Genomics of Evolutionary Novelty in Hybrids and Polyploids

It has long been recognized that hybridization and polyploidy are prominent processes in plant evolution. Although classically recognized as significant in speciation and adaptation, recognition of the importance of interspecific gene flow has dramatically increased during the genomics era, concomitant with an unending flood of empirical examples, with or without genome doubling. Interspecific gene flow is thus increasingly thought to lead to evolutionary innovation and diversification, via adaptive introgression, homoploid hybrid speciation and allopolyploid speciation. Less well understood, however, are the suite of genetic and genomic mechanisms set in motion by the merger of differentiated genomes, and the temporal scale over which recombinational complexity mediated by gene flow might be expressed and exposed to natural selection. We focus on these issues here, considering the types of molecular genetic and genomic processes that might be set in motion by the saltational event of genome merger between two diverged species, either with or without genome doubling, and how these various processes can contribute to novel phenotypes. Genetic mechanisms include the infusion of new alleles and the genesis of novel structural variation including translocations and inversions, homoeologous exchanges, transposable element mobilization and novel insertional effects, presence-absence variation and copy number variation. Polyploidy generates massive transcriptomic and regulatory alteration, presumably set in motion by disrupted stoichiometries of regulatory factors, small RNAs and other genome interactions that cascade from single-gene expression change up through entire networks of transformed regulatory modules. We highlight both these novel combinatorial possibilities and the range of temporal scales over which such complexity might be generated, and thus exposed to natural selection and drift

Online learning via dynamic reranking for Computer Assisted Translation

New techniques for online adaptation in computer assisted translation are explored and compared to previously existing approaches. Under the online adaptation paradigm, the translation system needs to adapt itself to real-world changing scenarios, where training and tuning may only take place once, when the system is set-up for the first time. For this purpose, post-edit information, as described by a given quality measure, is used as valuable feedback within a dynamic reranking algorithm. Two possible approaches are presented and evaluated. The first one relies on the well-known perceptron algorithm, whereas the second one is a novel approach using the Ridge regression in order to compute the optimum scaling factors within a state-of-the-art SMT system. Experimental results show that such algorithms are able to improve translation quality by learning from the errors produced by the system on a sentence-by-sentence basis.This paper is based upon work supported by the EC (FEDER/FSE) and the Spanish MICINN under projects MIPRCV “Consolider Ingenio 2010” (CSD2007-00018) and iTrans2 (TIN2009-14511). Also supported by the Spanish MITyC under the erudito.com (TSI-020110-2009-439) project, by the Generalitat Valenciana under grant Prometeo/2009/014 and scholarship GV/2010/067 and by the UPV under grant 20091027Martínez Gómez, P.; Sanchis Trilles, G.; Casacuberta Nolla, F. (2011). Online learning via dynamic reranking for Computer Assisted Translation. En Computational Linguistics and Intelligent Text Processing. Springer Verlag (Germany). 