arXiv subjects

Amir Alansary

Publications and source records attributed to Amir Alansary.

At least 19 recordsLinked to original sources

arXiv2022

CortexODE: Learning Cortical Surface Reconstruction by Neural ODEs

We present CortexODE, a deep learning framework for cortical surface reconstruction. CortexODE leverages neural ordinary differential equations (ODEs) to deform an input surface into a target shape by learning a diffeomorphic flow. The trajectories of the points on the surface are modeled as ODEs, where the derivatives of their coordinates are parameterized via a learnable Lipschitz-continuous deformation network. This provides theoretical guarantees for the prevention of self-intersections. CortexODE can be integrated to an automatic learning-based pipeline, which reconstructs cortical surfaces efficiently in less than 5 seconds. The pipeline utilizes a 3D U-Net to predict a white matter segmentation from brain Magnetic Resonance Imaging (MRI) scans, and further generates a signed distance function that represents an initial surface. Fast topology correction is introduced to guarantee homeomorphism to a sphere. Following the isosurface extraction step, two CortexODE models are trained to deform the initial surface to white matter and pial surfaces respectively. The proposed pipeline is evaluated on large-scale neuroimage datasets in various age groups including neonates (25-45 weeks), young adults (22-36 years) and elderly subjects (55-90 years). Our experiments demonstrate that the CortexODE-based pipeline can achieve less than 0.2mm average geometric error while being orders of magnitude faster compared to conventional processing pipelines.

eess.IV↗

arXiv2022

CAS-Net: Conditional Atlas Generation and Brain Segmentation for Fetal MRI

Fetal Magnetic Resonance Imaging (MRI) is used in prenatal diagnosis and to assess early brain development. Accurate segmentation of the different brain tissues is a vital step in several brain analysis tasks, such as cortical surface reconstruction and tissue thickness measurements. Fetal MRI scans, however, are prone to motion artifacts that can affect the correctness of both manual and automatic segmentation techniques. In this paper, we propose a novel network structure that can simultaneously generate conditional atlases and predict brain tissue segmentation, called CAS-Net. The conditional atlases provide anatomical priors that can constrain the segmentation connectivity, despite the heterogeneity of intensity values caused by motion or partial volume effects. The proposed method is trained and evaluated on 253 subjects from the developing Human Connectome Project (dHCP). The results demonstrate that the proposed method can generate conditional age-specific atlas with sharp boundary and shape variance. It also segment multi-category brain tissues for fetal MRI with a high overall Dice similarity coefficient (DSC) of $85.2\%$ for the selected 9 tissue labels.

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arXiv2022

Split HE: Fast Secure Inference Combining Split Learning and Homomorphic Encryption

This work presents a novel protocol for fast secure inference of neural networks applied to computer vision applications. It focuses on improving the overall performance of the online execution by deploying a subset of the model weights in plaintext on the client's machine, in the fashion of SplitNNs. We evaluate our protocol on benchmark neural networks trained on the CIFAR-10 dataset using SEAL via TenSEAL and discuss runtime and security performances. Empirical security evaluation using Membership Inference and Model Extraction attacks showed that the protocol was more resilient under the same attacks than a similar approach also based on SplitNN. When compared to related work, we demonstrate improvements of 2.5x-10x for the inference time and 14x-290x in communication costs.

cs.CR↗

arXiv2021

FedRAD: Federated Robust Adaptive Distillation

The robustness of federated learning (FL) is vital for the distributed training of an accurate global model that is shared among large number of clients. The collaborative learning framework by typically aggregating model updates is vulnerable to model poisoning attacks from adversarial clients. Since the shared information between the global server and participants are only limited to model parameters, it is challenging to detect bad model updates. Moreover, real-world datasets are usually heterogeneous and not independent and identically distributed (Non-IID) among participants, which makes the design of such robust FL pipeline more difficult. In this work, we propose a novel robust aggregation method, Federated Robust Adaptive Distillation (FedRAD), to detect adversaries and robustly aggregate local models based on properties of the median statistic, and then performing an adapted version of ensemble Knowledge Distillation. We run extensive experiments to evaluate the proposed method against recently published works. The results show that FedRAD outperforms all other aggregators in the presence of adversaries, as well as in heterogeneous data distributions.

