Kai Sun

Jingqing Zhang, Kai Sun, Akshay Jagadeesh et al.

Recent studies have demonstrated promising performance of ChatGPT and GPT-4 on several medical domain tasks. However, none have assessed its performance using a large-scale real-world electronic health record database, nor have evaluated its utility in providing clinical diagnostic assistance for patients across a full range of disease presentation. We performed two analyses using ChatGPT and GPT-4, one to identify patients with specific medical diagnoses using a real-world large electronic health record database and the other, in providing diagnostic assistance to healthcare workers in the prospective evaluation of hypothetical patients. Our results show that GPT-4 across disease classification tasks with chain of thought and few-shot prompting can achieve performance as high as 96% F1 scores. For patient assessment, GPT-4 can accurately diagnose three out of four times. However, there were mentions of factually incorrect statements, overlooking crucial medical findings, recommendations for unnecessary investigations and overtreatment. These issues coupled with privacy concerns, make these models currently inadequate for real world clinical use. However, limited data and time needed for prompt engineering in comparison to configuration of conventional machine learning workflows highlight their potential for scalability across healthcare applications.

Xiaoyu Zhang, Yuting Xing, Kai Sun et al.

High-dimensional omics data contains intrinsic biomedical information that is crucial for personalised medicine. Nevertheless, it is challenging to capture them from the genome-wide data due to the large number of molecular features and small number of available samples, which is also called 'the curse of dimensionality' in machine learning. To tackle this problem and pave the way for machine learning aided precision medicine, we proposed a unified multi-task deep learning framework named OmiEmbed to capture biomedical information from high-dimensional omics data with the deep embedding and downstream task modules. The deep embedding module learnt an omics embedding that mapped multiple omics data types into a latent space with lower dimensionality. Based on the new representation of multi-omics data, different downstream task modules were trained simultaneously and efficiently with the multi-task strategy to predict the comprehensive phenotype profile of each sample. OmiEmbed support multiple tasks for omics data including dimensionality reduction, tumour type classification, multi-omics integration, demographic and clinical feature reconstruction, and survival prediction. The framework outperformed other methods on all three types of downstream tasks and achieved better performance with the multi-task strategy comparing to training them individually. OmiEmbed is a powerful and unified framework that can be widely adapted to various application of high-dimensional omics data and has a great potential to facilitate more accurate and personalised clinical decision making.

Nguyen Truong, Gyu Myoung Lee, Kai Sun et al.

Blockchain technology has been envisaged to commence an era of decentralised applications and services (DApps) without the need for a trusted intermediary. Such DApps open a marketplace in which services are delivered to end-users by contributors which are then incentivised by cryptocurrencies in an automated, peer-to-peer, and trustless fashion. However, blockchain, consolidated by smart contracts, only ensures on-chain data security, autonomy and integrity of the business logic execution defined in smart contracts. It cannot guarantee the quality of service of DApps, which entirely depends on the services' performance. Thus, there is a critical need for a trust system to reduce the risk of dealing with fraudulent counterparts in a blockchain network. These reasons motivate us to develop a fully decentralised trust framework deployed on top of a blockchain platform, operating along with DApps in the marketplace to demoralise deceptive entities while encouraging trustworthy ones. The trust system works as an underlying decentralised service providing a feedback mechanism for end-users and maintaining trust relationships among them in the ecosystem accordingly. We believe this research fortifies the DApps ecosystem by introducing an universal trust middleware for DApps as well as shedding light on the implementation of a decentralised trust system.

Nguyen Truong, Kai Sun, Siyao Wang et al.

