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Wen Yan

Publications and source records attributed to Wen Yan.

At least 55 records · Page 3Linked to original sources

Cross-Modality Image Registration using a Training-Time Privileged Third Modality

In this work, we consider the task of pairwise cross-modality image registration, which may benefit from exploiting additional images available only at training time from an additional modality that is different to those being registered. As an example, we focus on aligning intra-subject multiparametric Magnetic Resonance (mpMR) images, between T2-weighted (T2w) scans and diffusion-weighted scans with high b-value (DWI$_{high-b}$). For the application of localising tumours in mpMR images, diffusion scans with zero b-value (DWI$_{b=0}$) are considered easier to register to T2w due to the availability of corresponding features. We propose a learning from privileged modality algorithm, using a training-only imaging modality DWI$_{b=0}$, to support the challenging multi-modality registration problems. We present experimental results based on 369 sets of 3D multiparametric MRI images from 356 prostate cancer patients and report, with statistical significance, a lowered median target registration error of 4.34 mm, when registering the holdout DWI$_{high-b}$ and T2w image pairs, compared with that of 7.96 mm before registration. Results also show that the proposed learning-based registration networks enabled efficient registration with comparable or better accuracy, compared with a classical iterative algorithm and other tested learning-based methods with/without the additional modality. These compared algorithms also failed to produce any significantly improved alignment between DWI$_{high-b}$ and T2w in this challenging application.

cs.CV↗

Towards the cellular-scale simulation of motor-driven cytoskeletal assemblies

The cytoskeleton -- a collection of polymeric filaments, molecular motors, and crosslinkers -- is a foundational example of active matter, and in the cell assembles into organelles that guide basic biological functions. Simulation of cytoskeletal assemblies is an important tool for modeling cellular processes and understanding their surprising material properties. Here we present aLENS, a novel computational framework to surmount the limits of conventional simulation methods. We model molecular motors with crosslinking kinetics that adhere to a thermodynamic energy landscape, and integrate the system dynamics while efficiently and stably enforcing hard-body repulsion between filaments -- molecular potentials are entirely avoided in imposing steric constraints. Utilizing parallel computing, we simulate different mixtures of tens to hundreds of thousands of cytoskeletal filaments and crosslinking motors, recapitulating self-emergent phenomena such as bundle formation and buckling, and elucidating how motor type, thermal fluctuations, internal stresses, and confinement determine the evolution of active matter aggregates.

cond-mat.soft↗

The impact of using voxel-level segmentation metrics on evaluating multifocal prostate cancer localisation

Dice similarity coefficient (DSC) and Hausdorff distance (HD) are widely used for evaluating medical image segmentation. They have also been criticised, when reported alone, for their unclear or even misleading clinical interpretation. DSCs may also differ substantially from HDs, due to boundary smoothness or multiple regions of interest (ROIs) within a subject. More importantly, either metric can also have a nonlinear, non-monotonic relationship with outcomes based on Type 1 and 2 errors, designed for specific clinical decisions that use the resulting segmentation. Whilst cases causing disagreement between these metrics are not difficult to postulate. This work first proposes a new asymmetric detection metric, adapting those used in object detection, for planning prostate cancer procedures. The lesion-level metrics is then compared with the voxel-level DSC and HD, whereas a 3D UNet is used for segmenting lesions from multiparametric MR (mpMR) images. Based on experimental results we report pairwise agreement and correlation 1) between DSC and HD, and 2) between voxel-level DSC and recall-controlled precision at lesion-level, with Cohen's [0.49, 0.61] and Pearson's [0.66, 0.76] (p-values}<0.001) at varying cut-offs. However, the differences in false-positives and false-negatives, between the actual errors and the perceived counterparts if DSC is used, can be as high as 152 and 154, respectively, out of the 357 test set lesions. We therefore carefully conclude that, despite of the significant correlations, voxel-level metrics such as DSC can misrepresent lesion-level detection accuracy for evaluating localisation of multifocal prostate cancer and should be interpreted with caution.

eess.IV↗

Image quality assessment by overlapping task-specific and task-agnostic measures: application to prostate multiparametric MR images for cancer segmentation

