Combinatorial Approaches for Mass Spectra Recalibration

Mass spectrometry has become one of the most popular analysis techniques in Proteomics and Systems Biology. With the creation of larger datasets, the automated recalibration of mass spectra becomes important to ensure that every peak in the sample spectrum is correctly assigned to some peptide and protein. Algorithms for recalibrating mass spectra have to be robust with respect to wrongly assigned peaks, as well as efficient due to the amount of mass spectrometry data. The recalibration of mass spectra leads us to the problem of finding an optimal matching between mass spectra under measurement errors. We have developed two deterministic methods that allow robust computation of such a matching: The first approach uses a computational geometry interpretation of the problem, and tries to find two parallel lines with constant distance that stab a maximal number of points in the plane. The second approach is based on finding a maximal common approximate subsequence, and improves existing algorithms by one order of magnitude exploiting the sequential nature of the matching problem. We compare our results to a computational geometry algorithm using a topological line-sweep

Orthogonal weighted linear L1 and L∞ approximation and applications

AbstractLet S={s1,s2,...,sn} be a set of sites in Ed, where every site si has a positive real weight ωi. This paper gives algorithms to find weighted orthogonal L∞ and L1 approximating hyperplanes for S. The algorithm for the weighted orthogonal L1 approximation is shown to require O(nd) worst-case time and O(n) space for d ≥ 2. The algorithm for the weighted orthogonal L∞ approximation is shown to require O(n log n) worst-case time and O(n) space for d = 2, and O(n⌊dl2 + 1⌋) worst-case time and O(n⌊(d+1)/2⌋) space for d > 2. In the latter case, the expected time complexity may be reduced to O(n⌊(d+1)/2⌋). The L∞ approximation algorithm can be modified to solve the problem of finding the width of a set of n points in Ed, and the problem of finding a stabbing hyperplane for a set of n hyperspheres in Ed with varying radii. The time and space complexities of the width and stabbing algorithms are seen to be the same as those of the L∞ approximation algorithm

Algorithms for the Analysis of Spatio-Temporal Data from Team Sports

Modern object tracking systems are able to simultaneously record trajectories—sequences of time-stamped location points—for large numbers of objects with high frequency and accuracy. The availability of trajectory datasets has resulted in a consequent demand for algorithms and tools to extract information from these data. In this thesis, we present several contributions intended to do this, and in particular, to extract information from trajectories tracking football (soccer) players during matches. Football player trajectories have particular properties that both facilitate and present challenges for the algorithmic approaches to information extraction. The key property that we look to exploit is that the movement of the players reveals information about their objectives through cooperative and adversarial coordinated behaviour, and this, in turn, reveals the tactics and strategies employed to achieve the objectives. While the approaches presented here naturally deal with the application-specific properties of football player trajectories, they also apply to other domains where objects are tracked, for example behavioural ecology, traffic and urban planning