arXiv subjects

Yike Guo

Publications and source records attributed to Yike Guo.

At least 217 records · Page 12Linked to original sources

arXiv2021

Verifying Design through Generative Visualization of Neural Activities

Current neuroscience focused approaches for evaluating the effectiveness of a design do not use direct visualisation of mental activity. A recurrent neural network is used as the encoder to learn latent representation from electroencephalogram (EEG) signals, recorded while subjects looked at 50 categories of images. A generative adversarial network (GAN) conditioned on the EEG latent representation is trained for reconstructing these images. After training, the neural network is able to reconstruct images from brain activity recordings. To demonstrate the proposed method in the context of the mental association with a design, we performed a study that indicates an iconic design image could inspire the subject to create cognitive associations with branding and valued products. The proposed method could have the potential in verifying designs by visualizing the cognitive understanding of underlying brain activity.

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arXiv2021

Privacy Preservation in Federated Learning: An insightful survey from the GDPR Perspective

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.

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arXiv2021

A General Framework for Revealing Human Mind with auto-encoding GANs

Addressing the question of visualising human mind could help us to find regions that are associated with observed cognition and responsible for expressing the elusive mental image, leading to a better understanding of cognitive function. The traditional approach treats brain decoding as a classification problem, reading the mind through statistical analysis of brain activity. However, human thought is rich and varied, that it is often influenced by more of a combination of object features than a specific type of category. For this reason, we propose an end-to-end brain decoding framework which translates brain activity into an image by latent space alignment. To find the correspondence from brain signal features to image features, we embedded them into two latent spaces with modality-specific encoders and then aligned the two spaces by minimising the distance between paired latent representations. The proposed framework was trained by simultaneous electroencephalogram and functional MRI data, which were recorded when the subjects were viewing or imagining a set of image stimuli. In this paper, we focused on implementing the fMRI experiment. Our experimental results demonstrated the feasibility of translating brain activity to an image. The reconstructed image matches image stimuli approximate in both shape and colour. Our framework provides a promising direction for building a direct visualisation to reveal human mind.

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arXiv2021

A Blockchain-based Trust System for Decentralised Applications: When trustless needs trust

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.

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arXiv2021

BU-Trace: A Permissionless Mobile System for Privacy-Preserving Intelligent Contact Tracing

The coronavirus disease 2019 (COVID-19) pandemic has caused an unprecedented health crisis for the global. Digital contact tracing, as a transmission intervention measure, has shown its effectiveness on pandemic control. Despite intensive research on digital contact tracing, existing solutions can hardly meet users' requirements on privacy and convenience. In this paper, we propose BU-Trace, a novel permissionless mobile system for privacy-preserving intelligent contact tracing based on QR code and NFC technologies. First, a user study is conducted to investigate and quantify the user acceptance of a mobile contact tracing system. Second, a decentralized system is proposed to enable contact tracing while protecting user privacy. Third, an intelligent behavior detection algorithm is designed to ease the use of our system. We implement BU-Trace and conduct extensive experiments in several real-world scenarios. The experimental results show that BU-Trace achieves a privacy-preserving and intelligent mobile system for contact tracing without requesting location or other privacy-related permissions.

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arXiv2021

Adversarially trained LSTMs on reduced order models of urban air pollution simulations

This paper presents an approach to improve computational fluid dynamics simulations forecasts of air pollution using deep learning. Our method, which integrates Principal Components Analysis (PCA) and adversarial training, is a way to improve the forecast skill of reduced order models obtained from the original model solution. Once the reduced-order model (ROM) is obtained via PCA, a Long Short-Term Memory network (LSTM) is adversarially trained on the ROM to make forecasts. Once trained, the adversarially trained LSTM outperforms a LSTM trained in a classical way. The study area is in London, including velocities and a concentration tracer that replicates a busy traffic junction. This adversarially trained LSTM-based approach is used on the ROM in order to produce faster forecasts of the air pollution tracer.

