Fitness Landscape Research Articles

The Compact Genetic Algorithm Struggles on Cliff Functions

AbstractEstimation of distribution algorithms (EDAs) are general-purpose optimizers that maintain a probability distribution over a given search space. This probability distribution is updated through sampling from the distribution and a reinforcement learning process which rewards solution components that have shown to be part of good quality samples. The compact genetic algorithm (cGA) is a non-elitist EDA able to deal with difficult multimodal fitness landscapes that are hard to solve by elitist algorithms. We investigate the cGA on the Cliff function for which it was shown recently that non-elitist evolutionary algorithms and artificial immune systems optimize it in expected polynomial time. We point out that the cGA faces major difficulties when solving the Cliff function and investigate its dynamics both experimentally and theoretically. Our experimental results indicate that the cGA requires exponential time for all values of the update strength 1/K. We show theoretically that, under sensible assumptions, there is a negative drift when sampling around the location of the cliff. Experiments further suggest that there is a phase transition for K where the expected optimization time drops from $$n^{\Theta (n)}$$ n Θ ( n ) to $$2^{\Theta (n)}$$ 2 Θ ( n ) .

Adaptive peak price with lazy updates for short-term portfolio optimization

Adaptive peak price with lazy updates for short-term portfolio optimization

Two fitness inference schemes compared using allele frequencies from 1,068,391 sequences sampled in the UK during the COVID-19 pandemic.

Throughout the course of the SARS-CoV-2 pandemic, genetic variation has contributed to the spread and persistence of the virus. For example, various mutations have allowed SARS-CoV-2 to escape antibody neutralization or to bind more strongly to the receptors that it uses to enter human cells. Here, we compared two methods that estimate the fitness effects of viral mutations using the abundant sequence data gathered over the course of the pandemic. Both approaches are grounded in population genetics theory but with different assumptions. One approach, tQLE, features an epistatic fitness landscape and assumes that alleles are nearly in linkage equilibrium. Another approach, MPL, assumes a simple, additive fitness landscape, but allows for any level of correlation between alleles. We characterized differences in the distributions of fitness values inferred by each approach and in the ranks of fitness values that they assign to sequences across time. We find that in a large fraction of weeks the two methods are in good agreement as to their top-ranked sequences, \textit{i.e.} as to which sequences observed that week are most fit. We also find that agreement between the ranking of sequences varies with genetic unimodality in the population in a given week.&#xD.

Evolutionary origins of temporal discounting: Modeling how time and uncertainty constrain optimal decision-making strategies across taxa.

The propensity of humans and non-human animals to discount future returns for short-term benefits is well established. This contrasts with the ability of organisms to unfold complex developmental sequences over months or years efficiently. Research has focused on various descriptive and predictive parameters of 'temporal discounting' in behavior, and researchers have proposed models to explain temporal preference in terms of fitness-maximizing outcomes. Still, the underlying ultimate cause of this phenomenon has not been deeply explored across taxa. Here, we propose an ultimate (i.e., evolutionary) causal explanation for the selection of temporal discounting largely conserved across taxa. We propose that preference for a short-term reward (e.g., heightened impulsivity) often is less than optimal and likely is the product of constraints imposed on natural selection with respect to predicting events in a temporal framework in the context of future uncertainty. Using a simple Newtonian model for time across a fitness landscape in which movement by organisms is only possible in one direction, we examine several factors that influence the ability of an organism to choose a distant reward over a more temporally proximate reward: including the temporal distance of the far reward, the relative value of the distant reward, and the effect of uncertainty about the value and presence of the distant reward. Our results indicate that an organism may choose a more distant reward, but only if it is not too far into the future and has a substantially higher-value fitness payoff relative to the short-term reward. Notably, any uncertainty about the distant reward made it extremely unlikely for an organism to choose the delayed reward strategy compared to choosing a closer reward, even if the distant reward had a much higher payoff because events that are uncertain are only partially visible to natural selection pressures. The results help explain why natural selection is constrained to promote more optimal behavioral strategies and why it has difficulty selecting a distant reward over a lower-value short-term reward. The degree of uncertainty is an especially salient ecological variable in promoting and preferencing short-term behavioral strategies across taxa. These results further help illustrate why, from an ultimate causal perspective, human and non-human taxa have difficulty making more optimal long-term decisions.

