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Antiviral peptides (AVPs) represent a promising strategy for addressing the global challenges of viral infections and their growing resistances to traditional drugs. Lab-based AVP discovery methods are resource-intensive, highlighting the need for efficient computational alternatives. In this study, we developed five non-trained but supervised multi-query similarity search models (MQSSMs) integrated into the StarPep toolbox. Rigorous testing and validation across diverse AVP datasets confirmed the models' robustness and reliability. The top-performing model, M13+, demonstrated impressive results, with an accuracy of 0.969 and a Matthew's correlation coefficient of 0.71. To assess their competitiveness, the top five models were benchmarked against 14 publicly available machine-learning and deep-learning AVP predictors. The MQSSMs outperformed these predictors, highlighting their efficiency in terms of resource demand and public accessibility. Another significant achievement of this study is the creation of the most comprehensive dataset of antiviral sequences to date. In general, these results suggest that MQSSMs are promissory tools to develop good alignment-based models that can be successfully applied in the screening of large datasets for new AVP discovery. [ABSTRACT FROM AUTHOR]

Simple Summary: The duration of pupa development on a cadaver holds the potential for estimating the time of colonization (TOC), which is often correlated with the postmortem interval (PMI) of decomposed bodies. Establishing an objective, precise, and efficient method for inferring pupa age has become paramount in forensic entomology. In this study, we observed temporal variations in the reflection spectrum of Chrysomya megacephala (Diptera: Calliphoridae) pupa, detectable through hyperspectral imaging (HSI). Additionally, we proposed that the eXtreme Gradient Boosting Regression (XGBR) model represents an optimal approach for estimating pupa development time based on HSI data. Estimating the age of pupa during the development time of the blow fly Chrysomya megacephala (Diptera: Calliphoridae) is of forensic significance as it assists in determining the time of colonization (TOC), which could help to determine the postmortem interval (PMI). However, establishing an objective, accurate, and efficient method for pupa age inference is still a leading matter of concern among forensic entomologists. In this study, we utilized hyperspectral imaging (HSI) technology to analyze the reflectance changes of pupa development under different temperatures (15 °C, 20 °C, 25 °C, and 30 °C). The spectrograms showed a downtrend under all temperatures. We used PCA to reduce the dimensionality of the spectral data, and then machine learning models (RF, SVR-RBF, SVR-POLY, XGBR, and Lasso) were built. RF, SVR with RBF kernel, and XGBR could show promise in accurate developmental time estimation using accumulated degree days. Among these, the XGBR model consistently exhibited the most minor errors, ranging between 3.9156 and 7.3951 (MAE). This study has identified the value of further refinement of HSI in forensic applications involving entomological specimens, and identified the considerable potential of HSI in forensic practice. [ABSTRACT FROM AUTHOR]

Machine learning (ML) has become an increasingly popular choice of scientific research for many students due to its application in various fields. However, students often have difficulty starting with machine learning concepts due to too much focus on programming. Therefore, they are deprived of a more profound knowledge of machine learning concepts. The purpose of this research study was the analysis of introductory courses in machine learning at some of the best-ranked universities in the world and existing software tools used in those courses and designed to assist in learning machine learning concepts. Most university courses are based on the Python programming language and tools realized in this language. Other tools with less focus on programming are quite difficult to master. The research further led to the proposal of a new practical tool that users can use to learn without needing to know any programming language or programming skills. The simulator includes three methods: linear regression, decision trees, and k-nearest neighbors. In the research, several case studies are presented with applications of all realized ML methods based on real problems. [ABSTRACT FROM AUTHOR]

Background: The application of machine learning (ML) tools (MLTs) to support clinical trials outputs in evidence-based health informatics can be an effective, useful, feasible, and acceptable way to advance medical research and provide precision medicine. Methods: In this study, the author used the rapid review approach and snowballing methods. The review was conducted in the following databases: PubMed, Scopus, COCHRANE LIBRARY, clinicaltrials.gov, Semantic Scholar, and the first six pages of Google Scholar from the 10 July–15 August 2022 period. Results: Here, 49 articles met the required criteria and were included in this review. Accordingly, 32 MLTs and platforms were identified in this study that applied the automatic extraction of knowledge from clinical trial outputs. Specifically, the initial use of automated tools resulted in modest to satisfactory time savings compared with the manual management. In addition, the evaluation of performance, functionality, usability, user interface, and system requirements also yielded positive results. Moreover, the evaluation of some tools in terms of acceptance, feasibility, precision, accuracy, efficiency, efficacy, and reliability was also positive. Conclusions: In summary, design based on the application of clinical trial results in ML is a promising approach to apply more reliable solutions. Future studies are needed to propose common standards for the assessment of MLTs and to clinically validate the performance in specific healthcare and technical domains. [ABSTRACT FROM AUTHOR]

