Multiple Quantum Hypothesis Testing Expressions and Classical-Quantum Channel Converse Bounds

Alternative exact expressions are derived for the minimum error probability of a hypothesis test discriminating among $M$ quantum states. The first expression corresponds to the error probability of a binary hypothesis test with certain parameters; the second involves the optimization of a given information-spectrum measure. Particularized in the classical-quantum channel coding setting, this characterization implies the tightness of two existing converse bounds; one derived by Matthews and Wehner using hypothesis-testing, and one obtained by Hayashi and Nagaoka via an information-spectrum approach.Comment: Presented at the 2016 IEEE International Symposium on Information Theory, July 10-15, 2016, Barcelona, Spai

Error Probability Bounds for Gaussian Channels under Maximal and Average Power Constraints

This paper studies the performance of block coding on an additive white Gaussian noise channel under different power limitations at the transmitter. Lower bounds are presented for the minimum error probability of codes satisfying maximal and average power constraints. These bounds are tighter than previous results in the finite blocklength regime, and yield a better understanding on the structure of good codes under an average power limitation. Evaluation of these bounds for short and moderate blocklengths is also discussed.Comment: Submitted to the IEEE Transactions on Information Theory. This article was presented in part at the 2019 IEEE International Symposium on Information Theory, Paris, France (ISIT 2019) and at the 2020 International Z\"urich Seminar on Communication and Information, Z\"urich, Switzerland (IZS 2020

Robust Signaling for Bursty Interference

This paper studies a bursty interference channel, where the presence/absence of interference is modeled by a block-i.i.d.\ Bernoulli process that stays constant for a duration of $T$ symbols (referred to as coherence block) and then changes independently to a new state. We consider both a quasi-static setup, where the interference state remains constant during the whole transmission of the codeword, and an ergodic setup, where a codeword spans several coherence blocks. For the quasi-static setup, we study the largest rate of a coding strategy that provides reliable communication at a basic rate and allows an increased (opportunistic) rate when there is no interference. For the ergodic setup, we study the largest achievable rate. We study how non-causal knowledge of the interference state, referred to as channel-state information (CSI), affects the achievable rates. We derive converse and achievability bounds for (i) local CSI at the receiver-side only; (ii) local CSI at the transmitter- and receiver-side, and (iii) global CSI at all nodes. Our bounds allow us to identify when interference burstiness is beneficial and in which scenarios global CSI outperforms local CSI. The joint treatment of the quasi-static and ergodic setup further allows for a thorough comparison of these two setups.Comment: 67 pages, 39 figure

On the Sum Capacity of A Class of Cyclically Symmetric Deterministic Interference Channels

Certain deterministic interference channels have been shown to accurately model Gaussian interference channels in the asymptotic low-noise regime. Motivated by this correspondence, we investigate a K user-pair, cyclically symmetric, deterministic interference channel in which each receiver experiences interference only from its neighboring transmitters (Wyner model). We establish the sum capacity for a large set of channel parameters, thus generalizing previous results for the 2-pair case.Comment: 5 pages; submitted to IEEE International Symposium on Information Theory (ISIT 2009

The Error Probability of Generalized Perfect Codes

This paper has been presented at : IEEE International Symposium on Information Theory 2018We introduce a definition of perfect and quasi-perfect codes for symmetric channels parametrized by an auxiliary output distribution. This new definition generalizes previous definitions and encompasses maximum distance separable codes. The error probability of these codes, whenever they exist, is shown to attain the meta-converse lower bound.This work has been funded in part by the European Research Council (ERC) under grants 714161 and 725411, by the Spanish Ministry of Economy and Competitiveness under Grants TEC2016-78434-C3 and IJCI-2015-27020, by the National Science Foundation under Grant CCF-1513915 and by the Center for Science of Information, an NSF Science and Technology Center under Grant CCF-0939370

