Analyzing analytical methods: The case of phonology in neural models of spoken language

Given the fast development of analysis techniques for NLP and speech processing systems, few systematic studies have been conducted to compare the strengths and weaknesses of each method. As a step in this direction we study the case of representations of phonology in neural network models of spoken language. We use two commonly applied analytical techniques, diagnostic classifiers and representational similarity analysis, to quantify to what extent neural activation patterns encode phonemes and phoneme sequences. We manipulate two factors that can affect the outcome of analysis. First, we investigate the role of learning by comparing neural activations extracted from trained versus randomly-initialized models. Second, we examine the temporal scope of the activations by probing both local activations corresponding to a few milliseconds of the speech signal, and global activations pooled over the whole utterance. We conclude that reporting analysis results with randomly initialized models is crucial, and that global-scope methods tend to yield more consistent results and we recommend their use as a complement to local-scope diagnostic methods.Comment: ACL 202

Speech Recognition for the iCub Platform

This paper describes open source software (available at https://github.com/robotology/natural- speech) to build automatic speech recognition (ASR) systems and run them within the YARP platform. The toolkit is designed (i) to allow non-ASR experts to easily create their own ASR system and run it on iCub, and (ii) to build deep learning-based models specifically addressing the main challenges an ASR system faces in the context of verbal human-iCub interactions. The toolkit mostly consists of Python, C++ code and shell scripts integrated in YARP. As additional contribution, a second codebase (written in Matlab) is provided for more expert ASR users who want to experiment with bio-inspired and developmental learning-inspired ASR systems. Specifically, we provide code for two distinct kinds of speech recognition: "articulatory" and "unsupervised" speech recognition. The first is largely inspired by influential neurobiological theories of speech perception which assume speech perception to be mediated by brain motor cortex activities. Our articulatory systems have been shown to outperform strong deep learning- based baselines. The second type of recognition systems, the "unsupervised" systems, do not use any supervised information (contrary to most ASR systems, including our articulatory systems). To some extent, they mimic an infant who has to discover the basic speech units of a language by herself. In addition, we provide resources consisting of pre-trained deep learning models for ASR, and a 2,5-hours speech dataset of spoken commands, the VoCub dataset, which can be used to adapt an ASR system to the typical acoustic environments in which iCub operates

Digital terrain analysis of the Haute-Mentue catchment an scale effect for hydrological modelling with TOPMODEL

International audienceIt is widely recognised that topography plays an important role in the generation of runoff. The scale of a digital elevation model has been found to have some impacts on the results of hydrological modelling in several studies. In particular it has been shown that the representation of the statistical distribution of the topographic index used by TOPMODEL is sensitive to the scale of the digital terrain model. The objectives of this study are to develop an analysis of the topography and scale effects for the Haute-Mentue catchment and to test the role of different spatial resolution on parameter calibration. The major result is that the spatial scale is important for the parameter values, but not determinant for the modelling results if a pertinent methodology is adopted for the determination of digital watershed representation. Keywords: digital elevation model, topographic index, scale problems, TOPMODEL</p

Stitching proteins into membranes, not sew simple

Most integral membrane proteins located within the endomembrane system of eukaryotic cells are first assembled co-translationally into the endoplasmic reticulum (ER) before being sorted and trafficked to other organelles. The assembly of membrane proteins is mediated by the ER translocon, which allows passage of lumenal domains through and lateral integration of transmembrane (TM) domains into the ER membrane. It may be convenient to imagine multi-TM domain containing membrane proteins being assembled by inserting their first TM domain in the correct orientation, with subsequent TM domains inserting with alternating orientations. However a simple threading model of assembly, with sequential insertion of one TM domain into the membrane after another, does not universally stand up to scrutiny. In this article we review some of the literature illustrating the complexities of membrane protein assembly. We also present our own thoughts on aspects that we feel are poorly understood. In short we hope to convince the readers that threading of membrane proteins into membranes is 'not sew simple' and a topic that requires further investigation

A Single Polar Residue and Distinct Membrane Topologies Impact the Function of the Infectious Bronchitis Coronavirus E Protein

