Publications from our Researchers
Several of our current PhD candidates and fellow researchers at the Data Science Institute have published, or in the proccess of publishing, papers to present their research.
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Journal articleKermani NZ, Pavlidis S, Riley JH, et al., 2019,
Prediction of longitudinal inflammatory phenotypes using baseline sputum transcriptomics in UBIOPRED
, EUROPEAN RESPIRATORY JOURNAL, Vol: 54, ISSN: 0903-1936 -
Journal articleTiotiu A, Kermani NZ, Agapow P, et al., 2019,
Differential macrophage activation in asthmatic sputum using U-BIOPRED transcriptomics
, EUROPEAN RESPIRATORY JOURNAL, Vol: 54, ISSN: 0903-1936 -
Journal articleCofré R, Videla L, Rosas F, 2019,
An introduction to the non-equilibrium steady states of maximum entropy spike trains
, Entropy, Vol: 21, Pages: 1-28, ISSN: 1099-4300Although most biological processes are characterized by a strong temporal asymmetry, several popular mathematical models neglect this issue. Maximum entropy methods provide a principled way of addressing time irreversibility, which leverages powerful results and ideas from the literature of non-equilibrium statistical mechanics. This tutorial provides a comprehensive overview of these issues, with a focus in the case of spike train statistics. We provide a detailed account of the mathematical foundations and work out examples to illustrate the key concepts and results from non-equilibrium statistical mechanics.
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Conference paperWang S, Dai C, Mo Y, et al., 2019,
Automatic Brain Tumour Segmentation and Biophysics-Guided Survival Prediction
, MICCAI BraTS 2019 ChallengeGliomas are the most common malignant brain tumourswith intrinsicheterogeneity. Accurate segmentation of gliomas and theirsub-regions onmulti-parametric magnetic resonance images (mpMRI)is of great clinicalimportance, which defines tumour size, shape andappearance and providesabundant information for preoperative diag-nosis, treatment planning andsurvival prediction. Recent developmentson deep learning have significantlyimproved the performance of auto-mated medical image segmentation. In thispaper, we compare severalstate-of-the-art convolutional neural network modelsfor brain tumourimage segmentation. Based on the ensembled segmentation, wepresenta biophysics-guided prognostic model for patient overall survivalpredic-tion which outperforms a data-driven radiomics approach. Our methodwonthe second place of the MICCAI 2019 BraTS Challenge for theoverall survivalprediction.
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Conference paperDuan J, Schlemper J, Qin C, et al., 2019,
VS-Net: variable splitting network for accelerated parallel MRI reconstruction
, International Conference on Medical Image Computing and Computer-Assisted Intervention, Publisher: Springer International Publishing, Pages: 713-722, ISSN: 0302-9743In this work, we propose a deep learning approach for parallel magnetic resonance imaging (MRI) reconstruction, termed a variable splitting network (VS-Net), for an efficient, high-quality reconstruction of undersampled multi-coil MR data. We formulate the generalized parallel compressed sensing reconstruction as an energy minimization problem, for which a variable splitting optimization method is derived. Based on this formulation we propose a novel, end-to-end trainable deep neural network architecture by unrolling the resulting iterative process of such variable splitting scheme. VS-Net is evaluated on complex valued multi-coil knee images for 4-fold and 6-fold acceleration factors. We show that VS-Net outperforms state-of-the-art deep learning reconstruction algorithms, in terms of reconstruction accuracy and perceptual quality. Our code is publicly available at https://github.com/j-duan/VS-Net.
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Journal articleDuan J, Bello G, Schlemper J, et al., 2019,
Automatic 3D bi-ventricular segmentation of cardiac images by a shape-refined multi-task deep learning approach
, IEEE Transactions on Medical Imaging, Vol: 38, Pages: 2151-2164, ISSN: 0278-0062Deep learning approaches have achieved state-of-the-art performance incardiac magnetic resonance (CMR) image segmentation. However, most approaches have focused on learning image intensity features for segmentation, whereas the incorporation of anatomical shape priors has received less attention. In this paper, we combine a multi-task deep learning approach with atlas propagation to develop a shape-constrained bi-ventricular segmentation pipeline for short-axis CMR volumetric images. The pipeline first employs a fully convolutional network (FCN) that learns segmentation and landmark localisation tasks simultaneously. The architecture of the proposed FCN uses a 2.5D representation, thus combining the computational advantage of 2D FCNs networks and the capability of addressing 3D spatial consistency without compromising segmentation accuracy. Moreover, the refinement step is designed to explicitly enforce a shape constraint and improve segmentation quality. This step is effective for overcoming image artefacts (e.g. due to different breath-hold positions and large slice thickness), which preclude the creation of anatomically meaningful 3D cardiac shapes. The proposed pipeline is fully automated, due to network's ability to infer landmarks, which are then used downstream in the pipeline to initialise atlas propagation. We validate the pipeline on 1831 healthy subjects and 649 subjects with pulmonary hypertension. Extensive numerical experiments on the two datasets demonstrate that our proposed method is robust and capable of producing accurate, high-resolution and anatomically smooth bi-ventricular3D models, despite the artefacts in input CMR volumes.