The Error Probability of Generalized Perfect Codes via the Meta-Converse

We introduce a definition of perfect and quasiperfect codes for discrete symmetric channels based on the packing and covering properties of generalized spheres whose shape is tilted using an auxiliary probability measure. This notion generalizes previous definitions of perfect and quasiperfect codes and encompasses maximum distance separable codes. The error probability of these codes, whenever they exist, is shown to coincide with the estimate provided by the metaconverse lower bound. We illustrate how the proposed definition naturally extends to cover almost-lossless source-channel coding and lossy compression.ER

GB3.0: a platform for plant bio-design that connects functional DNA elements with associated biological data

This is a pre-copyedited, author-produced version of an article accepted for publication in Nucleic Acids Research following peer review. The version of record Vázquez-Vilar, M.; Quijano-Rubio, A.; Fernandez Del Carmen, MA.; Sarrion-Perdigones, A.; Ochoa-Fernández, R.; Ziarsolo Areitioaurtena, P.; Blanca Postigo, JM.... (2017). GB3.0: a platform for plant bio-design that connects functional DNA elements with associated biological data. Nucleic Acids Research. 45(4):2196-2209. doi:10.1093/nar/gkw1326 is available online at: http://doi.org/10.1093/nar/gkw1326.[EN] Modular DNA assembly simplifies multigene engineering in Plant Synthetic Biology. Furthermore, the recent adoption of a common syntax to facilitate the exchange of plant DNA parts (phytobricks) is a promising strategy to speed up genetic engineering. Following this lead, here, we present a platform for plant biodesign that incorporates functional descriptions of phytobricks obtained under pre-defined experimental conditions, and systematically registers the resulting information as metadata for documentation. To facilitate the handling of functional descriptions, we developed a new version (v3.0) of the GoldenBraid (GB) webtool that integrates the experimental data and displays it in the form of datasheets. We report the use of the Luciferase/Renilla (Luc/Ren) transient agroinfiltration assay in Nicotiana benthamiana as a standard to estimate relative transcriptional activities conferred by regulatory phytobricks, and show the consistency and reproducibility of this method in the characterization of a synthetic phytobrick based on the CaMV35S promoter. Furthermore, we illustrate the potential for combinatorial optimization and incremental innovation of the GB3.0 platform in two separate examples, (i) the development of a collection of orthogonal transcriptional regulators based on phiC31 integrase and (ii) the design of a small genetic circuit that connects a glucocorticoid switch to a MYB/bHLH transcriptional activation module.Spanish Ministry of Economy and Competitiveness [BIO2013-42193-R and BIO2016-78601-R projects to A.G. and D.O.]. Funding for open access charge: Spanish Ministry of Economy and Competitiveness [BIO2013-42193-R and BIO2016-78601-R projects to A.G. and D.O.].Vázquez-Vilar, M.; Quijano-Rubio, A.; Fernández Del Carmen, MA.; Sarrion-Perdigones, A.; Ochoa-Fernández, R.; Ziarsolo Areitioaurtena, P.; Blanca Postigo, JM.... (2017). GB3.0: a platform for plant bio-design that connects functional DNA elements with associated biological data. Nucleic Acids Research. 