Víctor Valls

Hoang Thanh Lam, Marco Luca Sbodio, Marcos Martínez Galindo et al.

Recent research on predicting the binding affinity between drug molecules and proteins use representations learned, through unsupervised learning techniques, from large databases of molecule SMILES and protein sequences. While these representations have significantly enhanced the predictions, they are usually based on a limited set of modalities, and they do not exploit available knowledge about existing relations among molecules and proteins. In this study, we demonstrate that by incorporating knowledge graphs from diverse sources and modalities into the sequences or SMILES representation, we can further enrich the representation and achieve state-of-the-art results for drug-target binding affinity prediction in the established Therapeutic Data Commons (TDC) benchmarks. We release a set of multimodal knowledge graphs, integrating data from seven public data sources, and containing over 30 million triples. Our intention is to foster additional research to explore how multimodal knowledge enhanced protein/molecule embeddings can improve prediction tasks, including prediction of binding affinity. We also release some pretrained models learned from our multimodal knowledge graphs, along with source code for running standard benchmark tasks for prediction of biding affinity.

Víctor Valls, Mykhaylo Zayats, Alessandra Pascale

Graph Neural Networks (GNNs) have gained popularity in healthcare and other domains due to their ability to process multi-modal and multi-relational graphs. However, efficient training of GNNs remains challenging, with several open research questions. In this paper, we investigate how the flow of embedding information within GNNs affects the prediction of links in Knowledge Graphs (KGs). Specifically, we propose a mathematical model that decouples the GNN connectivity from the connectivity of the graph data and evaluate the performance of GNNs in a clinical triage use case. Our results demonstrate that incorporating domain knowledge into the GNN connectivity leads to better performance than using the same connectivity as the KG or allowing unconstrained embedding propagation. Moreover, we show that negative edges play a crucial role in achieving good predictions, and that using too many GNN layers can degrade performance.

Gabriele Agliardi, Giorgio Cortiana, Anton Dekusar et al.

Fidelity quantum kernels have shown promise in classification tasks, particularly when a group structure in the data can be identified and exploited through a covariant feature map. In fact, there exist classification problems on which covariant kernels provide a provable advantage, thus establishing a separation between quantum and classical learners. However, their practical application poses two challenges: on one side, the group structure may be unknown and approximate in real-world data, and on the other side, scaling to the `utility' regime (above 100 qubits) is affected by exponential concentration. In this work, we address said challenges by applying fidelity kernels to real-world data with unknown structure, related to the scheduling of a fleet of electric vehicles, and to synthetic data generated from the union of subspaces, which is then close to many relevant real-world datasets. Furthermore, we propose a novel error mitigation strategy specifically tailored for fidelity kernels, called Bit Flip Tolerance (BFT), to alleviate the exponential concentration in our utility-scale experiments. Our multiclass classification reaches accuracies comparable to classical SVCs up to 156 qubits, thus constituting the largest experimental demonstration of quantum machine learning on IBM devices to date. For the real-world data experiments, the effect of the proposed BFT becomes manifest on 40+ qubits, where mitigated accuracies reach 80%, in line with classical, compared to 33% without BFT. Through the union-of-subspace synthetic dataset with 156 qubits, we demonstrate a mitigated accuracy of 80%, compared to 83% of classical models, and 37% of unmitigated quantum, using a test set of limited size.