RXLR effector genes mediate regional adaptation of Phytophthora infestans

AbstractLocal adaptation has been a central theme of eco-evolutionary research for decades. It is generally assumed that plant pathogens are locally adapted due to their standing interactions with biotic and abiotic factors in the ecosystem. Effectors, secreted small proteins encoded by pathogens, play critical roles in host–pathogen interactions, by activating host genotype-specific resistance, suppressing plant immunity, and playing other functions. In this study, we investigated the potential involvement of RXLR effector genes in ecological adaptation by examining the simple sequence repeat (SSR), virulence, and effector profiles in Phytophthora infestans isolates collected from two geographic regions differing in ecological environments. Genotypic analyses with SSR markers and virulence assays showed that the pathogen from the two regions shared genetic background but differed in virulence spectrums. High-throughput sequencing and expression analysis of 24 selected P. infestans isolates further showed variations in the RXLR effector repertoire, ranging from 536 to 548 for each isolate and the expression of effector genes was highly associated with the accumulation of homologous sRNA. Regional specific alleles were detected at 94 RXLR effector genes, and a specific accumulation of homologous 25–26 nt sRNAs was found at 67 RXLR effector genes. Two of the regional specific RXLR effector genes were confirmed to be virulence factors. Taken together, these results suggest that genomic and epigenetic variations in RXLR effector genes contribute significantly to the ecological adaptation of P. infestans populations and that regional specific effector genes will help to understand the adaptive landscape of pathogens and efficient use of host resistance genes.

A Microfluidic Multiplex Sorter for Strain Development

AbstractSelecting strains with superior traits from strain improvement strategies is challenging, as it involves navigating the fitness landscape by applying selective pressures that drive variants from peaks of improvement to valleys over time. In recent years, the screening and selection is conducted via droplet microfluidic methods due to its high throughput capabilities. However, the oft‐used binary strategy, targeting only the high levels of improved traits, may not reflect the overall enhancement. A multiplexed sorting method capable of applying an additional threshold to sort traits by phenotypic strength is reported. The novel approach uses a droplet‐digital microfluidic sorter to screen different volumes of droplets using the same device design and sorting parameters. This method is used to sort glucoamylase enzyme mutants with two levels of activity (medium and high) from libraries of diastatic yeast that have been mutated with non‐genetically modified techniques. Using the multiplex system, medium‐performing strains with enhanced (up to 60%) fermentation kinetics in synthetic beverage media, which would have been missed with a binary screening approach, are identified. The multiplex sorting strategy efficiently finds strains with superior fermentation traits in the fitness landscape without requiring extensive screening rounds and mutations.

Fitness and Sports Academy Integration Web Application

In the modern health and fitness landscape, gyms and athletes face unique challenges in managing schedules, tracking workouts, and fostering engagement. Existing systems often lack comprehensive tools to connect gym owners and customers effectively, impeding workout management and client retention. This paper presents a gym management and athlete engagement web application, developed with the MERN stack and leveraging Firebase for real-time data updates. By incorporating features such as personalized workout tracking, feedback systems, and integrated payment processing, this application aims to enhance gym operations and user experience. The research also explores the application of machine learning algorithms for injury prevention and personalized recommendations. Evaluation of the platform demonstrates significant improvements in user engagement, workout tracking, and gym management. This study highlights the potential of technology-driven solutions to address fitness industry challenges, creating scalable systems for gym management, athlete engagement, and personalized fitness plans. In the era of digital fitness, gym users, trainers, and gym owners increasingly rely on technology to track progress, foster community, and manage services. FitConnect aims to bridge this gap by providing a comprehensive fitness networking platform with real-time workout tracking, role-based functionalities, and payment integration. Unlike conventional fitness apps, FitConnect introduces a collaborative ecosystem where users can connect with trainers, join gym sessions, and manage subscriptions efficiently. Leveraging scalable architecture and user-friendly interfaces, this project combines essential fitness tracking with networking capabilities to create an integrated solution for fitness enthusiasts and professionals alike. This paper explores the design, development, and deployment strategies used to create this platform and assesses its impact on improving user engagement, goal tracking, and service management..