Image quality assessment (IQA) in medical imaging can be used to ensure that downstream clinical tasks can be reliably performed. Quantifying the impact of an image on the specific target tasks, also named as task amenability, is needed. A task-specific IQA has recently been proposed to learn an image-amenability-predicting controller simultaneously with a target task predictor. This allows for the trained IQA controller to measure the impact an image has on the target task performance, when this task is performed using the predictor, e.g. segmentation and classification neural networks in modern clinical applications. In this work, we propose an extension to this task-specific IQA approach, by adding a task-agnostic IQA based on auto-encoding as the target task. Analysing the intersection between low-quality images, deemed by both the task-specific and task-agnostic IQA, may help to differentiate the underpinning factors that caused the poor target task performance. For example, common imaging artefacts may not adversely affect the target task, which would lead to a low task-agnostic quality and a high task-specific quality, whilst individual cases considered clinically challenging, which can not be improved by better imaging equipment or protocols, is likely to result in a high task-agnostic quality but a low task-specific quality. We first describe a flexible reward shaping strategy which allows for the adjustment of weighting between task-agnostic and task-specific quality scoring. Furthermore, we evaluate the proposed algorithm using a clinically challenging target task of prostate tumour segmentation on multiparametric magnetic resonance (mpMR) images, from 850 patients. The proposed reward shaping strategy, with appropriately weighted task-specific and task-agnostic qualities, successfully identified samples that need re-acquisition due to defected imaging process.

eess.IV↗

Hydrodynamic instabilities and collective dynamics in activity-balanced pusher-puller mixtures

Microorganisms living in microfluidic environments often form multi-species swarms, where they can leverage collective motions to achieve enhanced transport and spreading. Nevertheless, there is a general lack of physical understandings of the origins of the multiscale unstable dynamics observed within these systems. Here, we build a computational model to study binary suspensions of rear- and front-actuated microswimmers, or respectively the so-called "pusher" and "puller" particles, that have different populations and swimming speeds. We perform direct particle simulations to reveal that collective system dynamics are possible even in the scenario of an "activity-balanced" mixture, which produces near zero mean extra stress. We first construct a continuum kinetic model to describe the initial transient period when the system is near uniform isotropy and then perform linear stability analysis to reveal the system's finite-wavelength hydrodynamic instabilities, in contrast with the long-wavelength instabilities of pure pusher/puller suspensions. Then, we carry out slender-body discrete particle simulations to resolve both the short time instabilities and the the longtime dynamics, which feature non-trivial density fluctuations and spatially-correlated motions, distinct from those of single-species.

physics.flu-dyn↗

Few-shot image segmentation for cross-institution male pelvic organs using registration-assisted prototypical learning

The ability to adapt medical image segmentation networks for a novel class such as an unseen anatomical or pathological structure, when only a few labelled examples of this class are available from local healthcare providers, is sought-after. This potentially addresses two widely recognised limitations in deploying modern deep learning models to clinical practice, expertise-and-labour-intensive labelling and cross-institution generalisation. This work presents the first 3D few-shot interclass segmentation network for medical images, using a labelled multi-institution dataset from prostate cancer patients with eight regions of interest. We propose an image alignment module registering the predicted segmentation of both query and support data, in a standard prototypical learning algorithm, to a reference atlas space. The built-in registration mechanism can effectively utilise the prior knowledge of consistent anatomy between subjects, regardless whether they are from the same institution or not. Experimental results demonstrated that the proposed registration-assisted prototypical learning significantly improved segmentation accuracy (p-values<0.01) on query data from a holdout institution, with varying availability of support data from multiple institutions. We also report the additional benefits of the proposed 3D networks with 75% fewer parameters and an arguably simpler implementation, compared with existing 2D few-shot approaches that segment 2D slices of volumetric medical images.

eess.IV↗

Optimal Predefined-time Trajectory Planning for a Free-floating Space Robot

With the development of human space exploration, the space environment is gradually filled with abandoned satellite debris and unknown micrometeorites, which will seriously affect capture motion of space robot. Hence, a novel fast collision-avoidance trajectory planning strategy for a dual-arm free-floating space robot (FFSR) with predefined-time pose feedback will be mainly studied to achieve micron-level tracking accuracy of end-effector in this paper. However, similar to control, the exponential feedback results in larger initial joint angular velocity relative to proportional feedback. Firstly, a pose-error-based kinematic model of the FFSR will be derived from a control perspective. Then, a cumulative dangerous field (CDF) collision-avoidance algorithm is applied in predefined-time trajectory planning to achieve micron-level collision-avoidance trajectory tracking precision. In the end, a GA-based optimization algorithm is used to optimize the predefined-time parameter to obtain a motion trajectory of low joint angular velocity of robotic arms. The simulation results verify our conjecture and conclusion.