45(4):2196-2209. https://doi.org/10.1093/nar/gkw1326S21962209454Dalal, J., Yalamanchili, R., La Hovary, C., Ji, M., Rodriguez-Welsh, M., Aslett, D., … Qu, R. (2015). A novel gateway-compatible binary vector series (PC-GW) for flexible cloning of multiple genes for genetic transformation of plants. Plasmid, 81, 55-62. doi:10.1016/j.plasmid.2015.06.003Cha-aim, K., Fukunaga, T., Hoshida, H., & Akada, R. (2009). Reliable fusion PCR mediated by GC-rich overlap sequences. Gene, 434(1-2), 43-49. doi:10.1016/j.gene.2008.12.014Nour-Eldin, H. H., Geu-Flores, F., & Halkier, B. A. (2010). USER Cloning and USER Fusion: The Ideal Cloning Techniques for Small and Big Laboratories. Methods in Molecular Biology, 185-200. doi:10.1007/978-1-60761-723-5_13Engler, C., Kandzia, R., & Marillonnet, S. (2008). A One Pot, One Step, Precision Cloning Method with High Throughput Capability. PLoS ONE, 3(11), e3647. doi:10.1371/journal.pone.0003647Blake, W. J., Chapman, B. A., Zindal, A., Lee, M. E., Lippow, S. M., & Baynes, B. M. (2010). Pairwise selection assembly for sequence-independent construction of long-length DNA. Nucleic Acids Research, 38(8), 2594-2602. doi:10.1093/nar/gkq123De Paoli, H. C., Tuskan, G. A., & Yang, X. (2016). An innovative platform for quick and flexible joining of assorted DNA fragments. Scientific Reports, 6(1). doi:10.1038/srep19278Engler, C., Gruetzner, R., Kandzia, R., & Marillonnet, S. (2009). Golden Gate Shuffling: A One-Pot DNA Shuffling Method Based on Type IIs Restriction Enzymes. PLoS ONE, 4(5), e5553. doi:10.1371/journal.pone.0005553Weber, E., Engler, C., Gruetzner, R., Werner, S., & Marillonnet, S. (2011). A Modular Cloning System for Standardized Assembly of Multigene Constructs. PLoS ONE, 6(2), e16765. doi:10.1371/journal.pone.0016765Sarrion-Perdigones, A., Falconi, E. E., Zandalinas, S. I., Juárez, P., Fernández-del-Carmen, A., Granell, A., & Orzaez, D. (2011). GoldenBraid: An Iterative Cloning System for Standardized Assembly of Reusable Genetic Modules. PLoS ONE, 6(7), e21622. doi:10.1371/journal.pone.0021622Patron, N. J., Orzaez, D., Marillonnet, S., Warzecha, H., Matthewman, C., Youles, M., … Rogers, C. (2015). Standards for plant synthetic biology: a common syntax for exchange ofDNAparts. New Phytologist, 208(1), 13-19. doi:10.1111/nph.13532Liu, W., & Stewart, C. N. (2015). Plant synthetic biology. Trends in Plant Science, 20(5), 309-317. doi:10.1016/j.tplants.2015.02.004Wang, Y.-H., Wei, K. Y., & Smolke, C. D. (2013). Synthetic Biology: Advancing the Design of Diverse Genetic Systems. Annual Review of Chemical and Biomolecular Engineering, 4(1), 69-102. doi:10.1146/annurev-chembioeng-061312-103351Engler, C., Youles, M., Gruetzner, R., Ehnert, T.