineering

PhD

About

52
Publications
7,669
Reads
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200
Citations

Publications

Publications (52)
Article
The Quickhull algorithm for determining the convex hull of a finite set of points was independently conducted by Eddy in 1977 and Bykat in 1978. Inspired by the idea of this algorithm, we present a new efficient algorithm, for determining the connected orthogonal convex hull of a finite set of points through extreme points of the hull, that still k...
Article
Without traditional cultures, metagenomics studies the microorganisms sampled from the environment. In those studies, the binning step results serve as an input for the next step of metagenomic projects such as assembly and annotation. The main challenging issue of this process is due to the lack of explicit features of metagenomic reads, especiall...
Article
The study of metagenomic sequences brings a deep understanding of microbial communities. One of the crucial steps in metagenomic projects is to classify sequences into different organisms, named the binning problem. In the emerging methods for classification, deep learning is a potential technology to be applicable with high accuracy. However, it i...
Article
Full-text available
Runoff prediction has recently become an essential task with respect to assessing the impact of climate change to people’s livelihoods and production. However, the runoff time series always exhibits nonlinear and non-stationary features, which makes it very difficult to be accurately predicted. Machine learning have been recently proved to be a pow...
Conference Paper
Full-text available
In recent years, Internet of Things (IoT) and Machine Learning (ML) has been applied successfully in agriculture. These technologies increase productivity as well as reduce labor significantly. In this paper, we focus on improving the autonomous cow estrus detection system in terms of energy consumption and precision. In previous detection pipeline...
Chapter
Metagenomic binning refers to the means of clustering or assigning taxonomy to metagenomic sequences or contigs. Due to the massive abundance of organisms in metagenomic samples, the number of nucleotide sequences skyrockets, and thus leading to the complexity of binning algorithms. Unsupervised classification is gaining a reputation in recent year...
Chapter
The stable marriage problem with ties (SMT) is a variant of the stable marriage problem in which people are permitted to express ties in their preference lists. In this paper, an algorithm based on bidirectional searching is presented for trying to find strongly egalitarian and sex-equal stable matchings. We indicate that the use of two simultaneou...
Article
Full-text available
Metagenomics is a powerful approach to study environment samples which do not require the isolation and cultivation of individual organisms. One of the essential tasks in a metagenomic project is to identify the origin of reads, referred to as taxonomic assignment. Due to the fact that each metagenomic project has to analyze large-scale datasets, t...
Conference Paper
Full-text available
In this study, MIKE NAM, artificial neural networks (ANNs), and a hybridization of ANNs and Particle Swarm Optimization (ANN-PSO) are utilized to predict the Dak Nong runoff. ANNs are trained by the back-propagation (BP) procedure which is based on the gradient descent algorithm and an incorporating algorithm of PSO and BP. Moreover, to improve the...
Conference Paper
Full-text available
Yield assessment is one of the main interests at regional and national levels of agriculture management. The accuracy of the assessment is not highly expected inherently and, moreover, some costly and sophisticated tools (e.g., satellite images) have been usually involved without a careful consideration of their investment. In this paper, a novel a...
Conference Paper
The paper review methods to binning metagenomic, such as: use k-mer to find the features, use k-mer to create a document to find hidden models, then groups sequence base on this models. To increase performance, mostly reduce the size of original data, binning directly from representation sequences. There are problems when reducing the size and only...
Conference Paper
In the past few decades, boosting crop yield has been extensively regarded in many agricultural countries, especially Vietnam. Due to food demands and impossibility of crop-field area increasing, precision farming is essential to improve agricultural production and productivity. In this paper, we propose a novel framework based on some advanced tec...
Conference Paper
Full-text available
Calibrations and validations of Computational Fluid Dynamics (CFD) applications are significantly time-consuming. To reduce the execution time of the CFD applications, parallel-computing approach is often employed. In addition, high performance computing systems and cloud computing solutions are also appropriate tools to the CFD applications. One o...
Article
In this paper, we use a multiple shooting approach in solving boundary value problems for ODE to introduce a novel iterative algorithm for computing an approximate shortest path between two points on the surface of a convex polytope in 3D. Namely, the polytope is partitioned into subpolytopes, shooting points and a Straightness condition are establ...
Conference Paper
