We describe an algorithm, IsoRank, for global alignment of two protein-protein interaction (PPI) networks. IsoRank aims to maximize the overall match between the two networks; in contrast, much of previous work has focused on the local alignment problem— identifying many possible alignments, each corresponding to a local region of similarity. IsoRank is guided by the intuition that a protein sh...

We propose a new retrieval system based on musical structure using symbolic structural queries. The aim is to compare musical form in audio files without extracting explicitly the underlying audio structure. From a given or arbitrary segmentation, an audio file is segmented. Irrespective of the audio feature choice, we then compute a selfsimilarity matrix whose coefficients correspond to the es...

The intra-nuclear organisation of proteins is based on possibly transient interactions with morphologically defined compartments like the nucleolus. The fluidity of trafficking challenges the development of models that accurately identify compartment membership for novel proteins. A growing inventory of nucleolar proteins is here used to train a support-vector machine to recognise sequence feat...

We prove that the space of smooth Riemannian metrics on the three-ball with non-negative Ricci curvature and strictly convex boundary is path-connected; and, moreover, that the associated moduli space (i.e., modulo orientation-preserving diffeomorphisms of the threeball) is contractible. As an application, using results of Maximo, Nunes, and Smith [MNS], we show the existence of properly embedd...

In this paper, we present an evaluation of two different sentence alignment techniques. One is the well-known SIMR algorithm based on word correspondences on both sides of a bitext. The other one is the ALINOR algorithm, which is based on the similarity of the markup on both sides of a bitext. Both algorithms are accurate in 1-1 alignment, but ALINOR works slightly better in the case of N-M ali...

The algorithm of Gotoh computes in two passes of MN steps the alignment of a pair of sequences of lengths M and N, subject to a constraint on the form of the gap weighting function. This compares with the previous algorithm of Waterman et al. which runs in M2N steps. Gotoh also gave a method using two passes of (L+2)MN steps in the case where gap weights remain constant for gaps of length great...