1278377
A Tree Obscured By Vines: Horizontal Gene Transfer and the Median Tree Method of Estimating Species Phylogeny
A phylogeny is a tree graph representation of genealogical relationships between biological objects. It is of general interest to estimate the phylogeny of whole organisms (species trees) using bio-molecular sequences. When multiple sequences are available for each organism such as with whole genome data, individual phylogenies estimated by each molecule (gene trees) may not be concordant. The lack of concordance may be due to actual biological mechanisms such as horizontal transfer of the molecules. Here, we present a new phylogeny estimation method designed to estimate the species tree despite such horizontal transfer. It uses the idea that horizontal transfer distorts distance relationships between pairs of species but a median estimate of the distances is robust to such distortions. We demonstrate the utility of our method using a simulation study.
32992816
A Combinatorial Toolbox for Protein Sequence Design and Landscape Analysis in the Grand Canonical Model
In modern biology, one of the most important research problems is to understand how protein sequences fold into their native 3D structures. To investigate this problem at a high level, one wishes to analyze the protein landscapes, i.e., the structures of the space of all protein sequences and their native 3D structures. Perhaps the most basic computational problem at this level is to take a target 3D structure as input and design a fittest protein sequence with respect to one or more fitness functions of the target 3D structure. We develop a toolbox of combinatorial techniques for protein landscape analysis in the Grand Canonical model of Sun, Brem, Chan, and Dill. The toolbox is based on linear programming, network flow, and a linear-size representation of all minimum cuts of a network. It not only substantially expands the network flow technique for protein sequence design in Kleinberg's seminal work but also is applicable to a considerably broader collection of computational problems than those considered by Kleinberg. We have used this toolbox to obtain a number of efficient algorithms and hardness results. We have further used the algorithms to analyze 3D structures drawn from the Protein Data Bank and have discovered some novel relationships between such native 3D structures and the Grand Canonical model.
199137
Scaling of Accuracy in Extremely Large Phylogenetic Trees
The accuracy of phylogenetic inference was examined in simulated data sets up to nearly 10,000 taxa, the size of the largest set of homologous genes in existing molecular sequence databases. Even with a simple search algorithm (maximum parsimony without branch swapping), the number of characters needed to estimate 80% of a tree correctly can scale remarkably well at optimal substitution rates (on the order of log N, where N is the number of taxa). In other words, the number of taxa in an analysis can be doubled and only an arithmetic increase in the number of characters is required to maintain the same level of accuracy. Even substitution rates that are much higher than normally used in phylogenetic studies did not affect the scaling too adversely. However, scaling is usually worse than log N for more stringent levels of accuracy. Moreover, errors are not distributed randomly throughout the tree. Shallow nodes are remarkably easy to reconstruct and display favourable log-linear scaling. The deepest nodes are extremely difficult to reconstruct accurately, even with branch swapping, and the scaling is poor. Therefore, the strategy of sequencing large numbers of homologous genes may not always provide global solutions to extreme phylogenetic problems and alternative strategies may be required.
14012710
Interference-Minimizing Colorings of Regular Graphs
Communications problems that involve frequency interference, such as the channel assignment problem in the design of cellular telephone networks, can be cast as graph coloring problems in which the frequencies (colors) assigned to an edge's vertices interfere if they are too similar. The paper considers situations modeled by vertex-coloring d-regular graphs with n vertices using a color set 1, 2,..., n, where colors i and j are said to interfere if their circular distance $\min \{ | i-j | , n- | i-j | \}$ does not exceed a given threshold value $\alpha$. Given a d-regular graph G and threshold $\alpha$, an interference-minimizing coloring is a coloring of vertices that minimizes the number of edges that interfere. Let $I_\alpha (G)$ denote the minimum number of interfering edges in such a coloring of $G$. For most triples $(n, \alpha ,d),$ we determine the minimum value of $I_\alpha (G)$ over all d-regular graphs and find graphs that attain it. In determining when this minimum value is 0, we prove that for $r \geq 3$ there exists a d-regular graph G on n vertices that is r-colorable whenever $d \leq (1- \frac{1}{r}) n-1$ and nd is even. We also study the maximum value of $I_\alpha (G)$ over all d-regular graphs and find graphs that attain this maximum in many cases.
