An analysis of the feasibility of short read sequencing

Several methods for ultra high-throughput DNA sequencing are currently under investigation. Many of these methods yield very short blocks of sequence information (reads). Here we report on an analysis showing the level of genome sequencing possible as a function of read length. It is shown that re-sequencing and de novo sequencing of the majority of a bacterial genome is possible with read lengths of 20-30 nt, and that reads of 50 nt can provide reconstructed contigs (a contiguous fragment of sequence data) of 1000 nt and greater that cover 80% of human chromosome 1

Global Landscape Structure and the Random MAX-SAT Phase Transition

We revisit the fitness landscape structure of random MAX-SAT instances, and address the question: what structural features change when we go from easy underconstrained instances to hard overconstrained ones? Some standard techniques such as autocorrelation analysis fail to explain what makes instances hard to solve for stochastic local search algorithms, indicating that deeper landscape features are required to explain the observed performance differences. We address this question by means of local optima network (LON) analysis and visualisation. Our results reveal that the number, size, and, most importantly, the connectivity pattern of local and global optima change significantly over the easy-hard transition. Our empirical results suggests that the landscape of hard MAX-SAT instances may feature sub-optimal funnels, that is, clusters of sub-optimal solutions where stochastic local search methods can get trapped

Experimental Rugged Fitness Landscape in Protein Sequence Space

The fitness landscape in sequence space determines the process of biomolecular evolution. To plot the fitness landscape of protein function, we carried out in vitro molecular evolution beginning with a defective fd phage carrying a random polypeptide of 139 amino acids in place of the g3p minor coat protein D2 domain, which is essential for phage infection. After 20 cycles of random substitution at sites 12–130 of the initial random polypeptide and selection for infectivity, the selected phage showed a 1.7×10(4)-fold increase in infectivity, defined as the number of infected cells per ml of phage suspension. Fitness was defined as the logarithm of infectivity, and we analyzed (1) the dependence of stationary fitness on library size, which increased gradually, and (2) the time course of changes in fitness in transitional phases, based on an original theory regarding the evolutionary dynamics in Kauffman's n-k fitness landscape model. In the landscape model, single mutations at single sites among n sites affect the contribution of k other sites to fitness. Based on the results of these analyses, k was estimated to be 18–24. According to the estimated parameters, the landscape was plotted as a smooth surface up to a relative fitness of 0.4 of the global peak, whereas the landscape had a highly rugged surface with many local peaks above this relative fitness value. Based on the landscapes of these two different surfaces, it appears possible for adaptive walks with only random substitutions to climb with relative ease up to the middle region of the fitness landscape from any primordial or random sequence, whereas an enormous range of sequence diversity is required to climb further up the rugged surface above the middle region

Benefits of a population: five mechanisms that advantage population-based algorithms

This paper identifies five distinct mechanisms by which a population-based algorithm might have an advantage over a solo-search algorithm in classical optimization. These mechanisms are illustrated through a number of toy problems. Simulations are presented comparing different search algorithms on these problems. The plausibility of these mechanisms occurring in classical optimization problems is discussed. The first mechanism we consider relies on putting together building blocks from different solutions. This is extended to include problems containing critical variables. The second mechanism is the result of focusing of the search caused by crossover. Also discussed in this context is strong focusing produced by averaging many solutions. The next mechanism to be examined is the ability of a population to act as a low-pass filter of the landscape, ignoring local distractions. The fourth mechanism is a population's ability to search different parts of the fitness landscape, thus hedging against bad luck in the initial position or the decisions it makes. The final mechanism is the opportunity of learning useful parameter values to balance exploration against exploitation

New Area Based Measures for Gait Recognition

Gait is a new biometric aimed to recognise a subject by the manner in which they walk. Gait has several advantages over other biometrics, most notably that it is non-invasise and perceivable at a distance when other biometrics are obscured. We present a new area based metric, called gait masks, which provides statistical data intimately related to the gait of the subject. Early results show promising results with a recognition rate of 90% on a small database of human subjects. In addition to this, we show how gait masks can also be used on subjects other than humans to provide information about the gait cycle of the subject

A Heuristic Bidding Strategy for Buying Multiple Goods in Multiple English Auctions.

This paper presents the design, implementation, and evaluation of a novel bidding algorithm that a software agent can use to obtain multiple goods from multiple overlapping English auctions. Specifically, an Earliest Closest First heuristic algorithm is proposed that uses neurofuzzy techniques to predict the expected closing prices of the auctions and to adapt the agent’s bidding strategy to reflect the type of environment in which it is situated. This algorithm first identifies the set of auctions that are most likely to give the agent the best return and then, according to its attitude to risk, it bids in some other auctions that have approximately similar expected returns, but which finish earlier than those in the best return set. We show through empirical evaluation against a number of methods proposed in the multiple auction literature that our bidding strategy performs effectively and robustly in a wide range of scenarios

An adaptive bidding agent for multiple English auctions: a neuro-fuzzy approach

This paper presents the design, implementation and evaluation of a novel bidding strategy for obtaining goods in multiple overlapping English auctions. The strategy uses fuzzy sets to express trade-offs between multi-attribute goods and exploits neuro-fuzzy techniques to predict the expected closing prices of the auctions and to adapt the gent’s bidding strategy to reflect the type of environment in which it is situated. We show, through empirical evaluation against a number of methods proposed in the multiple auction literature, that our strategy performs effectively and robustly in a wide range of scenarios