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  1. Article ; Online: Can We Convert Genotype Sequences Into Images for Cases/Controls Classification?

    Muhammad Muneeb / Samuel F. Feng / Andreas Henschel

    Frontiers in Bioinformatics, Vol

    2022  Volume 2

    Abstract: Converting genotype sequences into images offers advantages, such as genotype data visualization, classification, and comparison of genotype sequences. This study converted genotype sequences into images, applied two-dimensional convolutional neural ... ...

    Abstract Converting genotype sequences into images offers advantages, such as genotype data visualization, classification, and comparison of genotype sequences. This study converted genotype sequences into images, applied two-dimensional convolutional neural networks for case/control classification, and compared the results with the one-dimensional convolutional neural network. Surprisingly, the average accuracy of multiple runs of 2DCNN was 0.86, and that of 1DCNN was 0.89, yielding a difference of 0.03, which suggests that even the 2DCNN algorithm works on genotype sequences. Moreover, the results generated by the 2DCNN exhibited less variation than those generated by the 1DCNN, thereby offering greater stability. The purpose of this study is to draw the research community’s attention to explore encoding schemes for genotype data and machine learning algorithms that can be used on genotype data by changing the representation of the genotype data for case/control classification.
    Keywords genotype-phenotype prediction ; genetics ; bioinformatics ; applied machine learning ; image classification ; Computer applications to medicine. Medical informatics ; R858-859.7
    Subject code 006
    Language English
    Publishing date 2022-06-01T00:00:00Z
    Publisher Frontiers Media S.A.
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  2. Article ; Online: The dynamics of explore–exploit decisions reveal a signal-to-noise mechanism for random exploration

    Samuel F. Feng / Siyu Wang / Sylvia Zarnescu / Robert C. Wilson

    Scientific Reports, Vol 11, Iss 1, Pp 1-

    2021  Volume 15

    Abstract: Abstract Growing evidence suggests that behavioral variability plays a critical role in how humans manage the tradeoff between exploration and exploitation. In these decisions a little variability can help us to overcome the desire to exploit known ... ...

    Abstract Abstract Growing evidence suggests that behavioral variability plays a critical role in how humans manage the tradeoff between exploration and exploitation. In these decisions a little variability can help us to overcome the desire to exploit known rewards by encouraging us to randomly explore something else. Here we investigate how such ‘random exploration’ could be controlled using a drift-diffusion model of the explore–exploit choice. In this model, variability is controlled by either the signal-to-noise ratio with which reward is encoded (the ‘drift rate’), or the amount of information required before a decision is made (the ‘threshold’). By fitting this model to behavior, we find that while, statistically, both drift and threshold change when people randomly explore, numerically, the change in drift rate has by far the largest effect. This suggests that random exploration is primarily driven by changes in the signal-to-noise ratio with which reward information is represented in the brain.
    Keywords Medicine ; R ; Science ; Q
    Subject code 612
    Language English
    Publishing date 2021-02-01T00:00:00Z
    Publisher Nature Portfolio
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  3. Article ; Online: Corrigendum

    Herbert F. Jelinek / Mira Mousa / Eman Alefishat / Wael Osman / Ian Spence / Dengpan Bu / Samuel F. Feng / Jason Byrd / Paola A. Magni / Shafi Sahibzada / Guan K. Tay / Habiba S. Alsafar

    Frontiers in Veterinary Science, Vol

    Evolution, ecology, and zoonotic transmission of betacoronaviruses: A review

    2023  Volume 10

    Keywords zoonoses ; coronavirus ; SARS-CoV-2 ; zoonotic transmission ; ecology ; evolution ; Veterinary medicine ; SF600-1100
    Language English
    Publishing date 2023-02-01T00:00:00Z
    Publisher Frontiers Media S.A.
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  4. Article ; Online: Evolution, Ecology, and Zoonotic Transmission of Betacoronaviruses

    Herbert F. Jelinek / Mira Mousa / Eman Alefishat / Wael Osman / Ian Spence / Dengpan Bu / Samuel F. Feng / Jason Byrd / Paola A. Magni / Shafi Sahibzada / Guan K. Tay / Habiba S. Alsafar

    Frontiers in Veterinary Science, Vol

    A Review

    2021  Volume 8

    Abstract: Coronavirus infections have been a part of the animal kingdom for millennia. The difference emerging in the twenty-first century is that a greater number of novel coronaviruses are being discovered primarily due to more advanced technology and that a ... ...