6609:93-105. https://doi.org/10.1007/978-3-642-19437-5_8S931056609Brown, P., Pietra, S.D., Pietra, V.D., Mercer, R.: The mathematics of machine translation. In: Computational Linguistics, vol. 19, pp. 263–311 (1993)Zens, R., Och, F.J., Ney, H.: Phrase-based statistical machine translation. In: Jarke, M., Koehler, J., Lakemeyer, G. (eds.) KI 2002. LNCS (LNAI), vol. 2479, pp. 18–32. Springer, Heidelberg (2002)Koehn, P., Och, F.J., Marcu, D.: Statistical phrase-based translation. In: Proc. HLT/NAACL 2003, pp. 48–54 (2003)Callison-Burch, C., Fordyce, C., Koehn, P., Monz, C., Schroeder, J.: (meta-) evaluation of machine translation. In: Proc. of the Workshop on SMT. ACL, pp. 136–158 (2007)Papineni, K., Roukos, S., Ward, T.: Maximum likelihood and discriminative training of direct translation models. In: Proc. of ICASSP 1988, pp. 189–192 (1998)Och, F., Ney, H.: Discriminative training and maximum entropy models for statistical machine translation. In: Proc. of the ACL 2002, pp. 295–302 (2002)Och, F., Zens, R., Ney, H.: Efficient search for interactive statistical machine translation. In: Proc. of EACL 2003, pp. 387–393 (2003)Sanchis-Trilles, G., Casacuberta, F.: Log-linear weight optimisation via bayesian adaptation in statistical machine translation. In: Proceedings of COLING 2010, Beijing, China (2010)Callison-Burch, C., Bannard, C., Schroeder, J.: Improving statistical translation through editing. In: Proc. of 9th EAMT Workshop Broadening Horizons of Machine Translation and its Applications, Malta (2004)Barrachina, S., et al.: Statistical approaches to computer-assisted translation. Computational Linguistics 35, 3–28 (2009)Casacuberta, F., et al.: Human interaction for high quality machine translation. Communications of the ACM 52, 135–138 (2009)Ortiz-Martínez, D., García-Varea, I., Casacuberta, F.: Online learning for interactive statistical machine translation. In: Proceedings of NAACL HLT, Los Angeles (2010)España-Bonet, C., Màrquez, L.: Robust estimation of feature weights in statistical machine translation. In: 14th Annual Conference of the EAMT (2010)Reverberi, G., Szedmak, S., Cesa-Bianchi, N., et al.: Deliverable of package 4: Online learning algorithms for computer-assisted translation (2008)Crammer, K., Dekel, O., Keshet, J., Shalev-Shwartz, S., Singer, Y.: Online passive-aggressive algorithms. Journal of Machine Learning Research 7, 551–585 (2006)Snover, M., Dorr, B., Schwartz, R., Micciulla, L., Makhoul, J.: A study of translation edit rate with targeted human annotation. In: Proc. of AMTA, Cambridge, MA, USA (2006)Papineni, K., Roukos, S., Ward, T., Zhu, W.: Bleu: A method for automatic evaluation of machine translation. In: Proc. of ACL 2002 (2002)Rosenblatt, F.: The perceptron: A probabilistic model for information storage and organization in the brain. Psychological Review 65, 386–408 (1958)Collins, M.: Discriminative training methods for hidden markov models: Theory and experiments with perceptron algorithms. In: EMNLP 2002, Philadelphia, PA, USA, pp. 1–8 (2002)Koehn, P.: Europarl: A parallel corpus for statistical machine translation. In: Proc. of the MT Summit X, pp. 79–86 (2005)Koehn, P., et al.: Moses: Open source toolkit for statistical machine translation. In: Proc. of the ACL Demo and Poster Sessions, Prague, Czech Republic, pp. 177–180 (2007)Och, F.: Minimum error rate training for statistical machine translation. In: Proc. of ACL 2003, pp. 160–167 (2003)Kneser, R., Ney, H.: Improved backing-off for m-gram language modeling. In: IEEE Int. Conf. on Acoustics, Speech and Signal Processing II, pp. 181–184 (1995)Stolcke, A.: SRILM – an extensible language modeling toolkit. In: Proc. of ICSLP 2002, pp. 901–904 (2002