Full-text available
Binning and taxanomical classification are two challenging problems in bioinformatics. The paper proposes a method using Laten Dirichlet Allocation to find hidden topics embedded as characteristic within genomic sequences. From these topics, the method classifies the group of sequences by using Kullback Leibler to calculate the similarity based on...
Article
Full-text available
Background Taxonomic assignment is a crucial step in a metagenomic project which aims to identify the origin of sequences in an environmental sample. Among the existing methods, since composition-based algorithms are not sufficient for classifying short reads, recent algorithms use only the feature of similarity, or similarity-based combined featur...
Article
Full-text available
We consider the problem of determining a least expected time (LET) path that minimizes the number of transfers and the expected total travel time in a stochastic schedule-based transit network. A time-dependent model is proposed to represent the stochastic transit network where vehicle arrival times are fully stochastically correlated. An exact lab...
Conference Paper
Finding alternative paths to follow is essential to travelers in dense city bus networks. A simple method is to transform the city bus networks into directed graph and then apply a standard K-shortest-path algorithm to the graph to find alternative paths. However, as the constructed graph is often massive and complex, classical K-shortest-path algo...
Article
Full-text available
Flooding is a serious urban problem, especially in HoChiMinh city in recent years. Many researches for flow accumulation by terrain have been proposed. Accordingly, terrains are splitted to grids. Single or multiflow algorithms will theoretically show the accumulated water trend. So that, to reduce flooding, increasing road or extending drainage sy...
Article
Full-text available
Background Metagenomics is the study of genetic materials derived directly from complex microbial samples, instead of from culture. One of the crucial steps in metagenomic analysis, referred to as “binning”, is to separate reads into clusters that represent genomes from closely related organisms. Among the existing binning methods, unsupervised met...
Chapter
In this paper we describe an algorithm based on the idea of the direct multiple shooting method for solving approximately 2D geometric shortest path problems (introduced by An et al. in Journal of Computational and Applied Mathematics, 244 (2103), pp. 67-76). The algorithm divides the problem into suitable sub-problems, and then solves iteratively...
Conference Paper
Full-text available
Metagenomics is a research discipline of microbial commu- nities that studies directly on genetic materials obtained from environ- mental samples without isolating and culturing single organisms in lab- oratory. One of the crucial tasks in metagenomic projects is the identi- fication and taxonomic characterization of DNA sequences in the sam- ples....
Conference Paper
In this paper, we consider the problem of finding itineraries in bus networks under multiple independent optimization criteria, namely arrival time at destination and number of transfers. It is also allowed to walk from one stop to another if the two stops are located within a small distance. A time–dependent model is proposed to solve this problem...
Article
Full-text available
The binning of reads is a crucial step in metagenomic data analysis. While unsuper- vised methods which are based on composition features are only efficient for long reads, genome abundance-based methods are often used in the binning of short reads. Previous abundance-based binning approaches usually use fixed-length l-mer frequencies to separate r...
Conference Paper
Full-text available
As a crucial step in a metagenomic project, the binning of metagenomic sequences aims to classify sequences into groups of individual genomes or closely related organisms. Although most recent binning approaches are based on genomic signatures, finding an efficient signature for the binning is still being investigated by recent theoretical and empi...
Article
Full-text available
A binning of reads is asignificant problem in metagenomic data analysis.Due to lacking of reference database and a large percentage of unknown microbes in the environment, the performance of supervised binning approaches are low. Thus, clustering method (or unsupervised binning method) is efficient to analyze DNA reads collected from microbial comm...
Conference Paper
Full-text available
As a crucial step in metagenomic analysis, the binning of reads aims to classify the reads into different groups that represent individual species or closely related organisms. This paper presents a new binning approach for metagenomic reads basing on species abundances and not requiring any reference databases. The proposed approach consists of th...
Article
Determining Euclidean shortest paths between two points in a domain is a fundamental problem in computing geometry and has many applications in GIS, robotics, computer graphics, CAD, etc. To date, solving Euclidean shortest path problems inside simple polygons has usually relied on triangulation of the entire polygons and graph theory. The question...
Article
Full-text available
