Pattern matching and pattern discovery algorithms for protein topologies

We describe algorithms for pattern matching and pattern learning in TOPS diagrams (formal descriptions of protein topologies). These problems can be reduced to checking for subgraph isomorphism and finding maximal common subgraphs in a restricted class of ordered graphs. We have developed a subgraph isomorphism algorithm for ordered graphs, which performs well on the given set of data. The maximal common subgraph problem then is solved by repeated subgraph extension and checking for isomorphisms. Despite the apparent inefficiency such approach gives an algorithm with time complexity proportional to the number of graphs in the input set and is still practical on the given set of data. As a result we obtain fast methods which can be used for building a database of protein topological motifs, and for the comparison of a given protein of known secondary structure against a motif database

Persistent topology of the reionisation bubble network. I: Formalism & Phenomenology

We present a new formalism for studying the topology of HII regions during the Epoch of Reionisation, based on persistent homology theory. With persistent homology, it is possible to follow the evolution of topological features over time. We introduce the notion of a persistence field as a statistical summary of persistence data and we show how these fields can be used to identify different stages of reionisation. We identify two new stages common to all bubble ionisation scenarios. Following an initial pre-overlap and subsequent overlap stage, the topology is first dominated by neutral filaments (filament stage) and then by enclosed patches of neutral hydrogen undergoing outside-in ionisation (patch stage). We study how these stages are affected by the degree of galaxy clustering. We also show how persistence fields can be used to study other properties of the ionisation topology, such as the bubble size distribution and the fractal-like topology of the largest ionised region.Comment: 18 pages, 12 figures, 1 table. Submitted to MNRA

Algorithms for the Problems of Length-Constrained Heaviest Segments

We present algorithms for length-constrained maximum sum segment and maximum density segment problems, in particular, and the problem of finding length-constrained heaviest segments, in general, for a sequence of real numbers. Given a sequence of n real numbers and two real parameters L and U (L <= U), the maximum sum segment problem is to find a consecutive subsequence, called a segment, of length at least L and at most U such that the sum of the numbers in the subsequence is maximum. The maximum density segment problem is to find a segment of length at least L and at most U such that the density of the numbers in the subsequence is the maximum. For the first problem with non-uniform width there is an algorithm with time and space complexities in O(n). We present an algorithm with time complexity in O(n) and space complexity in O(U). For the second problem with non-uniform width there is a combinatorial solution with time complexity in O(n) and space complexity in O(U). We present a simple geometric algorithm with the same time and space complexities. We extend our algorithms to respectively solve the length-constrained k maximum sum segments problem in O(n+k) time and O(max{U, k}) space, and the length-constrained $k$ maximum density segments problem in O(n min{k, U-L}) time and O(U+k) space. We present extensions of our algorithms to find all the length-constrained segments having user specified sum and density in O(n+m) and O(nlog (U-L)+m) times respectively, where m is the number of output. Previously, there was no known algorithm with non-trivial result for these problems. We indicate the extensions of our algorithms to higher dimensions. All the algorithms can be extended in a straight forward way to solve the problems with non-uniform width and non-uniform weight.Comment: 21 pages, 12 figure

From coinductive proofs to exact real arithmetic: theory and applications

Based on a new coinductive characterization of continuous functions we extract certified programs for exact real number computation from constructive proofs. The extracted programs construct and combine exact real number algorithms with respect to the binary signed digit representation of real numbers. The data type corresponding to the coinductive definition of continuous functions consists of finitely branching non-wellfounded trees describing when the algorithm writes and reads digits. We discuss several examples including the extraction of programs for polynomials up to degree two and the definite integral of continuous maps