scholarly journals Inevitability of Red Queen evolution driven by organismic complexity and simple feedback via environmental modification

2021 ◽  
Author(s):  
Daniel S Fisher
Keyword(s):  
Fitness Landscape ◽  
Adaptive Dynamics ◽  
High Dimensional ◽  
Red Queen ◽  
Future Evolution ◽  
Population Growth Rates ◽  
Slowing Down ◽  
Rate Of Increase ◽  
Evolutionary Trajectories ◽  
Low Dimensional

Evolution in complex high-dimensional phenotype spaces can be very different than the caricature of uphill evolutionary trajectories in a low-dimensional fitness landscape. And slight modifications of the environment can have large consequences for the future evolution. Here, the simplest approximation of evolution, an almost-always clonal population evolving by small effect mutations under deterministic "adaptive" dynamics, is studied. The complexities of organisms and their interactions with their environments are caricatured by population growth rates being smoothly varying random functions in very high dimensional phenotype spaces. In a fixed environment, there are huge numbers of fitness maxima, yet evolutionary trajectories wander around amongst saddles, gradually slowing down but still wandering widely and without committing to any maximum. But with even very small changes of the environment caused by the phenotypic changes, after an initial transient the evolution continues forever without further slowing down. In this Red Queen "phase" the apparent rate of increase of the fitness saturates (at a feedback strength-dependent rate) and the trajectories perpetually wander over large phenotypic distances. Organismic complexities, caricatured by a large number of constraints on the molecular-level phenotype, together with the simplest possible interactions of the organisms with their environment, are shown to be sufficient to cause such Red Queen dynamics. Arguments are made for the ubiquity of such behavior.

scholarly journals Adaptive walks on high-dimensional fitness landscapes and seascapes with distance-dependent statistics

2018 ◽  
Author(s):  
Atish Agarwala ◽  
Daniel S. Fisher
Keyword(s):  
Evolutionary Dynamics ◽  
Fitness Landscape ◽  
Broad Class ◽  
Fitness Landscapes ◽  
High Dimensional ◽  
General Function ◽  
Long Distance ◽  
Future Evolution ◽  
Adaptive Mutations ◽  
Adaptive Walks

AbstractThe dynamics of evolution is intimately shaped by epistasis — interactions between genetic elements which cause the fitness-effect of combinations of mutations to be non-additive. Analyzing evolutionary dynamics that involves large numbers of epistatic mutations is intrinsically difficult. A crucial feature is that the fitness landscape in the vicinity of the current genome depends on the evolutionary history. A key step is thus developing models that enable study of the effects of past evolution on future evolution. In this work, we introduce a broad class of high-dimensional random fitness landscapes for which the correlations between fitnesses of genomes are a general function of genetic distance. Their Gaussian character allows for tractable computational as well as analytic understanding. We study the properties of these landscapes focusing on the simplest evolutionary process: random adaptive (uphill) walks. Conventional measures of “ruggedness” are shown to not much affect such adaptive walks. Instead, the long-distance statistics of epistasis cause all properties to be highly conditional on past evolution, determining the statistics of the local landscape (the distribution of fitness-effects of available mutations and combinations of these), as well as the global geometry of evolutionary trajectories. In order to further explore the effects of conditioning on past evolution, we model the effects of slowly changing environments. At long times, such fitness “seascapes” cause a statistical steady state with highly intermittent evolutionary dynamics: populations undergo bursts of rapid adaptation, interspersed with periods in which adaptive mutations are rare and the population waits for more new directions to be opened up by changes in the environment. Finally, we discuss prospects for studying more complex evolutionary dynamics and on broader classes of high-dimensional landscapes and seascapes.

scholarly journals On the deformability of an empirical fitness landscape by microbial evolution

2018 ◽  
Vol 115 (44) ◽  
pp. 11286-11291 ◽  
Author(s):  
Djordje Bajić ◽  
Jean C. C. Vila ◽  
Zachary D. Blount ◽  
Alvaro Sánchez
Keyword(s):  
Environmental Effects ◽  
Evolutionary Dynamics ◽  
Fitness Landscape ◽  
Adaptive Dynamics ◽  
Microbial Evolution ◽  
Fitness Landscapes ◽  
Complex Genetics ◽  
Evolutionary Innovation ◽  
Genotype Space ◽  
Evolutionary Trajectories