Self-learning salp swarm algorithm for global optimization and its application in multi-layer perceptron model training

Optimization problems are common across various fields, and one effective solution is the swarm intelligence algorithm.It is essential for the algorithm to deliver high-quality solutions for problems with varying characteristics. However, most existing swarm intelligence rely on fixed and monotonic search strategies, which limits their ability to handle the diverse and complex situations encountered when solving real-world optimization problems with unknown fitness landscapes. To extend the applicability of swarm intelligence and thus offer users an efficient black-box optimizer for various applications, a novel self-learning mechanism is proposed and applied to the Salp Swarm Algorithm (SSA) to develop the self-learning salp swarm algorithm (SLSSA) in this paper. In SLSSA, four distinct search strategies, including a novel multiple food sources search strategy, are adopted to strengthen the search agents’ abilities to conquer various difficulties in the search space. To improve the efficiency of the search process, the self-learning strategy dynamically determines the execution probability of each search strategy according to the quality of solutions it produced previously. Moreover, a parameter setting method is proposed in this paper, which eliminates the need for a trial-and-error approach and allows for straightforward configuration of the parameters that optimize the performance of SLSSA. In comparison with several highly regarded state-of-the-art peer algorithms, the performance of SLSSA in solving the CEC2014 benchmark functions was thoroughly examined. Subsequently, SLSSA was applied to train multi-layer perceptron classifiers and test on the UCI machine-learning datasets. The experimental results and analysis on benchmark functions and multi-layer perceptron classifier training problems demonstrate that SLSSA outperforms the competing algorithms in terms of solution accuracy, stability, and overall convergence speed. Moreover, computational time comparisons reveal that SLSSA achieves significant performance improvement with only a marginal increase in time cost compared to the original SSA.

Continuous evolution of user-defined genes at 1 million times the genomic mutation rate.

When nature evolves a gene over eons at scale, it produces a diversity of homologous sequences with patterns of conservation and change that contain rich structural, functional, and historical information about the gene. However, natural gene diversity accumulates slowly and likely excludes large regions of functional sequence space, limiting the information that is encoded and extractable. We introduce upgraded orthogonal DNA replication (OrthoRep) systems that radically accelerate the evolution of chosen genes under selection in yeast. When applied to a maladapted biosynthetic enzyme, we obtained collections of extensively diverged sequences with patterns that revealed structural and environmental constraints shaping the enzyme's activity. Our upgraded OrthoRep systems should support the discovery of factors influencing gene evolution, uncover previously unknown regions of fitness landscapes, and find broad applications in biomolecular engineering.

Soft Actor-Critic Approach to Self-Adaptive Particle Swarm Optimisation

Particle swarm optimisation (PSO) is a swarm intelligence algorithm that finds candidate solutions by iteratively updating the positions of particles in a swarm. The decentralised optimisation methodology of PSO is ideally suited to problems with multiple local minima and deceptive fitness landscapes, where traditional gradient-based algorithms fail. PSO performance depends on the use of a suitable control parameter (CP) configuration, which governs the trade-off between exploration and exploitation in the swarm. CPs that ensure good performance are problem-dependent. Unfortunately, CPs tuning is computationally expensive and inefficient. Self-adaptive particle swarm optimisation (SAPSO) algorithms aim to adaptively adjust CPs during the optimisation process to improve performance, ideally while reducing the number of performance-sensitive parameters. This paper proposes a reinforcement learning (RL) approach to SAPSO by utilising a velocity-clamped soft actor-critic (SAC) that autonomously adapts the PSO CPs. The proposed SAC-SAPSO obtains a 50% to 80% improvement in solution quality compared to various baselines, has either one or zero runtime parameters, is time-invariant, and does not result in divergent particles.

