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Learning Natural Selection from the Site Frequency Spectrum [chapter]

Roy Ronen, Nitin Udpa, Eran Halperin, Vineet Bafna
2013 Lecture Notes in Computer Science  
Many tests have been proposed to identify the genomic signatures of natural selection by quantifying the skew in the site frequency spectrum (SFS) under selection relative to neutrality.  ...  Using supervised learning on extensive simulated data, we characterize the features of the scaled SFS that best separate different types of selective sweeps from neutrality.  ...  E.H. is a faculty fellow of the Edmond J. Safra Program at Tel Aviv University and was supported in part by the German Israeli Foundation (grant 0603806851).  ... 
doi:10.1007/978-3-642-37195-0_19 fatcat:tei3mngagbazpefxk3hl5xeqnm

Learning Natural Selection from the Site Frequency Spectrum

R. Ronen, N. Udpa, E. Halperin, V. Bafna
2013 Genetics  
Many tests have been proposed to identify the genomic signatures of natural selection by quantifying the skew in the site frequency spectrum (SFS) under selection relative to neutrality.  ...  Using supervised learning on extensive simulated data, we characterize the features of the scaled SFS that best separate different types of selective sweeps from neutrality.  ...  E.H. is a faculty fellow of the Edmond J. Safra Program at Tel Aviv University and was supported in part by the German Israeli Foundation (grant 0603806851).  ... 
doi:10.1534/genetics.113.152587 pmid:23770700 pmcid:PMC3761300 fatcat:joj2wql425gqtfy6mebm7xkvha

VULNERABILITY INDEX ASSESSMENT USING NEURAL NETWORKS (VIANN): A CASE STUDY OF NICOSIA, CYPRUS

H. Dindar, K. Dimililer, Ö. C. Özdağ, C. Atalar, M. Akgün, A. Özyankı
2017 ISPRS Annals of the Photogrammetry, Remote Sensing and Spatial Information Sciences  
The value of vulnerability index (Kg) has been evaluated by using the fundamental frequency and amplification factor.  ...  The sites are classified by their vulnerability index values using binary coding: [1 0 0] for the acceleration sensitive zone, [0 1 0] for the velocity sensitive zone, and [0 0 1] for the displacement  ...  The results of this study constitute a part of Hilmi Dindar's PhD thesis at the Institute of Natural and Applied Sciences in Dokuz Eylül University.  ... 
doi:10.5194/isprs-annals-iv-4-w4-189-2017 fatcat:lfkcnvsbfbdrpex2v5cxkwvlwq

Two Days of Spectrum Use in Europe

Alexandros Palaios, Janne Riihijarvi, Petri Mahonen, Vladimir Atanasovski, Liljana Gavrilovska, Peter Van Wesemael, Antoine Dejonghe, Peter Scheele
2012 Proceedings of the 7th International Conference on Cognitive Radio Oriented Wireless Networks  
We present preliminary analysis of the obtained data set, and particularly highlight similarities and differences in spectrum use between selected measurement locations.  ...  We describe in detail the measurement setup, including the coordinated preparation activities carried out across the different measurement sites.  ...  We would also like to warmly thank all the participants to the two days measurement campaign from the FARAMIR consortium.  ... 
doi:10.4108/icst.crowncom.2012.249475 dblp:conf/crowncom/PalaiosRMAGWDS12 fatcat:gsggssfkibbtlce3qvaph5vqce

Selection plays the hand it was dealt: evidence that human adaptation commonly targets standing genetic variation

Rajiv C. McCoy, Joshua M. Akey
2017 Genome Biology  
Adaptation by natural selection is responsible for the extraordinary diversity of life on Earth, as well as the striking matching of organisms to their environments.  ...  Controversy surrounding the role of positive selection in shaping genetic variation Understanding the frequency, mechanisms, and specific targets of past adaptation constitutes a central goal of human  ...  allele frequency spectrum, and increased linkage disequilibrium in regions flanking the selected site.  ... 
doi:10.1186/s13059-017-1280-5 pmid:28760139 pmcid:PMC5537971 fatcat:myphkduh7bexblgy5fehyyibnu

