Alice Del Vecchio

Paul Scherer, Alison Pouplin, Alice Del Vecchio et al.

Active learning (AL) is a sub-field of ML focused on the development of methods to iteratively and economically acquire data by strategically querying new data points that are the most useful for a particular task. Here, we introduce PyRelationAL, an open source library for AL research. We describe a modular toolkit based around a two step design methodology for composing pool-based active learning strategies applicable to both single-acquisition and batch-acquisition strategies. This framework allows for the mathematical and practical specification of a broad number of existing and novel strategies under a consistent programming model and abstraction. Furthermore, we incorporate datasets and active learning tasks applicable to them to simplify comparative evaluation and benchmarking, along with an initial group of benchmarks across datasets included in this library. The toolkit is compatible with existing ML frameworks. PyRelationAL is maintained using modern software engineering practices -- with an inclusive contributor code of conduct -- to promote long term library quality and utilisation. PyRelationAL is available under a permissive Apache licence on PyPi and at https://github.com/RelationRx/pyrelational.

Thomas Gaudelet, Alice Del Vecchio, Eli M Carrami et al.

Interventions play a pivotal role in the study of complex biological systems. In drug discovery, genetic interventions (such as CRISPR base editing) have become central to both identifying potential therapeutic targets and understanding a drug's mechanism of action. With the advancement of CRISPR and the proliferation of genome-scale analyses such as transcriptomics, a new challenge is to navigate the vast combinatorial space of concurrent genetic interventions. Addressing this, our work concentrates on estimating the effects of pairwise genetic combinations on the cellular transcriptome. We introduce two novel contributions: Salt, a biologically-inspired baseline that posits the mostly additive nature of combination effects, and Peper, a deep learning model that extends Salt's additive assumption to achieve unprecedented accuracy. Our comprehensive comparison against existing state-of-the-art methods, grounded in diverse metrics, and our out-of-distribution analysis highlight the limitations of current models in realistic settings. This analysis underscores the necessity for improved modelling techniques and data acquisition strategies, paving the way for more effective exploration of genetic intervention effects.

Alice Del Vecchio, Andreea Deac, Pietro Liò et al.

Antibodies are proteins in the immune system which bind to antigens to detect and neutralise them. The binding sites in an antibody-antigen interaction are known as the paratope and epitope, respectively, and the prediction of these regions is key to vaccine and synthetic antibody development. Contrary to prior art, we argue that paratope and epitope predictors require asymmetric treatment, and propose distinct neural message passing architectures that are geared towards the specific aspects of paratope and epitope prediction, respectively. We obtain significant improvements on both tasks, setting the new state-of-the-art and recovering favourable qualitative predictions on antigens of relevance to COVID-19.