cs.RO↗

Kernel Aggregated Fast Multipole Method: Efficient summation of Laplace and Stokes kernel functions

Many different simulation methods for Stokes flow problems involve a common computationally intense task -- the summation of a kernel function over $O(N^2)$ pairs of points. One popular technique is the Kernel Independent Fast Multipole Method (KIFMM), which constructs a spatial adaptive octree for all points and places a small number of equivalent multipole and local equivalent points around each octree box, and completes the kernel sum with $O(N)$ cost, using these equivalent points. Simpler kernels can be used between these equivalent points to improve the efficiency of KIFMM. Here we present further extensions and applications to this idea, to enable efficient summations and flexible boundary conditions for various kernels. We call our method the Kernel Aggregated Fast Multipole Method (KAFMM), because it uses different kernel functions at different stages of octree traversal. We have implemented our method as an open-source software library STKFMM based on the high performance library PVFMM, with support for Laplace kernels, the Stokeslet, regularized Stokeslet, Rotne-Prager-Yamakawa (RPY) tensor, and the Stokes double-layer and traction operators. Open and periodic boundary conditions are supported for all kernels, and the no-slip wall boundary condition is supported for the Stokeslet and RPY tensor. The package is designed to be ready-to-use as well as being readily extensible to additional kernels.

math.NA↗

Controlling False Positive/Negative Rates for Deep-Learning-Based Prostate Cancer Detection on Multiparametric MR images

Prostate cancer (PCa) is one of the leading causes of death for men worldwide. Multi-parametric magnetic resonance (mpMR) imaging has emerged as a non-invasive diagnostic tool for detecting and localising prostate tumours by specialised radiologists. These radiological examinations, for example, for differentiating malignant lesions from benign prostatic hyperplasia in transition zones and for defining the boundaries of clinically significant cancer, remain challenging and highly skill-and-experience-dependent. We first investigate experimental results in developing object detection neural networks that are trained to predict the radiological assessment, using these high-variance labels. We further argue that such a computer-assisted diagnosis (CAD) system needs to have the ability to control the false-positive rate (FPR) or false-negative rate (FNR), in order to be usefully deployed in a clinical workflow, informing clinical decisions without further human intervention. This work proposes a novel PCa detection network that incorporates a lesion-level cost-sensitive loss and an additional slice-level loss based on a lesion-to-slice mapping function, to manage the lesion- and slice-level costs, respectively. Our experiments based on 290 clinical patients concludes that 1) The lesion-level FNR was effectively reduced from 0.19 to 0.10 and the lesion-level FPR was reduced from 1.03 to 0.66 by changing the lesion-level cost; 2) The slice-level FNR was reduced from 0.19 to 0.00 by taking into account the slice-level cost; (3) Both lesion-level and slice-level FNRs were reduced with lower FP/FPR by changing the lesion-level or slice-level costs, compared with post-training threshold adjustment using networks without the proposed cost-aware training.

eess.IV↗

On Parameter Selection of Nonsingular Predefined-time Terminal Sliding Mode With the Fixed-time Convergence Guarantee

This paper study the parameter selection of predefined-time sliding mode and try to design a general nonsingular predefined-time terminal sliding mode. 1). On parameter selection: Some existing predefined-time sliding modes are designed to focus on the reaching time and ignore the characterization of the equilibrium point i.e. x_e= 0. In actual engineer, the system can only converge to a small neighborhood near the equilibrium point because of the existence of uncertainty i.e. x_e \to 0. The actual equilibrium point should be deduced by taking the limit but not directly solve the equilibrium point. Hence, the actual selection of exponential term is suggested to be not 1 to make system convergence to the equilibrium point within predefined time. 2). On singularity-avoidance: Based on the exponential feature of predefined-time stability systems, a mathematic concept of switching sliding mode \cite{su1994adaptive} is applied in the design of nonsingular predefined-time terminal sliding mode. However, this class of sliding mode switching method will cause a singular problem, which can be described as control input u \to \infty if the system state x \to 0 and any-order time derivative of x is not 0. Hence, a non-singular selection condition for each recursive sliding mode surface is explored in this paper to realize the global finiteness of control input. In addition, an unnecessary chattering of control input will also be caused by the sliding mode switching frequency, and a novel switching condition will be applied in the controller to reduce this chattering. Simulations will be carried out to validate the effect of the novel nonsingular predefined-time sliding mode control method to some extent.

