Efficiently computing weighted proximity relationships in spatial databases

Spatial data mining recently emerges from a number of real applications, such as real-estate marketing, urban planning, weather forecasting, medical image analysis, road traffic accident analysis, etc. It demands for efficient solutions for many new, expensive, and complicated problems. In this paper, we investigate the problem of evaluating the top k distinguished “features” for a “cluster” based on weighted proximity relationships between the cluster and features. We measure proximity in an average fashion to address possible nonuniform data distribution in a cluster. Combining a standard multi-step paradigm with new lower and upper proximity bounds, we presented an efficient algorithm to solve the problem. The algorithm is implemented in several different modes. Our experiment results not only give a comparison among them but also illustrate the efficiency of the algorithm.

On Solving the Maximum Betweenness Problem Using Genetic Algorithms

In this paper a genetic algorithm (GA) is applied on Maximum Betweennes Problem (MBP). The maximum of the objective function is obtained by finding a permutation which satisfies a maximal number of betweenness constraints. Every permutation considered is genetically coded with an integer representation. Standard operators are used in the GA. Instances in the experimental results are randomly generated. For smaller dimensions, optimal solutions of MBP are obtained by total enumeration. For those instances, the GA reached all optimal solutions except one. The GA also obtained results for larger instances of up to 50 elements and 1000 triples. The running time of execution and finding optimal results is quite short.

Solving Maximum Clique Problem for Protein Structure Similarity

Computing the similarity between two protein structures is a crucial task in molecular biology, and has been extensively investigated. Many protein structure comparison methods can be modeled as maximum weighted clique problems in specific k-partite graphs, referred here as alignment graphs. In this paper we present both a new integer programming formulation for solving such clique problems and a dedicated branch and bound algorithm for solving the maximum cardinality clique problem. Both approaches have been integrated in VAST, a software for aligning protein 3D structures largely used in the National Center for Biotechnology Information, an original clique solver which uses the well known Bron and Kerbosch algorithm (BK). Our computational results on real protein alignment instances show that our branch and bound algorithm is up to 116 times faster than BK.

Using Inside-Outside Algorithm for Estimation of the Offspring Distribution in Multitype Branching Processes

Multitype branching processes (MTBP) model branching structures, where the nodes of the resulting tree are particles of different types. Usually such a process is not observable in the sense of the whole tree, but only as the “generation” at a given moment in time, which consists of the number of particles of every type. This requires an EM-type algorithm to obtain a maximum likelihood (ML) estimate of the parameters of the branching process. Using a version of the inside-outside algorithm for stochastic context-free grammars (SCFG), such an estimate could be obtained for the offspring distribution of the process.

An efficient, approximate path-following algorithm for elastic net based nonlinear spike enhancement

Unwanted spike noise in a digital signal is a common problem in digital filtering. However, sometimes the spikes are wanted and other, superimposed, signals are unwanted, and linear, time invariant (LTI) filtering is ineffective because the spikes are wideband - overlapping with independent noise in the frequency domain. So, no LTI filter can separate them, necessitating nonlinear filtering. However, there are applications in which the noise includes drift or smooth signals for which LTI filters are ideal. We describe a nonlinear filter formulated as the solution to an elastic net regularization problem, which attenuates band-limited signals and independent noise, while enhancing superimposed spikes. Making use of known analytic solutions a novel, approximate path-following algorithm is given that provides a good, filtered output with reduced computational effort by comparison to standard convex optimization methods. Accurate performance is shown on real, noisy electrophysiological recordings of neural spikes.

A Variable Neighborhood Search Approach for Solving the Maximum Set Splitting Problem

This paper presents a Variable neighbourhood search (VNS) approach for solving the Maximum Set Splitting Problem (MSSP). The algorithm forms a system of neighborhoods based on changing the component for an increasing number of elements. An efficient local search procedure swaps the components of pairs of elements and yields a relatively short running time. Numerical experiments are performed on the instances known in the literature: minimum hitting set and Steiner triple systems. Computational results show that the proposed VNS achieves all optimal or best known solutions in short times. The experiments indicate that the VNS compares favorably with other methods previously used for solving the MSSP. ACM Computing Classification System (1998): I.2.8.

