Generalised Dice overlap as a deep learning loss function for highly unbalanced segmentations

Deep-learning has proved in recent years to be a powerful tool for image analysis and is now widely used to segment both 2D and 3D medical images. Deep-learning segmentation frameworks rely not only on the choice of network architecture but also on the choice of loss function. When the segmentation process targets rare observations, a severe class imbalance is likely to occur between candidate labels, thus resulting in sub-optimal performance. In order to mitigate this issue, strategies such as the weighted cross-entropy function, the sensitivity function or the Dice loss function, have been proposed. In this work, we investigate the behavior of these loss functions and their sensitivity to learning rate tuning in the presence of different rates of label imbalance across 2D and 3D segmentation tasks. We also propose to use the class re-balancing properties of the Generalized Dice overlap, a known metric for segmentation assessment, as a robust and accurate deep-learning loss function for unbalanced tasks

Diffeomorphic Demons using Normalised Mutual Information, Evaluation on Multi-Modal Brain MR Images

The demons algorithm is a fast non-parametric non-rigid registration method. In recent years great efforts have been made to improve the approach; the state of the art version yields symmetric inverse-consistent large-deformation diffeomorphisms. However, only limited work has explored inter-modal similarity metrics, with no practical evaluation on multi-modality data. We present a diffeomorphic demons implementation using the analytical gradient of Normalised Mutual Information (NMI) in a conjugate gradient optimiser. We report the first qualitative and quantitative assessment of the demons for inter-modal registration. Experiments to spatially normalise real MR images, and to recover simulated deformation fields, demonstrate (i) similar accuracy from NMI-demons and classical demons when the latter may be used, and (ii) similar accuracy for NMI-demons on T1w-T1w and T1w-T2w registration, demonstrating its potential in multi-modal scenarios

Diffeomorphic demons using normalized mutual information, evaluation on multimodal brain MR images

The demons algorithm is a fast non-parametric non-rigid registration method. In recent years great efforts have been made to improve the approach; the state of the art version yields symmetric inverse-consistent largedeformation diffeomorphisms. However, only limited work has explored inter-modal similarity metrics, with no practical evaluation on multi-modality data. We present a diffeomorphic demons implementation using the analytical gradient of Normalised Mutual Information (NMI) in a conjugate gradient optimiser. We report the first qualitative and quantitative assessment of the demons for inter-modal registration. Experiments to spatially normalise real MR images, and to recover simulated deformation fields, demonstrate (i) similar accuracy from NMI-demons and classical demons when the latter may be used, and (ii) similar accuracy for NMI-demons on T1w-T1w and T1w-T2w registration, demonstrating its potential in multi-modal scenarios

Disease-emergence dynamics and control in a socially-structured wildlife species

Once a pathogen is introduced in a population, key factors governing rate of spread include contact structure, supply of susceptible individuals and pathogen life-history. We examined the interplay of these factors on emergence dynamics and efficacy of disease prevention and response. We contrasted transmission dynamics of livestock viruses with different life-histories in hypothetical populations of feral swine with different contact structures (homogenous, metapopulation, spatial and network). Persistence probability was near 0 for the FMDV-like case under a wide range of parameter values and contact structures, while persistence was probable for the CSFV-like case. There were no sets of conditions where the FMDV-like pathogen persisted in every stochastic simulation. Even when population growth rates were up to 300% annually, the FMDV-like pathogen persisted in \u3c25% of simulations regardless of transmission probabilities and contact structure. For networks and spatial contact structure, persistence probability of the FMDV-like pathogen was always \u3c10%. Because of its low persistence probability, even very early response to the FMDV-like pathogen in feral swine was unwarranted while response to the CSFV-like pathogen was generally effective. When pre-emergence culling of feral swine caused population declines, it was effective at decreasing outbreak size of both diseases by ≥80%