Active learning for dialogue act labelling

Active learning is a useful technique that allows for a considerably reduction of the amount of data we need to manually label in order to reach a good performance of a statistical model. In order to apply active learning to a particular task we need to previously define an effective selection criteria, that picks out the most informative samples at each iteration of active learning process. This is still an open problem that we are going to face in this work, in the task of dialogue annotation at dialogue act level. We present two different criteria, weighted number of hypothesis and entropy, that we have applied to the Sample Selection Algorithm for the task of dialogue act labelling, that retrieved appreciably improvements in our experimental approach. © 2011 Springer-Verlag.Work supported by the EC (FEDER/FSE) and the Spanish MEC/MICINN under the MIPRCV “Consolider Ingenio 2010” program (CSD2007-00018), MITTRAL (TIN2009-14633-C03-01) projects and the FPI scholarship (BES-2009-028965). Also supported by the Generalitat Valenciana under grant Prometeo/2009/014 and GV/2010/067Ghigi, F.; Tamarit Ballester, V.; Martínez-Hinarejos, C.; Benedí Ruiz, JM. (2011). Active learning for dialogue act labelling. En Lecture Notes in Computer Science. Springer Verlag (Germany). 6669:652-659. https://doi.org/10.1007/978-3-642-21257-4_81S6526596669Alcácer, N., Benedí, J.M., Blat, F., Granell, R., Martínez, C.D., Torres, F.: Acquisition and Labelling of a Spontaneous Speech Dialogue Corpus. In: SPECOM, Greece, pp. 583–586 (2005)Benedí, J.M., Lleida, E., Varona, A., Castro, M.J., Galiano, I., Justo, R., López, I., Miguel, A.: Design and acquisition of a telephone spontaneous speech dialogue corpus in spanish: DIHANA. In: Fifth LREC, Genova, Italy, pp. 1636–1639 (2006)Bunt, H.: Context and dialogue control. THINK Quarterly 3 (1994)Casacuberta, F., Vidal, E., Picó, D.: Inference of finite-state transducers from regular languages. Pat. Recognition 38(9), 1431–1443 (2005)Dybkjær, L., Minker, W. (eds.): Recent Trends in Discourse and Dialogue. Text, Speech and Language Technology, vol. 39. Springer, Dordrecht (2008)Gorin, A., Riccardi, G., Wright, J.: How may I help you? Speech Comm. 23, 113–127 (1997)Hwa, R.: Sample selection for statistical grammar induction. In: Proceedings of the 2000 Joint SIGDAT, pp. 45–52. Association for Computational Linguistics, Morristown (2000)Lavie, A., Levin, L., Zhan, P., Taboada, M., Gates, D., Lapata, M.M., Clark, C., Broadhead, M., Waibel, A.: Expanding the domain of a multi-lingual speech-to-speech translation system. In: Proceedings of the Workshop on Spoken Language Translation, ACL/EACL 1997 (1997)Martínez-Hinarejos, C.D., Tamarit, V., Benedí, J.M.: Improving unsegmented dialogue turns annotation with N-gram transducers. In: Proceedings of the 23rd Pacific Asia Conference on Language, Information and Computation (PACLIC23), vol. 1, pp. 345–354 (2009)Robinson, D.W.: Entropy and uncertainty, vol. 10, pp. 493–506 (2008)Stolcke, A., Coccaro, N., Bates, R., Taylor, P., van Ess-Dykema, C., Ries, K., Shriberg, E., Jurafsky, D., Martin, R., Meteer, M.: Dialogue act modelling for automatic tagging and recognition of conversational speech. Computational Linguistics 26(3), 1–34 (2000)Tamarit, V., Benedí, J., Martínez-Hinarejos, C.: Estimating the number of segments for improving dialogue act labelling. In: Proceedings of the First International Workshop of Spoken Dialog Systems Technology (2009)Young, S.: Probabilistic methods in spoken dialogue systems. Philosophical Trans. Royal Society (Series A) 358(1769), 1389–1402 (2000

Brown representability for space-valued functors

In this paper we prove two theorems which resemble the classical cohomological and homological Brown representability theorems. The main difference is that our results classify small contravariant functors from spaces to spaces up to weak equivalence of functors. In more detail, we show that every small contravariant functor from spaces to spaces which takes coproducts to products up to homotopy and takes homotopy pushouts to homotopy pullbacks is naturally weekly equivalent to a representable functor. The second representability theorem states: every contravariant continuous functor from the category of finite simplicial sets to simplicial sets taking homotopy pushouts to homotopy pullbacks is equivalent to the restriction of a representable functor. This theorem may be considered as a contravariant analog of Goodwillie's classification of linear functors.Comment: 19 pages, final version, accepted by the Israel Journal of Mathematic

A model structure for coloured operads in symmetric spectra

We describe a model structure for coloured operads with values in the category of symmetric spectra (with the positive model structure), in which fibrations and weak equivalences are defined at the level of the underlying collections. This allows us to treat R-module spectra (where R is a cofibrant ring spectrum) as algebras over a cofibrant spectrum-valued operad with R as its first term. Using this model structure, we give suficient conditions for homotopical localizations in the category of symmetric spectra to preserve module structures.Comment: 16 page

Forecasting in the light of Big Data

Predicting the future state of a system has always been a natural motivation for science and practical applications. Such a topic, beyond its obvious technical and societal relevance, is also interesting from a conceptual point of view. This owes to the fact that forecasting lends itself to two equally radical, yet opposite methodologies. A reductionist one, based on the first principles, and the naive inductivist one, based only on data. This latter view has recently gained some attention in response to the availability of unprecedented amounts of data and increasingly sophisticated algorithmic analytic techniques. The purpose of this note is to assess critically the role of big data in reshaping the key aspects of forecasting and in particular the claim that bigger data leads to better predictions. Drawing on the representative example of weather forecasts we argue that this is not generally the case. We conclude by suggesting that a clever and context-dependent compromise between modelling and quantitative analysis stands out as the best forecasting strategy, as anticipated nearly a century ago by Richardson and von Neumann