Solving shortest path problems inside simple polygons is a very classical problem in motion planning. To date, it has usually relied on triangulation of the polygons. The question: "Can one devise a simple O(n) time algorithm for computing the shortest path between two points in a simple polygon (with n vertices), without resorting to a (complicate...
Conference Paper
We address an application of vehicle routing problem (VRP) in the real life, namely waste collection problem. Constraints are considered including conflicts between waste properties, time windows of the waste, and multiple landfills. A combination of flow and set partitioning formulation is suggested to model the problem in case of multi-objective...
Article
Full-text available
We use the idea of the direct multiple shooting method (presented by Bock in Proceedings of the 9th IFAC World Congress Budapest, Pergamon Press, 1984, for solving optimal control problems) to introduce an algorithm for solving some approximate shortest path problems in motion planning. The algorithm is based on a direct multiple shooting discretiz...
Conference Paper
This paper considers a virtual machine allocation problem. Each physical machine in cloud has a lot of virtual machines. Each job needs to use a number of virtual machines during a given and fixed period. The objective aims to minimize the cost induced by total execution time on each physical machine. This allocation problem is proved to be N P-har...
Conference Paper
This paper investigates the performance of several solvers for mixed-integer linear programming (MILP) on a scheduling problem with job splitting properties and availability constraints. The jobs are splitable and lower bound on the size of each sub-job is imposed. The scheduling objective aims to find a feasible schedule that minimizes the makespa...
Article
Full-text available
Influenza virus is one of the causes of flu in human beings as well as in animals. Vietnam, with its tropical climate, is one of the countries located in heavily affected areas of the influenza virus. Building a localized information system of flu viruses for Vietnam provinces is quite necessary not only for research but also for other communities....
Conference Paper
This paper describes some techniques based on polygon aggregation in reducing time for visibility graph in case of many obstacles. In path planning, the approaches are commonly used such as search-based, sampling-based or combinatorial planning. And visibility graph is one of the roadmaps of combinatorial planning. Building a visibility graph is a...
Article
Full-text available
Within a research to develop a computational fluid dynamics (CFD) solver for aeronautical engineering, we target to one of the aerodynamics shape optimization problems, namely Airfoil Optimization problem in two-dimensional space. Generally, a numerical solution approach for this problem consists of an outer loop driving optimization process (e.g.,...
Conference Paper
Full-text available
Although many studies have targeted homogeneous and heterogeneous traffic flow, they are normally little or no attention to driver reaction passing intersection. Understanding complex movement within an intersection is the critical task which can explain the reason of traffic jam especially in big cities (for example, Ho Chi Minh City, Hanoi). This...
Conference Paper
A grid environment is a collection of a large number of geographically distributed resources managed by various organizations. And it is considered as a powerful computing infrastructure to solve large and complex problems. To support the software development, until now, many grid programming languages have been investigated. Most of them use propr...
Article
Crew pairing problems are often solved using column generation in a branch-and-price framework. The oscillation of dual points is the main reason which leads to instability in the standard implementation of this method. One device to deal with the problem is to use the trust-region idea to stabilize the path of dual points. Therefore, a so-called s...
Conference Paper
Crew pairing problems are often solved using column generation in a branch-and-price framework. The main idea of this approach consists of solving linear programming relaxations for a subset of variables and employing pricing for introducing additional variables with negative reduced costs. Since the dual variables are not bounded, this leads to in...
Article
Crew pairing is one of the most critical processes in airline management operations. Taking a timetable as input, the objective of this process is to find an optimal way to partition flights of the timetable without breaking rules and regulations which are enforced by an airline. The problem has attracted many scientists in recent decades. The main...
Article
When solving crew scheduling problems by column generation, the main task is to solve the pricing problem for introducing new columns. This problem is NP-hard and usually requires more than 90% of the overall computation time in all of our experiments as well as in experiments reported in the literature. Therefore it is critical to achieve good per...

Projects

Projects (2)
Project
Apply advanced technology in Vietnamese agriculture
Project
The first is find out Latent Dirichlet Allocation (LDA) algorithms The second is use LDA to find models and use them to clustering metagenomic data. and finally, Classification metagenomic