Ensemble Monte Carlo calculations with five novel moves

We introduce five novel types of Monte Carlo (MC) moves that brings the number of moves of ensemble MC calculations from three to eight. So far such calculations have relied on affine invariant stretch moves that were originally introduced by Christen (2007) [8], walk moves by Goodman and Weare (2010) [16] and quadratic moves by Militzer (2023) [31,32]. Ensemble MC methods have been very popular because they harness information about the fitness landscape from a population of walkers rather than relying on expert knowledge. Here we modified the affine method and employed a simplex of points to set the stretch direction. We adopt the simplex concept to quadratic moves. We also generalize quadratic moves to arbitrary order. Finally, we introduce directed moves that employ the values of the probability density while all other types of moves rely solely on the location of the walkers. We apply all algorithms to the Rosenbrock density in 2 and 20 dimensions and to the ring potential in 12 and 24 dimensions. We evaluate their efficiency by comparing error bars, autocorrelation time, travel time, and the level of cohesion that measures whether any walkers were left behind. Our code is open source.

CNN Intelligent diagnosis method for bearing incipient faint faults based on adaptive stochastic resonance-wave peak cross correlation sliding sampling

As a representative of deep learning networks, convolutional neural networks (CNN) have been widely used in bearing fault diagnosis with good results. However, the signal length and segmentation of the input CNN can have a significant impact on diagnostic accuracy. In addition, the signal-to-noise ratio of early bearing faults is usually very low, which makes it difficult for traditional CNNs to accurately identify and classify these faults. To solve this problem, this paper proposes an adaptive stochastic resonance wave peak cross-correlation sliding sampling method. Firstly, the adaptive stochastic resonance is used to reduce the noise of the original signal, and then the data is divided from the position of the signal wave peak, the correlation coefficient between the divided signals is calculated, and the maximum value is found to determine the size of the division window. Finally, it is converted into a 2D image by Gramian Angular Field and input into CNN for diagnostic classification. The design methodology was validated using the Case Western Reserve University bearing dataset. Subsequently, three validation strategies were established on a self-built platform, including mixed diagnosis of 10 different bearing states, variable speed diagnosis, and low sampling data diagnosis. The proposed method outperforms the conventional CNN by 10% in the Case Western Reserve University dataset test set. The variable speed test set is 24.67% and 31.17% higher, respectively. It is 30% higher in low sampling data diagnosis.

An Analysis of Differential Evolution Population Size

The performance of the differential evolution algorithm (DE) is known to be highly sensitive to the values assigned to its control parameters. While numerous studies of the DE control parameters do exist, these studies have limitations, particularly in the context of setting the population size regardless of problem-specific characteristics. Moreover, the complex interrelationships between DE control parameters are frequently overlooked. This paper addresses these limitations by critically analyzing the existing guidelines for setting the population size in DE and assessing their efficacy for problems of various modalities. Moreover, the relative importance and interrelationship between DE control parameters using the functional analysis of variance (fANOVA) approach are investigated. The empirical analysis uses thirty problems of varying complexities from the IEEE Congress on Evolutionary Computation (CEC) 2014 benchmark suite. The results suggest that the conventional one-size-fits-all guidelines for setting DE population size possess the possibility of overestimating initial population sizes. The analysis further explores how varying population sizes impact DE performance across different fitness landscapes, highlighting important interactions between population size and other DE control parameters. This research lays the groundwork for subsequent research on thoughtful selection of optimal population sizes for DE algorithms, facilitating the development of more efficient adaptive DE strategies.

