Phylogenetic signal in characters from Aristotle’s History of Animals

The influential Greek philosopher Aristotle (384-322 BCE) is almost unanimously acclaimed as the founder of zoology. There is a consensus that he was interested in attributes of animals, but whether or not he tried to develop a zoological taxonomy remains controversial. Fürst von Lieven and Humar compiled a data matrix from Aristotle’s Historia animalium and showed, through a parsimony analysis published in 2008, that these data produced a hierarchy that matched several taxa recognized by Aristotle. However, their analysis leaves some questions unanswered because random data can sometimes yield fairly resolved trees. In this study, we update the scores of many cells and add four new characters to the data matrix (147 taxa scored for 161 characters) and quote passages from Aristotle’s Historia animalium to justify these changes. We confirm the presence of a phylogenetic signal in these data through a test using skewness in length distribution of a million random trees, which shows that many of the characters discussed by Aristotle were systematically relevant. Our parsimony analyses on the updated matrix recover far more trees than reported by Fürst von Lieven and Humar, but their consensus includes many taxa that Aristotle recognized and apparently named for the first time, such as selachē (selachians) and dithyra (Bivalvia Linnaeus, 1758). This study suggests that even though taxonomy was obviously not Aristotle’s chief interest in Historia animalium, it was probably among his secondary interests. These results may pave the way for further taxonomic studies in Aristotle’s zoological writings in general. Despite being almost peripheral to Aristotle’s writings, his taxonomic contributions are clearly major achievements.

Estimated path information gain-based robot exploration under perceptual uncertainty

At present, the frontier-based exploration has been one of the mainstream methods in autonomous robot exploration. Among the frontier-based algorithms, the method of searching frontiers based on rapidly exploring random trees consumes less computing resources with higher efficiency and performs well in full-perceptual scenarios. However, in the partially perceptual cases, namely when the environmental structure is beyond the perception range of robot sensors, the robot often lingers in a restricted area, and the exploration efficiency is reduced. In this article, we propose a decision-making method for robot exploration by integrating the estimated path information gain and the frontier information. The proposed method includes the topological structure information of the environment on the path to the candidate frontier in the frontier selection process, guiding the robot to select a frontier with rich environmental information to reduce perceptual uncertainty. Experiments are carried out in different environments with the state-of-the-art RRT-exploration method as a reference. Experimental results show that with the proposed strategy, the efficiency of robot exploration has been improved obviously.

Gray-Level Co-occurrence Matrix Analysis for the Detection of Discrete, Ethanol-Induced, Structural Changes in Cell Nuclei: An Artificial Intelligence Approach

Gray-level co-occurrence matrix (GLCM) analysis is a contemporary and innovative computational method for the assessment of textural patterns, applicable in almost any area of microscopy. The aim of our research was to perform the GLCM analysis of cell nuclei in Saccharomyces cerevisiae yeast cells after the induction of sublethal cell damage with ethyl alcohol, and to evaluate the performance of various machine learning (ML) models regarding their ability to separate damaged from intact cells. For each cell nucleus, five GLCM parameters were calculated: angular second moment, inverse difference moment, GLCM contrast, GLCM correlation, and textural variance. Based on the obtained GLCM data, we applied three ML approaches: neural network, random trees, and binomial logistic regression. Statistically significant differences in GLCM features were observed between treated and untreated cells. The multilayer perceptron neural network had the highest classification accuracy. The model also showed a relatively high level of sensitivity and specificity, as well as an excellent discriminatory power in the separation of treated from untreated cells. To the best of our knowledge, this is the first study to demonstrate that it is possible to create a relatively sensitive GLCM-based ML model for the detection of alcohol-induced damage in Saccharomyces cerevisiae cell nuclei.

Comparison of GEOBIA classification algorithms based on Worldview-3 imagery in the extraction of coastal coniferous forest

Šume primorskih četinjača, sa svojom ekološkom, ekonomskom, estetskom i društvenom funkcijom, predstavljaju važan dio europskih šumskih zajednica. Osnovni cilj ovoga rada je usporediti najkorištenije GEOBIA (engl. Geographic Object-Based Image Analysis) klasifikacijske algoritme (engl. Random Trees – RT, Maximum Likelihood – ML, Support Vector Machine – SVM) s ciljem izdvajanja šuma primorskih četinjača na visoko-rezolucijskom WorldView-3 snimku unutar topografskog slijevnog područja naselja Split. Metodološki okvir istraživanja uključuje (1) izvođenje izoštrenog multispektralnog snimka (WV-3_MS-a); (2) testiranje segmentacijskih korisničko-definiranih parametara; (3) dodavanje testnih uzoraka; (4) klasifikaciju segmentiranog modela; (5) procjenu točnosti klasifikacijskih algoritama, te (6) procjenu točnosti završnog modela. RT se prema korištenim pokazateljima (correctness – COR, completeness – COM i overall quality – OQ) pokazao kao najbolji algoritam. Iterativno postavljanje segmentacijskih parametara omogućilo je detekciju najprikladnijih vrijednosti za generiranje segmentacijskog modela. Utvrđeno je da sjene mogu uzrokovati značajne probleme ako se klasificiranje vrši na visoko-rezolucijskim snimkama. Modificiranim Cohen’s kappa coefficient (K) pokazateljem izračunata je točnost konačnog modela od 87,38%. WV-3_MS se može smatrati kvalitetnim podatkom za detekciju šuma primorskih četinjača primjenom GEOBIA metode.

