Applying Parallel and Distributed Models on Bio-Inspired Algorithms via a Clustering Method

In the world of optimization, especially concerning metaheuristics, solving complex problems represented by applying big data and constraint instances can be difficult. This is mainly due to the difficulty of implementing efficient solutions that can solve complex optimization problems in adequate time, which do exist in different industries. Big data has demonstrated its efficiency in solving different concerns in information management. In this paper, an approach based on multiprocessing is proposed wherein clusterization and parallelism are used together to improve the search process of metaheuristics when solving large instances of complex optimization problems, incorporating collaborative elements that enhance the quality of the solution. The proposal deals with machine learning algorithms to improve the segmentation of the search space. Particularly, two different clustering methods belonging to automatic learning techniques, are implemented on bio-inspired algorithms to smartly initialize their solution population, and then organize the resolution from the beginning of the search. The results show that this approach is competitive with other techniques in solving a large set of cases of a well-known NP-hard problem without incorporating too much additional complexity into the metaheuristic algorithms.

A Probabilistic Formulation of the Diffusion Coefficient in Porous Media as Function of Porosity

We investigate the upscaling of diffusive transport parameters using a stochastic framework. At sub-REV (representative elementary volume) scale, the complexity of the pore space geometry leads to a significant scatter of the observed diffusive transport. We study a large set of volumes reconstructed from focused ion beam-scanning electron microscopy data. Each individual volume provides us sub-REV measurements on porosity and the so-called transport-ability, being a dimensionless parameter representing the ratio of diffusive flux through the porous volume to that through an empty volume. The detected scatter of the transport-ability is mathematically characterized through a probability distribution function (PDF) with a mean and variance as function of porosity, which includes implicitly the effect of pore structure differences among sub-REV volumes. We then investigate domain size effects and predict when REV scale is reached. While the scatter in porosity observations decreases linearly with increasing sample size as expected, the observed scatter in transport-ability does not converge to zero. Our results confirm that differences in pore structure impact transport parameters at all scales. Consequently, the use of PDFs to describe the relationship of effective transport coefficients to porosity is advantageous to deterministic semiempirical functions. We discuss the consequences and advocate the use of PDFs for effective parameters in both continuum equations and data interpretation of experimental or computational work. The presented statistics-based upscaling technique of sub-REV microscopy data provides a new tool in understanding, describing and predicting macroscopic transport behavior of microporous media.

DeepGOZero: Improving protein function prediction from sequence and zero-shot learning based on ontology axioms

Motivation: Protein functions are often described using the Gene Ontology (GO) which is an ontology consisting of over 50,000 classes and a large set of formal axioms. Predicting the functions of proteins is one of the key challenges in computational biology and a variety of machine learning methods have been developed for this purpose. However, these methods usually require significant amount of training data and cannot make predictions for GO classes which have only few or no experimental annotations. Results: We developed DeepGOZero, a machine learning model which improves predictions for functions with no or only a small number of annotations. To achieve this goal, we rely on a model-theoretic approach for learning ontology embeddings and combine it with neural networks for protein function prediction. DeepGOZero can exploit formal axioms in the GO to make zero-shot predictions, i.e., predict protein functions even if not a single protein in the training phase was associated with that function. Furthermore, the zero-shot prediction method employed by DeepGOZero is generic and can be applied whenever associations with ontology classes need to be predicted. Availability: http://github.com/bio-ontology-research-group/deepgozero

On the Performance of Energy Criterion Method in Wi-Fi Transient Signal Detection

In the development of radiofrequency fingerprinting (RFF), one of the major challenges is to extract subtle and robust features from transmitted signals of wireless devices to be used in accurate identification of possible threats to the wireless network. To overcome this challenge, the use of the transient region of the transmitted signals could be one of the best options. For an efficient transient-based RFF, it is also necessary to accurately and precisely estimate the transient region of the signal. Here, the most important difficulty can be attributed to the detection of the transient starting point. Thus, several methods have been developed to detect transient start in the literature. Among them, the energy criterion method based on the instantaneous amplitude characteristics (EC-a) was shown to be superior in a recent study. The study reported the performance of the EC-a method for a set of Wi-Fi signals captured from a particular Wi-Fi device brand. However, since the transient pattern varies according to the type of wireless device, the device diversity needs to be increased to achieve more reliable results. Therefore, this study is aimed at assessing the efficiency of the EC-a method across a large set of Wi-Fi signals captured from various Wi-Fi devices for the first time. To this end, Wi-Fi signals are first captured from smartphones of five brands, for a wide range of signal-to-noise ratio (SNR) values defined as low (−3 to 5 dB), medium (5 to 15 dB), and high (15 to 30 dB). Then, the performance of the EC-a method and well-known methods was comparatively assessed, and the efficiency of the EC-a method was verified in terms of detection accuracy.