cs.LG↗

arXiv2020

An Epidemiological Modelling Approach for Covid19 via Data Assimilation

The global pandemic of the 2019-nCov requires the evaluation of policy interventions to mitigate future social and economic costs of quarantine measures worldwide. We propose an epidemiological model for forecasting and policy evaluation which incorporates new data in real-time through variational data assimilation. We analyze and discuss infection rates in China, the US and Italy. In particular, we develop a custom compartmental SIR model fit to variables related to the epidemic in Chinese cities, named SITR model. We compare and discuss model results which conducts updates as new observations become available. A hybrid data assimilation approach is applied to make results robust to initial conditions. We use the model to do inference on infection numbers as well as parameters such as the disease transmissibility rate or the rate of recovery. The parameterisation of the model is parsimonious and extendable, allowing for the incorporation of additional data and parameters of interest. This allows for scalability and the extension of the model to other locations or the adaption of novel data sources.

stat.AP↗

arXiv2020

A Bayesian Updating Scheme for Pandemics: Estimating the Infection Dynamics of COVID-19

Epidemic models play a key role in understanding and responding to the emerging COVID-19 pandemic. Widely used compartmental models are static and are of limited use to evaluate intervention strategies with the emerging pandemic. Applying the technology of data assimilation, we propose a Bayesian updating approach for estimating epidemiological parameters using observable information for the purpose of assessing the impacts of different intervention strategies. We adopt a concise renewal model and propose new parameters by disentangling the reduction of instantaneous reproduction number Rt into mitigation and suppression factors for quantifying intervention impacts at a finer granularity. Then we developed a data assimilation framework for estimating these parameters including constructing an observation function and developing a Bayesian updating scheme. A statistical analysis framework is then built to quantify the impact of intervention strategies by monitoring the evolution of these estimated parameters. By Investigating the impacts of intervention measures of European countries, the United States and Wuhan with the framework, we reveal the effects of interventions in these countries and the resurgence risk in the USA.

q-bio.PE↗

arXiv2020

Suggestive Annotation of Brain Tumour Images with Gradient-guided Sampling

Machine learning has been widely adopted for medical image analysis in recent years given its promising performance in image segmentation and classification tasks. As a data-driven science, the success of machine learning, in particular supervised learning, largely depends on the availability of manually annotated datasets. For medical imaging applications, such annotated datasets are not easy to acquire. It takes a substantial amount of time and resource to curate an annotated medical image set. In this paper, we propose an efficient annotation framework for brain tumour images that is able to suggest informative sample images for human experts to annotate. Our experiments show that training a segmentation model with only 19% suggestively annotated patient scans from BraTS 2019 dataset can achieve a comparable performance to training a model on the full dataset for whole tumour segmentation task. It demonstrates a promising way to save manual annotation cost and improve data efficiency in medical imaging applications.

cs.CV↗

arXiv2020

Deep Generative Model-based Quality Control for Cardiac MRI Segmentation

In recent years, convolutional neural networks have demonstrated promising performance in a variety of medical image segmentation tasks. However, when a trained segmentation model is deployed into the real clinical world, the model may not perform optimally. A major challenge is the potential poor-quality segmentations generated due to degraded image quality or domain shift issues. There is a timely need to develop an automated quality control method that can detect poor segmentations and feedback to clinicians. Here we propose a novel deep generative model-based framework for quality control of cardiac MRI segmentation. It first learns a manifold of good-quality image-segmentation pairs using a generative model. The quality of a given test segmentation is then assessed by evaluating the difference from its projection onto the good-quality manifold. In particular, the projection is refined through iterative search in the latent space. The proposed method achieves high prediction accuracy on two publicly available cardiac MRI datasets. Moreover, it shows better generalisation ability than traditional regression-based methods. Our approach provides a real-time and model-agnostic quality control for cardiac MRI segmentation, which has the potential to be integrated into clinical image analysis workflows.

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arXiv2020

Efficient Deep Representation Learning by Adaptive Latent Space Sampling

Supervised deep learning requires a large amount of training samples with annotations (e.g. label class for classification task, pixel- or voxel-wised label map for segmentation tasks), which are expensive and time-consuming to obtain. During the training of a deep neural network, the annotated samples are fed into the network in a mini-batch way, where they are often regarded of equal importance. However, some of the samples may become less informative during training, as the magnitude of the gradient start to vanish for these samples. In the meantime, other samples of higher utility or hardness may be more demanded for the training process to proceed and require more exploitation. To address the challenges of expensive annotations and loss of sample informativeness, here we propose a novel training framework which adaptively selects informative samples that are fed to the training process. The adaptive selection or sampling is performed based on a hardness-aware strategy in the latent space constructed by a generative model. To evaluate the proposed training framework, we perform experiments on three different datasets, including MNIST and CIFAR-10 for image classification task and a medical image dataset IVUS for biophysical simulation task. On all three datasets, the proposed framework outperforms a random sampling method, which demonstrates the effectiveness of proposed framework.