Renormalization aspects of N=1 Super Yang-Mills theory in the Wess-Zumino gauge

The renormalization of N=1 Super Yang-Mills theory is analysed in the Wess-Zumino gauge, employing the Landau condition. An all orders proof of the renormalizability of the theory is given by means of the Algebraic Renormalization procedure. Only three renormalization constants are needed, which can be identified with the coupling constant, gauge field and gluino renormalization. The non-renormalization theorem of the gluon-ghost-antighost vertex in the Landau gauge is shown to remain valid in N=1 Super Yang-Mills. Moreover, due to the non-linear realization of the supersymmetry in the Wess-Zumino gauge, the renormalization factor of the gauge field turns out to be different from that of the gluino. These features are explicitly checked through a three loop calculation.Comment: 15 pages, minor text improvements, references added. Version accepted for publication in the EPJ

Predicting spatial spread of rabies in skunk populations using surveillance data reported by the public

Background: Prevention and control of wildlife disease invasions relies on the ability to predict spatio-temporal dynamics and understand the role of factors driving spread rates, such as seasonality and transmission distance. Passive disease surveillance (i.e., case reports by public) is a common method of monitoring emergence of wildlife diseases, but can be challenging to interpret due to spatial biases and limitations in data quantity and quality. Methodology/Principal findings: We obtained passive rabies surveillance data from dead striped skunks (Mephitis mephitis) in an epizootic in northern Colorado, USA. We developed a dynamic patch-occupancy model which predicts spatio-temporal spreading while accounting for heterogeneous sampling. We estimated the distance travelled per transmission event, direction of invasion, rate of spatial spread, and effects of infection density and season. We also estimated mean transmission distance and rates of spatial spread using a phylogeographic approach on a subsample of viral sequences from the same epizootic. Both the occupancy and phylogeographic approaches predicted similar rates of spatio-temporal spread. Estimated mean transmission distances were 2.3 km (95% Highest Posterior Density (HPD95): 0.02, 11.9; phylogeographic) and 3.9 km (95% credible intervals (CI95): 1.4, 11.3; occupancy). Estimated rates of spatial spread in km/year were: 29.8 (HPD95: 20.8, 39.8; phylogeographic, branch velocity, homogenous model), 22.6 (HPD95: 15.3, 29.7; phylogeographic, diffusion rate, homogenous model) and 21.1 (CI95: 16.7, 25.5; occupancy). Initial colonization probability was twice as high in spring relative to fall. Conclusions/Significance: Skunk-to-skunk transmission was primarily local (< 4 km) suggesting that if interventions were needed, they could be applied at the wave front. Slower viral invasions of skunk rabies in western USA compared to a similar epizootic in raccoons in the eastern USA implies host species or landscape factors underlie the dynamics of rabies invasions. Our framework provides a straightforward method for estimating rates of spatial spread of wildlife diseases

Forward-Backward Splitting in Deformable Image Registration: A Demons Approach

Efficient non-linear image registration implementations are key for many biomedical imaging applications. By using the classical demons approach, the associated optimization problem is solved by an alternate optimization scheme consisting of a gradient descent step followed by Gaussian smoothing. Despite being simple and powerful, the solution of the underlying relaxed formulation is not guaranteed to minimize the original global energy. Implicitly, however, this second step can be recast as the proximal map of the regularizer. This interpretation introduces a parallel to the more general Forward-Backward Splitting (FBS) scheme consisting of a forward gradient descent and proximal step. By shifting entirely to FBS, we can take advantage of the recent advances in FBS methods and solve the original, non-relaxed deformable registration problem for any type of differentiable similarity measure and convex regularization associated with a tractable proximal operator. Additionally, global convergence to a critical point is guaranteed under weak restrictions. For the first time in the context of image registration, we show that Tikhonov regularization breaks down to the simple use of B-Spline filtering in the proximal step. We demonstrate the versatility of FBS by encoding spatial transformation as displacement fields or free-form B-Spline deformations. We use state-of-the-art FBS solvers and compare their performance against the classical demons, the recently proposed inertial demons and the conjugate gradient optimizer. Numerical experiments performed on both synthetic and clinical data show the advantage of FBS in image registration in terms of both convergence and accuracy