Em Algorithm for MLE of a Probit Model for Multiple Ordinal Outcomes

The correlated probit model is frequently used for multiple ordered data since it allows to incorporate seamlessly different correlation structures. The estimation of the probit model parameters based on direct maximization of the limited information maximum likelihood is a numerically intensive procedure. We propose an extension of the EM algorithm for obtaining maximum likelihood estimates for a correlated probit model for multiple ordinal outcomes. The algorithm is implemented in the free software environment for statistical computing and graphics R. We present two simulation studies to examine the performance of the developed algorithm. We apply the model to data on 121 women with cervical or endometrial cancer. Patients developed normal tissue reactions as a result of post-operative external beam pelvic radiotherapy. In this work we focused on modeling the effects of a genetic factor on early skin and early urogenital tissue reactions and on assessing the strength of association between the two types of reactions. We established that there was an association between skin reactions and polymorphism XRCC3 codon 241 (C>T) (rs861539) and that skin and urogenital reactions were positively correlated. ACM Computing Classification System (1998): G.3.

An Algorithm to Mine Normalized Weighted Sequential Patterns Using a Prefix-projected Database

Sequential pattern mining is an important subject in data mining with broad applications in many different areas. However, previous sequential mining algorithms mostly aimed to calculate the number of occurrences (the support) without regard to the degree of importance of different data items. In this paper, we propose to explore the search space of subsequences with normalized weights. We are not only interested in the number of occurrences of the sequences (supports of sequences), but also concerned about importance of sequences (weights). When generating subsequence candidates we use both the support and the weight of the candidates while maintaining the downward closure property of these patterns which allows to accelerate the process of candidate generation.

DFIG machine design for maximizing power output based on surrogate optimization algorithm

This paper presents a surrogate-model-based optimization of a doubly-fed induction generator (DFIG) machine winding design for maximizing power yield. Based on site-specific wind profile data and the machine's previous operational performance, the DFIG's stator and rotor windings are optimized to match the maximum efficiency with operating conditions for rewinding purposes. The particle swarm optimization-based surrogate optimization techniques are used in conjunction with the finite element method to optimize the machine design utilizing the limited available information for the site-specific wind profile and generator operating conditions. A response surface method in the surrogate model is developed to formulate the design objectives and constraints. Besides, the machine tests and efficiency calculations follow IEEE standard 112-B. Numerical and experimental results validate the effectiveness of the proposed technologies.

Investigating the effect of geographical distances and cultural proximity on the Hungarian wine trade

Wine is a very special product from an economic, cultural, and sociological point of view. Wine culture and wine trade play an important role in Hungary. The effect of cultural and geographical proximity on international trade has already been proven in the international trade literature. The size of bilateral trade flows between any two countries can be approximated by the gravity theory of trade. The gravity model provides empirical evidence of the relationship between the size of the economies, the distances between them, and their trade. This paper seeks to analyse the effect of cultural and geographical proximity on Hungary’s bilateral wine trade between 2000 and 2012, employing the gravity equation. The analysis is based on data from the World Bank WITS, WDI, as well as CEPII, and WTO databases. I apply OLS, Random Effects, Poisson, Pseudo-Poisson-Maximum-Likelihood and Heckman two stage estimators to calculate the gravity regression. The results show that in the case of Hungary, cultural similarity and trade liberalisation have a positive impact, while geographical distance, landlockedness, and contiguity have a negative impact on Hungarian wine exports.