A fitness landscape is a map between the genotype and its reproductive success in a given environment. The topography of fitness landscapes largely governs adaptive dynamics, constraining evolutionary trajectories and the predictability of evolution. Theory suggests that this topography can be deformed by mutations that produce substantial changes to the environment. Despite its importance, the deformability of fitness landscapes has not been systematically studied beyond abstract models, and little is known about its reach and consequences in empirical systems. Here we have systematically characterized the deformability of the genome-wide metabolic fitness landscape of the bacterium Escherichia coli. Deformability is quantified by the noncommutativity of epistatic interactions, which we experimentally demonstrate in mutant strains on the path to an evolutionary innovation. Our analysis shows that the deformation of fitness landscapes by metabolic mutations rarely affects evolutionary trajectories in the short range. However, mutations with large environmental effects produce long-range landscape deformations in distant regions of the genotype space that affect the fitness of later descendants. Our results therefore suggest that, even in situations in which mutations have strong environmental effects, fitness landscapes may retain their power to forecast evolution over small mutational distances despite the potential attenuation of that power over longer evolutionary trajectories. Our methods and results provide an avenue for integrating adaptive and eco-evolutionary dynamics with complex genetics and genomics.

scholarly journals On the deformability of an empirical fitness landscape by microbial evolution

2018 ◽  
Author(s):  
Djordje Bajić ◽  
Jean C.C. Vila ◽  
Zachary D. Blount ◽  
Alvaro Sánchez
Keyword(s):  
Evolutionary Dynamics ◽  
Fitness Landscape ◽  
Adaptive Dynamics ◽  
Microbial Evolution ◽  
Fitness Landscapes ◽  
Complex Genetics ◽  
Evolutionary Innovation ◽  
Genome Wide ◽  
Genotype Space ◽  
Evolutionary Trajectories

AbstractA fitness landscape is a map between the genotype and its reproductive success in a given environment. The topography of fitness landscapes largely governs adaptive dynamics, constraining evolutionary trajectories and the predictability of evolution. Theory suggests that this topography can be “deformed” by mutations that produce substantial changes to the environment. In spite of its importance, the deformability of fitness landscapes has not been systematically studied beyond abstract models, and little is known about its reach and consequences in empirical systems. Here we have systematically characterized the deformability of the genome-wide metabolic fitness landscape of the bacterium E. coli. Deformability is quantified by the non-commutativity of epistatic interactions, which we experimentally demonstrate in mutant strains on the path to an evolutionary innovation. Our analysis shows that the deformation of fitness landscapes by metabolic mutations rarely affects evolutionary trajectories in the short-range. However, mutations with large environmental effects leave these as a “legacy”, producing long-range landscape deformations in distant regions of the genotype space that affect the fitness of later descendants. Our methods and results provide the basis for an integration between adaptive and eco-evolutionary dynamics with complex genetics and genomics.

scholarly journals Classification of Brainwaves for Sleep Stages by High-Dimensional FFT Features from EEG Signals

2020 ◽  
Vol 10 (5) ◽  
pp. 1797 ◽  
Author(s):  
Mera Kartika Delimayanti ◽  
Bedy Purnama ◽  
Ngoc Giang Nguyen ◽  
Mohammad Reza Faisal ◽  
Kunti Robiatul Mahmudah ◽  
...  
Keyword(s):  
Machine Learning ◽  
Sleep Stage ◽  
Machine Learning Algorithms ◽  
High Dimensional ◽  
Sleep Stages ◽  
Eeg Signals ◽  
Stage Classification ◽  
Sleep Stage Classification ◽  
Low Dimensional