Spectral Features Control Temporal Plasticity in Auditory Cortex

Michael P. Kilgard, Pritesh K. Pandya, Jessica L. Vazquez, Daniel L. Rathbun, Navzer D. Engineer, Raluca Moucha
2001 Audiology & neuro-otology  
Additional experiments with more complex stimuli are needed to clarify how the cortex learns natural sounds such as speech.  ...  By systematically varying the acoustic parameters of the sound paired with NB activation, we have previously shown that tone frequency and amplitude modulation rate alter the topography and selectivity  ...  Acknowledgements: This work is supported by NIH grant DC-04354 and the Callier Excellence in Education Fund.  ... 
doi:10.1159/000046832 pmid:11694727 fatcat:b637ze73znefrmcozv6omzyr34

Development and Demonstration of Graphical User Interface Spectrum Sensing Algorithm using some Wireless Systems in South Africa

Jide Julius Popoola, Rex van Olst
2016 Journal of Applied Science & Process Engineering  
With this transformation, the demand for and usage of radio spectrum has increased exponentially making radio spectrum indeed a scarce natural resource.  ...  In order to solve this problem, the possibility of opening up the unused portions of licensed spectrum by sharing using cognitive radio technology has been in the spotlight for maximizing radio spectrum  ...  The principal author also acknowledges the financial assistance received from the University of the Witwatersrand's Postgraduate Merit Award (PMA).  ... 
doi:10.33736/jaspe.164.2015 fatcat:rgtz7hhj7rhyvjvicns67hzbye

POSITIVE FREQUENCY-DEPENDENT SELECTION ON WARNING COLOR IN ALPINE LEAF BEETLES

Matthias Borer, Tom Van Noort, Martine Rahier, Russell E. Naisbit
2010 Evolution  
Müller's theory of warning color and mimicry, despite forming a textbook example of frequency-dependent selection, has rarely been demonstrated in the wild.  ...  This may be largely due to the practical and statistical difficulties of measuring natural selection on mobile prey species.  ...  This might be a result of natural differences in the relative frequency of blue and green morphs at each site leading to variation in the strength of frequency-dependent selection, as well as differences  ... 
doi:10.1111/j.1558-5646.2010.01137.x pmid:21188752 fatcat:fotx3biso5gsnollzyh2onzqt4

A Machine Learning Study on the Thermostability Prediction of (R)-ω-Selective Amine Transaminase from Aspergillus terreus

Li-li Jia, Ting-ting Sun, Yan Wang, Yu Shen, David A. McClellan
2021 BioMed Research International  
The experimental data from 6 single-point mutated enzymes were used as a learning dataset to build models and predict the thermostability of 26 mutants.  ...  In this paper, a new sequence-activity relationship method was analyzed for its application in improving the thermal stability of Aspergillus terreus (R)-ω-selective amine transaminase.  ...  Acknowledgments This research was financially supported by the National Natural Science Foundation of China (Grant nos. 20904047, 21673207, and 21873087) and the Natural Science Foundation of Zhejiang  ... 
doi:10.1155/2021/2593748 pmid:34447850 pmcid:PMC8384528 fatcat:qylosys7yfdanmoahiqnzz4iiu

Population Graph-Based Multi-Model Ensemble Method for Diagnosing Autism Spectrum Disorder

Zarina Rakhimberdina, Xin Liu, and Tsuyoshi Murata
2020 Sensors  
With the advancement of brain imaging techniques and a variety of machine learning methods, significant progress has been made in brain disorder diagnosis, in particular Autism Spectrum Disorder.  ...  The development of machine learning models that can differentiate between healthy subjects and patients is of great importance.  ...  First, using graph filtering, we selected the best performing graphs by removing the contribution from high-frequency components.  ... 
doi:10.3390/s20216001 pmid:33105909 pmcid:PMC7660214 fatcat:cybol32tl5gb7jl7wvwd5adsgy