(Table 3) Barium barite and excess comparison, accumulation rates and productivity from surface sediments

Since Dymond et al. (1992, doi:10.1029/92PA00181) proposed the paleoproductivity algorithm based on "Bio-Ba", which relies on a strong correlation between Ba and organic carbon fluxes in sediment traps, this proxy has been applied in many paleoproductivity studies. Barite, the main carrier of particulate barium in the water column and the phase associated with carbon export, has also been suggested as a reliable paleoproductivity proxy in some locations. We demonstrate that Ba(excess) (total barium minus the fraction associated with terrigenous material) frequently overestimates Ba(barite) (barium associated with the mineral barite), most likely due to the inclusion of barium from phases other than barite and terrigenous silicates (e.g., carbonate, organic matter, opal, Fe-Mn oxides, and hydroxides). A comparison between overlying oceanic carbon export and carbon export derived from Ba(excess) shows that the Dymond et al. (1992) algorithm frequently underestimates carbon export but is still a useful carbon export indicator if all caveats are considered before the algorithm is applied. Ba(barite) accumulation rates from a wide range of core top sediments from different oceanic settings are highly correlated to surface ocean 14C and Chlorophyll a measurements of primary production. This relationship varies by ocean basin, but with the application of the appropriate f ratio to 14C and Chlorophyll a primary production estimates, the plot of Ba(barite) accumulation and carbon export for the equatorial Pacific, Atlantic, and Southern Ocean converges to a global relationship that can be used to reconstruct paleo carbon export.

Last glacial maximum sediment record of the southern Weddell Sea shelf

Abstract: The history of grounded ice-sheet extent on the southern Weddell Sea shelf during the Last Glacial Maximum (LGM) and the timing of post-LGM ice-sheet retreat are poorly constrained. Several glaciological models reconstructed widespread grounding and major thickening of the Antarctic Ice Sheet in the Weddell Sea sector at the LGM. In contrast, recently published onshore data and modelling results concluded only very limited LGM-thickening of glaciers and ice streams feeding into the modern Filchner and Ronne ice shelves. These studies concluded that during the LGM ice shelves rather than grounded ice covered the Filchner and Ronne troughs, two deep palaeo-ice stream troughs eroded into the southern Weddell Sea shelf. Here we review previously published and unpublished marine geophysical and geological data from the southern Weddell Sea shelf. The stratigraphy and geometry of reflectors in acoustic sub-bottom profiles are similar to those from other West Antarctic palaeo-ice stream troughs, where grounded ice had advanced to the shelf break at the LGM. Numerous cores from the southern Weddell Sea shelf recovered sequences with properties typical for subglacially deposited tills or subglacially compacted sediments. These data sets give evidence that grounded ice had advanced across the shelf during the past, thereby grounding in even the deepest parts of the Filchner and Ronne troughs. Radiocarbon dates from glaciomarine sediments overlying the subglacial deposits are limited, but indicate that the ice grounding occurred at the LGM and that ice retreat started before ~15.1 corrected 14C kyrs before present (BP) on the outer shelf and before ~7.7 corrected 14C kyrs BP on the inner shelf, which is broadly synchronous with ice retreat in other Antarctic sectors. The apparent mismatch between the ice-sheet reconstructions from marine and terrestrial data can be attributed to ice streams with very low surface profiles (similar to those of "ice plains") that had advanced through Filchner Trough and Ronne Trough at the LGM. Considering the global sea-level lowstand of ~130 metres below present, a low surface slope of the expanded LGM-ice sheet in the southern Weddell Sea can reconcile grounding-line advance to the shelf break with limited thickening of glaciers and ice streams in the hinterland. This scenario implies that ice-sheet growth in the Weddell Sea sector during the LGM and ice-sheet drawdown throughout the last deglaciation could only have made minor contributions to the major global sea-level fluctuations during these times.