-M., Werner, S., Jones, J. D. G., … Marillonnet, S. (2014). A Golden Gate Modular Cloning Toolbox for Plants. ACS Synthetic Biology, 3(11), 839-843. doi:10.1021/sb4001504Canton, B., Labno, A., & Endy, D. (2008). Refinement and standardization of synthetic biological parts and devices. Nature Biotechnology, 26(7), 787-793. doi:10.1038/nbt1413Sarrion-Perdigones, A., Vazquez-Vilar, M., Palaci, J., Castelijns, B., Forment, J., Ziarsolo, P., … Orzaez, D. (2013). GoldenBraid 2.0: A Comprehensive DNA Assembly Framework for Plant Synthetic Biology. PLANT PHYSIOLOGY, 162(3), 1618-1631. doi:10.1104/pp.113.217661Orzaez, D., Medina, A., Torre, S., Fernández-Moreno, J. P., Rambla, J. L., Fernández-del-Carmen, A., … Granell, A. (2009). A Visual Reporter System for Virus-Induced Gene Silencing in Tomato Fruit Based on Anthocyanin Accumulation. Plant Physiology, 150(3), 1122-1134. doi:10.1104/pp.109.139006Yoo, S.-D., Cho, Y.-H., & Sheen, J. (2007). Arabidopsis mesophyll protoplasts: a versatile cell system for transient gene expression analysis. Nature Protocols, 2(7), 1565-1572. doi:10.1038/nprot.2007.199Schneider, C. A., Rasband, W. S., & Eliceiri, K. W. (2012). NIH Image to ImageJ: 25 years of image analysis. Nature Methods, 9(7), 671-675. doi:10.1038/nmeth.2089Gutiérrez, S., Yvon, M., Thébaud, G., Monsion, B., Michalakis, Y., & Blanc, S. (2010). Dynamics of the Multiplicity of Cellular Infection in a Plant Virus. PLoS Pathogens, 6(9), e1001113. doi:10.1371/journal.ppat.1001113Vazquez-Vilar, M., Sarrion-Perdigones, A., Ziarsolo, P., Blanca, J., Granell, A., & Orzaez, D. (2015). Software-Assisted Stacking of Gene Modules Using GoldenBraid 2.0 DNA-Assembly Framework. Plant Functional Genomics, 399-420. doi:10.1007/978-1-4939-2444-8_20Vazquez-Vilar, M., Bernabé-Orts, J. M., Fernandez-del-Carmen, A., Ziarsolo, P., Blanca, J., Granell, A., & Orzaez, D. (2016). A modular toolbox for gRNA–Cas9 genome engineering in plants based on the GoldenBraid standard. Plant Methods, 12(1). doi:10.1186/s13007-016-0101-2Quinn, J. Y., Cox, R. S., Adler, A., Beal, J., Bhatia, S., Cai, Y., … Sauro, H. M. (2015). SBOL Visual: A Graphical Language for Genetic Designs. PLOS Biology, 13(12), e1002310. doi:10.1371/journal.pbio.1002310Thorpe, H. M., Wilson, S. E., & Smith, M. C. M. (2000). Control of directionality in the site-specific recombination system of the Streptomyces phage phiC31. Molecular Microbiology, 38(2), 232-241. doi:10.1046/j.1365-2958.2000.02142.xKhaleel, T., Younger, E., McEwan, A. R., Varghese, A. S., & Smith, M. C. M. (2011). A phage protein that binds φC31 integrase to switch its directionality. Molecular Microbiology, 80(6), 1450-1463. doi:10.1111/j.1365-2958.2011.07696.xOrt, D. R., Merchant, S. S., Alric, J., Barkan, A., Blankenship, R. E., Bock, R., … Zhu, X. G. (2015). Redesigning photosynthesis to sustainably meet global food and bioenergy demand. Proceedings of the National Academy of Sciences, 112(28), 8529-8536. doi:10.1073/pnas.1424031112Smolke, C. D. (2009). Building outside of the box: iGEM and the BioBricks Foundation. Nature Biotechnology, 27(12), 1099-1102. doi:10.1038/nbt1209-1099Cambray, G., Mutalik, V. K., & Arkin, A. P. (2011). Toward rational design of bacterial genomes. Current Opinion in Microbiology, 14(5), 624-630. doi:10.1016/j.mib.2011.08.001Mutalik, V. K., Guimaraes, J. C., Cambray, G., Mai, Q.-A., Christoffersen, M. J., Martin, L., … Arkin, A. P. (2013). Quantitative estimation of activity and quality for collections of functional genetic elements. Nature Methods, 10(4), 347-353. doi:10.1038/nmeth.2403Cambray, G., Guimaraes, J. C., Mutalik, V. K., Lam, C., Mai, Q.