Identification of DNA-binding proteins from only sequence information is one of the most challenging problems in the field of genome annotation. DNA-binding proteins play an important role in various biological processes such as DNA replication, repair, transcription and splicing. Existing experimental techniques for identifying DNA-binding proteins are time-consuming and expensive. Thus, prediction of DNA-binding proteins from sequences alone using computational methods can be useful to quickly annotate and guide the experimental process. Most of the methods developed for predicting DNA-binding proteins use the information from the evolutionary profile, called the position-specific scoring matrix (PSSM) profile, alone and the accuracies of such methods have been limited. Here, we propose a method, called StackDPPred, which utilizes features extracted from PSSM and residue specific contact-energy to help train a stacking based machine learning method for the effective prediction of DNA-binding proteins. Based on benchmark sequences of 1063 (518 DNA-binding and 545 non DNA-binding) proteins and using jackknife validation, StackDPPred achieved an ACC of 89.96%, MCC of 0.799 and AUC of 94.50%. This outcome outperforms several state-of-the-art approaches. Furthermore, when tested on recently designed two independent test datasets, StackDPPred outperforms existing approaches consistently. The proposed StackDPPred can be used for effective prediction of DNA-binding proteins from sequence alone. Online server is at http://bmll.cs.uno.edu/add and code-data is at http://cs.uno.edu/∼tamjid/Software/StackDPPred/code_data.zip. Supplementary data are available at Bioinformatics online.

In this article, we present a novel approach for forecasting significant wave heights in oceanic waters. We propose an algorithm based on the WaveWatch III, differencing, and a transformer neural network (Transformer). The data becomes stationary after first-order differencing, performed with the observed significant wave height and the wave height forecasts obtained from WaveWatch III. We perform a case study on a group of 92 buoys using WaveWatch III hindcasts. The Transformer model then provides the statistical forecasts of the residuals. The Transformer-based proposed framework obtains the root mean square error of 0.231 m for two days ahead forecasting. Our proposed method outperforms existing state-of-the-art machine learning and numerical approaches for significant wave heights prediction. Our results suggest that combining numerical and machine learning approaches gives better performance than using either alone.

To encourage proper employee scheduling for managing crew load, restaurants need accurate sales forecasting. This paper proposes a case study on many machine learning (ML) models using real-world sales data from a mid-sized restaurant. Trendy recurrent neural network (RNN) models are included for direct comparison to many methods. To test the effects of trend and seasonality, we generate three different datasets to train our models with and to compare our results. To aid in forecasting, we engineer many features and demonstrate good methods to select an optimal sub-set of highly correlated features. We compare the models based on their performance for forecasting time steps of one-day and one-week over a curated test dataset. The best results seen in one-day forecasting come from linear models with a sMAPE of only 19.6%. Two RNN models, LSTM and TFT, and ensemble models also performed well with errors less than 20%. When forecasting one-week, non-RNN models performed poorly, giving results worse than 20% error. RNN models extended better with good sMAPE scores giving 19.5% in the best result. The RNN models performed worse overall on datasets with trend and seasonality removed, however many simpler ML models performed well when linearly separating each training instance.

This paper presents the impact of twins and the measures for their removal from the population of genetic algorithm (GA) when applied to effective conformational searching. It is conclusively shown that a twin removal strategy for a GA provides considerably enhanced performance when investigating solutions to complex ab initio protein structure prediction (PSP) problems in low-resolution model. Without twin removal, GA crossover and mutation operations can become ineffectual as generations lose their ability to produce significant differences, which can lead to the solution stalling. The paper relaxes the definition of chromosomal twins in the removal strategy to not only encompass identical, but also highly correlated chromosomes within the GA population, with empirical results consistently exhibiting significant improvements solving PSP problems.