An Extended Stable Marriage Problem Algorithm for Clone Detection

Code cloning negatively affects industrial software and threatens intellectual property. This paper presents a novel approach to detecting cloned software by using a bijective matching technique. The proposed approach focuses on increasing the range of similarity measures and thus enhancing the precision of the detection. This is achieved by extending a well-known stable-marriage problem (SMP) and demonstrating how matches between code fragments of different files can be expressed. A prototype of the proposed approach is provided using a proper scenario, which shows a noticeable improvement in several features of clone detection such as scalability and accuracy.Comment: 20 pages, 10 figures, 6 table

Hyperspectral classification of Cyperus esculentus clones and morphologically similar weeds

Cyperus esculentus (yellow nutsedge) is one of the world's worst weeds as it can cause great damage to crops and crop production. To eradicate C. esculentus, early detection is key-a challenging task as it is often confused with other Cyperaceae and displays wide genetic variability. In this study, the objective was to classify C. esculentus clones and morphologically similar weeds. Hyperspectral reflectance between 500 and 800 nm was tested as a measure to discriminate between (I) C. esculentus and morphologically similar Cyperaceae weeds, and between (II) different clonal populations of C. esculentus using three classification models: random forest (RF), regularized logistic regression (RLR) and partial least squares-discriminant analysis (PLS-DA). RLR performed better than RF and PLS-DA, and was able to adequately classify the samples. The possibility of creating an affordable multispectral sensing tool, for precise in-field recognition of C. esculentus plants based on fewer spectral bands, was tested. Results of this study were compared against simulated results from a commercially available multispectral camera with four spectral bands. The model created with customized bands performed almost equally well as the original PLS-DA or RLR model, and much better than the model describing multispectral image data from a commercially available camera. These results open up the opportunity to develop a dedicated robust tool for C. esculentus recognition based on four spectral bands and an appropriate classification model

MP 2012-02

Final report to BP.The Prudhoe Bay oil fields, Alaska were discovered in 1968, and commercial production commenced in 1977 with the completion of the Trans-Alaska Pipeline. Oil production has been declining since 1989, although additional exploratory drilling continues. Support facilities for oil production are built on permafrost soils that surface-thaw in summer to form extensive wetlands composed of moist meadows, sedge marshes, moist sedge-dwarf shrub tundra, grass marshes, small ponds and lakes (Walker and Acevedo 1987). To prevent thawing and subsidence of subsurface, ice-rich soils, gravel pads, 2m (6 ft) or more thickness have been built to support drilling sites as well as roads, airstrips and building pads (Kidd et al. 2006). As well sites are decommissioned, the gravel is wholly or partially removed resulting in the need for site rehabilitation and/or restoration to support wetland plants and, in some instances, enhance wildlife habitat (McKendrick 1991, Jorgenson and Joyce 1994, Kidd et al. 2004, 2006). Since the 1970s, methods to revegetate arctic wetlands have included a variety of planting techniques, seed treatments, seeding with native and non-native species (mostly grasses), and fertilizer applications (Chapin and Chapin 1980; Bishop and Chapin 1989, Jorgenson 1988, Kidd and Rossow 1998, Kidd et al. 2004, 2006, Maslen and Kershaw 1989, McKendrick 1987, 1991, 2000, McKendrick et al. 1980, McKendrick and Mitchell 1978, Mitchell et al. 1974). Treatments also have included sprigging and plug transplantation (Kidd et al. 2004, 2006), surface manipulation (Streever et al. 2003), as well as natural re-colonization (Ebersole 1987, Schwarzenbach 1996). These methods have been partially successful. The gravelly soils often are dry, nutrient-poor, and have a higher pH and lower organic matter content than surrounding soils, so natural recolonization does not occur readily (Bishop and Chapin 1989, Jorgenson and Joyce 1994). Methods such as sprigging and plug transplanting are slow, labor intensive and expensive compared to direct seeding. Fertilization, especially with phosphorus, is recommended for long-term survival of plants grown on gravelly sandy soils (BP Exploration and McKendrick 2004). Two common species in the arctic coastal wetlands are water sedge, Carex aquatilis Wahlenb. and cotton sedge, Eriophorum angustifolium Honck. Carex aquatilis in particular forms large populations that spread vegetatively by rhizomes and often dominate these wetland environments (Shaver and Billings 1975). Despite their abundance, these species have not been considered for revegetation because of poor seed germination and inadequate information on seed development and viability (Dr. William Streever, BP Alaska, pers. comm.). Both Carex and Eriophorum in arctic environments produce abundant seeds, but seed viability and germination often is low and highly variable among years and locations (Archibold 1984, Billings and Mooney 1968, Ebersole 1989, Gartner et al. 1983). Germination recommendations for both species vary by location and have included an array of pretreatments such as light, alternating temperatures, cold stratification, scarification, and high and low temperature dry storage (Amen 1966, Billings and Mooney 1960, Bliss 1958, Hunt and Moore 2003, Johnson et al. 1965, Phillips 1954 and Steinfeld 2001). The purpose of this project was to explore methods of seed germination of Carex aquatilis and Eriophorum angustifolium, to learn the conditions for germination and dormancy control mechanisms, and identify seed treatments that might enhance germination for eventual use in direct-seeding or plug production for arctic wetland revegetation

Influence of chance, history, and adaptation on digital evolution

We evolved multiple clones of populations of digital organisms to study the effects of chance, history, and adaptation in evolution. We show that clones adapted to a specific environment can adapt to new environments quickly and efficiently, although their history remains a significant factor in their fitness. Adaptation is most significant (and the effects of history less so) if the old and new environments are dissimilar. For more similar environments, adaptation is slower while history is more prominent. For both similar and dissimilar transfer environments, populations quickly lose the ability to perform computations (the analogue of beneficial chemical reactions) that are no longer rewarded in the new environment. Populations that developed few computational "genes" in their original environment were unable to acquire them in the new environment

Experimental evolution reveals high insecticide tolerance in Daphnia inhabiting farmland ponds

Exposure of nontarget populations to agricultural chemicals is an important aspect of global change. We quantified the capacity of natural Daphnia magna populations to locally adapt to insecticide exposure through a selection experiment involving carbaryl exposure and a control. Carbaryl tolerance after selection under carbaryl exposure did not increase significantly compared to the tolerance of the original field populations. However, there was evolution of a decreased tolerance in the control experimental populations compared to the original field populations. The magnitude of this decrease was positively correlated with land use intensity in the neighbourhood of the ponds from which the original populations were sampled. The genetic change in carbaryl tolerance in the control rather than in the carbaryl treatment suggests widespread selection for insecticide tolerance in the field associated with land use intensity and suggests that this evolution comes at a cost. Our data suggest a strong impact of current agricultural land use on nontarget natural Daphnia populations

The Mpemba effect in spin glasses is a persistent memory effect

The Mpemba effect occurs when a hot system cools faster than an initially colder one, when both are refrigerated in the same thermal reservoir. Using the custom built supercomputer Janus II, we study the Mpemba effect in spin glasses and show that it is a non-equilibrium process, governed by the coherence length \xi of the system. The effect occurs when the bath temperature lies in the glassy phase, but it is not necessary for the thermal protocol to cross the critical temperature. In fact, the Mpemba effect follows from a strong relationship between the internal energy and \xi that turns out to be a sure-tell sign of being in the glassy phase. Thus, the Mpemba effect presents itself as an intriguing new avenue for the experimental study of the coherence length in supercooled liquids and other glass formers.Comment: Version accepted for publication in PNAS. 6 pages, 7 figure