A biological perspective on evolutionary computation

Mechanistic regulation of planarian shape during growth and degrowth

Adult planarians can grow when fed and degrow (shrink) when starved while maintaining their whole-body shape. It is unknown how the morphogens patterning the planarian axes are coordinated during feeding and starvation or how they modulate the necessary differential tissue growth or degrowth. Here, we investigate the dynamics of planarian shape together with a theoretical study of the mechanisms regulating whole-body proportions and shape. We found that the planarian body proportions scale isometrically following similar linear rates during growth and degrowth, but that fed worms are significantly wider than starved worms. By combining a descriptive model of planarian shape and size with a mechanistic model of anterior-posterior and medio-lateral signaling calibrated with a novel parameter optimization methodology, we theoretically demonstrate that the feedback loop between these positional information signals and the shape they control can regulate the planarian whole-body shape during growth. Furthermore, the computational model produced the correct shape and size dynamics during degrowth as a result of a predicted increase in apoptosis rate and pole signal during starvation. These results offer mechanistic insights into the dynamic regulation of whole-body morphologies.

Using the Grey Wolf Aquila Synergistic Algorithm for Design Problems in Structural Engineering

The Aquila Optimizer (AO) is a metaheuristic algorithm that is inspired by the hunting behavior of the Aquila bird. The AO approach has been proven to perform effectively on a range of benchmark optimization issues. However, the AO algorithm may suffer from limited exploration ability in specific situations. To increase the exploration ability of the AO algorithm, this work offers a hybrid approach that employs the alpha position of the Grey Wolf Optimizer (GWO) to drive the search process of the AO algorithm. At the same time, we applied the quasi-opposition-based learning (QOBL) strategy in each phase of the Aquila Optimizer algorithm. This strategy develops quasi-oppositional solutions to current solutions. The quasi-oppositional solutions are then utilized to direct the search phase of the AO algorithm. The GWO method is also notable for its resistance to noise. This means that it can perform effectively even when the objective function is noisy. The AO algorithm, on the other hand, may be sensitive to noise. By integrating the GWO approach into the AO algorithm, we can strengthen its robustness to noise, and hence, improve its performance in real-world issues. In order to evaluate the effectiveness of the technique, the algorithm was benchmarked on 23 well-known test functions and CEC2017 test functions and compared with other popular metaheuristic algorithms. The findings demonstrate that our proposed method has excellent efficacy. Finally, it was applied to five practical engineering issues, and the results showed that the technique is suitable for tough problems with uncertain search spaces.

Light-driven eco-evolutionary dynamics in a synthetic replicator system

Darwinian evolution involves the inheritance and selection of variations in reproducing entities. Selection can be based on, among others, interactions with the environment. Conversely, the replicating entities can also affect their environment generating a reciprocal feedback on evolutionary dynamics. The onset of such eco-evolutionary dynamics marks a stepping stone in the transition from chemistry to biology. Yet the bottom-up creation of a molecular system that exhibits eco-evolutionary dynamics has remained elusive. Here we describe the onset of such dynamics in a minimal system containing two synthetic self-replicators. The replicators are capable of binding and activating a co-factor, enabling them to change the oxidation state of their environment through photoredox catalysis. The replicator distribution adapts to this change and, depending on light intensity, one or the other replicator becomes dominant. This study shows how behaviour analogous to eco-evolutionary dynamics-which until now has been restricted to biology-can be created using an artificial minimal replicator system.

Bird's Eye View feature selection for high-dimensional data

In machine learning, an informative dataset is crucial for accurate predictions. However, high dimensional data often contains irrelevant features, outliers, and noise, which can negatively impact model performance and consume computational resources. To tackle this challenge, the Bird's Eye View (BEV) feature selection technique is introduced. This approach is inspired by the natural world, where a bird searches for important features in a sparse dataset, similar to how a bird search for sustenance in a sprawling jungle. BEV incorporates elements of Evolutionary Algorithms with a Genetic Algorithm to maintain a population of top-performing agents, Dynamic Markov Chain to steer the movement of agents in the search space, and Reinforcement Learning to reward and penalize agents based on their progress. The proposed strategy in this paper leads to improved classification performance and a reduced number of features compared to conventional methods, as demonstrated by outperforming state-of-the-art feature selection techniques across multiple benchmark datasets.

