Human-chimpanzee alignment: Ortholog Exponentials and Paralog Power Laws

Genomic subsequences conserved between closely related species such as human and chimpanzee exhibit an exponential length distribution, in contrast to the algebraic length distribution observed for sequences shared between distantly related genomes. We find that the former exponential can be further decomposed into an exponential component primarily composed of orthologous sequences, and a truncated algebraic component primarily composed of paralogous sequences.Comment: Main text: 31 pages, 13 figures, 1 table; Supplementary materials: 9 pages, 9 figures, 1 tabl

Globally Normalized Reader

Rapid progress has been made towards question answering (QA) systems that can extract answers from text. Existing neural approaches make use of expensive bi-directional attention mechanisms or score all possible answer spans, limiting scalability. We propose instead to cast extractive QA as an iterative search problem: select the answer's sentence, start word, and end word. This representation reduces the space of each search step and allows computation to be conditionally allocated to promising search paths. We show that globally normalizing the decision process and back-propagating through beam search makes this representation viable and learning efficient. We empirically demonstrate the benefits of this approach using our model, Globally Normalized Reader (GNR), which achieves the second highest single model performance on the Stanford Question Answering Dataset (68.4 EM, 76.21 F1 dev) and is 24.7x faster than bi-attention-flow. We also introduce a data-augmentation method to produce semantically valid examples by aligning named entities to a knowledge base and swapping them with new entities of the same type. This method improves the performance of all models considered in this work and is of independent interest for a variety of NLP tasks.Comment: Presented at EMNLP 201

Quasi-classical Gravity effect on neutrino oscillations in a gravitational field of an heavy astrophysical object

In the framework of quantum field theory, a graviton interacts locally with a quantum state having definite mass, i.e. the gravitational mass eigenstate, while a weak boson interacts with a state having definite flavor, i.e. the flavor eigenstate. An interaction of a neutrino with an energetic graviton may trigger the collapse of the neutrino to a definite mass eigenstate with probability expressed in terms of PMNS mixing matrix elements. Thus, gravitons would induce quantum decoherence of a coherent neutrino flavor state similarly to how weak bosons induce quantum decoherence of a neutrino in a definite mass state. We demonstrate that such an essentially quantum gravity effect may have strong consequences for neutrino oscillation phenomena in astrophysics due to relatively large scattering cross sections of relativistic neutrinos undergoing large-angle radiation of energetic gravitons in gravitational field of a classical massive source (i.e. the quasi-classical case of gravitational Bethe-Heitler scattering). This graviton-induced {\it decoherence} is compared to {\it decoherence} due to propagation in the presence of the Earth matter effect. Based on this study, we propose a new technique for the indirect detection of energetic gravitons by measuring the flavor composition of astrophysical neutrinos.Comment: 25 pages, 4 figures, minor revision with clarifications, main conclusions are unchange

Evolution of the Potential Energy Surface with Size for Lennard-Jones Clusters

Disconnectivity graphs are used to characterize the potential energy surfaces of Lennard-Jones clusters containing 13, 19, 31, 38, 55 and 75 atoms. This set includes members which exhibit either one or two `funnels' whose low-energy regions may be dominated by a single deep minimum or contain a number of competing structures. The graphs evolve in size due to these specific size effects and an exponential increase in the number of local minima with the number of atoms. To combat the vast number of minima we investigate the use of monotonic sequence basins as the fundamental topographical unit. Finally, we examine disconnectivity graphs for a transformed energy landscape to explain why the transformation provides a useful approach to the global optimization problem.Comment: 13 pages, 8 figures, revte

Faster Approximate Multicommodity Flow Using Quadratically Coupled Flows

The maximum multicommodity flow problem is a natural generalization of the maximum flow problem to route multiple distinct flows. Obtaining a $1-\epsilon$ approximation to the multicommodity flow problem on graphs is a well-studied problem. In this paper we present an adaptation of recent advances in single-commodity flow algorithms to this problem. As the underlying linear systems in the electrical problems of multicommodity flow problems are no longer Laplacians, our approach is tailored to generate specialized systems which can be preconditioned and solved efficiently using Laplacians. Given an undirected graph with m edges and k commodities, we give algorithms that find $1-\epsilon$ approximate solutions to the maximum concurrent flow problem and the maximum weighted multicommodity flow problem in time \tilde{O}(m^{4/3}\poly(k,\epsilon^{-1}))

Your turn: experiments in narrative and play

Carson and Miller’s artists’ book, 'The Exquisite Fold', utilises the book as a site for play and storytelling. Both acts are interpretative; they are ways through which both child and adult attempt to understand the world that surrounds them. In 'Your Turn' the process of making 'The Exquisite Fold' is explored in terms of both its content and its very particular physical construction. Through this examination the ideas that underpin the book are drawn out; the potential for the book to be played with (particularly as a place to play with narrative) and, in turn, the impulse to uncover meaning through narrative and play