The coronavirus E protein is a small membrane protein with a single predicted hydrophobic domain (HD), and has a poorly defined role in infection. The E protein is thought to promote virion assembly, which occurs in the Golgi region of infected cells. It has also been implicated in the release of infectious particles after budding. The E protein has ion channel activity in vitro, although a role for channel activity in infection has not been established. Furthermore, the membrane topology of the E protein is of considerable debate, and the protein may adopt more than one topology during infection. We previously showed that the HD of the infectious bronchitis virus (IBV) E protein is required for the efficient release of infectious virus, an activity that correlated with disruption of the secretory pathway. Here we report that a single residue within the hydrophobic domain, Thr16, is required for secretory pathway disruption. Substitutions of other residues for Thr16 were not tolerated. Mutations of Thr16 did not impact virus assembly as judged by virus-like particle production, suggesting that alteration of secretory pathway and assembly are independent activities. We also examined how the membrane topology of IBV E affected its function by generating mutant versions that adopted either a transmembrane or membrane hairpin topology. We found that a transmembrane topology was required for disrupting the secretory pathway, but was less efficient for virus-like particle production. The hairpin version of E was unable to disrupt the secretory pathway or produce particles. The findings reported here identify properties of the E protein that are important for its function, and provide insight into how the E protein may perform multiple roles during infection

Dynamic insertion of membrane proteins at the endoplasmic reticulum

Most eukaryotic membrane proteins are cotranslationally integrated into the endoplasmic reticulum membrane by the Sec61 translocation complex. They are targeted to the translocon by hydrophobic signal sequences which induce the translocation of either their N- or C-terminal sequence. Signal sequence orientation is largely determined by charged residues flanking the apolar sequence (the positive-inside rule), folding properties of the N-terminal segment, and the hydrophobicity of the signal. Recent in vivo experiments suggest that N-terminal signals initially insert into the translocon head-on to yield a translocated Nterminus. Driven by a local electrical potential, the signal may invert its orientation and translocate the C-terminal sequence. Increased hydrophobicity slows down inversion by stabilizing the initial bound state. In vitro crosslinking studies indicate that signals rapidly contact lipids upon entering the translocon. Together with the recent crystal structure of the homologous SecYEβ translocation complex of Methanococcus jannaschii, which did not reveal an obvious hydrophobic binding site for signals within the pore, a model emerges in which the translocon allows the lateral partitioning of hydrophobic segments between the aqueous pore and the lipid membrane. Signals may return into the pore for reorientation until translation is terminated. Subsequent transmembrane segments in multispanning proteins behave similarly and contribute to the overall topology of the protein. This thesis was aimed at investigating the integration of single- and doublespanning membrane proteins in mammalian cells. The first part consisted of probing the environment of the signal while its orientation is determined by inserting different hydrophobic residues at various positions throughout a uniform oligo-leucine signal sequence. The resulting topologies revealed a strikingly symmetric position dependence specifically for bulky aromatic amino acids, reflecting the structure of a lipid bilayer. The results support the model that during topogenesis in vivo the signal sequence is exposed to the lipid membrane. The second part consisted of the determination of the kinetics of double-spanning protein topogenesis. The results confirmed that major reorientation of the polypeptide my occur when a second topogenic sequence, conflicting with a first one, enters the translocon. They also showed that the time window for protein reorientation differs for different types of substrate

Conformation des polyélectrolyes dans des films nanométriques assemblés couche par couche

The Layer-by-Layer assembly allows the build-up of multimaterial films with various properties showing a stratified structure. This work describes the structural strudies of multilayer films of polyelectrolytes with neutron scattering measurements.Ageing effect on films was determined by neutron reflectometry. We observed a slight shrink of the films after 5 years and a strong expansion after 15 years.We also showed that the proximity of the substrate and the air at the surface have an influence on the structure of the layers at the extremities of the films, leading to an inhomogeneous structure perpendicularly to the surface.Finally, we studied the conformation of polyelectrolyte chains in the multilayer films ; we determined that PSS chains in dipped films have a flattened coil conformation, whereas the polyelectrolyte chains in solution have a spherical conformation.L’assemblage couche-par-couche permet de fabriquer des films multimatériaux aux propriétés variées présentant une structure stratifiée. Ce travail décrit les études structurelles des films multicouches de polyélectrolytes à l’aide de mesures de diffusion de neutrons.L’effet du vieillissement des films a été déterminé par réflectométrie des neutrons. Nous avons observé un léger tassement des films après 5 ans et une forte expansion après 15 ans.Nous avons aussi montré que le substrat et l’air en surface ont une influence sur la structure des couches proches des extrémités des films, conduisant à une structure inhomogène perpendiculairement à la surface.Nous avons finalement étudié la conformation des chaînes de polyélectrolytes dans les films multicouches ; nous avons déterminé que les chaînes de PSS dans des films préparés par trempage ont une conformation en pelotes aplaties, contrairement aux chaînes de polyélectrolytes en solution qui présentent une conformation sphérique