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The Capacity of Some Pólya String Models [article]

Ohad Elishco, Farzad Farnoud, Moshe Schwartz, Jehoshua Bruck
2018 arXiv   pre-print
Unlike previous works that study the combinatorial capacity of string-duplication systems, or various string statistics, this work provides exact capacity or bounds on it, for several probabilistic models  ...  In particular, we study the capacity of noisy string-duplication systems, including the tandem-duplication, end-duplication, and interspersed-duplication systems.  ...  We therefore suggest extensions of the Pólya urn models to what we call Pólya string models, in which the balls form a string, which may be circular or linear, similar to bases of a DNA molecule.  ... 
arXiv:1808.06062v1 fatcat:wywo2uxvynat7irigtque2uuva

The capacity of some Pólya string models

Ohad Elishco, Farzad Farnoud, Moshe Schwartz, Jehoshua Bruck
2016 2016 IEEE International Symposium on Information Theory (ISIT)  
We study random stringduplication systems, called Pólya string models, motivated by certain random mutation processes in the genome of living organisms.  ...  Unlike previous works that study the combinatorial capacity of string-duplication systems, or peripheral properties such as symbol frequency, this work provides exact capacity or bounds on it, for several  ...  In particular, this highlights the difference between an urn model and a string model. As we shall see, the capacity differs between some of the cases.  ... 
doi:10.1109/isit.2016.7541303 dblp:conf/isit/ElishcoFSB16 fatcat:m2nnled3qncbbjca433nlljrii

Table of contents

2019 IEEE Transactions on Information Theory  
Bruck The Entropy Rate of Some Pólya String Models 8180 SOURCE CODING R. Nomura Overflow Probability of Variable-Length Codes With Codeword Cost 8194 S. Foldes, D. S. Parker, and S.  ...  Ulukus The Capacity of Private Information Retrieval With Partially Known Private Side Information 8222 K. Banawan and S.  ... 
doi:10.1109/tit.2019.2942444 fatcat:p46r4x4dpnhpladn5nzb3ndybi

JBrainy: Micro-benchmarking Java Collections with Interference

Noric Couderc, Emma Söderberg, Christoph Reichenbach
2020 Companion of the ACM/SPEC International Conference on Performance Engineering  
For sets, we found LinkedHashSet to yield the best performance in 78% of the benchmarks.  ...  Software developers use collection data structures extensively and are often faced with the task of picking which collection to use.  ...  Pólya Pro les To address the limitation with multi-operation pro les, we propose a third model, which we call Pólya Pro les.  ... 
doi:10.1145/3375555.3383760 dblp:conf/wosp/CoudercSR20 fatcat:ngktatdj6zel7ozwiephsaiz4m

Long noncoding RNAs are rarely translated in two human cell lines

B. Banfai, H. Jia, J. Khatun, E. Wood, B. Risk, W. E. Gundling, A. Kundaje, H. P. Gunawardena, Y. Yu, L. Xie, K. Krajewski, B. D. Strahl (+5 others)
2012 Genome Research  
encoding genomic loci, and RNA-seq data generated by ENCODE in long polyA+ and polyA-fractions in the cell lines K562 and GM12878.  ...  The most important covariate for predicting translation was, surprisingly, the Cytosol polyA-fraction in both cell lines.  ...  In particular, we defined the ''signature'' of a gene to be a binary string encoding every terminal node into which the gene fell in the fitted model.  ... 
doi:10.1101/gr.134767.111 pmid:22955977 pmcid:PMC3431482 fatcat:ahinzmbfwvfgznrunnkmgej7jq

Empirical assessment of competitive hybridization and noise in ultra high density canine tiling arrays

Cali E Willet, Laura Bunbury-Cruickshank, Diane van Rooy, Georgina Child, Mohammad R Shariflou, Peter C Thomson, Claire M Wade
2013 BMC Bioinformatics  
To prevent the introduction of noise from this source, the degree of competition should be regulated by minimizing variation in density across the target region.  ...  Results: A high density array was designed to a 1.5 megabase region of the canine genome to explore the potential for probe competition to introduce noise.  ...  Acknowledgements The authors would like to thank Stephen Macchia for computational support. Author details  ... 
doi:10.1186/1471-2105-14-231 pmid:23870167 pmcid:PMC3733988 fatcat:2qwwjeywhzbwnkhvnuv3ibzilu

Design of an Epitope-Based Vaccine Ensemble for Animal Trypanosomiasis by Computational Methods

Lucas Michel-Todó, Pascal Bigey, Pedro A Reche, María-Jesus Pinazo, Joaquim Gascón, Julio Alonso-Padilla
2020 Vaccines  
Therefore, the availability of a prophylactic vaccine would represent a major breakthrough towards the management and control of the disease.  ...  African animal trypanosomiasis is caused by vector-transmitted parasites of the genus Trypanosoma.  ...  Acknowledgments: The authors want to thank the help support provided by IEDB-AR Solutions Centre to all the queries raised throughout the study.  ... 
doi:10.3390/vaccines8010130 pmid:32188062 fatcat:n7scl5dgnzg6blvo6bhgvqh4ym

