Protein–protein interactions (PPIs) are fundamental processes governing cellular functions, crucial for understanding biological systems at the molecular level. Compared to experimental methods for PPI prediction and site identification, computational deep learning approaches represent an affordable and efficient solution to tackle these problems. Since protein structure can be summarized as a graph, graph neural networks (GNNs) represent the ideal deep learning architecture for the task. In this work, PPI prediction is modeled as a node-focused binary classification task using a GNN to determine whether a generic residue is part of the interface. Biological data were obtained from the Protein Data Bank in Europe (PDBe), leveraging the Protein Interfaces, Surfaces, and Assemblies (PISA) service. To gain a deeper understanding of how proteins interact, the data obtained from PISA were assembled into three datasets: Whole, Interface, and Chain, consisting of data on the whole protein, couples of interacting chains, and single chains, respectively. These three datasets correspond to three different nuances of the problem: identifying interfaces between protein complexes, between chains of the same protein, and interface regions in general. The results indicate that GNNs are capable of solving each of the three tasks with very good performance levels.

Graph Neural Networks have proven to be very valuable models for the solution of a wide variety of problems on molecular graphs, as well as in many other research fields involving graph-structured data. Molecules are heterogeneous graphs composed of atoms of different species. Composite graph neural networks process heterogeneous graphs with multiple-state-updating networks, each one dedicated to a particular node type. This approach allows for the extraction of information from s graph more efficiently than standard graph neural networks that distinguish node types through a one-hot encoded type of vector. We carried out extensive experimentation on eight molecular graph datasets and on a large number of both classification and regression tasks. The results we obtained clearly show that composite graph neural networks are far more efficient in this setting than standard graph neural networks.

Drug side effects (DSEs), or adverse drug reactions (ADRs), constitute an important health risk, given the approximately 197,000 annual DSE deaths in Europe alone. Therefore, during the drug development process, DSE detection is of utmost importance, and the occurrence of ADRs prevents many candidate molecules from going through clinical trials. Thus, early prediction of DSEs has the potential to massively reduce drug development times and costs. In this work, data are represented in a non-euclidean manner, in the form of a graph-of-graphs domain. In such a domain, structures of molecule are represented by molecular graphs, each of which becomes a node in the higher-level graph. In the latter, nodes stand for drugs and genes, and arcs represent their relationships. This relational nature represents an important novelty for the DSE prediction task, and it is directly used during the prediction. For this purpose, the MolecularGNN model is proposed. This new classifier is based on graph neural networks, a connectionist model capable of processing data in the form of graphs. The approach represents an improvement over a previous method, called DruGNN, as it is also capable of extracting information from the graph-based molecular structures, producing a task-based neural fingerprint (NF) of the molecule which is adapted to the specific task. The architecture has been compared with other GNN models in terms of performance, showing that the proposed approach is very promising.

Predicting drug side effects before they occur is a critical task for keeping the number of drug–related hospitalizations low and for improving drug discovery processes. Automatic predictors of side–effects generally are not able to process the structure of the drug, resulting in a loss of information. Graph neural networks have seen great success in recent years, thanks to their ability of exploiting the information conveyed by the graph structure and labels. These models have been used in a wide variety of biological applications, among which the prediction of drug side–effects on a large knowledge graph. Exploiting the molecular graph encoding the structure of the drug represents a novel approach, in which the problem is formulated as a multi–class multi–label graph–focused classification. We developed a methodology to carry out this task, using recurrent Graph Neural Networks, and building a dataset from freely accessible and well established data sources. The results show that our method has an improved classification capability, under many parameters and metrics, with respect to previously available predictors. The method is not ready for clinical tests yet, as the specificity is still below the preliminary 25 $\%$ threshold. Future efforts will aim at improving this aspect.

Eye-tracking can offer a novel clinical practice and a non-invasive tool to detect neuropathological syndromes. In this paper, we show some analysis on data obtained from the visual sequential search test. Indeed, such a test can be used to evaluate the capacity of looking at objects in a specific order, and its successful execution requires the optimization of the perceptual resources of foveal and extrafoveal vision. The main objective of this work is to detect if some patterns can be found within the data, to discern among people with chronic pain, extrapyramidal patients and healthy controls. We employed statistical tests to evaluate differences among groups, considering three novel indicators: blinking rate, average blinking duration and maximum pupil size variation. Additionally, to divide the three patient groups based on scan-path images—which appear very noisy and all similar to each other—we applied deep learning techniques to embed them into a larger transformed space. We then applied a clustering approach to correctly detect and classify the three cohorts. Preliminary experiments show promising results.