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Journal articleQureshi N, Kim S, Cantwell C, et al., 2019,
Voltage during atrial fibrillation is superior to voltage during sinus rhythm in localizing areas of delayed enhancement on magnetic resonance imaging: An assessment of the posterior left atrium in patients with persistent atrial fibrillation
, Heart Rhythm, Vol: 16, Pages: 1357-1367, ISSN: 1547-5271BackgroundBipolar electrogram voltage during sinus rhythm (VSR) has been used as a surrogate for atrial fibrosis in guiding catheter ablation of persistent AF, but the fixed rate and wavefront characteristics present during sinus rhythm may not accurately reflect underlying functional vulnerabilities responsible for AF maintenance.ObjectivesWe hypothesized that given adequate temporal sampling, the spatial distribution of mean AF voltage (VmAF) should better correlate with delayed-enhancement MRI (MRI-DE) detected atrial fibrosis than VSR.MethodsAF was mapped (8s) during index ablation for persistent AF (20 patients) using a 20-pole catheter (660±28 points/map). Following cardioversion, VSR was mapped (557±326 points/map). Electroanatomic and MRI-DE maps were co-registered in 14 patients.Results(i) The time course of VmAF was assessed from 1-40 AF-cycles (∼8s) at 1113 locations. VmAF stabilized with sampling >4s (mean voltage error=0.05mV). (ii) Paired point analysis of VmAF from segments acquired 30s apart (3,667-sites, 15-patients), showed strong correlation (r=0.95, p<0.001). (iii) Delayed-enhancement (DE) was assessed across the posterior left atrial (LA) wall, occupying 33±13%. VmAF distributions (median[IQR]) were 0.21[0.14-0.35]mV in DE vs. 0.52[0.34-0.77]mV in Non-DE regions. VSR distributions were 1.34[0.65-2.48]mV in DE vs. 2.37[1.27-3.97]mV in Non-DE. A VmAF threshold of 0.35mV yielded sensitivity/specificity 75%/79% in detecting MRI-DE, compared with 63%/67% for VSR (1.8mV threshold).ConclusionThe correlation between low-voltage and posterior LA MRI-DE is significantly improved when acquired during AF vs. sinus rhythm. With adequate sampling, mean AF voltage is a reproducible marker reflecting the functional response to the underlying persistent AF substrate.
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Conference paperDai C, Mo Y, Angelini E, et al., 2019,
Transfer learning from partial annotations for whole brain segmentation
, International Workshop on Medical Image Learning with Less Labels and Imperfect DataBrain 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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Conference paperGadotti A, Houssiau F, Rocher L, et al., 2019,
When the signal is in the noise: exploiting Diffix's sticky noise
, 28th USENIX Security Symposium (USENIX Security '19), Publisher: USENIX, Pages: 1081-1098Anonymized data is highly valuable to both businesses and researchers. A large body of research has however shown the strong limits of the de-identification release-and-forget model, where data is anonymized and shared. This has led to the development of privacy-preserving query-based systems. Based on the idea of “sticky noise”, Diffix has been recently pro-posed as a novel query-based mechanism satisfying alone the EU Article 29 Working Party’s definition of anonymization. According to its authors, Diffix adds less noise to answers than solutions based on differential privacy while allowing for an unlimited number of queries.This paper presents a new class of noise-exploitation attacks, exploiting the noise added by the system to infer privateinformation about individuals in the dataset. Our first differential attack uses samples extracted from Diffix in a likelihood ratio test to discriminate between two probability distributions.We show that using this attack against a synthetic best-case dataset allows us to infer private information with 89.4% accuracy using only 5 attributes. Our second cloning attack uses dummy conditions that conditionally strongly affect the output of the query depending on the value of the private attribute. Using this attack on four real-world datasets, we show that we can infer private attributes of at least 93% of the users in the dataset with accuracy between 93.3% and 97.1%, issuing a median of 304 queries per user. We show how to optimize this attack, targeting 55.4% of the users and achieving 91.7% accuracy, using a maximum of only 32 queries per user. Our attacks demonstrate that adding data-dependent noise, as done by Diffix, is not sufficient to prevent inference of private attributes. We furthermore argue that Diffix alone fails to satisfy Art. 29 WP’s definition of anonymization. We conclude by discussing how non-provable privacy-preserving systems can be combined with fundamental security principles su
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Journal articleRocher L, Hendrickx J, de Montjoye Y-A, 2019,
Estimating the success of re-identifications in incomplete datasets using generative models
, Nature Communications, Vol: 10, ISSN: 2041-1723While rich medical, behavioral, and socio-demographic data are key to modern data-driven research, their collection and use raise legitimate privacy concerns. Anonymizing datasets through de-identification and sampling before sharing them has been the main tool used to address those concerns. We here propose a generative copula-based method that can accurately estimate the likelihood of a specific person to be correctly re-identified, even in a heavily incomplete dataset. On 210 populations, our method obtains AUC scores for predicting individual uniqueness ranging from 0.84 to 0.97, with low false-discovery rate. Using our model, we find that 99.98% of Americans would be correctly re-identified in any dataset using 15 demographic attributes. Our results suggest that even heavily sampled anonymized datasets are unlikely to satisfy the modern standards for anonymization set forth by GDPR and seriously challenge the technical and legal adequacy of the de-identification release-and-forget model.