cs.LG↗

arXiv2021

PialNN: A Fast Deep Learning Framework for Cortical Pial Surface Reconstruction

Traditional cortical surface reconstruction is time consuming and limited by the resolution of brain Magnetic Resonance Imaging (MRI). In this work, we introduce Pial Neural Network (PialNN), a 3D deep learning framework for pial surface reconstruction. PialNN is trained end-to-end to deform an initial white matter surface to a target pial surface by a sequence of learned deformation blocks. A local convolutional operation is incorporated in each block to capture the multi-scale MRI information of each vertex and its neighborhood. This is fast and memory-efficient, which allows reconstructing a pial surface mesh with 150k vertices in one second. The performance is evaluated on the Human Connectome Project (HCP) dataset including T1-weighted MRI scans of 300 subjects. The experimental results demonstrate that PialNN reduces the geometric error of the predicted pial surface by 30% compared to state-of-the-art deep learning approaches.

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arXiv2021

Bayesian analysis of the prevalence bias: learning and predicting from imbalanced data

Datasets are rarely a realistic approximation of the target population. Say, prevalence is misrepresented, image quality is above clinical standards, etc. This mismatch is known as sampling bias. Sampling biases are a major hindrance for machine learning models. They cause significant gaps between model performance in the lab and in the real world. Our work is a solution to prevalence bias. Prevalence bias is the discrepancy between the prevalence of a pathology and its sampling rate in the training dataset, introduced upon collecting data or due to the practioner rebalancing the training batches. This paper lays the theoretical and computational framework for training models, and for prediction, in the presence of prevalence bias. Concretely a bias-corrected loss function, as well as bias-corrected predictive rules, are derived under the principles of Bayesian risk minimization. The loss exhibits a direct connection to the information gain. It offers a principled alternative to heuristic training losses and complements test-time procedures based on selecting an operating point from summary curves. It integrates seamlessly in the current paradigm of (deep) learning using stochastic backpropagation and naturally with Bayesian models.

cs.LG↗

arXiv2020

Geometric Deep Learning for Post-Menstrual Age Prediction based on the Neonatal White Matter Cortical Surface

Accurate estimation of the age in neonates is essential for measuring neurodevelopmental, medical, and growth outcomes. In this paper, we propose a novel approach to predict the post-menstrual age (PA) at scan, using techniques from geometric deep learning, based on the neonatal white matter cortical surface. We utilize and compare multiple specialized neural network architectures that predict the age using different geometric representations of the cortical surface; we compare MeshCNN, Pointnet++, GraphCNN, and a volumetric benchmark. The dataset is part of the Developing Human Connectome Project (dHCP), and is a cohort of healthy and premature neonates. We evaluate our approach on 650 subjects (727scans) with PA ranging from 27 to 45 weeks. Our results show accurate prediction of the estimated PA, with mean error less than one week.

cs.CV↗

arXiv2020

Communicative Reinforcement Learning Agents for Landmark Detection in Brain Images

Accurate detection of anatomical landmarks is an essential step in several medical imaging tasks. We propose a novel communicative multi-agent reinforcement learning (C-MARL) system to automatically detect landmarks in 3D brain images. C-MARL enables the agents to learn explicit communication channels, as well as implicit communication signals by sharing certain weights of the architecture among all the agents. The proposed approach is evaluated on two brain imaging datasets from adult magnetic resonance imaging (MRI) and fetal ultrasound scans. Our experiments show that involving multiple cooperating agents by learning their communication with each other outperforms previous approaches using single agents.

cs.CV↗

arXiv2020

Robust Aggregation for Adaptive Privacy Preserving Federated Learning in Healthcare