math.OC↗

A scalable computational platform for particulate Stokes suspensions

We describe a computational framework for simulating suspensions of rigid particles in Newtonian Stokes flow. One central building block is a collision-resolution algorithm that overcomes the numerical constraints arising from particle collisions. This algorithm extends the well-known complementarity method for non-smooth multi-body dynamics to resolve collisions in dense rigid body suspensions. This approach formulates the collision resolution problem as a linear complementarity problem with geometric `non-overlapping' constraints imposed at each timestep. It is then reformulated as a constrained quadratic programming problem and the Barzilai-Borwein projected gradient descent method is applied for its solution. This framework is designed to be applicable for any convex particle shape, e.g., spheres and spherocylinders, and applicable to any Stokes mobility solver, including the Rotne-Prager-Yamakawa approximation, Stokesian Dynamics, and PDE solvers (e.g., boundary integral and immersed boundary methods). In particular, this method imposes Newton's Third Law and records the entire contact network. Further, we describe a fast, parallel, and spectrally-accurate boundary integral method tailored for spherical particles, capable of resolving lubrication effects. We show weak and strong parallel scalings up to $8\times 10^4$ particles with approximately $4\times 10^7$ degrees of freedom on $1792$ cores. We demonstrate the versatility of this framework with several examples, including sedimentation of particle clusters, and active matter systems composed of ensembles of particles driven to rotate.

cs.CE↗

Complex dynamics of long, flexible fibers in shear

The macroscopic properties of polymeric fluids are inherited from the material properties of the fibers embedded in the solvent. The behavior of such passive fibers in flow has been of interest in a wide range of systems, including cellular mechanics, nutrient aquisition by diatom chains in the ocean, and industrial applications such as paper manufacturing. The rotational dynamics and shape evolution of fibers in shear depends upon the slenderness of the fiber and the non-dimensional "elasto-viscous" number that measures the ratio of the fluid's viscous forces to the fiber's elastic forces. For a small elasto-viscous number, the nearly-rigid fiber rotates in the shear, but when the elasto-viscous number reaches a threshhold, buckling occurs. For even larger elasto-viscous numbers, there is a transition to a "snaking behavior" where the fiber remains aligned with the shear axis, but its ends curl in, in opposite directions. These experimentally-observed behaviors have recently been characterized computationally using slender-body theory and immersed boundary computations. However, classical experiments with nylon fibers and recent experiments with actin filaments have demonstrated that for even larger elasto-viscous numbers, multiple buckling sites and coiling can occur. Using a regularized Stokeslet framework coupled with a kernel independent fast multipole method, we present simulations that capture these complex fiber dynamics.

cond-mat.soft↗

Computing collision stress in assemblies of active spherocylinders: applications of a fast and generic geometric method

In this work, we provide a solution to the problem of computing collision stress in particle-tracking simulations. First, a formulation for the collision stress between particles is derived as an extension of the virial stress formula to general-shaped particles with uniform or non-uniform density. Second, we describe a collision-resolution algorithm based on geometric constraint minimization which eliminates the stiff pairwise potentials in traditional methods. The method is validated with a comparison to the equation of state of Brownian spherocylinders. Then we demonstrate the application of this method in several emerging problems of soft active matter.

physics.flu-dyn↗

Flexibly imposing periodicity in kernel independent FMM: A Multipole-To-Local operator approach

An important but missing component in the application of the kernel independent fast multipole method (KIFMM) is the capability for flexibly and efficiently imposing singly, doubly, and triply periodic boundary conditions. In most popular packages such periodicities are imposed with the hierarchical repetition of periodic boxes, which may give an incorrect answer due to the conditional convergence of some kernel sums. Here we present an efficient method to properly impose periodic boundary conditions using a near-far splitting scheme. The near-field contribution is directly calculated with the KIFMM method, while the far-field contribution is calculated with a multipole-to-local (M2L) operator which is independent of the source and target point distribution. The M2L operator is constructed with the far-field portion of the kernel function to generate the far-field contribution with the downward equivalent source points in KIFMM. This method guarantees the sum of the near-field \& far-field converge pointwise to results satisfying periodicity and compatibility conditions. The computational cost of the far-field calculation observes the same $\mathcal{O}(N)$ complexity as FMM and is designed to be small by reusing the data computed by KIFMM for the near-field. The far-field calculations require no additional control parameters, and observes the same theoretical error bound as KIFMM. We present accuracy and timing test results for the Laplace kernel in singly periodic domains and the Stokes velocity kernel in doubly and triply periodic domains.