15382159
Hybrid recursive energy-based method for robust optical flow on large motion fields
We present a new reliable hybrid recursive method for optical flow estimation. The method efficiently combines the advantage of discrete motion estimation and optical flow estimation in a recursive block-to-pixel estimation scheme. Integrated local and global approaches using the robust statistic of anisotropic diffusion remove outliers from the estimated motion field. We separately describe the process with two frameworks i.e. an incremental updating framework and a robust energy minimization framework. With robust error norms of Perona and Marik anisotropic diffusion, the formulation usually leads to non-convex optimization problems. Thus, the solution has many local minima, and convergence to the global minima is not guaranteed. Our hybrid recursive energy-based method employs a hierarchical block-to-pixel estimation concept to prevent this problem. The experimental results prove the excellent performance on several large motion fields.
2978705
Reconstructing the Temporal Ordering of Biological Samples Using Microarray Data
MOTIVATION
Accurate time series for biological processes are difficult to estimate due to problems of synchronization, temporal sampling and rate heterogeneity. Methods are needed that can utilize multi-dimensional data, such as those resulting from DNA microarray experiments, in order to reconstruct time series from unordered or poorly ordered sets of observations.


RESULTS
We present a set of algorithms for estimating temporal orderings from unordered sets of sample elements. The techniques we describe are based on modifications of a minimum-spanning tree calculated from a weighted, undirected graph. We demonstrate the efficacy of our approach by applying these techniques to an artificial data set as well as several gene expression data sets derived from DNA microarray experiments. In addition to estimating orderings, the techniques we describe also provide useful heuristics for assessing relevant properties of sample datasets such as noise and sampling intensity, and we show how a data structure called a PQ-tree can be used to represent uncertainty in a reconstructed ordering.


AVAILABILITY
Academic implementations of the ordering algorithms are available as source code (in the programming language Python) on our web site, along with documentation on their use. The artificial 'jelly roll' data set upon which the algorithm was tested is also available from this web site. The publicly available gene expression data may be found at http://genome-www.stanford.edu/cellcycle/ and http://caulobacter.stanford.edu/CellCycle/.
701944
Simulation-Based Security Testing for Continuity of Essential Service
One of the most important characteristic of essential service in the computer network is its continuity. If the continuity of essential service is not guaranteed, it causes a big problem in normal operation of computer network. In our research, we suggest the simulation-based security testing for the continuity of essential service. Especially, the security testing sequence and Experimental Frame is designed to get indexes related to the continuity of essential service. We choose three testing indexes that represent the degree of service continuity and testing methods to get those indexes. Also, to explain the indexes and the testing methods, two testing examples are presented.
15453065
Device-Aware Cache Replacement Algorithm for Heterogeneous Mobile Storage Devices
Hard disks, most prevalent mass-storage devices, have high power consumption and high response time for random I/O requests. Recent remarkable technology improvement of flash memory has made it a rising secondary storage device but flash memory still has high cost per bit. Usage of heterogeneous storage devices such as a pair of a hard disk and a flash memory can provide reasonable cost, relatively acceptable response time, and low-power consumption. In this paper, we propose a novel buffer cache replacement algorithm which targets a mobile computing system with a heterogeneous storage pair of a hard disk and a flash memory. The algorithm partitions the cache per each device and adjusts the size of each partition based on the performance indices of the devices, and manages each partition according to workload patterns. Simulations show that the proposed algorithm yields a hit rate up to two times higher than LRU on the typical mobile traces according to the cache size and achieves also better system I/O response time and energy consumption.