Niccolò Pancino

Pietro Bongini, Elisa Messori, Niccolò Pancino et al.

Predicting drug side-effects before they occur is a key task in keeping the number of drug-related hospitalizations low and to improve 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.

Benedetta Tondi, Wei Guo, Niccolò Pancino et al.

Most of the approaches proposed so far to craft targeted adversarial examples against Deep Learning classifiers are highly suboptimal and typically rely on increasing the likelihood of the target class, thus implicitly focusing on one-hot encoding settings. In this paper, a more general, theoretically sound, targeted attack is proposed, which resorts to the minimization of a Jacobian-induced Mahalanobis distance term, taking into account the effort (in the input space) required to move the latent space representation of the input sample in a given direction. The minimization is solved by exploiting the Wolfe duality theorem, reducing the problem to the solution of a Non-Negative Least Square (NNLS) problem. The proposed algorithm (referred to as JMA) provides an optimal solution to a linearised version of the adversarial example problem originally introduced by Szegedy et al. The results of the experiments confirm the generality of the proposed attack which is proven to be effective under a wide variety of output encoding schemes. Noticeably, JMA is also effective in a multi-label classification scenario, being capable to induce a targeted modification of up to half the labels in complex multi-label classification scenarios, a capability that is out of reach of all the attacks proposed so far. As a further advantage, JMA requires very few iterations, thus resulting more efficient than existing methods.

Pietro Bongini, Franco Scarselli, Monica Bianchini et al.

Drug Side-Effects (DSEs) have a high impact on public health, care system costs, and drug discovery processes. Predicting the probability of side-effects, before their occurrence, is fundamental to reduce this impact, in particular on drug discovery. Candidate molecules could be screened before undergoing clinical trials, reducing the costs in time, money, and health of the participants. Drug side-effects are triggered by complex biological processes involving many different entities, from drug structures to protein-protein interactions. To predict their occurrence, it is necessary to integrate data from heterogeneous sources. In this work, such heterogeneous data is integrated into a graph dataset, expressively representing the relational information between different entities, such as drug molecules and genes. The relational nature of the dataset represents an important novelty for drug side-effect predictors. Graph Neural Networks (GNNs) are exploited to predict DSEs on our dataset with very promising results. GNNs are deep learning models that can process graph-structured data, with minimal information loss, and have been applied on a wide variety of biological tasks. Our experimental results confirm the advantage of using relationships between data entities, suggesting interesting future developments in this scope. The experimentation also shows the importance of specific subsets of data in determining associations between drugs and side-effects.