A Formal Grammar for Code-Switching
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Question Formation in Québec* Martin Elsig and Shana Poplack 1
Transplanted dialects and language change: question formation in Québec* Martin Elsig and Shana Poplack 1 Introduction Variability in question formation is a well-documented feature of French syntax. In yes/no questions, five distinct variant forms have been competing for centuries: inversion of (clitic) subject and verb (INV), as in (1), complex inversion (C-INV) (2), rising intonation (INT) (3), phrase-initial interroga- tive particle est-ce-que (ECQ) (4), and its post-verbal counterpart tu (TU) (5). (1) As-tu (INV) déjà parlé avec un vrai Français de France là? (XX.105.2768)1 ‘Have you ever spoken to a real Frenchman from France?’ (2) Et le roi est-il (C-INV) icitte? (XIX.036.3932) ‘And the king, is he here?’ (3) Ah, toi tu restes pas (INT) avec tes parents? (XX.112.1819) ‘Oh, you don’t live with your parents?’ (4) Mes bombes est-ce que (ECQ) je les largue ici? (XX.078.1502) ‘My bombs, do I throw them here?’ (5) Tu vas-tu (TU) être plus marié oubedonc moins marié? (XX.079.1471) ‘Are you gonna be more married or less married?’ Empirical studies of European varieties report that the variability illus- trated in (1-5) has resolved itself in favor of INT (3), with ECQ persisting as a minor contender. INV, once the quintessential interrogative marker, is now * The research reported here is part of a larger project entitled Confronting pre- scription and praxis in the evolution of grammar. We gratefully acknowledge the support of the Sonderforschungsbereich Mehrsprachigkeit to Elsig, and that of the SSHRC and the Killam Foundation to Poplack. -
Grammar String: a Novel Ncrna Secondary Structure Representation
Grammar string: a novel ncRNA secondary structure representation Rujira Achawanantakun, Seyedeh Shohreh Takyar, and Yanni Sun∗ Department of Computer Science and Engineering, Michigan State University, East Lansing, MI 48824 , USA ∗Email: [email protected] Multiple ncRNA alignment has important applications in homologous ncRNA consensus structure derivation, novel ncRNA identification, and known ncRNA classification. As many ncRNAs’ functions are determined by both their sequences and secondary structures, accurate ncRNA alignment algorithms must maximize both sequence and struc- tural similarity simultaneously, incurring high computational cost. Faster secondary structure modeling and alignment methods using trees, graphs, probability matrices have thus been developed. Despite promising results from existing ncRNA alignment tools, there is a need for more efficient and accurate ncRNA secondary structure modeling and alignment methods. In this work, we introduce grammar string, a novel ncRNA secondary structure representation that encodes an ncRNA’s sequence and secondary structure in the parameter space of a context-free grammar (CFG). Being a string defined on a special alphabet constructed from a CFG, it converts ncRNA alignment into sequence alignment with O(n2) complexity. We align hundreds of ncRNA families from BraliBase 2.1 using grammar strings and compare their consensus structure with Murlet using the structures extracted from Rfam as reference. Our experiments have shown that grammar string based multiple sequence alignment competes favorably in consensus structure quality with Murlet. Source codes and experimental data are available at http://www.cse.msu.edu/~yannisun/grammar-string. 1. INTRODUCTION both the sequence and structural conservations. A successful application of SCFG is ncRNA classifica- Annotating noncoding RNAs (ncRNAs), which are tion, which classifies query sequences into annotated not translated into protein but function directly as ncRNA families such as tRNA, rRNA, riboswitch RNA, is highly important to modern biology. -
120421-24Recombschedule FINAL.Xlsx
Friday 20 April 18:00 20:00 REGISTRATION OPENS in Fira Palace 20:00 21:30 WELCOME RECEPTION in CaixaForum (access map) Saturday 21 April 8:00 8:50 REGISTRATION 8:50 9:00 Opening Remarks (Roderic GUIGÓ and Benny CHOR) Session 1. Chair: Roderic GUIGÓ (CRG, Barcelona ES) 9:00 10:00 Richard DURBIN The Wellcome Trust Sanger Institute, Hinxton UK "Computational analysis of population genome sequencing data" 10:00 10:20 44 Yaw-Ling Lin, Charles Ward and Steven Skiena Synthetic Sequence Design for Signal Location Search 10:20 10:40 62 Kai Song, Jie Ren, Zhiyuan Zhai, Xuemei Liu, Minghua Deng and Fengzhu Sun Alignment-Free Sequence Comparison Based on Next Generation Sequencing Reads 10:40 11:00 178 Yang Li, Hong-Mei Li, Paul Burns, Mark Borodovsky, Gene Robinson and