Estimating Vehicle Turn-In Rate of Expressway Rest Areas via ETC Gantry Data – An ADPC-GMM Approach

Vehicle turn-in rate is a critical and widely adopted input for expressway rest area design and operation. With the implementation of expressway ETC gantries, the ERA turn-in rate can be further estimated by measuring the travel speed distribution via ETC gantry data. This paper proposed an adaptive density peak clustering Gaussian mixture model (ADPC-GMM) for ERA turn-in rate estimation. The ADPC algorithm is applied to generate the GMM’s inputs accommodating to the traffic characteristic of ERA expressway segments and GMM would further provide the turn-in rate estimation results. To validate the model precision, the turn-in rate data of four selected ERAs in Sichuan, China, as well as the ETC gantry data of their corresponding expressway sections are obtained. According to the estimation results, the MAE and RMSE are 0.0228 and 0.0267 for the passenger car scenario and 0.0264 and 0.0356 for the commercial truck scenario, respectively. These results are also at the lowest level compared with the results acquired from ordinary GMM, K-Means and DBSCAN algorithms. The proposed method has good applicability for vehicle turn-in rate estimation and can be deployed at different ERAs, especially those ERAs without traffic monitoring.

On the issue of forecasting crop yields for the purposes of adaptive landscape agriculture

Long-term monitoring (1998–2023) of the yield of clover-timothy grass stands of the first year of use was carried out in order to find patterns of influence of landscape environmental conditions on it in various agroclimatic conditions. The research was conducted within the moraine hill located at the Gubino VNIIMZ agro-testing site in the Tver region. Soil-forming rocks are two-membered deposits consisting of an upper layer composed of relatively light rocks, underlain by moraine bouldery loam. The grass stands were exploited without fertilizers in a single-cut mode on a field divided into 120 plots. Using regression analysis, the influence of landscape and soil environment factors was determined: relief, physical and agrochemical properties of soils on grass yield, as well as the dependence of the degree of this impact on climatic conditions. It was found that the yield of perennial grasses is most strongly influenced by various fractions of the granulometric composition of soils – from stones to dust (up to 16 % of its variability) and the altitude of the location (up to 38 %), since the thermal and water-air characteristics of soils and vegetation largely depend on them. Terrain characteristics such as steepness and curvature of the surface have a minor impact on grass yield (up to 12 %). The degree of influence of agro-landscape environmental factors on the growth of grasses is largely regulated by fluctuations in weather conditions. “Climate scenarios” of a specific factor – sets of weather parameters under which its effect on the production process of a crop is manifested – in the years of sowing and mowing, as a rule, do not differ fundamentally. Knowing the nature of the influence of climatic factors allows us to more accurately predict crop yields within an agricultural landscape and, thus, optimize the location of crops on the territory of a particular farm.

Performance degradation assessment of rolling bearings for electrostatic monitoring based on IDDAE and ADPC

Abstract To improve the early degradation detection capability of the electrostatic monitoring system for rolling bearings, a performance degradation evaluation method based on improved deep denoising autoencoder (IDDAE) and adaptive density peak clustering (ADPC) is proposed in this paper. Firstly, the fusion of electrostatic charge signal features with conventional time-domain, frequency-domain and time-frequency-domain features constitutes the characteristic parameter set of the electrostatic monitoring system indicating the status of the bearings. Then, in order to improve the feature extraction ability of DAE, the deep network DDAE is constructed, and L1 regularisation and Dropout mechanism are applied to avoid overfitting in the deep network, so as to achieve non-linear mapping dimensionality reduction of high-dimensional features. Moreover, to eliminate the error caused by manually selecting the clustering centre, the parameters are adaptively determined by entropy value method and comprehensive optimisation search on the basis of DPC, thus avoiding the "chain effect" that occurs in traditional DPC when data are incorrectly aggregated due to incorrect assignment of clustering centres. Consequently, an improved ADPC algorithm is used to establish a model to measure the health status of bearings, calculate the Mahalanobis distance (MD) be-tween the test set and the cluster centre, and quantitatively characterize the degree of performance degradation of rolling bearings. Finally, combining the 3σ principle, a repair method that can satisfy online monitoring and adapt to spurious fluctuations in different situations is established on a sliding window to obtain an improved index IMD that can accurately characterise the rolling bearing degradation process. The experimental results show that the proposed method can identify early bearing degradation earlier and has better monotonicity, robustness and tendency than other performance degradation assessment methods.

