MOTIVATION: Accurately predicting the impact of single-point mutations on protein stability is crucial for elucidating molecular mechanisms underlying diseases in life sciences and advancing protein engineering in biotechnology. With recent advances in deep learning and protein structure prediction, deep learning approaches are expected to surpass existing methods for predicting protein thermostability. However, structure-based deep learning models, specifically convolutional neural networks, are affected by orientation biases, leading to inconsistent predictions with respect to the input protein orientation. RESULTS: In this study, we present OrgNet, a novel orientation-gnostic deep learning model using 3D convolutional neural networks to predict protein thermostability change upon point mutation. OrgNet encodes protein structures as voxel grids, enabling the model to capture fine-grained, spatially localized atomic features. OrgNet implements spatial transforms to standardize input protein orientations, thus eliminating orientation bias problem. When evaluated on established benchmarks, including Ssym and S669, OrgNet achieves state-of-the-art performance, demonstrating superior accuracy and robust performance compared to existing methods. AVAILABILITY AND IMPLEMENTATION: OrgNet is available at https://github.com/i-Molecule/OrgNet.

The paper considers the problem of classification of agricultural crops. As is known, to solve this problem, it is much more efficient to use not instantaneous remote sensing data or calculated vegetation indices, but their historical series. Time series formed by index values for a fixed spatial point at different dates are characterized by a high level of missing values, caused primarily by cloudiness on some dates. A study of known methods of time series approximation has been carried out. The question of whether reducing the dimensionality of the approximated time series can improve the quality of crops classification is also investigated. In the experimental part of the work, NDVI time series calculated from the Sentinel-2 multispectral satellite data were used. The classification of corn, sunflower, wheat and soybeans was studied. The paper shows that UMAP usage for dimensionality reduction leads to 1.5 times increase of classification quality in terms of average the F1-measure compared to using the original dimension data. A new crop classification method based on cubic spline approximation of NDVI time series, extraction of features of low dimension by the UMAP algorithm and their classification by the k nearest neighbors method is proposed.

Mass spectrometry imaging (MSI) with high resolution in mass and space is an analytical method that produces distributions of ions on a sample surface. The algorithms for preprocessing and analysis of the raw data acquired from a mass spectrometer should be evaluated. To do that, the ion composition at every point of the sample should be known. This is possible via the employment of a simulated MSI dataset. In this work, we suggest a pipeline for a robust simulation of MSI datasets that resemble real data with an option to simulate the spectra acquired from any mass spectrometry instrument through the use of the experimental MSI datasets to extract simulation parameters.