We will review some of the major results in random graphs and some of the more challenging open problems. We will cover algorithmic and structural questions. We will touch on newer models, including those related to the WWW.

Random graphs

Rapid improvements in sequencing and array-based platforms are resulting in a flood of diverse genome-wide data, including data from exome and whole-genome sequencing, epigenetic surveys, expression profiling of coding and noncoding RNAs, single nucleotide polymorphism (SNP) and copy number profiling, and functional assays. Analysis of these large, diverse data sets holds the promise of a more comprehensive understanding of the genome and its relation to human disease. Experienced and knowledgeable human review is an essential component of this process, complementing computational approaches. This calls for efficient and intuitive visualization tools able to scale to very large data sets and to flexibly integrate multiple data types, including clinical data. However, the sheer volume and scope of data pose a significant challenge to the development of such tools.

Integrative Genomics Viewer

This paper presents a new reflectance model for rendering computer synthesized images. The model accounts for the relative brightness of different materials and light sources in the same scene. It describes the directional distribution of the reflected light and a color shift that occurs as the reflectance changes with incidence angle. The paper presents a method for obtaining the spectral energy distribution of the light reflected from an object made of a specific real material and discusses a procedure for accurately reproducing the color associated with the spectral energy distribution. The model is applied to the simulation of a metal and a plastic.

A reflectance model for computer graphics

Computational geometry

This article reviews machine learning methods for bioinformatics. It presents modelling methods, such as supervised classification, clustering and probabilistic graphical models for knowledge discovery, as well as deterministic and stochastic heuristics for optimization. Applications in genomics, proteomics, systems biology, evolution and text mining are also shown.

/pdf/machine-learning-in-bioinformatics-5gfm1x1ssk.pdf

Machine learning in bioinformatics

Summary: PhyloDraw is a unified viewing tool for phylogenetic trees. PhyloDraw supports various kinds of multi-alignment formats (Dialign2, Clustal-W, Phylip format, NEXUS, MEGA, and pairwise distance matrix) and visualizes various kinds of tree diagrams, e.g. rectangular cladogram, slanted cladogram, phylogram, unrooted tree, and radial tree. By using several control parameters, users can easily and interactively manipulate the shape of phylogenetic trees. This program can export the final tree layout to BMP (bitmap image format) and PostScript. Availability: http:// pearl.cs.pusan.ac.kr/ phylodraw/

PhyloDraw: a phylogenetic tree drawing system

It is very important to detect plagiarized programs in the field of computer science education. Therefore, many tools and algorithms have been developed for this purpose. Generally, these tools are operated in two phases. In phase 1, a program plagiarism detecting tool generates an intermediate representation from a given program set. The intermediate representation should reflect the structural characterization of the program. Most tools use the parse tree or token sequence by intermediate representation. In phase 2, the program looks for plagiarized material and evaluates the similarity of two programs. It is helpful to announce the plagiarized metarials between two programs to the instructor. In this paper, we present the static tracing method in order to improve program plagiarism detection accuracy. The static tracing method statically executes a program at the syntax-level and then extracts predefined keywords according to the order of the executed functions. The result of experiment proves this method can detect plagiarism more effectively than the previously released plagiarism detecting method.

A source code linearization technique for detecting plagiarized programs

We present an efficient method for rapid animation of mass-spring model with a large number of mass-points. Realistic cloth simulation requires large amount of time in general. This is not only because the calculation for one step requires much time but also because the cloth simulation easily tends to become unstable. Although the implicit method can make the simulation stable, it is still impossible to generate interactive animation when the number of mass-points is sufficiently large enough to represent realistic wrinkles. An efficient animation method proposed by M. Desbrun (1999) also involves O(n/sup 2/)-sized matrix so that it cannot be applied to models with a large number of mass-points. A stable approximate method without matrix operations has been introduced by M. Oshita and A. Makinouchi (2001), but its physical correctness is significantly impaired as the stiffness increases or the timestep becomes large. In this paper we propose a bilayered approach for efficient cloth animation with a large number of mass-points. The proposed method uses two mass-spring meshes. One of them is a rough mesh for representing global motion, and the other is a fine mesh for realistic wrinkles. The experimental results show that the method can be successfully used for real-time animation of plausible cloth models.

Bilayered approximate integration for rapid and plausible animation of virtual cloth with realistic wrinkles

Realistic animation of soft objects such as cloth is essential for plausible character animation. Many techniques have been proposed for the simulation of soft objects, and most of them are based on numerical integration. Among the techniques, the implicit integration method is the most likely technique for real time environments, since it allows large time steps for cloth simulation by ensuring the stability of systems. However the most critical flaw of the implicit method is that it involves a large linear system. The paper presents a fast animation technique for animating soft objects based on a mass-spring model with an approximated implicit method which does not involve linear system solving. The proposed technique stably updates the state of n mass-points in O(n) time when the number of total springs are O(n). Because the mass-spring model shows a superelastic effect, the excessively deformed springs (i.e., super-elongated springs) should be adjusted for reality. The paper presents an efficient inverse dynamics process to adjust the super-elongated springs.

Fast and stable animation of cloth with an approximated implicit method

This paper presents an efficient method for creating the animation of flexible objects. The mass-spring model was used to represent flexible objects. The easiest approach to creating animation with the mass-spring model is the explicit Euler method, but the method has a serious weakness in that it suffers from an instability problem. The implicit integration method is a possible solution, but a critical flaw of the implicit method is that it involves a large linear system. This paper presents an approximate implicit method for the mass-spring model. The proposed technique updates with stability the state of n mass points in O(n) time when the number of total springs is O(n). In order to increase the efficiency of simulation or reduce the numerical errors of the proposed approximate implicit method, the number of mass points must be as small as possible. However, coarse discretization with a small number of mass points generates an unrealistic appearance for a cloth model. By introducing a wrinkled cubic spline curve, we propose a new technique that generates realistic details of the cloth model, even though a small number of mass points are used for simulation.

/pdf/an-efficient-animation-of-wrinkled-cloth-with-approximate-2rifqv9xb1.pdf

Hwan-Gue Cho

Papers

PhyloDraw: a phylogenetic tree drawing system

A source code linearization technique for detecting plagiarized programs

Bilayered approximate integration for rapid and plausible animation of virtual cloth with realistic wrinkles

Fast and stable animation of cloth with an approximated implicit method

An efficient animation of wrinkled cloth with approximate implicit integration