A Convolutional Encoder Model for Neural Machine Translation

The prevalent approach to neural machine translation relies on bi-directional LSTMs to encode the source sentence. In this paper we present a faster and simpler architecture based on a succession of convolutional layers. This allows to encode the entire source sentence simultaneously compared to recurrent networks for which computation is constrained by temporal dependencies. On WMT'16 English-Romanian translation we achieve competitive accuracy to the state-of-the-art and we outperform several recently published results on the WMT'15 English-German task. Our models obtain almost the same accuracy as a very deep LSTM setup on WMT'14 English-French translation. Our convolutional encoder speeds up CPU decoding by more than two times at the same or higher accuracy as a strong bi-directional LSTM baseline.Comment: 13 page

The Coevolution of Blue-Light Photoreception and Circadian Rhythms

Sunlight is a primary source of energy for life. However, its UV component causes DNA damage. We suggest that the strong UV component of sunlight contributed to the selective pressure for the evolution of the specialized photoreceptor cryptochrome from photolyases involved in DNA repair and propose that early metazoans avoided irradiation by descending in the oceans during the daytime. We suggest further that it is not coincidental that blue-light photoreception evolved in an aquatic environment, since only blue light can penetrate to substantial depths in water. These photoreceptors were then also critical for sensing the decreased luminescence that signals the coming of night and the time to return to the surface. The oceans and the 24-h light-dark cycle therefore provided an optimal setting for an early evolutionary relationship between blue-light photoreception and circadian rhythmicit

A Primer on the Differential Calculus of 3D Orientations

The proper handling of 3D orientations is a central element in many optimization problems in engineering. Unfortunately many researchers and engineers struggle with the formulation of such problems and often fall back to suboptimal solutions. The existence of many different conventions further complicates this issue, especially when interfacing multiple differing implementations. This document discusses an alternative approach which makes use of a more abstract notion of 3D orientations. The relative orientation between two coordinate systems is primarily identified by the coordinate mapping it induces. This is combined with the standard exponential map in order to introduce representation-independent and minimal differentials, which are very convenient in optimization based methods

5-Hydroxymethylcytosine Is Not Present in Appreciable Quantities in Arabidopsis DNA

5-Hydroxymethylcytosine (5-hmC) is an intermediate in active demethylation in metazoans, as well as a potentially stable epigenetic mark. Previous reports investigating 5-hydroxymethylcytosine in plants have reached conflicting conclusions. We systematically investigated whether 5-hmC is present in plant DNA using a range of methods. Using the model organism Arabidopsis thaliana, in addition to other plant species, we assayed the amount or distribution of 5-hydroxymethylcytosine by thin-layer chromatography, immunoprecipitation-chip, ELISA, enzymatic radiolabeling, and mass spectrometry. The failure to observe 5-hydroxymethylcytosine by thin-layer chromatography established an upper bound for the possible fraction of the nucleotide in plant DNA. Antibody-based methods suggested that there were low levels of 5-hmC in plant DNA, but these experiments were potentially confounded by cross-reactivity with the abundant base 5-methylcytosine. Enzymatic radiolabeling and mass spectrometry, the most sensitive methods for detection that we used, failed to detect 5-hydroxymethylcytosine in A. thaliana genomic DNA isolated from a number of different tissue types and genetic backgrounds. Taken together, our results led us to conclude that 5-hmC is not present in biologically relevant quantities within plant genomic DNA.National Science Foundation (U.S.). Graduate Research Fellowship Progra