Jian Ma TrueSight: Self-training Algorithm for Splice Junction Detection using RNA-seq 11:00 11:30 coffee break Session 2. Chair: Bonnie BERGER (MIT, Cambrige US) 11:30 11:50 139 Son Pham, Dmitry Antipov, Alexander Sirotkin, Glenn Tesler, Pavel Pevzner and Max Alekseyev PATH-SETS: A Novel Approach for Comprehensive Utilization of Mate-Pairs in Genome Assembly 11:50 12:10 171 Yan Huang, Yin Hu and Jinze Liu A Robust Method for Transcript Quantification with RNA-seq Data 12:10 12:30 120 Zhanyong Wang, Farhad Hormozdiari, Wen-Yun Yang, Eran Halperin and Eleazar Eskin CNVeM: Copy Number Variation detection Using Uncertainty of Read Mapping 12:30 12:50 205 Dmitri Pervouchine Evidence for widespread association of mammalian splicing and conserved long range RNA structures 12:50 13:10 169 Melissa Gymrek, David Golan, Saharon Rosset and Yaniv Erlich lobSTR: A Novel Pipeline for Short Tandem Repeats Profiling in Personal Genomes 13:10 13:30 217 Rory Stark Differential oestrogen receptor binding is associated with clinical outcome in breast cancer 13:30 15:00 lunch break Session 3. -
Shana Poplack and Marjory Meechan 1 Introduction
10 PATTERNS OF LANGUAGE MIXTURE: NOMINAL STRUCTURE IN WOLOF-FRENCH AND FONGBE• FRENCH BILINGUAL DISCOURSE Shana Poplack and Marjory Meechan 1 Introduction A primary goal of any study of language mixture is to determine the properties of the internal grammars of bilinguals. Specifically, what grammar is utilised at the point where languages meet? Do speakers operate with a single base grammar which is on occasion overlaid with lexical items from another language or are different grammars activated at different times? If the latter is the case, what structural principles govern their juxtaposition? In this chapter, we demonstrate how the variationist method yields straightforward answers to these questions and further, assert that it is the only method which can irrefutably do so. Empirical studies of bilingual performance data have revealed that the utter• ance-internal combination of elements from more than one grammar may surface in a number of different forms, some of which are illustrated in (I), where French• origin items (italicised) alternate with Wolof items. (I) amoon naa fi nak benn copine koo xam ni daf ma have+PAST I LOC CON] IND friend that+you know that she me attacherwoon debut d' annee mais sarna idees yooyoo attach+PAST beginning of year but POSS ideas DEM tax ba leegi mu jappantewoon ak man, c'est que moom cause that now she dispute+past with me it's that she feministe la quoi ta man je defendais des idees yoo feminist it's what so me I defend+PAST IND ideas that+you xamenta ni g;}m mu ma ko sax. -
Michael S. Waterman: Breathing Mathematics Into Genes >>>
ISSUE 13 Newsletter of Institute for Mathematical Sciences, NUS 2008 Michael S. Waterman: Breathing Mathematics into Genes >>> setting up of the Center for Computational and Experimental Genomics in 2001, Waterman and his collaborators and students continue to provide a road map for the solution of post-genomic computational problems. For his scientific contributions he was elected fellow or member of prestigious learned bodies like the American Academy of Arts and Sciences, National Academy of Sciences, American Association for the Advancement of Science, Institute of Mathematical Statistics, Celera Genomics and French Acadèmie des Sciences. He was awarded a Gairdner Foundation International Award and the Senior Scientist Accomplishment Award of the International Society of Computational Biology. He currently holds an Endowed Chair at USC and has held numerous visiting positions in major universities. In addition to research, he is actively involved in the academic and social activities of students as faculty master Michael Waterman of USC’s International Residential College at Parkside. Interview of Michael S. Waterman by Y.K. Leong Waterman has served as advisor to NUS on genomic research and was a member of the organizational committee Michael Waterman is world acclaimed for pioneering and of the Institute’s thematic program Post-Genome Knowledge 16 fundamental work in probability and algorithms that has Discovery (Jan – June 2002). On one of his advisory tremendous impact on molecular biology, genomics and visits to NUS, Imprints took the opportunity to interview bioinformatics. He was a founding member of the Santa him on 7 February 2007. The following is an edited and Cruz group that launched the Human Genome Project in enhanced version of the interview in which he describes the 1990, and his work was instrumental in bringing the public excitement of participating in one of the greatest modern and private efforts of mapping the human genome to their scientific adventures and of unlocking the mystery behind completion in 2003, two years ahead of schedule. -
