Filippo Castiglione

Sen Yan, Etienne Goffinet, Fabrizio Gabellieri et al.

Nuclear Magnetic Resonance (NMR) spectroscopy is a crucial analytical technique used for molecular structure elucidation, with applications spanning chemistry, biology, materials science, and medicine. However, the frequency resolution of NMR spectra is limited by the "field strength" of the instrument. High-field NMR instruments provide high-resolution spectra but are prohibitively expensive, whereas lower-field instruments offer more accessible, but lower-resolution, results. This paper introduces an AI-driven approach that not only enhances the frequency resolution of NMR spectra through super-resolution techniques but also provides multi-scale functionality. By leveraging a diffusion model, our method can reconstruct high-field spectra from low-field NMR data, offering flexibility in generating spectra at varying magnetic field strengths. These reconstructions are comparable to those obtained from high-field instruments, enabling finer spectral details and improving molecular characterization. To date, our approach is one of the first to overcome the limitations of instrument field strength, achieving NMR super-resolution through AI. This cost-effective solution makes high-resolution analysis accessible to more researchers and industries, without the need for multimillion-dollar equipment.

Etienne Goffinet, Raghvendra Mall, Ankita Singh et al.

An accurate binding affinity prediction between T-cell receptors and epitopes contributes decisively to develop successful immunotherapy strategies. Some state-of-the-art computational methods implement deep learning techniques by integrating evolutionary features to convert the amino acid residues of cell receptors and epitope sequences into numerical values, while some other methods employ pre-trained language models to summarize the embedding vectors at the amino acid residue level to obtain sequence-wise representations. Here, we propose a highly reliable novel method, MATE-Pred, that performs multi-modal attention-based prediction of T-cell receptors and epitopes binding affinity. The MATE-Pred is compared and benchmarked with other deep learning models that leverage multi-modal representations of T-cell receptors and epitopes. In the proposed method, the textual representation of proteins is embedded with a pre-trained bi-directional encoder model and combined with two additional modalities: a) a comprehensive set of selected physicochemical properties; b) predicted contact maps that estimate the 3D distances between amino acid residues in the sequences. The MATE-Pred demonstrates the potential of multi-modal model in achieving state-of-the-art performance (+8.4\% MCC, +5.5\% AUC compared to baselines) and efficiently capturing contextual, physicochemical, and structural information from amino acid residues. The performance of MATE-Pred projects its potential application in various drug discovery regimes.

Peteris Daugulis, Vija Vagale, Emiliano Mancini et al.

The problem of choosing appropriate values for missing data is often encountered in the data science. We describe a novel method containing both traditional mathematics and machine learning elements for prediction (imputation) of missing data. This method is based on the notion of distance between shifted linear subspaces representing the existing data and candidate sets. The existing data set is represented by the subspace spanned by its first principal components. Solutions for the case of the Euclidean metric are given.

Etienne Goffinet, Sen Yan, Fabrizio Gabellieri et al.

Nuclear Magnetic Resonance (NMR) spectrometry uses electro-frequency pulses to probe the resonance of a compound's nucleus, which is then analyzed to determine its structure. The acquisition time of high-resolution NMR spectra remains a significant bottleneck, especially for complex biological samples such as proteins. In this study, we propose a novel and efficient sub-sampling strategy based on a diffusion model trained on protein NMR data. Our method iteratively reconstructs under-sampled spectra while using model uncertainty to guide subsequent sampling, significantly reducing acquisition time. Compared to state-of-the-art strategies, our approach improves reconstruction accuracy by 52.9\%, reduces hallucinated peaks by 55.6%, and requires 60% less time in complex NMR experiments. This advancement holds promise for many applications, from drug discovery to materials science, where rapid and high-resolution spectral analysis is critical.