Biologically meaningful regulatory logic enhances the convergence rate in Boolean networks and bushiness of their state transition graph.

Boolean models of gene regulatory networks (GRNs) have gained widespread traction as they can easily recapitulate cellular phenotypes via their attractor states. Their overall dynamics are embodied in a state transition graph (STG). Indeed, two Boolean networks (BNs) with the same network structure and attractors can have drastically different STGs depending on the type of Boolean functions (BFs) employed. Our objective here is to systematically delineate the effects of different classes of BFs on the structural features of the STG of reconstructed Boolean GRNs while keeping network structure and biological attractors fixed, and explore the characteristics of BFs that drive those features. Using $10$ reconstructed Boolean GRNs, we generate ensembles that differ in BFs and compute from their STGs the dynamics' rate of contraction or 'bushiness' and rate of 'convergence', quantified with measures inspired from cellular automata (CA) that are based on the garden-of-Eden (GoE) states. We find that biologically meaningful BFs lead to higher STG 'bushiness' and 'convergence' than random ones. Obtaining such 'global' measures gets computationally expensive with larger network sizes, stressing the need for feasible proxies. So we adapt Wuensche's $Z$-parameter in CA to BFs in BNs and provide four natural variants, which, along with the average sensitivity of BFs computed at the network level, comprise our descriptors of local dynamics and we find some of them to be good proxies for bushiness. Finally, we provide an excellent proxy for the 'convergence' based on computing transient lengths originating at random states rather than GoE states.

A framework for real-time operation of urban detention reservoirs: Application of the cellular automata and rainfall nowcasting.

Detention reservoirs are employed in urban drainage systems to reduce peak flows downstream of reservoirs. In addition to the volume of detention reservoirs, their operational policies could significantly affect their performance. This paper presents a framework for the real-time coordinated operation of detention reservoirs using deep-learning-based rainfall nowcasting data. Considering the short concentration time of urban basins, the real-time operating policies of urban detention reservoirs should be developed quickly. In the proposed framework, a cellular automata (CA)-based optimization algorithm is linked with the storm water management model (SWMM) to optimize real-time operating policies of gates at the inlets and outlets of detention reservoirs. As CA-based optimization models are not population-based, their computational costs are much less than population-based metaheuristic optimization techniques such as genetic algorithms. To evaluate the applicability and efficiency of the framework, it is applied to the east drainage catchment (EDC) of Tehran metropolitan area in Iran. The results illustrate that the proposed framework could reduce the overflow volume by up to 60%. For complete flood control in the study area, in addition to the real-time operation of detention reservoirs, constructing five tunnels with a total length of 13200 m is recommended. To evaluate the performance of the CA-based optimization model, its results are compared with those obtained from the non-dominated sorting genetic algorithm III (NSGA-III). It is shown that the CA-based model provides similar results with only 5% of the run-time of NSGA-III. A sensitivity analysis is also performed to evaluate the effects of optimization models' parameters on their performance.

A cellular automata model coupled with partitioning CNN-LSTM and PLUS models for urban land change simulation.

Urbanisation is a key aspect of land use change (LUC), and accurately modelling of urban LUC is crucial for sustainable development. Cellular automata (CA) are widely used in LUC research. However, previous studies have overlooked the significant temporal dependence and spatial heterogeneity associated with LUC. To address these gaps, this study proposes a novel model called KCLP-CA, which integrates k-means, a convolutional neural network (CNN), a long and short-term memory neural network (LSTM), and the popular patch-generation land use model (PLUS). Initially, k-means and CNN are utilised to address spatial heterogeneity, while LSTM tackles temporal dependence. The LSTM and land expansion analysis strategy (LEAS) models of PLUS are employed to obtain land use conversion probability maps. Finally, a simulation of land use dynamic change was conducted using a linear weighted fusion conversion probability map that accounts for random factors. To validate the KCLP-CA model, land use data collected from Hangzhou between 1995 and 2000 were employed. The results showed that the KCLP-CA model outperformed traditional methods, including artificial neural networks and random forest model, with the figure of merit (FoM) index increasing from 2.12% to 4.19%. Random forest analysis of drivers impacting LUC revealed that distance to water and road network density exerted the greatest influence on urban land development in Hangzhou. Incorporation of various policy planning factors affecting urban development yielded simulation results aligning more closely with reality, resulting in a FoM index increase of 1.64-1.76%. In summary, the model developed in this study combines the strengths of two sub models to deliver an accurate and effective simulation of future land use.

Adaptive reservoir operation considering water quantity and quality objectives: Application of parallel cellular automata and sub-seasonal streamflow forecasts.