Gene and Genome Duplication David Sankoff
681 Gene and genome duplication David Sankoff Genomic sequencing projects have revealed the productivity of tetraploidization. I also summarize some mathematical processes duplicating genes or entire chromosome segments. modeling and algorithmics inspired by duplication phenomena. Substantial proportions of the yeast, Arabidopsis and human gene complements are made up of duplicates. This has prompted much Gene duplication interest in the processes of duplication, functional divergence and Li et al. [2] find that duplicated genes, as identified through loss of genes, has renewed the debate on whether an early fairly selective criteria, account for ~15% of the protein genes vertebrate genome was tetraploid, and has inspired mathematical in the human genome (counting both genes in each pair). In a models and algorithms in computational biology. survey of eukaryotic genome sequences, Lynch and Conery [3••], using a somewhat different filter, accounted for ~8%, Addresses 10% and 20% of the gene complement of the fly, yeast and Centre de recherches mathématiques, Université de Montréal, worm genomes, respectively. (Other estimates put the figure CP 6128 succursale Centre-Ville, Montreal, Québec H3C 3J7, Canada; at 16% for yeast and 25% for Arabidopsis [4•].) They estimated e-mail: [email protected] highly variable rates of gene duplication, averaging ~0.01 per Current Opinion in Genetics & Development 2001, 11:681–684 gene per Myr (million years). On the basis of ratios of silent and replacement rearrangements, they found that there is 0959-437X/01/$ — see front matter © 2001 Elsevier Science Ltd. All rights reserved. typically a period of neutral or (occasionally) even slightly accelerated evolution, lasting a few Myr at most, with one of Abbreviation the copies eventually being silenced in a large majority of Myr million years cases, and the remaining ones undergoing relatively stringent purifying selection. -
Code-Switching 589
Sociolinguistics Soziolinguistik An International Handbook of the Science of Language and Society Ein internationales Handbuch zur Wissenschaft von Sprache und Gesellschaft 2nd completely revised and extended edition 2., vollstandig neu bearbeitete und erweiterte Auflage Edited by / Herausgegeben von Ulrich Ammon . Norbert Dittmar Klaus 1. Mattheier . Peter Trudgill Volume 1 / 1. Teilband Offprint I Sonderdruck Walter de Gruyter . Berlin· New York 70. Code-Switching 589 70. Code-Switching/Sprachwechsel 1. Linguistic manifestations of language conjunctions and their conjuncts), but these contact were soon met with a host of counter- 2. Theories of CS examples. 3. Fitting theory to data The first general account of the distribu- 4. The data of cs tion of stemmed from the observation 5. Community strategies for CS es 6. Summary that es is favored at the kinds of syntactic 7. Literature (selected) boundaries which occur in both languages. The Equivalence Constraint (Poplack 1980) states that switched sentences are made up 1. Linguistic manifestations of of concatenated fragments of alternating language contact languages, each of which is grammatical in the language of its provenance (see also Code-switching (eS) is but one of a number Lipski 1978; Muysken 2000; Pfaff 1979). of the linguistic manifestations of language The boundary between adjacent fragments contact and mixing, which variously include occurs between two constituents that are borrowing on the lexical and syntactic levels, ordered in the same way in both languages, language transfer, linguistic convergence, ensuring the linear coherence of sentence interference, language attrition, language structure without omitting or duplicating death, pidginization and creolization, among lexical content. others. There is little consensus in the litera- That general principles, rather than atom- ture over which aspects should be subsumed istic constraints, govern es is now widely under the label code-switching. -
Curriculum Vitae
