Automation of Function Assignment in the Models of Speech Production and Second Language Acquisition

This article explores the concept of function assignment in first language (L1) and second language (L2) speech production, compares automation of function assignment in L1 and L2 speech production, pursues factors hampering automation of function assignment in L2 speech production, and discusses how to improve automation of function assignment in L2 speech production. Grammatical encoding, of which function assignment is one of the subordinate processes, is also one of the processes in L2 speech production. While function assignment in L1 speech production is mostly automatic, it demands much attentional resources and is executed under conscious supervision in L2 speech production. L2 learners’ incomplete knowledge of the target language and their limited working memory resources hamper automation of function assignment in L2 speech production. Furthermore, as per generative models of learning, to improve automation of function assignment, teachers can either adopt strategies or improve instructional designs targeting this subprocess. Together, this conceptual paper gives a comprehensive overview of automation of function assignment, explores its impact on second language acquisition (SLA), and reveals that it is feasible to facilitate automation of function assignment in L2 speech production by improving instructional designs, especially the presentation methods of sentence elements.

Open Issues for Protein Function Assignment in Haloferax volcanii and Other Halophilic Archaea

Background: Annotation ambiguities and annotation errors are a general challenge in genomics. While a reliable protein function assignment can be obtained by experimental characterization, this is expensive and time-consuming, and the number of such Gold Standard Proteins (GSP) with experimental support remains very low compared to proteins annotated by sequence homology, usually through automated pipelines. Even a GSP may give a misleading assignment when used as a reference: the homolog may be close enough to support isofunctionality, but the substrate of the GSP is absent from the species being annotated. In such cases, the enzymes cannot be isofunctional. Here, we examined a variety of such issues in halophilic archaea (class Halobacteria), with a strong focus on the model haloarchaeon Haloferax volcanii. Results: Annotated proteins of Hfx. volcanii were identified for which public databases tend to assign a function that is probably incorrect. In some cases, an alternative, probably correct, function can be predicted or inferred from the available evidence, but this has not been adopted by public databases because experimental validation is lacking. In other cases, a probably invalid specific function is predicted by homology, and while there is evidence that this assigned function is unlikely, the true function remains elusive. We listed 50 of those cases, each with detailed background information, so that a conclusion about the most likely biological function can be drawn. For reasons of brevity and comprehension, only the key aspects are listed in the main text, with detailed information being provided in a corresponding section of the Supplementary Materials. Conclusions: Compiling, describing and summarizing these open annotation issues and functional predictions will benefit the scientific community in the general effort to improve the evaluation of protein function assignments and more thoroughly detail them. By highlighting the gaps and likely annotation errors currently in the databases, we hope this study will provide a framework for experimentalists to systematically confirm (or disprove) our function predictions or to uncover yet more unexpected functions.

Open issues for protein function assignment in Haloferax volcanii and other halophilic archaea

Background: Annotation ambiguities and annotation errors are a general challenge in genomics. While a reliable protein function assignment can be obtained by experimental characterization, this is expensive and time-consuming, and the number of such Gold Standard Proteins (GSP) with experimental support remains very low compared to proteins annotated by sequence homology, usually through automated pipelines. Even a GSP may give a misleading assignment when used as a reference: the homolog may be close enough to support isofunctionality, but the substrate of the GSP is absent from the species being annotated. In such cases the enzymes cannot be isofunctional. Here, we examine a variety of such issues in halophilic archaea (class Halobacteria), with a strong focus on the model haloarchaeon Haloferax volcanii. Results: Annotated proteins of Hfx. volcanii were identified for which public databases tend to assign a function that is probably incorrect. In some cases, an alternative, probably correct, function can be predicted or inferred from the available evidence but this has not been adopted by public databases because experimental validation is lacking. In other cases, a probably invalid specific function is predicted by homology, and while there is evidence that this assigned function is unlikely, the true function remains elusive. We list 50 of those cases, each with detailed background information so that a conclusion about the most likely biological function can be drawn. For reasons of brevity and comprehension, only key aspects are listed in the main text, with detailed information being provided in a corresponding section of the Supplementary Material. Conclusions: Compiling, describing and summarizing these open annotation issues and functional predictions will benefit the scientific community in the general effort to improve the evaluation of protein function assignments and more thoroughly detail them. By highlighting the gaps and likely annotation errors currently in the databases, we hope this study will provide a framework for experimentalists to sytematically confirm (or disprove) our function predictions or to uncover yet unexpected functions.