Single-cell transcriptomics reveal potent extrafollicular B cell response linked with granzyme K+ CD8 T cell activation in lupus kidney

ObjectivesB and T cells constitute the majority of infiltrating lymphocytes in the kidney and represent the local perpetrators in lupus nephritis (LN), but the underlying pathogenic mechanisms are not well...

SeqDance: A Protein Language Model for Representing Protein Dynamic Properties.

Proteins perform their functions by folding amino acid sequences into dynamic structural ensembles. Despite the important role of protein dynamics, their complexity and the absence of efficient representation methods have limited their integration into studies on protein function and mutation fitness, especially in deep learning applications. To address this, we present SeqDance, a protein language model designed to learn representation of protein dynamic properties directly from sequence alone. SeqDance is pre-trained on dynamic biophysical properties derived from over 30,400 molecular dynamics trajectories and 28,600 normal mode analyses. Our results show that SeqDance effectively captures local dynamic interactions, co-movement patterns, and global conformational features, even for proteins lacking homologs in the pre-training set. Additionally, we showed that SeqDance enhances the prediction of protein fitness landscapes, disorder-to-order transition binding regions, and phase-separating proteins. By learning dynamic properties from sequence, SeqDance complements conventional evolution- and static structure-based methods, offering new insights into protein behavior and function.

Phytoclimatological study in the high plains of Sétif: application of the bioclimatic classification system (Algeria)

The Global Bioclimatic Classification System (WBCS) by Rivas-Martínez is an effective approach to reflect and study the role of climate in determining the potential distribution of natural vegetation at various temporal and spatial scales. In particular, the diversity of physical characteristics in the Setifian high plains leads to the complexity of large-scale phytogeographic belts. Isobioclimates, unique combinations of bioclimatic indices (continentality, ombrotype, and thermotype), have been created for the study area based on Rivas-Martínez's global bioclimatic classification system for current and future climate scenarios, using the parallel climate model from CMIP5 (Coupled Model Intercomparison Project) under the intermediate greenhouse gas emission scenario (RCP4.5). Precipitation and temperature data from the "WorldClim" dataset were used as the data source. These climatic variables were reduced to a spatial resolution of 1 km. The objective is to understand how the climate is evolving in this region, what the consequences are, and what the future holds for these natural ecosystems. A phytosociological study complemented by satellite image analysis reveals a high diversity of pre-forestry formations. The digitally mapped results were used to 1) assess the relative redistribution of isobioclimates and the magnitude of change, 2) identify and locate the new projected isobioclimates, and 3) explore the compositional changes in vegetation types among analogous isobioclimatic zones. The ordination of the relationships between vegetation and bioclimates shows a strong correlation between Rivas-Martinez indices and the distribution and composition of vegetation. Changes in ombrotype, thermotype, bioclimate, ombrotype, and isobioclimate differed between the current and future series. The resulting map presents 9 isobioclimatic units, which are advantageous for confirming the diagnosis of bioclimatic characteristics and describing the relationships between climatic variables and the corresponding distributions of natural vegetation. We identified eight different isobioclimates for the current period (1979-2013) and seven for the future period (2050), three thermotype horizons for both the current and future periods, and finally, four ombrotype horizons for the period (1979-2013), while two ombrohorizons represent the period (2050). This approach is useful for explaining territorial diversity in environmental applications related to ecological adaptation assessment, nature conservation, landscape regionalization, and planning.

On Recombination.

The predominant explanations for including chromosomal recombination during meiosis are that it serves as a mechanism for repair or as a mechanism for increased adaptability. However, neither gives a clear immediate selective advantage to the reproducing organism itself. This letter revisits the idea that sex emerged and is maintained because it enables a simple form of fitness landscape smoothing to explain why recombination evolved. Although recombination was originally included in the idea, as with the other explanations, no immediate benefit was identified. That a benefit exists if the dividing cell(s) form a simple colony of the resulting haploids for some time after reproduction is explored here and shown to further increase the benefits of the landscape smoothing process.