Sedimentary record of the western Amundsen Sea Embayment after the last glacial maximum

Reliable dating of glaciomarine sediments deposited on the Antarctic shelf since the Last Glacial Maximum (LGM) is very challenging because of the general absence of calcareous (micro-) fossils and the recycling of fossil organic matter. As a consequence, radiocarbon (14C) ages of the acid-insoluble organic fraction (AIO) of the sediments bear uncertainties that are very difficult to quantify. In this paper we present the results of three different chronostratigraphic methods to date a sedimentary unit consisting of diatomaceous ooze and diatomaceous mud that was deposited following the last deglaciation at five core sites on the inner shelf in the western Amundsen Sea (West Antarctica). In three cores conventional 14C dating of the AIO in bulk sediment samples yielded age reversals down-core, but at all sites the AIO 14C ages obtained from diatomaceous ooze within the diatom-rich unit yielded similar uncorrected 14C ages ranging from 13,517±56 to 11,543±47 years before present (yr BP). Correction of these ages by subtracting the core-top ages, which are assumed to reflect present-day deposition (as indicated by 21044 Pb dating of the sediment surface at one core site), yielded ages between ca. 10,500 and 8,400 calibrated years before present (cal yr BP). Correction of the AIO ages of the diatomaceous ooze by only subtracting the marine reservoir effect (MRE) of 1,300 years indicated deposition of the diatom-rich sediments between 14,100 and 11,900 cal yr BP. Most of these ages are consistent with age constraints between 13.0 and 8.0 ka BP for the diatom-rich unit, which we obtained by correlating the relative palaeomagnetic intensity (RPI) records of three of the sediment cores with global and regional reference curves for palaeomagnetic intensity. As a third dating technique we applied conventional 53 radiocarbon dating of the AIO included in acid-cleaned diatom hard parts that were extracted from the diatomaceous ooze. This method yielded uncorrected 14C ages of only 5,111±38 and 5,106±38 yr BP, respectively. We reject these young ages, because they are likely to be overprinted by the adsorption of modern atmospheric carbon dioxide onto the surfaces of the extracted diatom hard parts prior to sample graphitisation and combustion for 14C dating. The deposition of the diatom-rich unit in the western Amundsen Sea suggests deglaciation of the inner shelf before ca. 13 ka BP. The deposition of diatomaceous oozes on other parts of the Antarctic shelf around the same time, however, seems to be coincidental rather than directly related.

Sediment age, abundance of planktonic foraminifera shells, degree of their dissolution, percentage of benthic foraminifera in total foram fauna, Core GC-11, Sea of Okhotsk

Taxonomic composition and distribution of planktonic foraminifera are studied in section of Core GC-11 penetrated through Upper Quaternary sediments of the Bowers Ridge western slope, south Bering Sea. It is shown that structure of foraminiferal assemblage and productivity varied substantially during the last 32000 calendar years in response to changes in surface water temperatures and water mass circulation in the North Pacific including the Bering Sea. Productivity was maximal during the deglaciation epoch, being notably lower in Holocene and minimal at glaciation time.

Sea-surface temperature and sea ice distribution of the Southern Ocean at the EPILOG Last Glacial Maximum

Based on the quantitative study of diatoms and radiolarians, summer sea-surface temperature (SSST) and sea ice distribution were estimated from 122 sediment core localities in the Atlantic, Indian and Pacific sectors of the Southern Ocean to reconstruct the last glacial environment at the EPILOG (19.5-16.0 ka or 23 000-19 000 cal yr. B.P.) time-slice. The statistical methods applied include the Imbrie and Kipp Method, the Modern Analog Technique and the General Additive Model. Summer SSTs reveal greater surface-water cooling than reconstructed by CLIMAP (Geol. Soc. Am. Map Chart. Ser. MC-36 (1981) 1), reaching a maximum (4-5 °C) in the present Subantarctic Zone of the Atlantic and Indian sector. The reconstruction of maximum winter sea ice (WSI) extent is in accordance with CLIMAP, showing an expansion of the WSI field by around 100% compared to the present. Although only limited information is available, the data clearly show that CLIMAP strongly overestimated the glacial summer sea ice extent. As a result of the northward expansion of Antarctic cold waters by 5-10° in latitude and a relatively small displacement of the Subtropical Front, thermal gradients were steepened during the last glacial in the northern zone of the Southern Ocean. Such reconstruction may, however, be inapposite for the Pacific sector. The few data available indicate reduced cooling in the southern Pacific and give suggestion for a non-uniform cooling of the glacial Southern Ocean.