Curriculum Vitae Tandy Warnow Grainger Distinguished Chair in Engineering 1 Contact Information Department of Computer Science The University of Illinois at Urbana-Champaign Email: [email protected] Homepage: http://tandy.cs.illinois.edu 2 Research Interests Phylogenetic tree inference in biology and historical linguistics, multiple sequence alignment, metage- nomic analysis, big data, statistical inference, probabilistic analysis of algorithms, machine learning, combinatorial and graph-theoretic algorithms, and experimental performance studies of algorithms. 3 Professional Appointments • Co-chief scientist, C3.ai Digital Transformation Institute, 2020-present • Grainger Distinguished Chair in Engineering, 2020-present • Associate Head for Computer Science, 2019-present • Special advisor to the Head of the Department of Computer Science, 2016-present • Associate Head for the Department of Computer Science, 2017-2018. • Founder Professor of Computer Science, the University of Illinois at Urbana-Champaign, 2014- 2019 • Member, Carl R. Woese Institute for Genomic Biology. Affiliate of the National Center for Supercomputing Applications (NCSA), Coordinated Sciences Laboratory, and the Unit for Criticism and Interpretive Theory. Affiliate faculty member in the Departments of Mathe- matics, Electrical and Computer Engineering, Bioengineering, Statistics, Entomology, Plant Biology, and Evolution, Ecology, and Behavior, 2014-present. • National Science Foundation, Program Director for Big Data, July 2012-July 2013. • Member, Big Data Senior Steering Group of NITRD (The Networking and Information Tech- nology Research and Development Program), subcomittee of the National Technology Council (coordinating federal agencies), 2012-2013 • Departmental Scholar, Institute for Pure and Applied Mathematics, UCLA, Fall 2011 • Visiting Researcher, University of Maryland, Spring and Summer 2011. 1 • Visiting Researcher, Smithsonian Institute, Spring and Summer 2011. • Professeur Invit´e,Ecole Polytechnique F´ed´erale de Lausanne (EPFL), Summer 2010. -
Structure-Based Realignment of Non-Coding Rnas in Multiple Whole Genome Alignments
Structure-based Realignment of Non-coding RNAs in Multiple Whole Genome Alignments. by Michael Ku Yu Submitted to the Department of Electrical Engineering and Computer Science in partial fulfillment of the requirements for the degree of ARCHIVES Masters of Engineering in Computer Science and Engineering MASSACHUE N U TE at the OF TECH IOLOY MASSACHUSETTS INSTITUTE OF TECHNOLOGY JUN 2 1 2011 June 2011 LIBRARI ES @ Massachusetts Institute of Technology 2011. All rights reserved. '$7 A uthor ............ .. .. ... ............. Department of Electrical Wgineering and Computer Science May 20, 2011 Certified by..................................... ...... Bonnie Berger Professor of Applied Mathematics and Computer Science Thesis Supervisor Accepted by.... ....................................... Christopher J. Terman Chairman, Department Committee on Graduate Theses 2 Structure-based Realignment of Non-coding RNAs in Multiple Whole Genome Alignments by Michael Ku Yu Submitted to the Department of Electrical Engineering and Computer Science on May 20, 2011, in partial fulfillment of the requirements for the degree of Masters of Engineering in Computer Science and Engineering Abstract Whole genome alignments have become a central tool in biological sequence analy- sis. A major application is the de novo prediction of non-coding RNAs (ncRNAs) from structural conservation visible in the alignment. However, current methods for constructing genome alignments do so by explicitly optimizing for sequence simi- larity but not structural similarity. Therefore, de novo prediction of ncRNAs with high structural but low sequence conservation is intrinsically challenging in a genome alignment because the conservation signal is typically hidden. This study addresses this problem with a method for genome-wide realignment of potential ncRNAs ac- cording to structural similarity. -
New Cambridge History of the English Language
New Cambridge History of the English Language Volume V: English in North America and the Caribbean Editors: Natalie Schilling (Georgetown), Derek Denis (Toronto), Raymond Hickey (Essen) I The United States 1. Language change and the history of American English (Walt Wolfram) 2. The dialectology of Anglo-American English (Natalie Schilling) 3. The roots and development of New England English (James N. Stanford) 4. The history of the Midland-Northern boundary (Matthew J. Gordon) 5. The spread of English westwards (Valerie Fridland and Tyler Kendall) 6. American English in the city (Barbara Johnstone) 7. English in the southern United States (Becky Childs and Paul E. Reed) 8. Contact forms of American English (Cristopher Font-Santiago and Joseph Salmons) African American English 9. The roots of African American English (Tracey L. Weldon) 10. The Great Migration and regional variation in the speech of African Americans (Charlie Farrington) 11. Urban African American English (Nicole Holliday) 12. A longitudinal panel survey of African American English (Patricia Cukor-Avila) Latinx English 13. Puerto Rican English in Puerto Rico and in the continental United States (Rosa E. Guzzardo Tamargo) 14. The English of Americans of Mexican and Central American heritage (Erik R. Thomas) II Canada 15. Anglophone settlement and the creation of Canadian English (Charles Boberg) NewCHEL Vol 5: English in North America and the Caribbean Page 2 of 2 16. The open-class lexis of Canadian English: History, structure, and social correlations (Stefan Dollinger) 17. Ontario English: Loyalists and beyond (Derek Denis, Bridget Jankowski and Sali A. Tagliamonte) 18. The Prairies and the West of Canada (Alex D’Arcy and Nicole Rosen) 19. -
