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Fingerprint Analysis of the Noisy Prisoner's Dilemma Using a Finite-State Representation

Ashlock, D.,Eun-Youn Kim,Ashlock, W. IEEE 2009 Ieee transactions on computational intelligence an Vol.1 No.2
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Fingerprinting is a technique that permits automatic classification of strategies for playing a game. In this paper, the evolution of strategies for playing the iterated prisoner's dilemma (IPD) at three different noise levels is analyzed using fingerprinting and other techniques including a novel quantity, evolutionary velocity, derived from fingerprinting. The results are at odds with initial expectations and permit the detection of a critical difference in the evolution of agents with and without noise. Noise during fitness evaluation places a larger fraction of an agent's genome under selective pressure, resulting in substantially more efficient training. In this case, efficiency is the production of superior competitive ability at a lower evolutionary velocity. Prisoner's dilemma playing agents are evolved for 6400 generations, taking samples at eight exponentially spaced epochs. This permits assessment of the change in populations over long evolutionary time. Agents are evaluated for competitive ability between those evolved for different lengths of time and between those evolved using distinct noise levels. The presence of noise during agent training is found to convey a commanding competitive advantage. A novel analysis is done in which a tournament is run with no two agents from the same evolutionary line and one third of agents from each noise level studied. This analysis simulates contributed agent tournaments without any genetic relation between agents. It is found that in early epochs the agents evolved without noise have the best average tournament rank, but that in later epochs they have the worst.
2
MULTI-K: accurate classification of microarray subtypes using ensemble k-means clustering

Kim, Eun-Youn,Kim, Seon-Young,Ashlock, Daniel,Nam, Dougu BioMed Central 2009 BMC bioinformatics Vol.10 No.-
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BackgroundUncovering subtypes of disease from microarray samples has important clinical implications such as survival time and sensitivity of individual patients to specific therapies. Unsupervised clustering methods have been used to classify this type of data. However, most existing methods focus on clusters with compact shapes and do not reflect the geometric complexity of the high dimensional microarray clusters, which limits their performance.ResultsWe present a cluster-number-based ensemble clustering algorithm, called MULTI-K, for microarray sample classification, which demonstrates remarkable accuracy. The method amalgamates multiple k-means runs by varying the number of clusters and identifies clusters that manifest the most robust co-memberships of elements. In addition to the original algorithm, we newly devised the entropy-plot to control the separation of singletons or small clusters. MULTI-K, unlike the simple k-means or other widely used methods, was able to capture clusters with complex and high-dimensional structures accurately. MULTI-K outperformed other methods including a recently developed ensemble clustering algorithm in tests with five simulated and eight real gene-expression data sets.ConclusionThe geometric complexity of clusters should be taken into account for accurate classification of microarray data, and ensemble clustering applied to the number of clusters tackles the problem very well. The C++ code and the data sets tested are available from the authors.

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