A Compression System for Unicode Files Using an Enhanced Lzw Method

Rincy Thayyalakkal Anto, Rajesh Ramachandran
2020 Pertanika journal of science & technology  
The system of the present work comprises a compression module, configured to compress the Unicode data by creating the dictionary entries in Unicode format.  ...  The decompression module is configured to decompress the compressed file with the help of unique Unicode character table obtained from the compression module and the encoded output.  ...  ACKNOWLEDGEMENT We thank the Bharathiar University Research Centre, Coimbatore for all the facilities extended so far during the period of research.  ... 
doi:10.47836/pjst.28.4.16 fatcat:pq3sbgos2rdndfi26ngnl37m5q

Switching time between overt and covert speech: Generative attention

Robert J. Weber, James Blagowsky, Reed Mankin
1982 Memory & Cognition  
The results supported the symbolic model.  ...  In addition, two models -of response intensity representation were contrasted: a symbolic or digital model, with intensity altered by parameter substitution, and an analog model, with intensity represented  ...  between the symbolic and analogic models of central representation of intensity.  ... 
doi:10.3758/bf03202437 fatcat:d7kviirw2bb25d5wx4pm2dxveq

Evolution of k-mer Frequencies and Entropy in Duplication and Substitution Mutation Systems [article]

Hao Lou, Farzad Farnoud, Moshe Schwartz, Jehoshua Bruck
2018 arXiv   pre-print
At the same time, due to the complexity of these processes, designing tractable stochastic models and analyzing them are challenging.  ...  An understanding of the statistical properties resulting from these mutation processes is of value in a variety of tasks related to biological sequence data, e.g., estimation of model parameters and compression  ...  These results can be viewed as extensions of results for Pólya urn models. In such models, a random ball is chosen from an urn containing balls of different colors.  ... 
arXiv:1812.02250v1 fatcat:2bcdwvre2rckjadzkacmntprkm

Counting Runs of Ones with Overlapping Parts in Binary Strings Ordered Linearly and Circularly

Frosso S. Makri, Zaharias M. Psillakis, Anastasios N. Arapis
2013 International Journal of Statistics and Probability  
On a binary (0 − 1) string of length n the -overlapping counting scheme of runs of 1 s of a fixed length k is considered.  ...  The numbers of binary strings of length n, ordered on a line or on a circle, with a specific number of -overlapping runs of 1s of length k are also provided via closed expressions.  ...  Acknowledgements The authors would like to thank the Editor and the two anonymous reviewers for the thorough reading, useful comments and suggestions which helped to improve the paper.  ... 
doi:10.5539/ijsp.v2n3p50 fatcat:khcisronbrbnfoddpkpkbaqgze

Gene Therapy for Heart Disease: Modified mRNA Perspectives [chapter]

Lior Zangi, Ravinder K. Kaundal, Keerat Kaur
2021 Cardiomyopathy - Disease of the Heart Muscle [Working Title]  
With increasing knowledge of the basic molecular mechanisms guiding the progress of this disease, it is now possible to target the key pathological players through gene therapy.  ...  In this chapter, we outline the compositional changes made to mRNA to enhance its translational capacity and discuss the available carrier molecules currently being employed to deliver modRNA to the heart  ...  pumping capacity of the heart muscle.  ... 
doi:10.5772/intechopen.97184 fatcat:pg5vvladtzatjgm6mxbhuswlai

Fostering creativity through instruction rich in mathematical problem solving and problem posing

Edward A. Silver
1997 Zentralblatt für Didaktik der Mathematik  
Through the use of such tasks and activities, teachers can increase their students' capacity with respect to the core dimensions of creativity; namely, fluency, flexibility, and novelty.  ...  Although creativity is often viewed as being associated with the notions of "genius" or exceptional ability, it can be productive for mathematics educators to view creativity instead as an orientation  ...  An example of argument that uses the divisibility properties associated with numbers in the string of consecutive integers is the following: One of the four numbers in the string must be even and another  ... 
doi:10.1007/s11858-997-0003-x fatcat:c2utc57nkzdr7anzsnszkyreui

MicroRNA Target Detection and Analysis for Genes Related to Breast Cancer Using MDLcompress

Scott C Evans, Antonis Kourtidis, T Stephen Markham, Jonathan Miller, Douglas S Conklin, Andrew S Torres
2007 EURASIP Journal on Bioinformatics and Systems Biology  
The ability to quantify cost in bits for phrases in the MDL model allows prediction of regions where SNPs may have the most impact on biological activity.  ...  The deep recursion of MDLcompress, together with its explicit two-part coding, enables it to identify biologically meaningful sequence without needlessly restrictive priors.  ...  The content and information do not necessarily reflect the position or policy of the government and no official endorsement should be inferred.  ... 
doi:10.1186/1687-4153-2007-43670 fatcat:k67qmsaiwzfjlcka5cidy7zxpe

MicroRNA Target Detection and Analysis for Genes Related to Breast Cancer Using MDLcompress

Scott C. Evans, Antonis Kourtidis, T. Stephen Markham, Jonathan Miller, Douglas S. Conklin, Andrew S. Torres
2007 EURASIP Journal on Bioinformatics and Systems Biology  
The ability to quantify cost in bits for phrases in the MDL model allows prediction of regions where SNPs may have the most impact on biological activity.  ...  The deep recursion of MDLcompress, together with its explicit two-part coding, enables it to identify biologically meaningful sequence without needlessly restrictive priors.  ...  The content and information do not necessarily reflect the position or policy of the government and no official endorsement should be inferred.  ... 
doi:10.1155/2007/43670 pmid:18317504 pmcid:PMC3171339 fatcat:dxyxzntkwvbgth76ana2jsn75q
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