Federated learning (FL) has enabled training models collaboratively from multiple data owning parties without sharing their data. Given the privacy regulations of patient's healthcare data, learning-based systems in healthcare can greatly benefit from privacy-preserving FL approaches. However, typical model aggregation methods in FL are sensitive to local model updates, which may lead to failure in learning a robust and accurate global model. In this work, we implement and evaluate different robust aggregation methods in FL applied to healthcare data. Furthermore, we show that such methods can detect and discard faulty or malicious local clients during training. We run two sets of experiments using two real-world healthcare datasets for training medical diagnosis classification tasks. Each dataset is used to simulate the performance of three different robust FL aggregation strategies when facing different poisoning attacks. The results show that privacy preserving methods can be successfully applied alongside Byzantine-robust aggregation techniques. We observed in particular how using differential privacy (DP) did not significantly impact the final learning convergence of the different aggregation strategies.

cs.CR↗

arXiv2019

Flexible Conditional Image Generation of Missing Data with Learned Mental Maps

Real-world settings often do not allow acquisition of high-resolution volumetric images for accurate morphological assessment and diagnostic. In clinical practice it is frequently common to acquire only sparse data (e.g. individual slices) for initial diagnostic decision making. Thereby, physicians rely on their prior knowledge (or mental maps) of the human anatomy to extrapolate the underlying 3D information. Accurate mental maps require years of anatomy training, which in the first instance relies on normative learning, i.e. excluding pathology. In this paper, we leverage Bayesian Deep Learning and environment mapping to generate full volumetric anatomy representations from none to a small, sparse set of slices. We evaluate proof of concept implementations based on Generative Query Networks (GQN) and Conditional BRUNO using abdominal CT and brain MRI as well as in a clinical application involving sparse, motion-corrupted MR acquisition for fetal imaging. Our approach allows to reconstruct 3D volumes from 1 to 4 tomographic slices, with a SSIM of 0.7+ and cross-correlation of 0.8+ compared to the 3D ground truth.

eess.IV↗

arXiv2019

Multiple Landmark Detection using Multi-Agent Reinforcement Learning

The detection of anatomical landmarks is a vital step for medical image analysis and applications for diagnosis, interpretation and guidance. Manual annotation of landmarks is a tedious process that requires domain-specific expertise and introduces inter-observer variability. This paper proposes a new detection approach for multiple landmarks based on multi-agent reinforcement learning. Our hypothesis is that the position of all anatomical landmarks is interdependent and non-random within the human anatomy, thus finding one landmark can help to deduce the location of others. Using a Deep Q-Network (DQN) architecture we construct an environment and agent with implicit inter-communication such that we can accommodate K agents acting and learning simultaneously, while they attempt to detect K different landmarks. During training the agents collaborate by sharing their accumulated knowledge for a collective gain. We compare our approach with state-of-the-art architectures and achieve significantly better accuracy by reducing the detection error by 50%, while requiring fewer computational resources and time to train compared to the naive approach of training K agents separately.

cs.CV↗

arXiv2019

Controlling Meshes via Curvature: Spin Transformations for Pose-Invariant Shape Processing

We investigate discrete spin transformations, a geometric framework to manipulate surface meshes by controlling mean curvature. Applications include surface fairing -- flowing a mesh onto say, a reference sphere -- and mesh extrusion -- e.g., rebuilding a complex shape from a reference sphere and curvature specification. Because they operate in curvature space, these operations can be conducted very stably across large deformations with no need for remeshing. Spin transformations add to the algorithmic toolbox for pose-invariant shape analysis. Mathematically speaking, mean curvature is a shape invariant and in general fully characterizes closed shapes (together with the metric). Computationally speaking, spin transformations make that relationship explicit. Our work expands on a discrete formulation of spin transformations. Like their smooth counterpart, discrete spin transformations are naturally close to conformal (angle-preserving). This quasi-conformality can nevertheless be relaxed to satisfy the desired trade-off between area distortion and angle preservation. We derive such constraints and propose a formulation in which they can be efficiently incorporated. The approach is showcased on subcortical structures.