Algorithms for High-Throughput Sequencing Data
Univerzita Komenského v Bratislave Fakulta matematiky, fyziky a informatiky Vladimír Boºa Autoreferát dizerta£nej práce Algorithms for high-throughput sequencing data na získanie akademického titulu philosophiae doctor v odbore doktorandského ²túdia: 9.2.1. - informatika Bratislava 2017 Dizerta£ná práca bola vypracovaná v dennej forme doktorandského ²túdia na Katedre ap- likovanej informatiky Fakulty matematiky, fyziky a informatiky Univerzity Komenského v Bratislave. Predkladate©: Vladimír Boºa Katedra aplikovanej informatiky Fakulta matematiky, fyziky a informatiky Univerzita Komenského Bratislava kolite©: Mgr. Tomá² Vina°, PhD. Katedra aplikovanej informatiky Fakulta matematiky, fyziky a informatiky Univerzita Komenského Bratislava Odbor: 9.2.1. - informatika Predseda odborovej komisie: prof. RNDr. Rastislav Krá©ovi£, PhD. Katedra informatiky Fakulta matematiky, fyziky a informatiky Univerzita Komenského Bratislava 1 Overview Knowledge of DNA sequences has become indispensable for basic biological research and in numerous applied elds like diagnostics, forensic biology, etc. It is also important for understanding cancer, ghting antibiotic resistant bacteria, etc. With decreasing cost of the DNA sequencing we are able to sequence more organisms, but consequently we have to handle much bigger amounts of data. Usual length of DNA sequence of an organism is between millions and billions of characters. For example, human DNA has approximatelly three billions bases. Unfortunately, we are still not able to read the whole DNA sequence at once, we can only read it in small pieces called reads. Usual length of reads vary between hundred to tens of thousands of bases depending on the sequencing technology. Thus, our only option is to try to computationaly reconstruct original sequence, using overlap information between reads. This process is called sequence assembly. -
REVISITING PHONETIC INTEGRATION in BILINGUAL BORROWING Shana Poplack Suzanne Robillard
REVISITING PHONETIC INTEGRATION IN BILINGUAL BORROWING Shana Poplack Suzanne Robillard University of Ottawa University of Ottawa Nathalie Dion John C. Paolillo University of Ottawa Indiana University Bloomington This article investigates whether speakers marshal phonetic integration as a strategy to dis - tinguish language-contact phenomena. Systematic comparison of the behavior of individuals, diagnostics, and language-mixing types (code -switches, established loanwords, and nonce bor - rowings) reveals variability at every level of the adaptation process, providing strong evidence that bilinguals do not phonetically distinguish other -language words, nonce or dictionary -attested, in a uniform way. This is in striking contrast to the community -wide morphosyntactic treatment they afford this same material when borrowing it: immediate, quasi -categorical, and consistent. This confirms that phonetic and morphosyntactic integration are independent. Only the latter is a reliable metric for distinguishing language-mixing types.* Keywords : metrics for distinguishing language-contact phenomena, phonetic integration, lexical borrowing, loanword adaptation, nonce borrowings, code -switches, loanword phonology 1. Introduction . Research on spontaneous language mixing has shown that bilin - guals tend overwhelmingly to imbue the words they borrow with the morphological and syntactic features of the recipient language, and that such integration occurs well be - fore the borrowings have achieved the status of bona fide loanwords (e.g. Adalar & Tagliamonte 1998, Budzhak -Jones 1998, Eze 1997, Ghafar Samar & Meechan 1998, Poplack 2018, Poplack & Dion 2012, Poplack & Meechan 1998a, Turpin 1995). In - deed, where the extralinguistic characteristics of loanword status (frequency of use and diffusion across the community) are lacking, this quasi -immediate adoption of the grammatical apparatus of the recipient language is the principal basis on which we can identify loanwords as borrowed.