    Abstract Coronavirus infections have been a part of the animal kingdom for millennia. The difference emerging in the twenty-first century is that a greater number of novel coronaviruses are being discovered primarily due to more advanced technology and that a greater number can be transmitted to humans, either directly or via an intermediate host. This has a range of effects from annual infections that are mild to full-blown pandemics. This review compares the zoonotic potential and relationship between MERS, SARS-CoV, and SARS-CoV-2. The role of bats as possible host species and possible intermediate hosts including pangolins, civets, mink, birds, and other mammals are discussed with reference to mutations of the viral genome affecting zoonosis. Ecological, social, cultural, and environmental factors that may play a role in zoonotic transmission are considered with reference to SARS-CoV, MERS, and SARS-CoV-2 and possible future zoonotic events.
    Keywords zoonoses ; coronavirus ; SARS-CoV-2 ; zoonotic transmission ; ecology ; evolution ; Veterinary medicine ; SF600-1100
    Language English
    Publishing date 2021-05-01T00:00:00Z
    Publisher Frontiers Media S.A.
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  5. Article ; Online: A Multi-Area Stochastic Model for a Covert Visual Search Task.

    Michael A Schwemmer / Samuel F Feng / Philip J Holmes / Jacqueline Gottlieb / Jonathan D Cohen

    PLoS ONE, Vol 10, Iss 8, p e

    2015  Volume 0136097

    Abstract: Decisions typically comprise several elements. For example, attention must be directed towards specific objects, their identities recognized, and a choice made among alternatives. Pairs of competing accumulators and drift-diffusion processes provide good ...

    Abstract Decisions typically comprise several elements. For example, attention must be directed towards specific objects, their identities recognized, and a choice made among alternatives. Pairs of competing accumulators and drift-diffusion processes provide good models of evidence integration in two-alternative perceptual choices, but more complex tasks requiring the coordination of attention and decision making involve multistage processing and multiple brain areas. Here we consider a task in which a target is located among distractors and its identity reported by lever release. The data comprise reaction times, accuracies, and single unit recordings from two monkeys' lateral interparietal area (LIP) neurons. LIP firing rates distinguish between targets and distractors, exhibit stimulus set size effects, and show response-hemifield congruence effects. These data motivate our model, which uses coupled sets of leaky competing accumulators to represent processes hypothesized to occur in feature-selective areas and limb motor and pre-motor areas, together with the visual selection process occurring in LIP. Model simulations capture the electrophysiological and behavioral data, and fitted parameters suggest that different connection weights between LIP and the other cortical areas may account for the observed behavioral differences between the animals.
    Keywords Medicine ; R ; Science ; Q
    Subject code 612
    Language English
    Publishing date 2015-01-01T00:00:00Z
    Publisher Public Library of Science (PLoS)
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  6. Article ; Online: Travel ban effects on SARS-CoV-2 transmission lineages in the UAE as inferred by genomic epidemiology

    Andreas Henschel / Samuel F. Feng / Rifat A. Hamoudi / Gihan Daw Elbait / Ernesto Damiani / Fathimathuz Waasia / Guan K. Tay / Bassam H. Mahboub / Maimunah Hemayet Uddin / Juan Acuna / Eman Alefishat / Rabih Halwani / Herbert F. Jelinek / Farah Mustafa / Nawal Alkaabi / Habiba S. Alsafar / on behalf of the UAE COVID-19 Collaborative Partnership

    PLoS ONE, Vol 17, Iss

    2022  Volume 3

    Abstract: Global and local whole genome sequencing of SARS-CoV-2 enables the tracing of domestic and international transmissions. We sequenced Viral RNA from 37 sampled Covid-19 patients with RT-PCR-confirmed infections across the UAE and developed time-resolved ... ...

    Abstract Global and local whole genome sequencing of SARS-CoV-2 enables the tracing of domestic and international transmissions. We sequenced Viral RNA from 37 sampled Covid-19 patients with RT-PCR-confirmed infections across the UAE and developed time-resolved phylogenies with 69 local and 3,894 global genome sequences. Furthermore, we investigated specific clades associated with the UAE cohort and, their global diversity, introduction events and inferred domestic and international virus transmissions between January and June 2020. The study comprehensively characterized the genomic aspects of the virus and its spread within the UAE and identified that the prevalence shift of the D614G mutation was due to the later introductions of the G-variant associated with international travel, rather than higher local transmissibility. For clades spanning different emirates, the most recent common ancestors pre-date domestic travel bans. In conclusion, we observe a steep and sustained decline of international transmissions immediately following the introduction of international travel restrictions.
    Keywords Medicine ; R ; Science ; Q
    Language English
    Publishing date 2022-01-01T00:00:00Z
    Publisher Public Library of Science (PLoS)
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

    Full text online

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