math.NA↗

Universal image systems for non-periodic and periodic Stokes flows above a no-slip wall

It is well-known that by placing judiciously chosen image point forces and doublets to the Stokeslet above a flat wall, the no-slip boundary condition can be conveniently imposed on the wall [Blake, J. R. Math. Proc. Camb. Philos. Soc. 70(2), 1971: 303.]. However, to further impose periodic boundary conditions on directions parallel to the wall usually involves tedious derivations because single or double periodicity in Stokes flow may require the periodic unit to have no net force, which is not satisfied by the well-known image system. In this work we present a force-neutral image system. This neutrality allows us to represent the Stokes image system in a universal formulation for non-periodic, singly periodic and doubly periodic geometries. This formulation enables the black-box style usage of fast kernel summation methods. We demonstrate the efficiency and accuracy of this new image method with the periodic kernel independent fast multipole method in both non-periodic and doubly periodic geometries. We then extend this new image system to other widely used Stokes fundamental solutions, including the Laplacian of the Stokeslet and the Rotne-Prager-Yamakawa tensor.

math.NA↗

Anisotropic swim stress in active matter with nematic order

Active Brownian Particles (ABPs) transmit a swim pressure $Π^{swim}=nζD^{swim}$ to the container boundaries, where $ζ$ is the drag coefficient, $D^{swim}$ is the swim diffusivity and $n$ is the uniform bulk number density far from the container walls. In this work we extend the notion of the isotropic swim pressure to the anisotropic tensorial swim stress $\mathbfσ^{swim} = - n ζ\mathbf{D}^{swim}$, which is related to the anisotropic swim diffusivity $\mathbf{D}^{swim}$. We demonstrate this relationship with ABPs that achieve nematic orientational order via a bulk external field. The anisotropic swim stress is obtained analytically for dilute ABPs in both 2D and 3D systems, and the anisotropy is shown to grow exponentially with the strength of the external field. We verify that the normal component of the anisotropic swim stress applies a pressure $Π^{swim}=-(\mathbfσ^{swim}\cdot\mathbf{n})\cdot\mathbf{n}$ on a wall with normal vector $\mathbf{n}$, and, through Brownian dynamics simulations, this pressure is shown to be the force per unit area transmitted by the active particles. Since ABPs have no friction with a wall, the difference between the normal and tangential stress components -- the normal stress difference -- generates a net flow of ABPs along the wall, which is a generic property of active matter systems.

cond-mat.soft↗

Unsupervised End-to-end Learning for Deformable Medical Image Registration

We propose a registration algorithm for 2D CT/MRI medical images with a new unsupervised end-to-end strategy using convolutional neural networks. The contributions of our algorithm are threefold: (1) We transplant traditional image registration algorithms to an end-to-end convolutional neural network framework, while maintaining the unsupervised nature of image registration problems. The image-to-image integrated framework can simultaneously learn both image features and transformation matrix for registration. (2) Training with additional data without any label can further improve the registration performance by approximately 10 %. (3) The registration speed is 100x faster than traditional methods. The proposed network is easy to implement and can be trained efficiently. Experiments demonstrate that our system achieves state-of-the-art results on 2D brain registration and achieves comparable results on 2D liver registration. It can be extended to register other organs beyond liver and brain such as kidney, lung, and heart.

cs.CV↗

The curved kinetic boundary layer of active matter

The finite reorient-time of swimmers leads to a finite run length $\ell$ and the kinetic accumulation boundary layer on the microscopic length scale $δ$ on a non-penetrating wall. That boundary layer is the microscopic origin of the swim pressure, and is impacted by the geometry of the boundary [Yan \& Brady, \textit{J. Fluid. Mech.}, 2015, \textbf{785}, R1]. In this work we extend the analysis to analytically solve the boundary layer on an arbitrary-shaped body distorted by the local mean curvature. The solution gives the swim pressure distribution and the total force (torque) on an arbitrarily shaped body immersed in swimmers, with a general scaling of the curvature effect $Π^{swim}\simλδ^2/L$.

cond-mat.soft↗