-A., Thimmaiah, T., … Endy, D. (2013). Measurement and modeling of intrinsic transcription terminators. Nucleic Acids Research, 41(9), 5139-5148. doi:10.1093/nar/gkt163Mutalik, V. K., Guimaraes, J. C., Cambray, G., Lam, C., Christoffersen, M. J., Mai, Q.-A., … Endy, D. (2013). Precise and reliable gene expression via standard transcription and translation initiation elements. Nature Methods, 10(4), 354-360. doi:10.1038/nmeth.2404Bartley, B., Beal, J., Clancy, K., Misirli, G., Roehner, N., Oberortner, E., … Sauro, H. (2015). Synthetic Biology Open Language (SBOL) Version 2.0.0. Journal of Integrative Bioinformatics, 12(2). doi:10.1515/jib-2015-272Angov, E. (2011). Codon usage: Nature’s roadmap to expression and folding of proteins. Biotechnology Journal, 6(6), 650-659. doi:10.1002/biot.201000332Hillson, N. J., Rosengarten, R. D., & Keasling, J. D. (2011). j5 DNA Assembly Design Automation Software. ACS Synthetic Biology, 1(1), 14-21. doi:10.1021/sb2000116Brazma, A., Hingamp, P., Quackenbush, J., Sherlock, G., Spellman, P., Stoeckert, C., … Vingron, M. (2001). Minimum information about a microarray experiment (MIAME)—toward standards for microarray data. Nature Genetics, 29(4), 365-371. doi:10.1038/ng1201-365Taylor, C. F., Paton, N. W., Lilley, K. S., Binz, P.-A., Julian, R. K., Jones, A. R., … Hermjakob, H. (2007). The minimum information about a proteomics experiment (MIAPE). Nature Biotechnology, 25(8), 887-893. doi:10.1038/nbt1329Yang, Y., Li, R., & Qi, M. (2000). In vivo analysis of plant promoters and transcription factors by agroinfiltration of tobacco leaves. The Plant Journal, 22(6), 543-551. doi:10.1046/j.1365-313x.2000.00760.xKapila, J., De Rycke, R., Van Montagu, M., & Angenon, G. (1997). An Agrobacterium-mediated transient gene expression system for intact leaves. Plant Science, 122(1), 101-108. doi:10.1016/s0168-9452(96)04541-4Schaumberg, K. A., Antunes, M. S., Kassaw, T. K., Xu, W., Zalewski, C. S., Medford, J. I., & Prasad, A. (2015). Quantitative characterization of genetic parts and circuits for plant synthetic biology. Nature Methods, 13(1), 94-100. doi:10.1038/nmeth.3659Dafny-Yelin, M., & Tzfira, T. (2007). Delivery of Multiple Transgenes to Plant Cells. Plant Physiology, 145(4), 1118-1128. doi:10.1104/pp.107.106104TZFIRA, T. (2004). Agrobacterium T-DNA integration: molecules and models. Trends in Genetics, 20(8), 375-383. doi:10.1016/j.tig.2004.06.004De Buck, S., De Wilde, C., Van Montagu, M., & Depicker, A. (2000). Determination of the T-DNA Transfer and the T-DNA Integration Frequencies upon Cocultivation ofArabidopsis thalianaRoot Explants. Molecular Plant-Microbe Interactions, 13(6), 658-665. doi:10.1094/mpmi.2000.13.6.658Konermann, S., Brigham, M. D., Trevino, A. E., Joung, J., Abudayyeh, O. O., Barcena, C., … Zhang, F. (2014). Genome-scale transcriptional activation by an engineered CRISPR-Cas9 complex. Nature, 517(7536), 583-588. doi:10.1038/nature14136Gilbert, L. A., Horlbeck, M. A., Adamson, B., Villalta, J. E., Chen, Y., Whitehead, E. H., … Weissman, J. S. (2014). Genome-Scale CRISPR-Mediated Control of Gene Repression and Activation. Cell, 159(3), 647-661. doi:10.1016/j.cell.2014.09.029Moore, I., Samalova, M., & Kurup, S. (2006). Transactivated and chemically inducible gene expression in plants. The Plant Journal, 45(4), 651-683. doi:10.1111/j.1365-313x.2006.02660.xButelli, E., Titta, L., Giorgio, M., Mock, H.