Manual classification of sleep stage is a time-consuming but necessary step in the diagnosis and treatment of sleep disorders, and its automation has been an area of active study. The previous works have shown that low dimensional fast Fourier transform (FFT) features and many machine learning algorithms have been applied. In this paper, we demonstrate utilization of features extracted from EEG signals via FFT to improve the performance of automated sleep stage classification through machine learning methods. Unlike previous works using FFT, we incorporated thousands of FFT features in order to classify the sleep stages into 2–6 classes. Using the expanded version of Sleep-EDF dataset with 61 recordings, our method outperformed other state-of-the art methods. This result indicates that high dimensional FFT features in combination with a simple feature selection is effective for the improvement of automated sleep stage classification.

scholarly journals A Nonlinear Maximum Correntropy Information Filter for High-Dimensional Neural Decoding

Entropy ◽  
2021 ◽  
Vol 23 (6) ◽  
pp. 743
Author(s):  
Xi Liu ◽  
Shuhang Chen ◽  
Xiang Shen ◽  
Xiang Zhang ◽  
Yiwen Wang
Keyword(s):  
State Estimation ◽  
Measurement Model ◽  
High Dimensional ◽  
Neural Firing ◽  
The Neural Network ◽  
Information Filter ◽  
Critical Technology ◽  
Dimensional Measurements ◽  
Non Gaussian ◽  
Low Dimensional

Neural signal decoding is a critical technology in brain machine interface (BMI) to interpret movement intention from multi-neural activity collected from paralyzed patients. As a commonly-used decoding algorithm, the Kalman filter is often applied to derive the movement states from high-dimensional neural firing observation. However, its performance is limited and less effective for noisy nonlinear neural systems with high-dimensional measurements. In this paper, we propose a nonlinear maximum correntropy information filter, aiming at better state estimation in the filtering process for a noisy high-dimensional measurement system. We reconstruct the measurement model between the high-dimensional measurements and low-dimensional states using the neural network, and derive the state estimation using the correntropy criterion to cope with the non-Gaussian noise and eliminate large initial uncertainty. Moreover, analyses of convergence and robustness are given. The effectiveness of the proposed algorithm is evaluated by applying it on multiple segments of neural spiking data from two rats to interpret the movement states when the subjects perform a two-lever discrimination task. Our results demonstrate better and more robust state estimation performance when compared with other filters.

PSS Business Case Map: Supporting Idea Generation in PSS Design

2012 ◽  
Author(s):  
Fumiya Akasaka ◽  
Kazuki Fujita ◽  
Yoshiki Shimomura
Keyword(s):  
Idea Generation ◽  
Business Case ◽  
Literature Survey ◽  
The Self ◽  
High Dimensional ◽  
Self Organizing Map ◽  
Two Dimensional ◽  
Service Type ◽  
Business Cases ◽  
Low Dimensional

This paper proposes the PSS Business Case Map as a tool to support designers’ idea generation in PSS design. The map visualizes the similarities among PSS business cases in a two-dimensional diagram. To make the map, PSS business cases are first collected by conducting, for example, a literature survey. The collected business cases are then classified from multiple aspects that characterize each case such as its product type, service type, target customer, and so on. Based on the results of this classification, the similarities among the cases are calculated and visualized by using the Self-Organizing Map (SOM) technique. A SOM is a type of artificial neural network that is trained using unsupervised learning to produce a low-dimensional (typically two-dimensional) view from high-dimensional data. The visualization result is offered to designers in a form of a two-dimensional map, which is called the PSS Business Case Map. By using the map, designers can figure out the position of their current business and can acquire ideas for the servitization of their business.

scholarly journals Perspectives of the high-dimensional dynamics of neural microcircuits from the point of view of low-dimensional readouts

Complexity ◽  
2003 ◽  
Vol 8 (4) ◽  
pp. 39-50 ◽  
Author(s):  
Stefan Häusler ◽  
Henry Markram ◽  
Wolfgang Maass
Keyword(s):  
Point Of View ◽  
High Dimensional ◽  
Low Dimensional

Improved interactive color visualization approach for hyperspectral images

2021 ◽  
pp. 147387162110481
Author(s):  
Haijun Yu ◽  
Shengyang Li
Keyword(s):  
Real Time ◽  
Hyperspectral Images ◽  
High Dimensional ◽  
Interactive Control ◽  
Output Image ◽  
Dr Method ◽  
The Rich ◽  
Low Dimensional ◽  
Color Visualization ◽  
Fusion Coefficient

