Analyze Large Multidimensional Datasets Using Algebraic Topology

This paper presents an efficient algorithm to extract knowledge from high-dimensionality, high- complexity datasets using algebraic topology, namely simplicial complexes. Based on concept of isomorphism of relations, our method turn a relational table into a geometric object (a simplicial complex is a polyhedron). So, conceptually association rule searching is turned into a geometric traversal problem. By leveraging on the core concepts behind Simplicial Complex, we use a new technique (in computer science) that improves the performance over existing methods and uses far less memory. It was designed and developed with a strong emphasis on scalability, reliability, and extensibility. This paper also investigate the possibility of Hadoop integration and the challenges that come with the framework

Sixteen space-filling curves and traversals for d-dimensional cubes and simplices

This article describes sixteen different ways to traverse d-dimensional space recursively in a way that is well-defined for any number of dimensions. Each of these traversals has distinct properties that may be beneficial for certain applications. Some of the traversals are novel, some have been known in principle but had not been described adequately for any number of dimensions, some of the traversals have been known. This article is the first to present them all in a consistent notation system. Furthermore, with this article, tools are provided to enumerate points in a regular grid in the order in which they are visited by each traversal. In particular, we cover: five discontinuous traversals based on subdividing cubes into 2^d subcubes: Z-traversal (Morton indexing), U-traversal, Gray-code traversal, Double-Gray-code traversal, and Inside-out traversal; two discontinuous traversals based on subdividing simplices into 2^d subsimplices: the Hill-Z traversal and the Maehara-reflected traversal; five continuous traversals based on subdividing cubes into 2^d subcubes: the Base-camp Hilbert curve, the Harmonious Hilbert curve, the Alfa Hilbert curve, the Beta Hilbert curve, and the Butz-Hilbert curve; four continuous traversals based on subdividing cubes into 3^d subcubes: the Peano curve, the Coil curve, the Half-coil curve, and the Meurthe curve. All of these traversals are self-similar in the sense that the traversal in each of the subcubes or subsimplices of a cube or simplex, on any level of recursive subdivision, can be obtained by scaling, translating, rotating, reflecting and/or reversing the traversal of the complete unit cube or simplex.Comment: 28 pages, 12 figures. v2: fixed a confusing typo on page 12, line

Epistasis and Shapes of Fitness Landscapes

The relationship between the shape of a fitness landscape and the underlying gene interactions, or epistasis, has been extensively studied in the two-locus case. Gene interactions among multiple loci are usually reduced to two-way interactions. We present a geometric theory of shapes of fitness landscapes for multiple loci. A central concept is the genotope, which is the convex hull of all possible allele frequencies in populations. Triangulations of the genotope correspond to different shapes of fitness landscapes and reveal all the gene interactions. The theory is applied to fitness data from HIV and Drosophila melanogaster. In both cases, our findings refine earlier analyses and reveal previously undetected gene interactions.Comment: 31 pages, 7 figures; typos removed, Example 3.10 adde

Action potential energy efficiency varies among neuron types in vertebrates and invertebrates.

The initiation and propagation of action potentials (APs) places high demands on the energetic resources of neural tissue. Each AP forces ATP-driven ion pumps to work harder to restore the ionic concentration gradients, thus consuming more energy. Here, we ask whether the ionic currents underlying the AP can be predicted theoretically from the principle of minimum energy consumption. A long-held supposition that APs are energetically wasteful, based on theoretical analysis of the squid giant axon AP, has recently been overturned by studies that measured the currents contributing to the AP in several mammalian neurons. In the single compartment models studied here, AP energy consumption varies greatly among vertebrate and invertebrate neurons, with several mammalian neuron models using close to the capacitive minimum of energy needed. Strikingly, energy consumption can increase by more than ten-fold simply by changing the overlap of the Na+ and K+ currents during the AP without changing the APs shape. As a consequence, the height and width of the AP are poor predictors of energy consumption. In the Hodgkin–Huxley model of the squid axon, optimizing the kinetics or number of Na+ and K+ channels can whittle down the number of ATP molecules needed for each AP by a factor of four. In contrast to the squid AP, the temporal profile of the currents underlying APs of some mammalian neurons are nearly perfectly matched to the optimized properties of ionic conductances so as to minimize the ATP cost