Cheng Ye

Minghui Xu, Zongrui Zou, Ye Cheng et al.

Decentralized learning involves training machine learning models over remote mobile devices, edge servers, or cloud servers while keeping data localized. Even though many studies have shown the feasibility of preserving privacy, enhancing training performance or introducing Byzantine resilience, but none of them simultaneously considers all of them. Therefore we face the following problem: \textit{how can we efficiently coordinate the decentralized learning process while simultaneously maintaining learning security and data privacy?} To address this issue, in this paper we propose SPDL, a blockchain-secured and privacy-preserving decentralized learning scheme. SPDL integrates blockchain, Byzantine Fault-Tolerant (BFT) consensus, BFT Gradients Aggregation Rule (GAR), and differential privacy seamlessly into one system, ensuring efficient machine learning while maintaining data privacy, Byzantine fault tolerance, transparency, and traceability. To validate our scheme, we provide rigorous analysis on convergence and regret in the presence of Byzantine nodes. We also build a SPDL prototype and conduct extensive experiments to demonstrate that SPDL is effective and efficient with strong security and privacy guarantees.

Stephen Bonner, Ian P Barrett, Cheng Ye et al.

Knowledge Graphs (KG) and associated Knowledge Graph Embedding (KGE) models have recently begun to be explored in the context of drug discovery and have the potential to assist in key challenges such as target identification. In the drug discovery domain, KGs can be employed as part of a process which can result in lab-based experiments being performed, or impact on other decisions, incurring significant time and financial costs and most importantly, ultimately influencing patient healthcare. For KGE models to have impact in this domain, a better understanding of not only of performance, but also the various factors which determine it, is required. In this study we investigate, over the course of many thousands of experiments, the predictive performance of five KGE models on two public drug discovery-oriented KGs. Our goal is not to focus on the best overall model or configuration, instead we take a deeper look at how performance can be affected by changes in the training setup, choice of hyperparameters, model parameter initialisation seed and different splits of the datasets. Our results highlight that these factors have significant impact on performance and can even affect the ranking of models. Indeed these factors should be reported along with model architectures to ensure complete reproducibility and fair comparisons of future work, and we argue this is critical for the acceptance of use, and impact of KGEs in a biomedical setting.

Stephen Bonner, Ian P Barrett, Cheng Ye et al.

Drug discovery and development is a complex and costly process. Machine learning approaches are being investigated to help improve the effectiveness and speed of multiple stages of the drug discovery pipeline. Of these, those that use Knowledge Graphs (KG) have promise in many tasks, including drug repurposing, drug toxicity prediction and target gene-disease prioritisation. In a drug discovery KG, crucial elements including genes, diseases and drugs are represented as entities, whilst relationships between them indicate an interaction. However, to construct high-quality KGs, suitable data is required. In this review, we detail publicly available sources suitable for use in constructing drug discovery focused KGs. We aim to help guide machine learning and KG practitioners who are interested in applying new techniques to the drug discovery field, but who may be unfamiliar with the relevant data sources. The datasets are selected via strict criteria, categorised according to the primary type of information contained within and are considered based upon what information could be extracted to build a KG. We then present a comparative analysis of existing public drug discovery KGs and a evaluation of selected motivating case studies from the literature. Additionally, we raise numerous and unique challenges and issues associated with the domain and its datasets, whilst also highlighting key future research directions. We hope this review will motivate KGs use in solving key and emerging questions in the drug discovery domain.