Maximum Lyapunov exponent-based multiple chaotic slime mold algorithm for real-world optimization

Slime mold algorithm (SMA) is a nature-inspired algorithm that simulates the biological optimization mechanisms and has achieved great results in various complex stochastic optimization problems. Owing to the simulated biological search principle of slime mold, SMA has a unique advantage in global optimization problem. However, it still suffers from issues of missing the optimal solution or collapsing to local optimum when facing complicated problems. To conquer these drawbacks, we consider adding a novel multi-chaotic local operator to the bio-shock feedback mechanism of SMA to compensate for the lack of exploration of the local solution space with the help of the perturbation nature of the chaotic operator. Based on this, we propose an improved algorithm, namely MCSMA, by investigating how to improve the probabilistic selection of chaotic operators based on the maximum Lyapunov exponent (MLE), an inherent property of chaotic maps. We implement the comparison between MCSMA with other state-of-the-art methods on IEEE Congress on Evolution Computation (CEC) i.e., CEC2017 benchmark test suits and CEC2011 practical problems to demonstrate its potency and perform dendritic neuron model training to test the robustness of MCSMA on classification problems. Finally, the parameters' sensitivities of MCSMA, the utilization of the solution space, and the effectiveness of the MLE are adequately discussed.

A review of biowaste remediation and valorization for environmental sustainability: Artificial intelligence approach

Biowaste remediation and valorization for environmental sustainability focuses on prevention rather than cleanup of waste generation by applying the fundamental recovery concept through biowaste-to-bioenergy conversion systems - an appropriate approach in a circular bioeconomy. Biomass waste (biowaste) is discarded organic materials made of biomass (e.g., agriculture waste and algal residue). Biowaste is widely studied as one of the potential feedstocks in the biowaste valorization process due to its being abundantly available. In terms of practical implementations, feedstock variability from biowaste, conversion costs and supply chain stability prevent the widespread usage of bioenergy products. Biowaste remediation and valorization have used artificial intelligence (AI), a newly developed idea, to overcome these difficulties. This report analyzed 118 works that applied various AI algorithms to biowaste remediation and valorization-related research published between 2007 and 2022. Four common AI types are utilized in biowaste remediation and valorization: neural networks, Bayesian networks, decision tree, and multivariate regression. The neural network is the most frequent AI for prediction models, the Bayesian network is utilized for probabilistic graphical models, and the decision tree is trusted for providing tools to assist decision-making. Meanwhile, multivariate regression is employed to identify the relationship between experimental variables. AI is a remarkably effective tool in predicting data, which is reportedly better than the conventional approach owing to its characteristics of time-saving and high accuracy. The challenge and future work in biowaste remediation and valorization are briefly discussed to maximize the model's performance.

ARMO: automated and reliable multi-objective model for lymph node metastasis prediction in head and neck cancer

Objective. Accurate diagnosis of lymph node metastasis (LNM) is critical in treatment management for patients with head and neck cancer. Positron emission tomography and computed tomography are routinely used for identifying LNM status. However, for small or less fluorodeoxyglucose (FDG) avid nodes, there are always uncertainties in LNM diagnosis. We are aiming to develop a reliable prediction model is for identifying LNM.Approach. In this study, a new automated and reliable multi-objective learning model (ARMO) is proposed. In ARMO, a multi-objective model is introduced to obtain balanced sensitivity and specificity. Meanwhile, confidence is calibrated by introducing individual reliability, whilst the model uncertainty is estimated by a newly defined overall reliability in ARMO. In the training stage, a Pareto-optimal model set is generated. Then all the Pareto-optimal models are used, and a reliable fusion strategy that introduces individual reliability is developed for calibrating the confidence of each output. The overall reliability is calculated to estimate the model uncertainty for each test sample.Main results. The experimental results demonstrated that ARMO obtained more promising results, which the area under the curve, accuracy, sensitivity and specificity can achieve 0.97, 0.93, 0.88 and 0.94, respectively. Meanwhile, based on calibrated confidence and overall reliability, clinicians could pay particular attention to highly uncertain predictions.Significance. In this study, we developed a unified model that can achieve balanced prediction, confidence calibration and uncertainty estimation simultaneously. The experimental results demonstrated that ARMO can obtain accurate and reliable prediction performance.

Evolutionary Process for Engineering Optimization in Manufacturing Applications: Fine Brushworks of Single-Objective to Multi-Objective/Many-Objective Optimization

Single-objective to multi-objective/many-objective optimization (SMO) is a new paradigm in the evolutionary transfer optimization (ETO), since there are only “1 + 4” pioneering works on SMOs so far, that is, “1” is continuous and is firstly performed by Professors L. Feng and H.D. Wang, and “4” are firstly proposed by our group for discrete cases. As a new computational paradigm, theoretical insights into SMOs are relatively rare now. Therefore, we present a proposal on the fine brushworks of SMOs for theoretical advances here, which is based on a case study of a permutation flow shop scheduling problem (PFSP) in manufacturing systems via lenses of building blocks, transferring gaps, auxiliary task and asynchronous rhythms. The empirical studies on well-studied benchmarks enrich the rough strokes of SMOs and guide future designs and practices in ETO based manufacturing scheduling, and even ETO based evolutionary processes for engineering optimization in other cases.