GBA mutation promotes early mitochondrial dysfunction in 3D neurosphere models

Glucocerebrosidase (GBA) mutations are the most important genetic risk factor for the development of Parkinson disease (PD). GBA encodes the lysosomal enzyme glucocerebrosidase (GCase). Loss-of-GCase activity in cellular models has implicated lysosomal and mitochondrial dysfunction in PD disease pathogenesis, although the exact mechanisms remain unclear. We hypothesize that GBA mutations impair mitochondria quality control in a neurosphere model.We have characterized mitochondrial content, mitochondrial function and macroautophagy flux in 3D-neurosphere-model derived from neural crest stem cells containing heterozygous and homozygous N370SGBA mutations, under carbonyl cyanide-m-chlorophenyl-hydrazine (CCCP)- induced mitophagy.Our findings on mitochondrial markers and ATP levels indicate that mitochondrial accumulation occurs in mutant N370SGBA neurospheres under basal conditions, and clearance of depolarised mitochondria is impaired following CCCP-treatment. A significant increase in TFEB-mRNA levels, the master regulator of lysosomal and autophagy genes, may explain an unchanged macroautophagy flux in N370SGBA neurospheres. PGC1α-mRNA levels were also significantly increased following CCCP-treatment in heterozygote, but not homozygote neurospheres, and might contribute to the increased mitochondrial content seen in cells with this genotype, probably as a compensatory mechanism that is absent in homozygous lines.Mitochondrial impairment occurs early in the development of GCase-deficient neurons. Furthermore, impaired turnover of depolarised mitochondria is associated with early mitochondrial dysfunction.In summary, the presence of GBA mutation may be associated with higher levels of mitochondrial content in homozygous lines and lower clearance of damaged mitochondria in our neurosphere model

Design, development and field evaluation of a Spanish into sign language translation system

This paper describes the design, development and field evaluation of a machine translation system from Spanish to Spanish Sign Language (LSE: Lengua de Signos Española). The developed system focuses on helping Deaf people when they want to renew their Driver’s License. The system is made up of a speech recognizer (for decoding the spoken utterance into a word sequence), a natural language translator (for converting a word sequence into a sequence of signs belonging to the sign language), and a 3D avatar animation module (for playing back the signs). For the natural language translator, three technological approaches have been implemented and evaluated: an example-based strategy, a rule-based translation method and a statistical translator. For the final version, the implemented language translator combines all the alternatives into a hierarchical structure. This paper includes a detailed description of the field evaluation. This evaluation was carried out in the Local Traffic Office in Toledo involving real government employees and Deaf people. The evaluation includes objective measurements from the system and subjective information from questionnaires. The paper details the main problems found and a discussion on how to solve them (some of them specific for LSE)

Annual post-market environmental monitoring (PMEM) report on the cultivation of genetically modified maize MON 810 in 2014 from Monsanto Europe S.A.

Following a request from the European Commission, the Panel on Genetically Modified Organisms of the European Food Safety Authority (GMO Panel) assessed the annual post-market environmental monitoring (PMEM) report for the 2014 growing season of maize MON 810 provided by Monsanto Europe S.A. The GMO Panel concludes that the insect resistance monitoring data do not indicate a decrease in susceptibility of field Iberian populations of corn borers to the Cry1Ab protein over the 2014 season. However, as the methodology for insect resistance monitoring remained unchanged compared to previous PMEM reports, the GMO Panel reiterates its previous recommendations for improvement of the insect resistance management plan. The GMO Panel considers that the farmer alert system to report complaints regarding product performance could complement the information obtained from the laboratory bioassays, but encourages the consent holder to provide more information in order to be in a position to appraise its usefulness. The data on general surveillance activities do not indicate any unanticipated adverse effects on human and animal health or the environment arising from the cultivation of maize MON 810 cultivation in 2014. The GMO Panel reiterates its previous recommendations to improve the methodology for the analysis of farmer questionnaires and conduct of the literature review in future annual PMEM reports on maize MON 810. The GMO Panel urges the consent holder to consider how to make best use of the information recorded in national registers to optimise sampling for farmer questionnaires, and requests to continue reviewing and discussing relevant scientific publications on possible adverse effects of maize MON 810 on rove beetles. Also, the GMO Panel encourages relevant parties to continue developing a methodological framework to use existing networks in the broader context of environmental monitorin