cs.CV↗

arXiv2019

Regularizing Deep Multi-Task Networks using Orthogonal Gradients

Deep neural networks are a promising approach towards multi-task learning because of their capability to leverage knowledge across domains and learn general purpose representations. Nevertheless, they can fail to live up to these promises as tasks often compete for a model's limited resources, potentially leading to lower overall performance. In this work we tackle the issue of interfering tasks through a comprehensive analysis of their training, derived from looking at the interaction between gradients within their shared parameters. Our empirical results show that well-performing models have low variance in the angles between task gradients and that popular regularization methods implicitly reduce this measure. Based on this observation, we propose a novel gradient regularization term that minimizes task interference by enforcing near orthogonal gradients. Updating the shared parameters using this property encourages task specific decoders to optimize different parts of the feature extractor, thus reducing competition. We evaluate our method with classification and regression tasks on the multiDigitMNIST, NYUv2 and SUN RGB-D datasets where we obtain competitive results.

cs.LG↗

arXiv2019

Biologically inspired architectures for sample-efficient deep reinforcement learning

Deep reinforcement learning requires a heavy price in terms of sample efficiency and overparameterization in the neural networks used for function approximation. In this work, we use tensor factorization in order to learn more compact representation for reinforcement learning policies. We show empirically that in the low-data regime, it is possible to learn online policies with 2 to 10 times less total coefficients, with little to no loss of performance. We also leverage progress in second order optimization, and use the theory of wavelet scattering to further reduce the number of learned coefficients, by foregoing learning the topmost convolutional layer filters altogether. We evaluate our results on the Atari suite against recent baseline algorithms that represent the state-of-the-art in data efficiency, and get comparable results with an order of magnitude gain in weight parsimony.

cs.LG↗

arXiv2019

Automatic Brain Tumour Segmentation and Biophysics-Guided Survival Prediction

Gliomas are the most common malignant brain tumourswith intrinsic heterogeneity. Accurate segmentation of gliomas and theirsub-regions on multi-parametric magnetic resonance images (mpMRI)is of great clinical importance, which defines tumour size, shape andappearance and provides abundant information for preoperative diag-nosis, treatment planning and survival prediction. Recent developmentson deep learning have significantly improved the performance of auto-mated medical image segmentation. In this paper, we compare severalstate-of-the-art convolutional neural network models for brain tumourimage segmentation. Based on the ensembled segmentation, we presenta biophysics-guided prognostic model for patient overall survival predic-tion which outperforms a data-driven radiomics approach. Our methodwon the second place of the MICCAI 2019 BraTS Challenge for theoverall survival prediction.

eess.IV↗

arXiv2019

Unsupervised Annotation of Phenotypic Abnormalities via Semantic Latent Representations on Electronic Health Records

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.

cs.CL↗

arXiv2019

Blockchain-based Personal Data Management: From Fiction to Solution

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.

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arXiv2019

Transfer Learning from Partial Annotations for Whole Brain Segmentation

Brain MR image segmentation is a key task in neuroimaging studies. It is commonly conducted using standard computational tools, such as FSL, SPM, multi-atlas segmentation etc, which are often registration-based and suffer from expensive computation cost. Recently, there is an increased interest using deep neural networks for brain image segmentation, which have demonstrated advantages in both speed and performance. However, neural networks-based approaches normally require a large amount of manual annotations for optimising the massive amount of network parameters. For 3D networks used in volumetric image segmentation, this has become a particular challenge, as a 3D network consists of many more parameters compared to its 2D counterpart. Manual annotation of 3D brain images is extremely time-consuming and requires extensive involvement of trained experts. To address the challenge with limited manual annotations, here we propose a novel multi-task learning framework for brain image segmentation, which utilises a large amount of automatically generated partial annotations together with a small set of manually created full annotations for network training. Our method yields a high performance comparable to state-of-the-art methods for whole brain segmentation.

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arXiv2019

Integrated Multi-omics Analysis Using Variational Autoencoders: Application to Pan-cancer Classification

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.

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