A Coverage Criterion for Spaced Seeds and its Applications to Support Vector Machine String Kernels and k-Mer Distances

Spaced seeds have been recently shown to not only detect more alignments, but also to give a more accurate measure of phylogenetic distances (Boden et al., 2013, Horwege et al., 2014, Leimeister et al., 2014), and to provide a lower misclassification rate when used with Support Vector Machines (SVMs) (On-odera and Shibuya, 2013), We confirm by independent experiments these two results, and propose in this article to use a coverage criterion (Benson and Mak, 2008, Martin, 2013, Martin and No{\'e}, 2014), to measure the seed efficiency in both cases in order to design better seed patterns. We show first how this coverage criterion can be directly measured by a full automaton-based approach. We then illustrate how this criterion performs when compared with two other criteria frequently used, namely the single-hit and multiple-hit criteria, through correlation coefficients with the correct classification/the true distance. At the end, for alignment-free distances, we propose an extension by adopting the coverage criterion, show how it performs, and indicate how it can be efficiently computed.Comment: http://online.liebertpub.com/doi/abs/10.1089/cmb.2014.017

Deep Learning as a Parton Shower

We make the connection between certain deep learning architectures and the renormalisation group explicit in the context of QCD by using a deep learning network to construct a toy parton shower model. The model aims to describe proton-proton collisions at the Large Hadron Collider. A convolutional autoencoder learns a set of kernels that efficiently encode the behaviour of fully showered QCD collision events. The network is structured recursively so as to ensure self-similarity, and the number of trained network parameters is low. Randomness is introduced via a novel custom masking layer, which also preserves existing parton splittings by using layer-skipping connections. By applying a shower merging procedure, the network can be evaluated on unshowered events produced by a matrix element calculation. The trained network behaves as a parton shower that qualitatively reproduces jet-based observables.Comment: 26 pages, 13 figure

Evolutionary distances in the twilight zone -- a rational kernel approach

Phylogenetic tree reconstruction is traditionally based on multiple sequence alignments (MSAs) and heavily depends on the validity of this information bottleneck. With increasing sequence divergence, the quality of MSAs decays quickly. Alignment-free methods, on the other hand, are based on abstract string comparisons and avoid potential alignment problems. However, in general they are not biologically motivated and ignore our knowledge about the evolution of sequences. Thus, it is still a major open question how to define an evolutionary distance metric between divergent sequences that makes use of indel information and known substitution models without the need for a multiple alignment. Here we propose a new evolutionary distance metric to close this gap. It uses finite-state transducers to create a biologically motivated similarity score which models substitutions and indels, and does not depend on a multiple sequence alignment. The sequence similarity score is defined in analogy to pairwise alignments and additionally has the positive semi-definite property. We describe its derivation and show in simulation studies and real-world examples that it is more accurate in reconstructing phylogenies than competing methods. The result is a new and accurate way of determining evolutionary distances in and beyond the twilight zone of sequence alignments that is suitable for large datasets.Comment: to appear in PLoS ON

The Integration of Connectionism and First-Order Knowledge Representation and Reasoning as a Challenge for Artificial Intelligence

Intelligent systems based on first-order logic on the one hand, and on artificial neural networks (also called connectionist systems) on the other, differ substantially. It would be very desirable to combine the robust neural networking machinery with symbolic knowledge representation and reasoning paradigms like logic programming in such a way that the strengths of either paradigm will be retained. Current state-of-the-art research, however, fails by far to achieve this ultimate goal. As one of the main obstacles to be overcome we perceive the question how symbolic knowledge can be encoded by means of connectionist systems: Satisfactory answers to this will naturally lead the way to knowledge extraction algorithms and to integrated neural-symbolic systems.Comment: In Proceedings of INFORMATION'2004, Tokyo, Japan, to appear. 12 page

Coalgebras for Bisimulation of Weighted Automata over Semirings

Weighted automata are a generalization of nondeterministic automata that associate a weight drawn from a semiring $K$ with every transition and every state. Their behaviours can be formalized either as weighted language equivalence or weighted bisimulation. In this paper we explore the properties of weighted automata in the framework of coalgebras over (i) the category $\mathsf{SMod}$ of semimodules over a semiring $K$ and $K$-linear maps, and (ii) the category $\mathsf{Set}$ of sets and maps. We show that the behavioural equivalences defined by the corresponding final coalgebras in these two cases characterize weighted language equivalence and weighted bisimulation, respectively. These results extend earlier work by Bonchi et al. using the category $\mathsf{Vect}$ of vector spaces and linear maps as the underlying model for weighted automata with weights drawn from a field $K$. The key step in our work is generalizing the notions of linear relation and linear bisimulation of Boreale from vector spaces to semimodules using the concept of the kernel of a $K$-linear map in the sense of universal algebra. We also provide an abstract procedure for forward partition refinement for computing weighted language equivalence. Since for weighted automata defined over semirings the problem is undecidable in general, it is guaranteed to halt only in special cases. We provide sufficient conditions for the termination of our procedure. Although the results are similar to those of Bonchi et al., many of our proofs are new, especially those about the coalgebra in $\mathsf{SMod}$ characterizing weighted language equivalence