2551048
Computers Are from Mars, Organisms Are from Venus
Biology and computer science share a natural affinity. Physicist Erwin Schrodinger envisioned life as an aperiodic crystal, observing that the organizing structure of life is neither completely regular, like a pure crystal, nor completely chaotic and without structure, like dust in the wind. Perhaps this is why biological information has never satisfactorily yielded to classical mathematical analysis. Machine computations combine elegant algorithms with brute-force calculations, which seems a reasonable approach to this aperiodic structure. Likewise, computing seeks to create a machine that can flexibly solve diverse problems. In nature, such plastic problem solving resides uniquely in the domain of organic matter. Thus, examining how organisms solve problems can lead to new computation and algorithm development approaches that devour the problems that are so easy to approach using a computer, yet so difficult to tackle in the laboratory. The paper discusses the two most successful uses of computers in biology, comparative sequence analysis and in silico cloning. It considers DNA computing and genetic algorithms.
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.
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.
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.
10981925
Geometrical Learning Algorithm for Multilayer Neural Networks in a Binary Field
A geometrical expansion learning algorithm for multilayer neural networks using unipolar binary neurons with integer connection weights, which guarantees convergence for any Boolean function, is introduced. Neurons in the hidden layer develop as necessary without supervision. In addition, the computational amount is much less than that of the backpropagation algorithm. >
20426558
The ANSER Project
16878992
Improving use case driven analysis using goal and scenario authoring: A linguistics-based approach
Use case driven analysis does not facilitate effective requirements elicitation or provide rationale for the various artifacts that get generated during the requirements analysis phase. On the other hand, goal and scenario based approach is considered to be effective for elicitation but it does not lead to use cases. This paper discusses how to combine goal and scenario based requirements elicitation technique with use case driven analysis using natural language concepts. In our proposed approach, four levels of goals, scenario authoring rules, and linguistic techniques have been developed to identify use cases from text based goal and scenario descriptions. The artifacts resulting from our approach could be used as input to a use case diagramming tool to automate the process of use case diagram generation.
12515507
Using content-addressable networks for load balancing in desktop grids
Desktop grids have evolved to combine Peer-to-Peer and Grid computing techniques to improve the robustness, reliability and scalability of job execution infrastructures. However, efficiently matching incoming jobs to available system resources and achieving good load balance in a fully decentralized and heterogeneous computing environment is a challenging problem. In this paper, we extend our prior work with a new decentralized algorithm for maintaining approximate global load information, and a job pushing mechanism that uses the global information to push jobs towards underutilized portions of the system. The resulting system more effectively balances load and improves overall system throughput. Through a comparative analysis of experimental results across different system configurations and job profiles, performed via simulation, we show that our system can reliably execute Grid applications on a distributed set of resources both with low cost and with good load balance.
40331728
Efficient 2-D Convolution Algorithm with the Single-Data Multiple Kernel Approach
Abstract A fast implementation of convolution operation is described. The implementation takes advantage of various properties of commonly used kernels. First, the kernel elements are analyzed and rearranged, grouping the kernel elements of the same absolute value together and arranging trivial multiplication cases separately. Then the sequence of computing convolution sums is modified so that all the kernel elements could be multiplied by the same data element at each step. This new algorithm significantly reduces the number of multiplication operations for most widely used kernels. Our experiment shows that the performance improvement of two to seven over the direct implementation is achievable for most kernels. The required overhead (extra memory and preprocessing) is proportional to the kernel size and is negligible.