-P., Matros, A., Peterek, S., … Martin, C. (2008). Enrichment of tomato fruit with health-promoting anthocyanins by expression of select transcription factors. Nature Biotechnology, 26(11), 1301-1308. doi:10.1038/nbt.1506Müller, K., Siegel, D., Rodriguez Jahnke, F., Gerrer, K., Wend, S., Decker, E. L., … Zurbriggen, M. D. (2014). A red light-controlled synthetic gene expression switch for plant systems. Mol. BioSyst., 10(7), 1679-1688. doi:10.1039/c3mb70579jDavuluri, G. R., van Tuinen, A., Fraser, P. D., Manfredonia, A., Newman, R., Burgess, D., … Bowler, C. (2005). Fruit-specific RNAi-mediated suppression of DET1 enhances carotenoid and flavonoid content in tomatoes. Nature Biotechnology, 23(7), 890-895. doi:10.1038/nbt1108Zhang, Y., Butelli, E., Alseekh, S., Tohge, T., Rallapalli, G., Luo, J., … Martin, C. (2015). Multi-level engineering facilitates the production of phenylpropanoid compounds in tomato. Nature Communications, 6(1). doi:10.1038/ncomms9635Ori, N., Juarez, M. T., Jackson, D., Yamaguchi, J., Banowetz, G. M., & Hake, S. (1999). Leaf Senescence Is Delayed in Tobacco Plants Expressing the Maize Homeobox Gene knotted1 under the Control of a Senescence-Activated Promoter. The Plant Cell, 11(6), 1073-1080. doi:10.1105/tpc.11.6.1073Azuma, M., Morimoto, R., Hirose, M., Morita, Y., Hoshino, A., Iida, S., … Shiratake, K. (2015). A petal‐specific In MYB 1 promoter from Japanese morning glory: a useful tool for molecular breeding of floricultural crops. Plant Biotechnology Journal, 14(1), 354-363. doi:10.1111/pbi.12389Paine, J. A., Shipton, C. A., Chaggar, S., Howells, R. M., Kennedy, M. J., Vernon, G., … Drake, R. (2005). Improving the nutritional value of Golden Rice through increased pro-vitamin A content. Nature Biotechnology, 23(4), 482-487. doi:10.1038/nbt1082Houmard, N. M., Mainville, J. L., Bonin, C. P., Huang, S., Luethy, M. H., & Malvar, T. M. (2007). High-lysine corn generated by endosperm-specific suppression of lysine catabolism using RNAi. Plant Biotechnology Journal, 5(5), 605-614. doi:10.1111/j.1467-7652.2007.00265.xPadidam, M. (2003). Chemically regulated gene expression in plants. Current Opinion in Plant Biology, 6(2), 169-177. doi:10.1016/s1369-5266(03)00005-0Kinkema, M., Geijskes, R. J., Shand, K., Coleman, H. D., De Lucca, P. C., Palupe, A., … Sainz, M. B. (2013). An improved chemically inducible gene switch that functions in the monocotyledonous plant sugar cane. Plant Molecular Biology, 84(4-5), 443-454. doi:10.1007/s11103-013-0140-

Bayesian M-Ary Hypothesis Testing: The Meta-Converse and Verdu-Han Bounds Are Tight

Two alternative exact characterizations of the minimum error probability of Bayesian M-ary hypothesis testing are derived. The first expression corresponds to the error probability of an induced binary hypothesis test and implies the tightness of the meta-converse bound by Polyanskiy et al.; the second expression is a function of an information-spectrum measure and implies the tightness of a generalized Verdú-Han lower bound. The formulas characterize the minimum error probability of several problems in information theory and help to identify the steps where existing converse bounds are loose