Fast-RRT: A RRT-Based Optimal Path Finding Method

As a sampling-based pathfinding algorithm, Rapidly Exploring Random Trees (RRT) has been widely used in motion planning problems due to the ability to find a feasible path quickly. However, the RRT algorithm still has several shortcomings, such as the large variance in the search time, poor performance in narrow channel scenarios, and being far from the optimal path. In this paper, we propose a new RRT-based path find algorithm, Fast-RRT, to find a near-optimal path quickly. The Fast-RRT algorithm consists of two modules, including Improved RRT and Fast-Optimal. The former is aims to quickly and stably find an initial path, and the latter is to merge multiple initial paths to obtain a near-optimal path. Compared with the RRT algorithm, Fast-RRT shows the following improvements: (1) A Fast-Sampling strategy that only samples in the unreached space of the random tree was introduced to improve the search speed and algorithm stability; (2) A Random Steering strategy expansion strategy was proposed to solve the problem of poor performance in narrow channel scenarios; (3) By fusion and adjustment of paths, a near-optimal path can be faster found by Fast-RRT, 20 times faster than the RRT* algorithm. Owing to these merits, our proposed Fast-RRT outperforms RRT and RRT* in both speed and stability during experiments.

Comparing the topology of phylogenetic network generators

Phylogenetic networks represent evolutionary history of species and can record natural reticulate evolutionary processes such as horizontal gene transfer and gene recombination. This makes phylogenetic networks a more comprehensive representation of evolutionary history compared to phylogenetic trees. Stochastic processes for generating random trees or networks are important tools in evolutionary analysis, especially in phylogeny reconstruction where they can be utilized for validation or serve as priors for Bayesian methods. However, as more network generators are developed, there is a lack of discussion or comparison for different generators. To bridge this gap, we compare a set of phylogenetic network generators by profiling topological summary statistics of the generated networks over the number of reticulations and comparing the topological profiles.

Deep Learning of High-Resolution Aerial Imagery for Coastal Marsh Change Detection: A Comparative Study

Deep learning techniques are increasingly being recognized as effective image classifiers. Aside from their successful performance in past studies, the accuracies have varied in complex environments in comparison with the popularly applied machine learning classifiers. This study seeks to explore the feasibility for using a U-Net deep learning architecture to classify bi-temporal high resolution county scale aerial images to determine the spatial extent and changes of land cover classes that directly or indirectly impact tidal marsh. The image set used in the analysis is a collection of a 1-m resolution collection of National Agriculture Imagery Program (NAIP) tiles from 2009 and 2019 covering Beaufort County, South Carolina. The U-net CNN classification results were compared with two machine learning classifiers, the Random Trees (RT) and the Support Vector Machine (SVM). The results revealed a significant accuracy advantage in using the U-Net classifier (92.4%) as opposed to the SVM (81.6%) and RT (75.7%) classifiers for overall accuracy. From the perspective of a GIS analyst or coastal manager, the U-Net classifier is now an easily accessible nad powerful tool for mapping large areas. Change detection analysis indicated little areal change on marsh extent, though increased land development throughout the county has the potential to negatively impact the health of the marshes. Future work should explore applying the constructed U-Net classifier to coastal environments in large geographic areas, while also implementing other data sources (e.g., LIDAR, multispectral data) to enhance classification accuracy.

Stochastic rumors on random trees

The Maki–Thompson rumor model is defined by assuming that a population represented by a graph is subdivided into three classes of individuals; namely, ignorants, spreaders and stiflers. A spreader tells the rumor to any of its nearest ignorant neighbors at rate one. At the same rate, a spreader becomes a stifler after a contact with other nearest neighbor spreaders, or stiflers. In this work we study the model on random trees. As usual we define a critical parameter of the model as the critical value around which the rumor either becomes extinct almost-surely or survives with positive probability. We analyze the existence of phase-transition regarding the survival of the rumor, and we obtain estimates for the mean range of the rumor. The applicability of our results is illustrated with examples on random trees generated from some well-known discrete distributions.

Router and gateway node placement in wireless mesh networks for emergency rescue scenarios

The focus of this paper is on base functionalities required for UAV-based rapid deployment of an ad hoc communication infrastructure in the initial phases of rescue operations. The main idea is to use heterogeneous teams of UAVs to deploy communication kits that include routers, and are used in the generation of ad hoc Wireless Mesh Networks (WMN). Several fundamental problems are considered and algorithms are proposed to solve these problems. The Router Node Placement problem (RNP) and a generalization of it that takes into account additional constraints arising in actual field usage is considered first. The RNP problem tries to determine how to optimally place routers in a WMN. A new algorithm, the RRT-WMN algorithm, is proposed to solve this problem. It is based in part on a novel use of the Rapidly Exploring Random Trees (RRT) algorithm used in motion planning. A comparative empirical evaluation between the RRT-WMN algorithm and existing techniques such as the Covariance Matrix Adaptation Evolution Strategy (CMA-ES) and Particle Swarm Optimization (PSO), shows that the RRT-WMN algorithm has far better performance both in amount of time taken and regional coverage as the generalized RNP problem scales to realistic scenarios. The Gateway Node Placement Problem (GNP) tries to determine how to locate a minimal number of gateway nodes in a WMN backbone network while satisfying a number of Quality of Service (QoS) constraints.Two alternatives are proposed for solving the combined RNP-GNP problem. The first approach combines the RRT-WMN algorithm with a preexisting graph clustering algorithm. The second approach, WMNbyAreaDecomposition, proposes a novel divide-and-conquer algorithm that recursively partitions a target deployment area into a set of disjoint regions, thus creating a number of simpler RNP problems that are then solved concurrently. Both algorithms are evaluated on real-world GIS models of different size and complexity. WMNbyAreaDecomposition is shown to outperform existing algorithms using 73% to 92% fewer router nodes while at the same time satisfying all QoS requirements.