Distinct midbrain response statistics are associated with sound recognition and discrimination during the construction of natural sound textures [article]

Xiu Zhai, Fatemeh Khatami, Mina Sadeghi, Fengrong He, Heather L Read, Ian H Stevenson, Monty Escabi
2020 bioRxiv   pre-print
Here, using natural textures and synthetic variants with reduced statistics, we show that summary statistics modulate the correlations between frequency organized neuron ensembles in the awake rabbit inferior  ...  The perception of natural auditory textures, such as fire wind, and rain, has been proposed to arise through the integration of time-averaged summary sound statistics.  ...  This allowed us to estimate the frequency selectivity of each penetration site, and we only include locations that showed a tonotopic gradient in further analysis.  ... 
doi:10.1101/2020.01.30.914747 fatcat:7epx2jt5vzgm5iizkr7x5v7vly

FUZZY PATTERN CLASSIFICATION OF STRONG GROUND MOTION RECORDS

ARZHANG ALIMORADI, SHAHRAM PEZESHK, FARZAD NAEIM, HICHEM FRIGUI
2005 Journal of earthquake engineering  
Therefore, databases of SGM records of today present data of complex nature in high dimensions (many of the dimensions -or SGM parameters in time and frequency domain-are presently available from different  ...  The clusters are valid and stable in time and frequency domain and are meaningful even with respect to seismological features that were not included in the classification task.  ...  Langston, Professor of Seismology and Earth Structure at The University of Memphis is appreciated.  ... 
doi:10.1080/13632460509350544 fatcat:z4s6atzrffg2xd2qkgqmgvqidi

Seismic Ground Response Estimation Based on Convolutional Neural Networks (CNN)

Seokgyeong Hong, Huyen-Tram Nguyen, Jongwon Jung, Jaehun Ahn
2021 Applied Sciences  
The proposed model especially outperforms the conventional software when the natural periods range from 0.01 to 0.3 s.  ...  Whereas the conventional software overestimated the values of the amplitudes for most of the sites, the proposed CNN model predicts fairly well both the values of the amplitudes and the natural periods  ...  Conflicts of Interest: The authors declare no conflict of interest.  ... 
doi:10.3390/app112210760 fatcat:crwehu2dgfgzpftuezbrkfjqpm

Distinguishing between recent balancing selection and incomplete sweep using deep neural networks

Ulas Isildak, Alessandro Stella, Matteo Fumagalli
2021 Molecular Ecology Resources  
Despite its relevance, the detection of recent balancing selection from genomic data is challenging as its signatures are qualitatively similar to those left by ongoing positive selection.  ...  In this study we developed and implemented two deep neural networks and tested their performance to predict loci under recent selection, either due to balancing selection or incomplete sweep, from population  ...  We alsoF I G U R E 4 Prediction of sites under natural selection (Test 1, upper panel) or balancing selection vs. incomplete sweep (Test 2, second panel from top) on intermediate frequency variants in  ... 
doi:10.1111/1755-0998.13379 pmid:33749134 fatcat:rw74pgrgfrhhfdjusj4g2i4ujy

Case study of TV spectrum sensing model based on machine learning techniques

Abdalaziz Mohammad, Faroq Awin, Esam Abdel-Raheem
2021 Ain Shams Engineering Journal  
Spectrum sensing is an essential component in cognitive radios (CR). Machine learning (ML) algorithms are powerful techniques for designing a promising spectrum sensing model.  ...  Moreover, the Principal Component Analysis (PCA) is incorporated to speed up the learning of the classifiers.  ...  Kemal Tepe, the director of the Wireless Communication and Information Processing Laboratory (WiCIP Lab) at the University of Windsor, for using the lab facilities and TV spectrum database.  ... 
doi:10.1016/j.asej.2021.06.026 fatcat:yvf6dj26yvbqtkqekhhfvbufla
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