This paper presents a new framework for the adaptive reservoir operation considering water quantity and quality objectives. In this framework, using the European Centre for Medium-Range Weather Forecasts (ECMWF) database, the monthly precipitation forecasts, with up to 6-month lead time, are downscaled and bias corrected. The rainfall forecasts are used as inputs to a rainfall-runoff simulation model to predict sub-seasonal inflows to reservoir. The water storage at the end of a short-term planning horizon (e.g. 6 months) is obtained from some probabilistic optimal reservoir storage volume curves, which are developed using a long-term reservoir operation optimization model. The adaptive optimization model is linked with the CE-QUAL-W2 water quality simulation model to assess the quality of outflow from each gate as well as the in-reservoir water quality. At the first of each month, the inflow forecasts for the coming months are updated and operating policies for each gate are revised. To tackle the computational burden of the adaptive simulation-optimization model, it is run using Parallel Cellular Automata with Local Search (PCA-LS) optimization algorithm. To evaluate the applicability and efficiency of the framework, it is applied to the Karkheh dam, which is the largest reservoir in Iran. By comparing the run times of the PCA-LS and the Non-dominated Sorting Genetic Algorithms II (NSGA-II), it is shown that the computational time of PCA-LS is 95 % less than NSGA-II. According to the results, the difference between the objective function of the proposed adaptive optimization model and a perfect model, which uses the observed inflow data, is only 1.68 %. It shows the appropriate accuracy of the adaptive model and justifies using the proposed framework for the adaptive operation of reservoirs considering water quantity and quality objectives.

Spatial and temporal classification and prediction of LULC in Brahmani and Baitarni basin using integrated cellular automata models.

Monitoring the dynamics of land use and land cover (LULC) is imperative in the changing climate and evolving urbanization patterns worldwide. The shifts in land use have a significant impact on the hydrological response of watersheds across the globe. Several studies have applied machine learning (ML) algorithms using historical LULC maps along with elevation data and slope for predicting future LULC projections. However, the influence of other driving factors such as socio-economic and climatological factors has not been thoroughly explored. In the present study, a sensitivity analysis approach was adopted to understand the effect of both physical (elevation, slope, aspect, etc.) and socio-economic factors such as population density, distance to built-up, and distance to road and rail, as well as climatic factors (mean precipitation) on the accuracy of LULC prediction in the Brahmani and Baitarni (BB) basin of Eastern India. Additionally, in the absence of the recent LULC maps of the basin, three ML algorithms, i.e., random forest (RF), classified and regression trees (CART), and support vector machine (SVM) were utilized for LULC classification for the years 2007, 2014, and 2021 on Google earth engine (GEE) cloud computing platform. Among the three algorithms, RF performed best for classifying built-up areas along with all the other classes as compared to CART and SVM. The prediction results revealed that the proximity to built-up and population growth dominates in modeling LULC over physical factors such as elevation and slope. The analysis of historical data revealed an increase of 351% in built-up areas over the past years (2007-2021), with a corresponding decline in forest and water areas by 12% and 36% respectively. While the future predictions highlighted an increase in built-up class ranging from 11 to 38% during the years 2028-2070, the forested areas are anticipated to decline by 4 to 16%. The overall findings of the present study suggested that the BB basin, despite being primarily agricultural with a significant forest cover, is undergoing rapid expansion of built-up areas through the encroachment of agricultural and forested lands, which could have far-reaching implications for the region's ecosystem services and sustainability.

iAMP-CA2L: a new CNN-BiLSTM-SVM classifier based on cellular automata image for identifying antimicrobial peptides and their functional types.

Predicting antimicrobial peptides (AMPs') function is an important and difficult problem, particularly when AMPs have many multiplex functions, i.e. some AMPs simultaneously have two or three functional classes. By introducing the 'CNN-BiLSTM-SVM classifier' and 'cellular automata image', a new predictor, called iAMP-CA2L, has been developed that can be used to deal with the systems containing both monofunctional and multifunctional AMPs. iAMP-CA2L is a 2-level predictor. The 1st level is to identify whether a given query peptide is an AMP or a non-AMP, while the 2nd level is to predict if it belongs to one or more functional types. As demonstration, the jackknife cross-validation was performed with iAMP-CA2L on a benchmark dataset of AMPs classified into the following 10 functional classes: (1) antibacterial peptides, (2) antiviral peptides, (3) antifungal peptides, (4) antibiofilm peptides, (5) antiparasital peptides, (6) anti-HIV peptides, (7) anticancer (antitumor) peptides, (8) chemotactic peptides, (9) anti-MRSA peptides and (10) antiendotoxin peptides, where none of AMPs included has ≥90% pairwise sequence identity to any other in the same subset. Experiments show that iAMP-CA2L has greatly improved the prediction performance compared with the existing predictors. iAMP-CA2L is freely accessible to the public at the web site http://www.jci-bioinfo.cn/ iAMP-CA2L, and the predictor program has been uploaded to https://github.com/liujin66/iAMP-CA2L.