A Comparative Performance Study of Classification Models for Opinion Mining

Opinion mining has become a major part in today's economy. People would want to know more about a product and the customers opinion before buying it. Companies would also want to know the opinions of the customers. Therefore, analyzing the customer’s opinion is important. A new customer would consider a product as good by analyzing the opinions of other customers. The opinions are collected from various areas, which include blogs, web forums, and product review sites. Classifying these large set of opinions requires a good classifier. In view of this, a comparative study of three classification techniques - Naive Bayes classifier with Kernel Density Estimation (KDE), Support Vector Machine (SVM), Decision Tree and KNN was made. To evaluate the classifier accuracy, precision, recall and F-measure techniques are used. Experimental results show that the Naive Bayes with Kernel Density Estimation (KDE) classifier achieved higher accuracy among others.

Dynamic Network Formation for FSO Satellite Communication

Satellite network optimization is essential, particularly since the cost of manufacturing, launching and maintaining each satellite is significant. Moreover, classical communication optimization methods, such as Minimal Spanning Tree, cannot be applied directly in dynamic scenarios where the satellite constellation is constantly changing. Motivated by the rapid growth of the Star-Link constellation that, as of Q4 2021, consists of over 1600 operational LEO satellites with thousands more expected in the coming years, this paper focuses on the problem of constructing an optimal inter-satellite (laser) communication network. More formally, given a large set of LEO satellites, each equipped with a fixed number of laser links, we direct each laser module on each satellite such that the underlying laser network will be optimal with respect to a given objective function and communication demand. In this work, we present a novel heuristic to create an optimal dynamic optical network communication using an Ant Colony algorithm. This method takes into account both the time it takes to establish an optical link (acquisition time) and the bounded number of communication links, as each satellite has a fixed amount of optical communication modules installed. Based on a large number of simulations, we conclude that, although the underlying problem of bounded-degree-spanning-tree is NP-hard (even for static cases), the suggested ant-colony heuristic is able to compute cost-efficient solutions in semi-real-time.

Science goals and new mission concepts for future exploration of Titan’s atmosphere, geology and habitability: titan POlar scout/orbitEr and in situ lake lander and DrONe explorer (POSEIDON)

In response to ESA’s “Voyage 2050” announcement of opportunity, we propose an ambitious L-class mission to explore one of the most exciting bodies in the Solar System, Saturn’s largest moon Titan. Titan, a “world with two oceans”, is an organic-rich body with interior-surface-atmosphere interactions that are comparable in complexity to the Earth. Titan is also one of the few places in the Solar System with habitability potential. Titan’s remarkable nature was only partly revealed by the Cassini-Huygens mission and still holds mysteries requiring a complete exploration using a variety of vehicles and instruments. The proposed mission concept POSEIDON (Titan POlar Scout/orbitEr and In situ lake lander DrONe explorer) would perform joint orbital and in situ investigations of Titan. It is designed to build on and exceed the scope and scientific/technological accomplishments of Cassini-Huygens, exploring Titan in ways that were not previously possible, in particular through full close-up and in situ coverage over long periods of time. In the proposed mission architecture, POSEIDON consists of two major elements: a spacecraft with a large set of instruments that would orbit Titan, preferably in a low-eccentricity polar orbit, and a suite of in situ investigation components, i.e. a lake lander, a “heavy” drone (possibly amphibious) and/or a fleet of mini-drones, dedicated to the exploration of the polar regions. The ideal arrival time at Titan would be slightly before the next northern Spring equinox (2039), as equinoxes are the most active periods to monitor still largely unknown atmospheric and surface seasonal changes. The exploration of Titan’s northern latitudes with an orbiter and in situ element(s) would be highly complementary in terms of timing (with possible mission timing overlap), locations, and science goals with the upcoming NASA New Frontiers Dragonfly mission that will provide in situ exploration of Titan’s equatorial regions, in the mid-2030s.

