NMTPY: A Flexible Toolkit for Advanced Neural Machine Translation Systems

In this paper, we present nmtpy, a flexible Python toolkit based on Theano for training Neural Machine Translation and other neural sequence-to-sequence architectures. nmtpy decouples the specification of a network from the training and inference utilities to simplify the addition of a new architecture and reduce the amount of boilerplate code to be written. nmtpy has been used for LIUM's top-ranked submissions to WMT Multimodal Machine Translation and News Translation tasks in 2016 and 2017.Comment: 10 pages, 3 figure

Ms Pac-Man versus Ghost Team CEC 2011 competition

Games provide an ideal test bed for computational intelligence and significant progress has been made in recent years, most notably in games such as Go, where the level of play is now competitive with expert human play on smaller boards. Recently, a significantly more complex class of games has received increasing attention: real-time video games. These games pose many new challenges, including strict time constraints, simultaneous moves and open-endedness. Unlike in traditional board games, computational play is generally unable to compete with human players. One driving force in improving the overall performance of artificial intelligence players are game competitions where practitioners may evaluate and compare their methods against those submitted by others and possibly human players as well. In this paper we introduce a new competition based on the popular arcade video game Ms Pac-Man: Ms Pac-Man versus Ghost Team. The competition, to be held at the Congress on Evolutionary Computation 2011 for the first time, allows participants to develop controllers for either the Ms Pac-Man agent or for the Ghost Team and unlike previous Ms Pac-Man competitions that relied on screen capture, the players now interface directly with the game engine. In this paper we introduce the competition, including a review of previous work as well as a discussion of several aspects regarding the setting up of the game competition itself. © 2011 IEEE

Mass & secondary structure propensity of amino acids explain their mutability and evolutionary replacements

Why is an amino acid replacement in a protein accepted during evolution? The answer given by bioinformatics relies on the frequency of change of each amino acid by another one and the propensity of each to remain unchanged. We propose that these replacement rules are recoverable from the secondary structural trends of amino acids. A distance measure between high-resolution Ramachandran distributions reveals that structurally similar residues coincide with those found in substitution matrices such as BLOSUM: Asn Asp, Phe Tyr, Lys Arg, Gln Glu, Ile Val, Met → Leu; with Ala, Cys, His, Gly, Ser, Pro, and Thr, as structurally idiosyncratic residues. We also found a high average correlation (\overline{R} R = 0.85) between thirty amino acid mutability scales and the mutational inertia (I X ), which measures the energetic cost weighted by the number of observations at the most probable amino acid conformation. These results indicate that amino acid substitutions follow two optimally-efficient principles: (a) amino acids interchangeability privileges their secondary structural similarity, and (b) the amino acid mutability depends directly on its biosynthetic energy cost, and inversely with its frequency. These two principles are the underlying rules governing the observed amino acid substitutions. © 2017 The Author(s)