Shape matching and clustering in design

Generalising knowledge and matching patterns is a basic human trait in re-using past experiences. We often cluster (group) knowledge of similar attributes as a process of learning and or aid to manage the complexity and re-use of experiential knowledge [1, 2]. In conceptual design, an ill-defined shape may be recognised as more than one type. Resulting in shapes possibly being classified differently when different criteria are applied. This paper outlines the work being carried out to develop a new technique for shape clustering. It highlights the current methods for analysing shapes found in computer aided sketching systems, before a method is proposed that addresses shape clustering and pattern matching. Clustering for vague geometric models and multiple viewpoint support are explored

Sequence-based Multiscale Model (SeqMM) for High-throughput chromosome conformation capture (Hi-C) data analysis

In this paper, I introduce a Sequence-based Multiscale Model (SeqMM) for the biomolecular data analysis. With the combination of spectral graph method, I reveal the essential difference between the global scale models and local scale ones in structure clustering, i.e., different optimization on Euclidean (or spatial) distances and sequential (or genomic) distances. More specifically, clusters from global scale models optimize Euclidean distance relations. Local scale models, on the other hand, result in clusters that optimize the genomic distance relations. For a biomolecular data, Euclidean distances and sequential distances are two independent variables, which can never be optimized simultaneously in data clustering. However, sequence scale in my SeqMM can work as a tuning parameter that balances these two variables and deliver different clusterings based on my purposes. Further, my SeqMM is used to explore the hierarchical structures of chromosomes. I find that in global scale, the Fiedler vector from my SeqMM bears a great similarity with the principal vector from principal component analysis, and can be used to study genomic compartments. In TAD analysis, I find that TADs evaluated from different scales are not consistent and vary a lot. Particularly when the sequence scale is small, the calculated TAD boundaries are dramatically different. Even for regions with high contact frequencies, TAD regions show no obvious consistence. However, when the scale value increases further, although TADs are still quite different, TAD boundaries in these high contact frequency regions become more and more consistent. Finally, I find that for a fixed local scale, my method can deliver very robust TAD boundaries in different cluster numbers.Comment: 22 PAGES, 13 FIGURE

Topological structures in the equities market network

We present a new method for articulating scale-dependent topological descriptions of the network structure inherent in many complex systems. The technique is based on "Partition Decoupled Null Models,'' a new class of null models that incorporate the interaction of clustered partitions into a random model and generalize the Gaussian ensemble. As an application we analyze a correlation matrix derived from four years of close prices of equities in the NYSE and NASDAQ. In this example we expose (1) a natural structure composed of two interacting partitions of the market that both agrees with and generalizes standard notions of scale (eg., sector and industry) and (2) structure in the first partition that is a topological manifestation of a well-known pattern of capital flow called "sector rotation.'' Our approach gives rise to a natural form of multiresolution analysis of the underlying time series that naturally decomposes the basic data in terms of the effects of the different scales at which it clusters. The equities market is a prototypical complex system and we expect that our approach will be of use in understanding a broad class of complex systems in which correlation structures are resident.Comment: 17 pages, 4 figures, 3 table

Self-similarity, small-world, scale-free scaling, disassortativity, and robustness in hierarchical lattices

In this paper, firstly, we study analytically the topological features of a family of hierarchical lattices (HLs) from the view point of complex networks. We derive some basic properties of HLs controlled by a parameter $q$. Our results show that scale-free networks are not always small-world, and support the conjecture that self-similar scale-free networks are not assortative. Secondly, we define a deterministic family of graphs called small-world hierarchical lattices (SWHLs). Our construction preserves the structure of hierarchical lattices, while the small-world phenomenon arises. Finally, the dynamical processes of intentional attacks and collective synchronization are studied and the comparisons between HLs and Barab{\'asi}-Albert (BA) networks as well as SWHLs are shown. We show that degree distribution of scale-free networks does not suffice to characterize their synchronizability, and that networks with smaller average path length are not always easier to synchronize.Comment: 26 pages, 8 figure

Topological properties of hierarchical networks

Hierarchical networks are attracting a renewal interest for modelling the organization of a number of biological systems and for tackling the complexity of statistical mechanical models beyond mean-field limitations. Here we consider the Dyson hierarchical construction for ferromagnets, neural networks and spin-glasses, recently analyzed from a statistical-mechanics perspective, and we focus on the topological properties of the underlying structures. In particular, we find that such structures are weighted graphs that exhibit high degree of clustering and of modularity, with small spectral gap; the robustness of such features with respect to link removal is also studied. These outcomes are then discussed and related to the statistical mechanics scenario in full consistency. Lastly, we look at these weighted graphs as Markov chains and we show that in the limit of infinite size, the emergence of ergodicity breakdown for the stochastic process mirrors the emergence of meta-stabilities in the corresponding statistical mechanical analysis

Economic sector identification in a set of stocks traded at the New York Stock Exchange: a comparative analysis

We review some methods recently used in the literature to detect the existence of a certain degree of common behavior of stock returns belonging to the same economic sector. Specifically, we discuss methods based on random matrix theory and hierarchical clustering techniques. We apply these methods to a set of stocks traded at the New York Stock Exchange. The investigated time series are recorded at a daily time horizon. All the considered methods are able to detect economic information and the presence of clusters characterized by the economic sector of stocks. However, different methodologies provide different information about the considered set. Our comparative analysis suggests that the application of just a single method could not be able to extract all the economic information present in the correlation coefficient matrix of a set of stocks.Comment: 13 pages, 8 figures, 2 Table

Shape matching and clustering

Generalising knowledge and matching patterns is a basic human trait in re-using past experiences. We often cluster (group) knowledge of similar attributes as a process of learning and or aid to manage the complexity and re-use of experiential knowledge [1, 2]. In conceptual design, an ill-defined shape may be recognised as more than one type. Resulting in shapes possibly being classified differently when different criteria are applied. This paper outlines the work being carried out to develop a new technique for shape clustering. It highlights the current methods for analysing shapes found in computer aided sketching systems, before a method is proposed that addresses shape clustering and pattern matching. Clustering for vague geometric models and multiple viewpoint support are explored