Photosynthetic protein classification using genome neighborhood-based machine learning feature

Identification of novel photosynthetic proteins is important for understanding and improving photosynthetic efficiency. Synergistically, genomic context such as genome neighborhood can provide additional useful information to identify the photosynthetic proteins. We, therefore, expected that applying the computational approach, particularly machine learning (ML) with the genome neighborhood-based feature should facilitate the photosynthetic function assignment. Our results revealed a functional relationship between photosynthetic genes and their genomic neighbors, indicating the possibility to assign functions from their genome neighborhood profile. Therefore, we created a new method for extracting the patterns based on genome neighborhood network (GNN) and applied for the photosynthetic protein classification using ML algorithms. Random forest (RF) classifier using genome neighborhood-based features achieved the highest accuracy up to 94% in the classification of photosynthetic proteins and also showed better performance (Mathew’s correlation coefficient = 0.852) than other available tools including the sequence similarity search (0.497) and ML-based method (0.512). Furthermore, we demonstrated the ability of our model to identify novel photosynthetic proteins comparing to the other methods. Our classifier is available at http://bicep.kmutt.ac.th/photomod_standalone, https://bit.ly/2S0I2Ox and DockerHub: https://hub.docker.com/r/asangphukieo/photomod

TIPOLOGÍA DE ESTADOS DE COSAS Y ASIGNACIÓN DE FUNCIONES SEMÁNTICAS EN LA TEORÍA DE LA GRAMÁTICA FUNCIONAL: APROXIMACIONES CRÍTICAS

This paper is concerned with one specific area of S.C. Dik’s theory of Functional Grammar (FG) which has received a great deal of attention within the FG movement: the classi cation of States of Affairs and semantic functions. I will first focus on Dik’s (1978, 1989, 1997) proposals for a typology of SoAs, then presenting other alternative approaches by authors such as Rijksbaron (1989) and Goossens (1990), who suggested some interesting refinements of the 1978 and 1989 versions. Finally, the assignment of semantic and syntactic functions in FG will be brie y discussed, including some more recent advances and critical evaluations of Dik’s work.Keywords: States of Affairs (SoAs), semantic functions, syntactic functions, Functional GrammarTitle in English: Typology of States of Affairs and semantic function assignment in the theory of Functional Grammar: critical approachesResumen:Este trabajo pretende profundizar en un área de la teoría de la Gramática Funcional (GF) de S.C. Dik que ha recibido especial atención dentro del modelo: la clasificación de los estados de cosas y la asignación de funciones semánticas. En primer lugar, se analizan las propuestas de Dik (1978, 1989, 1997) presentándose a continuación las aportaciones de otros autores, como Rijksbaron (1989) y Goossens (1990), que introdujeron interesantes modificaciones respecto a las versiones de 1978 y 1989. Finalmente, se abordará brevemente el tema de la asignación de funciones semánticas y sintácticas en la GF, incluyendo algunas de las aportaciones y valoraciones críticas más recientes. Palabras clave: Estados de cosas (EdCs), funciones semánticas, funciones sintácticas, Gramática Funcional

Integrating a rich external valency dictionary with an implemented XLE/LFG grammar

This paper shows how Walenty, a valency dictionary of Polish, was automatically converted in order to be used with an XLE/LFG grammar of Polish, discussing issues such as the grammatical function assignment under unlike category coordination and imposing constraints for lexicalised dependents.