Class imbalance is a phenomenon of asymmetry that degrades the performance of traditional classification algorithms such as the Support Vector Machine (SVM) and Extreme Learning Machine (ELM). Various modifications of SVM and ELM have been proposed to handle the class imbalance problem, which focus on different aspects to resolve the class imbalance. The Universum Support Vector Machine (USVM) incorporates the prior information in the classification model by adding Universum data to the training data to handle the class imbalance problem. Various other modifications of SVM have been proposed which use Universum data in the classification model generation. Moreover, the existing ELM-based classification models intended to handle class imbalance do not consider the prior information about the data distribution for training. An ELM-based classification model creates two symmetry planes, one for each class. The Universum-based ELM classification model tries to create a third plane between the two symmetric planes using Universum data. This paper proposes a novel hybrid framework called Reduced-Kernel Weighted Extreme Learning Machine Using Universum Data in Feature Space (RKWELM-UFS) to handle the classification of binary class-imbalanced problems. The proposed RKWELM-UFS combines the Universum learning method with a Reduced-Kernelized Weighted Extreme Learning Machine (RKWELM) for the first time to inherit the advantages of both techniques. To generate efficient Universum samples in the feature space, this work uses the kernel trick. The performance of the proposed method is evaluated using 44 benchmark binary class-imbalanced datasets. The proposed method is compared with 10 state-of-the-art classifiers using AUC and G-mean. The statistical t-test and Wilcoxon signed-rank test are used to quantify the performance enhancement of the proposed RKWELM-UFS compared to other evaluated classifiers. [ABSTRACT FROM AUTHOR]

Meteorological data are extensively used to perform environmental learning. Soft Computing (SC) and Machine Learning (ML) techniques represent a valuable support in many research areas, but require datasets containing information related to the topic under study. Such datasets are not always available in an appropriate format and its preparation and pre-processing implies a lot of time and effort by researchers. This paper presents a novel software tool with a user-friendly GUI to create datasets by means of management and data integration of meteorological observations from two data sources: the National Data Buoy Center and the National Centers for Environmental Prediction and for Atmospheric Research Reanalysis Project. Such datasets can be created using buoys and reanalysis data through customisable procedures, in terms of temporal resolution, predictive and objective variables, and can be used by SC and ML methodologies for prediction tasks (classification or regression). The objective is providing the research community with an automated and versatile system for the casuistry that entails well-formed and quality data integration, potentially leading to better prediction models. The software tool can be used as a supporting tool for coastal and ocean engineering applications, sustainable energy production, or environmental modelling; as well as for decision-making in the design and building of coastal protection structures, marine transport, ocean energy converters, and well-planned running of offshore and coastal engineering activities. Finally, to illustrate the applicability of the proposed tool, a case study to classify waves depending on their significant height and to predict energy flux in the Gulf of Alaska is presented. [ABSTRACT FROM AUTHOR]

This paper proposes a machine learning approach dealing with genetic programming to build classifiers through logical rule induction. In this context, we define and test a set of mutation operators across from different clinical datasets to improve the performance of the proposal for each dataset. The use of genetic programming for rule induction has generated interesting results in machine learning problems. Hence, genetic programming represents a flexible and powerful evolutionary technique for automatic generation of classifiers. Since logical rules disclose knowledge from the analyzed data, we use such knowledge to interpret the results and filter the most important features from clinical data as a process of knowledge discovery. The ultimate goal of this proposal is to provide the experts in the data domain with prior knowledge (as a guide) about the structure of the data and the rules found for each class, especially to track dichotomies and inequality. The results reached by our proposal on the involved datasets have been very promising when used in classification tasks and compared with other methods. [ABSTRACT FROM AUTHOR]