Along with the blooming of AI and Machine Learning-based applications and services, data privacy and security have become a critical challenge. Conventionally, data is collected and aggregated in a data centre on which machine learning models are trained. This centralised approach has induced severe privacy risks to personal data leakage, misuse, and abuse. Furthermore, in the era of the Internet of Things and big data in which data is essentially distributed, transferring a vast amount of data to a data centre for processing seems to be a cumbersome solution. This is not only because of the difficulties in transferring and sharing data across data sources but also the challenges on complying with rigorous data protection regulations and complicated administrative procedures such as the EU General Data Protection Regulation (GDPR). In this respect, Federated learning (FL) emerges as a prospective solution that facilitates distributed collaborative learning without disclosing original training data whilst naturally complying with the GDPR. Recent research has demonstrated that retaining data and computation on-device in FL is not sufficient enough for privacy-guarantee. This is because ML model parameters exchanged between parties in an FL system still conceal sensitive information, which can be exploited in some privacy attacks. Therefore, FL systems shall be empowered by efficient privacy-preserving techniques to comply with the GDPR. This article is dedicated to surveying on the state-of-the-art privacy-preserving techniques which can be employed in FL in a systematic fashion, as well as how these techniques mitigate data security and privacy risks. Furthermore, we provide insights into the challenges along with prospective approaches following the GDPR regulatory guidelines that an FL system shall implement to comply with the GDPR.

Jingqing Zhang, Xiaoyu Zhang, Kai Sun et al.

The extraction of phenotype information which is naturally contained in electronic health records (EHRs) has been found to be useful in various clinical informatics applications such as disease diagnosis. However, due to imprecise descriptions, lack of gold standards and the demand for efficiency, annotating phenotypic abnormalities on millions of EHR narratives is still challenging. In this work, we propose a novel unsupervised deep learning framework to annotate the phenotypic abnormalities from EHRs via semantic latent representations. The proposed framework takes the advantage of Human Phenotype Ontology (HPO), which is a knowledge base of phenotypic abnormalities, to standardize the annotation results. Experiments have been conducted on 52,722 EHRs from MIMIC-III dataset. Quantitative and qualitative analysis have shown the proposed framework achieves state-of-the-art annotation performance and computational efficiency compared with other methods.

Nguyen Truong, Kai Sun, Yike Guo

The emerging blockchain technology has enabled various decentralised applications in a trustless environment without relying on a trusted intermediary. It is expected as a promising solution to tackle sophisticated challenges on personal data management, thanks to its advanced features such as immutability, decentralisation and transparency. Although certain approaches have been proposed to address technical difficulties in personal data management; most of them only provided preliminary methodological exploration. Alarmingly, when utilising Blockchain for developing a personal data management system, fictions have occurred in existing approaches and been promulgated in the literature. Such fictions are theoretically doable; however, by thoroughly breaking down consensus protocols and transaction validation processes, we clarify that such existing approaches are either impractical or highly inefficient due to the natural limitations of the blockchain and Smart Contracts technologies. This encourages us to propose a feasible solution in which such fictions are reduced by designing a novel system architecture with a blockchain-based "proof of permission" protocol. We demonstrate the feasibility and efficiency of the proposed models by implementing a clinical data sharing service built on top of a public blockchain platform. We believe that our research resolves existing ambiguity and take a step further on providing a practically feasible solution for decentralised personal data management.

Xiaoyu Zhang, Jingqing Zhang, Kai Sun et al.

Different aspects of a clinical sample can be revealed by multiple types of omics data. Integrated analysis of multi-omics data provides a comprehensive view of patients, which has the potential to facilitate more accurate clinical decision making. However, omics data are normally high dimensional with large number of molecular features and relatively small number of available samples with clinical labels. The "dimensionality curse" makes it challenging to train a machine learning model using high dimensional omics data like DNA methylation and gene expression profiles. Here we propose an end-to-end deep learning model called OmiVAE to extract low dimensional features and classify samples from multi-omics data. OmiVAE combines the basic structure of variational autoencoders with a classification network to achieve task-oriented feature extraction and multi-class classification. The training procedure of OmiVAE is comprised of an unsupervised phase without the classifier and a supervised phase with the classifier. During the unsupervised phase, a hierarchical cluster structure of samples can be automatically formed without the need for labels. And in the supervised phase, OmiVAE achieved an average classification accuracy of 97.49% after 10-fold cross-validation among 33 tumour types and normal samples, which shows better performance than other existing methods. The OmiVAE model learned from multi-omics data outperformed that using only one type of omics data, which indicates that the complementary information from different omics datatypes provides useful insights for biomedical tasks like cancer classification.