Probabilistic cellular automata modelling of intercellular interactions in airways: complex pattern formation in patients with chronic obstructive pulmonary disease.

Chronic obstructive pulmonary disease (COPD) is a highly prevalent lung disease characterized by chronic inflammation and tissue remodeling possibly induced by unusual interactions between fibrocytes and CD8+ T lymphocytes in the peribronchial area. To investigate this phenomenon, we developed a probabilistic cellular automata type model where the two types of cells follow simple local interaction rules taking into account cell death, proliferation, migration and infiltration. We conducted a rigorous mathematical analysis using multiscale experimental data obtained in control and disease conditions to estimate the model's parameters accurately. The simulation of the model is straightforward to implement, and two distinct patterns emerged that we can analyse quantitatively. In particular, we show that the change in fibrocyte density in the COPD condition is mainly the consequence of their infiltration into the lung during exacerbations, suggesting possible explanations for experimental observations in normal and COPD tissue. Our integrated approach that combines a probabilistic cellular automata model and experimental findings will provide further insights into COPD in future studies.

Evaluation of entropy and fractal dimension as biomarkers for tumor growth and treatment response using cellular automata.

Cell-based models provide a helpful approach for simulating complex systems that exhibit adaptive, resilient qualities, such as cancer. Their focus on individual cell interactions makes them a particularly appropriate strategy to study cancer therapies' effects, which are often designed to disrupt single-cell dynamics. In this work, we propose them as viable methods for studying the time evolution of cancer imaging biomarkers (IBM). We propose a cellular automata model for tumor growth and three different therapies: chemotherapy, radiotherapy, and immunotherapy, following well-established modeling procedures documented in the literature. The model generates a sequence of tumor images, from which a time series of two biomarkers: entropy and fractal dimension, is obtained. Our model shows that the fractal dimension increased faster at the onset of cancer cell dissemination. At the same time, entropy was more responsive to changes induced in the tumor by the different therapy modalities. These observations suggest that the prognostic value of the proposed biomarkers could vary considerably with time. Thus, it is essential to assess their use at different stages of cancer and for different imaging modalities. Another observation derived from the results was that both biomarkers varied slowly when the applied therapy attacked cancer cells scattered along the automatons' area, leaving multiple independent clusters of cells at the end of the treatment. Thus, patterns of change of simulated biomarkers time series could reflect on essential qualities of the spatial action of a given cancer intervention.

Urban growth boundaries optimization under low-carbon development: Combining multi-objective programming and patch cellular automata models.

Urban Growth Boundaries (UGBs) are a tool to control urban sprawl. However, the way to optimize future urban land uses and fix their boundaries is not clear. This paper presents a new framework to delimit UGBs while accounting for ecological, economic, and carbon storage benefits. Aggregate land-use constraints are included in a multi-objective optimization algorithm to capture non-inferior solutions on the Pareto Surface (PS) under different objective scenarios. A patch-level cellular automata simulation model is then used to spatially allocate these land uses, followed by a new two-step adjustment method to delineate the UGBs. This modeling is applied to Wuhan, China. The results show that: (1) One district (Caidian) will have a strong economic growth under low-carbon development. (2) The maximization of carbon storage reduces losses in ecological benefits, suggesting that carbon storage be considered in urban growth planning. (3) The combined model framework and two-step boundary adjustment method can help urban planners define different UGB scenarios and make science-based policy decisions.

Spatio-temporal change analysis and prediction of land use and land cover changes using CA-ANN model.

The spatial and temporal representation of land use and land cover (LULC) changes helps to understand the interactions between natural habitats and other areas and to plan for sustainability. Research on the models used to determine the spatio-temporal change of LULC and simulation of possible future scenarios provides a perspective for future planning and development strategies. Landsat 5 TM for 1990, Landsat 7 ETM + for 2006, and Landsat 8 OLI for 2022 satellite imageries were used to estimate spatial and temporal variations of transition potentials and future LULC simulation. Independent variables (DEM, slope, and distances to roads and buildings) and the cellular automata-artificial neural network (CA-ANN) model integrated in the MOLUSCE plugin of QGIS were used. The CA-ANN model was used to predict the LULC maps for 2038 and 2054, and the results suggest that artificial surfaces will continue to increase. The Düzce City center's artificial surfaces grew by 100% between 1990 and 2022, from 16.04 to 33.10 km2, and are projected to be 41.13 km2 and 50.32 km2 in 2038 and 2054, respectively. Artificial surfaces, which covered 20% of the study area in 1990, are estimated to cover 64.07% in 2054. If this trend continues, most of the 1st-class agricultural lands may be lost. The study's results can assist local governments in their land management strategies and aid them in planning for the future. The results suggest that policies are necessary to control the expansion of artificial surfaces, ensuring a balanced distribution of land use.