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Journal articleCofre R, Herzog R, Corcoran D, et al., 2019,
A comparison of the maximum entropy principle across biological spatial scales
Despite their obvious differences, biological systems at different scales tend to exhibit common organizational patterns. Unfortunately, these commonalities are usually obscured by the parcelled terminology employed by various scientific sub-disciplines. To explore these commonalities, this papers a comparative study of diverse applications of the maximum entropy principle, ranging from amino acids up to societies. By presenting these studies under a common language, this paper establishes a unified view over seemingly highly heterogeneous biological scenarios.
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Conference paperBai W, Chen C, Tarroni G, et al., 2019,
Self-supervised learning for cardiac MR image segmentation by anatomicalposition prediction
, International Conference on Medical Image Computing and Computer-Assisted Intervention (MICCAI)In the recent years, convolutional neural networks have transformed the field of medical image analysis due to their capacity to learn discriminative image features for a variety of classification and regression tasks. However, successfully learning these features requires a large amount of manuallyannotated data, which is expensive to acquire and limited by the availableresources of expert image analysts. Therefore, unsupervised, weakly-supervised and self-supervised feature learning techniques receive a lot of attention, which aim to utilise the vast amount of available data, while at the same time avoid or substantially reduce the effort of manual annotation. In this paper, we propose a novel way for training a cardiac MR image segmentation network, in which features are learnt in a self-supervised manner by predicting anatomical positions. The anatomical positions serve as a supervisory signal and do not require extra manual annotation. We demonstrate that this seemingly simple task provides a strong signal for feature learning and with self-supervised learning, we achieve a high segmentation accuracy that is better than or comparable to a U-net trained from scratch, especially at a small data setting. When only five annotated subjects are available, the proposed method improves the mean Dice metric from 0.811 to 0.852 for short-axis image segmentation, compared to the baseline U-net.
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ReportCrémer J, de Montjoye Y-A, Schweitzer H, 2019,
Competition policy for the digital era
, Competition policy for the digital era, Brussels, Publisher: EU Publications -
Conference paperJain S, Bensaid E, de Montjoye Y-A, 2019,
UNVEIL: capture and visualise WiFi data leakages
, The Web Conference 2019, Publisher: ACM, Pages: 3550-3554In the past few years, numerous privacy vulnerabilities have been discovered in the WiFi standards and their implementations for mobile devices. These vulnerabilities allow an attacker to collect large amounts of data on the device user, which could be used to infer sensitive information such as religion, gender, and sexual orientation. Solutions for these vulnerabilities are often hard to design and typically require many years to be widely adopted, leaving many devices at risk.In this paper, we present UNVEIL - an interactive and extendable platform to demonstrate the consequences of these attacks. The platform performs passive and active attacks on smartphones to collect and analyze data leaked through WiFi and communicate the analysis results to users through simple and interactive visualizations.The platform currently performs two attacks. First, it captures probe requests sent by nearby devices and combines them with public WiFi location databases to generate a map of locations previously visited by the device users. Second, it creates rogue access points with SSIDs of popular public WiFis (e.g. _Heathrow WiFi, Railways WiFi) and records the resulting internet traffic. This data is then analyzed and presented in a format that highlights the privacy leakage. The platform has been designed to be easily extendable to include more attacks and to be easily deployable in public spaces. We hope that UNVEIL will help raise public awareness of privacy risks of WiFi networks.
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Journal articleTarroni G, Oktay O, Bai W, et al., 2019,
Learning-based quality control for cardiac MR images
, IEEE Transactions on Medical Imaging, Vol: 38, Pages: 1127-1138, ISSN: 0278-0062The effectiveness of a cardiovascular magnetic resonance (CMR) scan depends on the ability of the operator to correctly tune the acquisition parameters to the subject being scanned and on the potential occurrence of imaging artefacts such as cardiac and respiratory motion. In the clinical practice, a quality control step is performed by visual assessment of the acquired images: however, this procedure is strongly operatordependent, cumbersome and sometimes incompatible with the time constraints in clinical settings and large-scale studies. We propose a fast, fully-automated, learning-based quality control pipeline for CMR images, specifically for short-axis image stacks. Our pipeline performs three important quality checks: 1) heart coverage estimation, 2) inter-slice motion detection, 3) image contrast estimation in the cardiac region. The pipeline uses a hybrid decision forest method - integrating both regression and structured classification models - to extract landmarks as well as probabilistic segmentation maps from both long- and short-axis images as a basis to perform the quality checks. The technique was tested on up to 3000 cases from the UK Biobank as well as on 100 cases from the UK Digital Heart Project, and validated against manual annotations and visual inspections performed by expert interpreters. The results show the capability of the proposed pipeline to correctly detect incomplete or corrupted scans (e.g. on UK Biobank, sensitivity and specificity respectively 88% and 99% for heart coverage estimation, 85% and 95% for motion detection), allowing their exclusion from the analysed dataset or the triggering of a new acquisition.
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