cs.CG↗

arXiv2018

Standard Plane Detection in 3D Fetal Ultrasound Using an Iterative Transformation Network

Standard scan plane detection in fetal brain ultrasound (US) forms a crucial step in the assessment of fetal development. In clinical settings, this is done by manually manoeuvring a 2D probe to the desired scan plane. With the advent of 3D US, the entire fetal brain volume containing these standard planes can be easily acquired. However, manual standard plane identification in 3D volume is labour-intensive and requires expert knowledge of fetal anatomy. We propose a new Iterative Transformation Network (ITN) for the automatic detection of standard planes in 3D volumes. ITN uses a convolutional neural network to learn the relationship between a 2D plane image and the transformation parameters required to move that plane towards the location/orientation of the standard plane in the 3D volume. During inference, the current plane image is passed iteratively to the network until it converges to the standard plane location. We explore the effect of using different transformation representations as regression outputs of ITN. Under a multi-task learning framework, we introduce additional classification probability outputs to the network to act as confidence measures for the regressed transformation parameters in order to further improve the localisation accuracy. When evaluated on 72 US volumes of fetal brain, our method achieves an error of 3.83mm/12.7 degrees and 3.80mm/12.6 degrees for the transventricular and transcerebellar planes respectively and takes 0.46s per plane. Source code is publicly available at https://github.com/yuanwei1989/plane-detection.

cs.CV↗

arXiv2018

Fast Multiple Landmark Localisation Using a Patch-based Iterative Network

We propose a new Patch-based Iterative Network (PIN) for fast and accurate landmark localisation in 3D medical volumes. PIN utilises a Convolutional Neural Network (CNN) to learn the spatial relationship between an image patch and anatomical landmark positions. During inference, patches are repeatedly passed to the CNN until the estimated landmark position converges to the true landmark location. PIN is computationally efficient since the inference stage only selectively samples a small number of patches in an iterative fashion rather than a dense sampling at every location in the volume. Our approach adopts a multi-task learning framework that combines regression and classification to improve localisation accuracy. We extend PIN to localise multiple landmarks by using principal component analysis, which models the global anatomical relationships between landmarks. We have evaluated PIN using 72 3D ultrasound images from fetal screening examinations. PIN achieves quantitatively an average landmark localisation error of 5.59mm and a runtime of 0.44s to predict 10 landmarks per volume. Qualitatively, anatomical 2D standard scan planes derived from the predicted landmark locations are visually similar to the clinical ground truth. Source code is publicly available at https://github.com/yuanwei1989/landmark-detection.

cs.CV↗

arXiv2018

Computing CNN Loss and Gradients for Pose Estimation with Riemannian Geometry

Pose estimation, i.e. predicting a 3D rigid transformation with respect to a fixed co-ordinate frame in, SE(3), is an omnipresent problem in medical image analysis with applications such as: image rigid registration, anatomical standard plane detection, tracking and device/camera pose estimation. Deep learning methods often parameterise a pose with a representation that separates rotation and translation. As commonly available frameworks do not provide means to calculate loss on a manifold, regression is usually performed using the L2-norm independently on the rotation's and the translation's parameterisations, which is a metric for linear spaces that does not take into account the Lie group structure of SE(3). In this paper, we propose a general Riemannian formulation of the pose estimation problem. We propose to train the CNN directly on SE(3) equipped with a left-invariant Riemannian metric, coupling the prediction of the translation and rotation defining the pose. At each training step, the ground truth and predicted pose are elements of the manifold, where the loss is calculated as the Riemannian geodesic distance. We then compute the optimisation direction by back-propagating the gradient with respect to the predicted pose on the tangent space of the manifold SE(3) and update the network weights. We thoroughly evaluate the effectiveness of our loss function by comparing its performance with popular and most commonly used existing methods, on tasks such as image-based localisation and intensity-based 2D/3D registration. We also show that hyper-parameters, used in our loss function to weight the contribution between rotations and translations, can be intrinsically calculated from the dataset to achieve greater performance margins.