Catalytic atroposelective synthesis of axially chiral benzonitriles via chirality control during bond dissociation and CN group formation

The applications of axially chiral benzonitriles and their derivatives remain mostly unexplored due to their synthetic difficulties. Here we disclose an unusual strategy for atroposelective access to benzonitriles via formation of the nitrile unit on biaryl scaffolds pre-installed with stereogenic axes in racemic forms. Our method starts with racemic 2-arylbenzaldehydes and sulfonamides as the substrates and N-heterocyclic carbenes as the organocatalysts to afford axially chiral benzonitriles in good to excellent yields and enantioselectivities. DFT calculations suggest that the loss of p-toluenesulfinate group is both the rate-determining and stereo-determining step. The axial chirality is controlled during the bond dissociation and CN group formation. The reaction features a dynamic kinetic resolution process modulated by both covalent and non-covalent catalytic interactions. The axially chiral benzonitriles from our method can be easily converted to a large set of functional molecules that show promising catalytic activities for chemical syntheses and anti-bacterial activities for plant protections.

Ensemble learning from ensemble docking: revisiting the optimum ensemble size problem

Despite considerable advances obtained by applying machine learning approaches in protein–ligand affinity predictions, the incorporation of receptor flexibility has remained an important bottleneck. While ensemble docking has been used widely as a solution to this problem, the optimum choice of receptor conformations is still an open question considering the issues related to the computational cost and false positive pose predictions. Here, a combination of ensemble learning and ensemble docking is suggested to rank different conformations of the target protein in light of their importance for the final accuracy of the model. Available X-ray structures of cyclin-dependent kinase 2 (CDK2) in complex with different ligands are used as an initial receptor ensemble, and its redundancy is removed through a graph-based redundancy removal, which is shown to be more efficient and less subjective than clustering-based representative selection methods. A set of ligands with available experimental affinity are docked to this nonredundant receptor ensemble, and the energetic features of the best scored poses are used in an ensemble learning procedure based on the random forest method. The importance of receptors is obtained through feature selection measures, and it is shown that a few of the most important conformations are sufficient to reach 1 kcal/mol accuracy in affinity prediction with considerable improvement of the early enrichment power of the models compared to the different ensemble docking without learning strategies. A clear strategy has been provided in which machine learning selects the most important experimental conformers of the receptor among a large set of protein–ligand complexes while simultaneously maintaining the final accuracy of affinity predictions at the highest level possible for available data. Our results could be informative for future attempts to design receptor-specific docking-rescoring strategies.

Ecological and environmental factors affecting transmission of sylvatic yellow fever in the 2017–2019 outbreak in the Atlantic Forest, Brazil

Background Yellow fever virus (YFV) is an arbovirus that, despite the existence of a safe and effective vaccine, continues to cause outbreaks of varying dimensions in the Americas and Africa. Between 2017 and 2019, Brazil registered un unprecedented sylvatic YFV outbreak whose severity was the result of its spread into zones of the Atlantic Forest with no signals of viral circulation for nearly 80 years. Methods To investigate the influence of climatic, environmental, and ecological factors governing the dispersion and force of infection of YFV in a naïve area such as the landscape mosaic of Rio de Janeiro (RJ), we combined the analyses of a large set of data including entomological sampling performed before and during the 2017–2019 outbreak, with the geolocation of human and nonhuman primates (NHP) and mosquito infections. Results A greater abundance of Haemagogus mosquitoes combined with lower richness and diversity of mosquito fauna increased the probability of finding a YFV-infected mosquito. Furthermore, the analysis of functional traits showed that certain functional groups, composed mainly of Aedini mosquitoes which includes Aedes and Haemagogus mosquitoes, are also more representative in areas where infected mosquitoes were found. Human and NHP infections were more common in two types of landscapes: large and continuous forest, capable of harboring many YFV hosts, and patches of small forest fragments, where environmental imbalance can lead to a greater density of the primary vectors and high human exposure. In both, we show that most human infections (~ 62%) occurred within an 11-km radius of the finding of an infected NHP, which is in line with the flight range of the primary vectors. Conclusions Together, our data suggest that entomological data and landscape composition analyses may help to predict areas permissive to yellow fever outbreaks, allowing protective measures to be taken to avoid human cases. Graphical Abstract