Hyperspectral images (HSIs) have become increasingly prominent as they can maintain the subtle spectral differences of the imaged objects. Designing approaches and tools for analyzing HSIs presents a unique set of challenges due to their high-dimensional characteristics. An improved color visualization approach is proposed in this article to achieve communication between users and HSIs in the field of remote sensing. Under the real-time interactive control and color visualization, this approach can help users intuitively obtain the rich information hidden in original HSIs. Using the dimensionality reduction (DR) method based on band selection, high-dimensional HSIs are reduced to low-dimensional images. Through drop-down boxes, users can freely specify images that participate in the combination of RGB channels of the output image. Users can then interactively and independently set the fusion coefficient of each image within an interface based on concentric circles. At the same time, the output image will be calculated and visualized in real time, and the information it reflects will also be different. In this approach, channel combination and fusion coefficient setting are two independent processes, which allows users to interact more flexibly according to their needs. Furthermore, this approach is also applicable for interactive visualization of other types of multi-layer data.

scholarly journals LSTM-Guided Coaching Assistant for Table Tennis Practice

Sensors ◽  
2018 ◽  
Vol 18 (12) ◽  
pp. 4112 ◽  
Author(s):  
Se-Min Lim ◽  
Hyeong-Cheol Oh ◽  
Jaein Kim ◽  
Juwon Lee ◽  
Jooyoung Park
Keyword(s):  
Time Series ◽  
State Space ◽  
Time Series Data ◽  
State Space Model ◽  
Skill Assessment ◽  
Series Data ◽  
High Dimensional ◽  
Table Tennis ◽  
Space Model ◽  
Low Dimensional

Recently, wearable devices have become a prominent health care application domain by incorporating a growing number of sensors and adopting smart machine learning technologies. One closely related topic is the strategy of combining the wearable device technology with skill assessment, which can be used in wearable device apps for coaching and/or personal training. Particularly pertinent to skill assessment based on high-dimensional time series data from wearable sensors is classifying whether a player is an expert or a beginner, which skills the player is exercising, and extracting some low-dimensional representations useful for coaching. In this paper, we present a deep learning-based coaching assistant method, which can provide useful information in supporting table tennis practice. Our method uses a combination of LSTM (Long short-term memory) with a deep state space model and probabilistic inference. More precisely, we use the expressive power of LSTM when handling high-dimensional time series data, and state space model and probabilistic inference to extract low-dimensional latent representations useful for coaching. Experimental results show that our method can yield promising results for characterizing high-dimensional time series patterns and for providing useful information when working with wearable IMU (Inertial measurement unit) sensors for table tennis coaching.

An applied mathematics perspective on stochastic modelling for climate

2008 ◽  
Vol 366 (1875) ◽  
pp. 2427-2453 ◽  
Author(s):  
Andrew J Majda ◽  
Christian Franzke ◽  
Boualem Khouider
Keyword(s):  
Stochastic Model ◽  
General Circulation ◽  
Applied Mathematics ◽  
Low Frequency ◽  
Lattice Models ◽  
Stochastic Modelling ◽  
General Circulation Models ◽  
Teleconnection Patterns ◽  
Slowing Down ◽  
Low Dimensional

Systematic strategies from applied mathematics for stochastic modelling in climate are reviewed here. One of the topics discussed is the stochastic modelling of mid-latitude low-frequency variability through a few teleconnection patterns, including the central role and physical mechanisms responsible for multiplicative noise. A new low-dimensional stochastic model is developed here, which mimics key features of atmospheric general circulation models, to test the fidelity of stochastic mode reduction procedures. The second topic discussed here is the systematic design of stochastic lattice models to capture irregular and highly intermittent features that are not resolved by a deterministic parametrization. A recent applied mathematics design principle for stochastic column modelling with intermittency is illustrated in an idealized setting for deep tropical convection; the practical effect of this stochastic model in both slowing down convectively coupled waves and increasing their fluctuations is presented here.

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