cs.CV↗

arXiv2018

Automatic View Planning with Multi-scale Deep Reinforcement Learning Agents

We propose a fully automatic method to find standardized view planes in 3D image acquisitions. Standard view images are important in clinical practice as they provide a means to perform biometric measurements from similar anatomical regions. These views are often constrained to the native orientation of a 3D image acquisition. Navigating through target anatomy to find the required view plane is tedious and operator-dependent. For this task, we employ a multi-scale reinforcement learning (RL) agent framework and extensively evaluate several Deep Q-Network (DQN) based strategies. RL enables a natural learning paradigm by interaction with the environment, which can be used to mimic experienced operators. We evaluate our results using the distance between the anatomical landmarks and detected planes, and the angles between their normal vector and target. The proposed algorithm is assessed on the mid-sagittal and anterior-posterior commissure planes of brain MRI, and the 4-chamber long-axis plane commonly used in cardiac MRI, achieving accuracy of 1.53mm, 1.98mm and 4.84mm, respectively.

cs.CV↗

arXiv2018

3D Reconstruction in Canonical Co-ordinate Space from Arbitrarily Oriented 2D Images

Limited capture range, and the requirement to provide high quality initialization for optimization-based 2D/3D image registration methods, can significantly degrade the performance of 3D image reconstruction and motion compensation pipelines. Challenging clinical imaging scenarios, which contain significant subject motion such as fetal in-utero imaging, complicate the 3D image and volume reconstruction process. In this paper we present a learning based image registration method capable of predicting 3D rigid transformations of arbitrarily oriented 2D image slices, with respect to a learned canonical atlas co-ordinate system. Only image slice intensity information is used to perform registration and canonical alignment, no spatial transform initialization is required. To find image transformations we utilize a Convolutional Neural Network (CNN) architecture to learn the regression function capable of mapping 2D image slices to a 3D canonical atlas space. We extensively evaluate the effectiveness of our approach quantitatively on simulated Magnetic Resonance Imaging (MRI), fetal brain imagery with synthetic motion and further demonstrate qualitative results on real fetal MRI data where our method is integrated into a full reconstruction and motion compensation pipeline. Our learning based registration achieves an average spatial prediction error of 7 mm on simulated data and produces qualitatively improved reconstructions for heavily moving fetuses with gestational ages of approximately 20 weeks. Our model provides a general and computationally efficient solution to the 2D/3D registration initialization problem and is suitable for real-time scenarios.

cs.CV↗

arXiv2017

Context-Sensitive Super-Resolution for Fast Fetal Magnetic Resonance Imaging

3D Magnetic Resonance Imaging (MRI) is often a trade-off between fast but low-resolution image acquisition and highly detailed but slow image acquisition. Fast imaging is required for targets that move to avoid motion artefacts. This is in particular difficult for fetal MRI. Spatially independent upsampling techniques, which are the state-of-the-art to address this problem, are error prone and disregard contextual information. In this paper we propose a context-sensitive upsampling method based on a residual convolutional neural network model that learns organ specific appearance and adopts semantically to input data allowing for the generation of high resolution images with sharp edges and fine scale detail. By making contextual decisions about appearance and shape, present in different parts of an image, we gain a maximum of structural detail at a similar contrast as provided by high-resolution data. We experiment on $145$ fetal scans and show that our approach yields an increased PSNR of $1.25$ $dB$ when applied to under-sampled fetal data \emph{cf.} baseline upsampling. Furthermore, our method yields an increased PSNR of $1.73$ $dB$ when utilizing under-sampled fetal data to perform brain volume reconstruction on motion corrupted captured data.

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