Definition Of Overlap Research Articles

Perception of overlap in multi-modal urban transit route choice

Capturing unobserved correlation between overlapping routes is a non-trivial problem in route choice modelling. For urban transit networks, research so far has been inconclusive on how this overlap is perceived by travellers. We estimate a series of path size correction logit (PSCL) models to account for alternative specifications of route overlap, including a new definition of overlap in terms of transfer nodes is proposed for multi-leg journeys. Our estimation is performed on smart card data from Amsterdam. The results indicate that the overlap between transit routes is valued positively when incorporated using either link-based, leg-based or transfer node-based PSC individually, with the transfer node-based PSC resulting in the best model fit. When considered simultaneously, the overlap of transfer nodes is valued positively by the travellers, but the subsequent overlap of journey legs is valued negatively, implying that travellers prefer having multiple (distinct) travel options at common transfer locations.

A Genetic Algorithm for Identifying Overlapping Communities in Social Networks Using an Optimized Search Space

There are currently many approaches to identify the community structure of a network, but relatively few specific to detect overlapping community structures. Likewise, there are few networks with ground truth overlapping nodes. For this reason,we introduce a new network, Pilgrim, with known overlapping nodes, and a new genetic algorithm for detecting such nodes. Pilgrim is comprised of a variety of structures including two communities with dense overlap,which is common in real social structures. This study initially explores the potential of the community detection algorithm LabelRank for consistent overlap detection; however, the deterministic nature of this algorithm restricts it to very few candidate solutions. Therefore, we propose a genetic algorithm using a restricted edge-based clustering technique to detect overlapping communities by maximizing an efficient overlapping modularity function. The proposed restriction to the edge-based representation precludes the possibility of disjoint communities, thereby, dramatically reducing the search space and decreasing the number of generations required to produce an optimal solution. A tunable parameterr allows the strictness of the definition of overlap to be adjusted allowing for refinement in the number of identified overlapping nodes. Our method, tested on several real social networks, yields results comparable to the most effective overlapping community detection algorithms to date.

The Effect of Algorithms on Copy Number Variant Detection

BackgroundThe detection of copy number variants (CNVs) and the results of CNV-disease association studies rely on how CNVs are defined, and because array-based technologies can only infer CNVs, CNV-calling algorithms can produce vastly different findings. Several authors have noted the large-scale variability between CNV-detection methods, as well as the substantial false positive and false negative rates associated with those methods. In this study, we use variations of four common algorithms for CNV detection (PennCNV, QuantiSNP, HMMSeg, and cnvPartition) and two definitions of overlap (any overlap and an overlap of at least 40% of the smaller CNV) to illustrate the effects of varying algorithms and definitions of overlap on CNV discovery.Methodology and Principal FindingsWe used a 56 K Illumina genotyping array enriched for CNV regions to generate hybridization intensities and allele frequencies for 48 Caucasian schizophrenia cases and 48 age-, ethnicity-, and gender-matched control subjects. No algorithm found a difference in CNV burden between the two groups. However, the total number of CNVs called ranged from 102 to 3,765 across algorithms. The mean CNV size ranged from 46 kb to 787 kb, and the average number of CNVs per subject ranged from 1 to 39. The number of novel CNVs not previously reported in normal subjects ranged from 0 to 212.Conclusions and SignificanceMotivated by the availability of multiple publicly available genome-wide SNP arrays, investigators are conducting numerous analyses to identify putative additional CNVs in complex genetic disorders. However, the number of CNVs identified in array-based studies, and whether these CNVs are novel or valid, will depend on the algorithm(s) used. Thus, given the variety of methods used, there will be many false positives and false negatives. Both guidelines for the identification of CNVs inferred from high-density arrays and the establishment of a gold standard for validation of CNVs are needed.

Path Size Modeling in Multimodal Route Choice Analysis

Travelers in multimodal networks make many choices (e.g., main mode, access modes, egress modes, boarding nodes, transfer nodes, and egress nodes). One way to address this complexity of choices is to analyze choice sets of multimodal routes. However, choice sets for multimodal networks are large, and of routes within choice sets is substantial. This paper focuses on in multimodal transport networks. An overview of the topic of and route choice modeling is given and is followed by an analysis of how might be defined in the context of multimodal networks. Three definitions of overlap are proposed, based on number of legs, time, or distance. The different definitions are analyzed using logit estimations, which show that must be accounted for. Furthermore, the definition of path size for multimodal transport networks should be different from that used for road networks: for multimodal transport networks, a definition using number of legs yields substanti...