Copy number variation and transposable elements feature in recent, ongoing adaptation at the Cyp6g1 locus

The increased transcription of the Cyp6g1 gene of Drosophila melanogaster, and consequent resistance to insecticides such as DDT, is a widely cited example of adaptation mediated by cis-regulatory change. A fragment of an Accord transposable element inserted upstream of the Cyp6g1 gene is causally associated with resistance and has spread to high frequencies in populations around the world since the 1940s. Here we report the existence of a natural allelic series at this locus of D. melanogaster, involving copy number variation of Cyp6g1, and two additional transposable element insertions (a P and an HMS-Beagle). We provide evidence that this genetic variation underpins phenotypic variation, as the more derived the allele, the greater the level of DDT resistance. Tracking the spatial and temporal patterns of allele frequency changes indicates that the multiple steps of the allelic series are adaptive. Further, a DDT association study shows that the most resistant allele, Cyp6g1-[BP], is greatly enriched in the top 5% of the phenotypic distribution and accounts for ~16% of the underlying phenotypic variation in resistance to DDT. In contrast, copy number variation for another candidate resistance gene, Cyp12d1, is not associated with resistance. Thus the Cyp6g1 locus is a major contributor to DDT resistance in field populations, and evolution at this locus features multiple adaptive steps occurring in rapid succession.

An Intelligent Human-Computer Interaction System for Decision Support

This paper proposes a novel architecture for
developing decision support systems. Unlike conventional decision support systems, the proposed architecture endeavors to reveal the decision-making process such that humans' subjectivity can be
incorporated into a computerized system and, at the same time, to
preserve the capability of the computerized system in processing information objectively. A number of techniques used in developing the decision support system are elaborated to make the decisionmarking
process transparent. These include procedures for high dimensional data visualization, pattern classification, prediction, and evolutionary computational search. An artificial data set is first
employed to compare the proposed approach with other methods. A simulated handwritten data set and a real data set on liver disease diagnosis are then employed to evaluate the efficacy of the proposed
approach. The results are analyzed and discussed. The potentials of the proposed architecture as a useful decision support system are demonstrated.

Visualizing and classifying data using a hybrid intelligent system

In this paper, a hybrid intelligent system that integrates the SOM (Self-Organizing Map) neural network, kMER (kernel-based Maximum Entropy learning Rule), and Probabilistic Neural Network (PNN) for data visualization and classification is proposed. The rationales of this Probabilistic SOM-kMER model are explained, and its applicability is demonstrated using two benchmark data sets. The results are analyzed and compared with those from a number of existing methods. Implication of the proposed hybrid system as a useful and usable data visualization and classification tool is discussed.

Dimensionality reduction of protein mass spectrometry data using random projection

Protein mass spectrometry (MS) pattern recognition has recently emerged as a new method for cancer diagnosis. Unfortunately, classification performance may degrade owing to the enormously high dimensionality of the data. This paper investigates the use of Random Projection in protein MS data dimensionality reduction. The effectiveness of Random Projection (RP) is analyzed and compared against Principal Component Analysis (PCA) by using three classification algorithms, namely Support Vector Machine, Feed-forward Neural Networks and K-Nearest Neighbour. Three real-world cancer data sets are employed to evaluate the performances of RP and PCA. Through the investigations, RP method demonstrated better or at least comparable classification performance as PCA if the dimensionality of the projection matrix is sufficiently large. This paper also explores the use of RP as a pre-processing step prior to PCA. The results show that without sacrificing classification accuracy, performing RP prior to PCA significantly improves the computational time.