Antibody design using deep learning: from sequence and structure design to affinity maturation.

Deep learning has achieved impressive results in various fields such as computer vision and natural language processing, making it a powerful tool in biology. Its applications now encompass cellular image classification, genomic studies and drug discovery. While drug development traditionally focused deep learning applications on small molecules, recent innovations have incorporated it in the discovery and development of biological molecules, particularly antibodies. Researchers have devised novel techniques to streamline antibody development, combining in vitro and in silico methods. In particular, computational power expedites lead candidate generation, scaling and potential antibody development against complex antigens. This survey highlights significant advancements in protein design and optimization, specifically focusing on antibodies. This includes various aspects such as design, folding, antibody-antigen interactions docking and affinity maturation.

On Inductive-Transductive Learning With Graph Neural Networks.

Many real-world domains involve information naturally represented by graphs, where nodes denote basic patterns while edges stand for relationships among them. The graph neural network (GNN) is a machine learning model capable of directly managing graph-structured data. In the original framework, GNNs are inductively trained, adapting their parameters based on a supervised learning environment. However, GNNs can also take advantage of transductive learning, thanks to the natural way they make information flow and spread across the graph, using relationships among patterns. In this paper, we propose a mixed inductive-transductive GNN model, study its properties and introduce an experimental strategy that allows us to understand and distinguish the role of inductive and transductive learning. The preliminary experimental results show interesting properties for the mixed model, highlighting how the peculiarities of the problems and the data can impact on the two learning strategies.