Exploring genetic influences on adverse outcome pathways using heuristic simulation and graph data science

Adverse outcome pathways provide a powerful tool for understanding the biological signaling cascades that lead to disease outcomes following toxicity. The framework outlines downstream responses known as key events, culminating in a clinically significant adverse outcome as a final result of the toxic exposure. Here we use the AOP framework combined with artificial intelligence methods to gain novel insights into genetic mechanisms that underlie toxicity-mediated adverse health outcomes. Specifically, we focus on liver cancer as a case study with diverse underlying mechanisms that are clinically significant. Our approach uses two complementary AI techniques: Generative modeling via automated machine learning and genetic algorithms, and graph machine learning. We used data from the US Environmental Protection Agency's Adverse Outcome Pathway Database (AOP-DB; aopdb.epa.gov) and the UK Biobank's genetic data repository. We use the AOP-DB to extract disease-specific AOPs and build graph neural networks used in our final analyses. We use the UK Biobank to retrieve real-world genotype and phenotype data, where genotypes are based on single nucleotide polymorphism data extracted from the AOP-DB, and phenotypes are case/control cohorts for the disease of interest (liver cancer) corresponding to those adverse outcome pathways. We also use propensity score matching to appropriately sample based on important covariates (demographics, comorbidities, and social deprivation indices) and to balance the case and control populations in our machine language training/testing datasets. Finally, we describe a novel putative risk factor for LC that depends on genetic variation in both the aryl-hydrocarbon receptor (AHR) and ATP binding cassette subfamily B member 11 (ABCB11) genes.

Chaotic Wind Driven Optimization with Fitness Distance Balance Strategy

Wind driven optimization (WDO) is a meta-heuristic algorithm based on swarm intelligence. The original selection method makes it easy to converge prematurely and trap in local optima. Maintaining population diversity can solve this problem well. Therefore, we introduce a new fitness-distance balance-based selection strategy to replace the original selection method, and add chaotic local search with selecting chaotic map based on memory to further improve the search performance of the algorithm. A chaotic wind driven optimization with fitness-distance balance strategy is proposed, called CFDBWDO. In the experimental section, we find the optimal parameter settings for the proposed algorithm. To verify the effect of the algorithm, we conduct comparative experiments on the CEC 2017 benchmark functions. The experimental results denote that the proposed algorithm has superior performance. Compared with WDO, CFDBWDO can gradually converge in function optimization. We further verify the practicality of the proposed algorithm with six real-world optimization problems, and the obtained results are all better than other algorithms.

Subpopulation-specific machine learning prognosis for underrepresented patients with double prioritized bias correction

Background

Many clinical datasets are intrinsically imbalanced, dominated by overwhelming majority groups. Off-the-shelf machine learning models that optimize the prognosis of majority patient types (e.g., healthy class) may cause substantial errors on the minority prediction class (e.g., disease class) and demographic subgroups (e.g., Black or young patients). In the typical one-machine-learning-model-fits-all paradigm, racial and age disparities are likely to exist, but unreported. In addition, some widely used whole-population metrics give misleading results.

Methods

We design a double prioritized (DP) bias correction technique to mitigate representational biases in machine learning-based prognosis. Our method trains customized machine learning models for specific ethnicity or age groups, a substantial departure from the one-model-predicts-all convention. We compare with other sampling and reweighting techniques in mortality and cancer survivability prediction tasks.

Results

We first provide empirical evidence showing various prediction deficiencies in a typical machine learning setting without bias correction. For example, missed death cases are 3.14 times higher than missed survival cases for mortality prediction. Then, we show DP consistently boosts the minority class recall for underrepresented groups, by up to 38.0%. DP also reduces relative disparities across race and age groups, e.g., up to 88.0% better than the 8 existing sampling solutions in terms of the relative disparity of minority class recall. Cross-race and cross-age-group evaluation also suggests the need for subpopulation-specific machine learning models.

Conclusions

Biases exist in the widely accepted one-machine-learning-model-fits-all-population approach. We invent a bias correction method that produces specialized machine learning prognostication models for underrepresented racial and age groups. This technique may reduce potentially life-threatening prediction mistakes for minority populations.