Foveation for Segmentation of Mega-Pixel Histology Images

Segmenting histology images is challenging because of the sheer size of the images with millions or even billions of pixels. Typical solutions pre-process each histology image by dividing it into patches of fixed size and/or down-sampling to meet memory constraints. Such operations incur information loss in the field-of-view (FoV) (i.e., spatial coverage) and the image resolution. The impact on segmentation performance is, however, as yet understudied. In this work, we first show under typical memory constraints (e.g., 10G GPU memory) that the trade-off between FoV and resolution considerably affects segmentation performance on histology images, and its influence also varies spatially according to local patterns in different areas (see Fig. 1). Based on this insight, we then introduce foveation module, a learnable “dataloader” which, for a given histology image, adaptively chooses the appropriate configuration (FoV/resolution trade-off) of the input patch to feed to the downstream segmentation model at each spatial location (Fig. 1). The foveation module is jointly trained with the segmentation network to maximise the task performance. We demonstrate, on the Gleason2019 challenge dataset for histopathology segmentation, that the foveation module improves segmentation performance over the cases trained with patches of fixed FoV/resolution trade-off. Moreover, our model achieves better segmentation accuracy for the two most clinically important and ambiguous classes (Gleason Grade 3 and 4) than the top performers in the challenge by 13.1% and 7.5%, and improves on the average performance of 6 human experts by 6.5% and 7.5%

Spectral isolation of naturally reductive metrics on simple Lie groups

We show that within the class of left-invariant naturally reductive metrics $\mathcal{M}_{\operatorname{Nat}}(G)$ on a compact simple Lie group $G$, every metric is spectrally isolated. We also observe that any collection of isospectral compact symmetric spaces is finite; this follows from a somewhat stronger statement involving only a finite part of the spectrum.Comment: 19 pages, new title and abstract, revised introduction, new result demonstrating that any collection of isospectral compact symmetric spaces must be finite, to appear Math Z. (published online Dec. 2009

Uncertainty in multitask learning: joint representations for probabilistic MR-only radiotherapy planning

Multi-task neural network architectures provide a mechanism that jointly integrates information from distinct sources. It is ideal in the context of MR-only radiotherapy planning as it can jointly regress a synthetic CT (synCT) scan and segment organs-at-risk (OAR) from MRI. We propose a probabilistic multi-task network that estimates: 1) intrinsic uncertainty through a heteroscedastic noise model for spatially-adaptive task loss weighting and 2) parameter uncertainty through approximate Bayesian inference. This allows sampling of multiple segmentations and synCTs that share their network representation. We test our model on prostate cancer scans and show that it produces more accurate and consistent synCTs with a better estimation in the variance of the errors, state of the art results in OAR segmentation and a methodology for quality assurance in radiotherapy treatment planning.Comment: Early-accept at MICCAI 2018, 8 pages, 4 figure

Multi-stage prediction networks for data harmonization

In this paper, we introduce multi-task learning (MTL) to data harmonization (DH); where we aim to harmonize images across different acquisition platforms and sites. This allows us to integrate information from multiple acquisitions and improve the predictive performance and learning efficiency of the harmonization model. Specifically, we introduce the Multi Stage Prediction (MSP) Network, a MTL framework that incorporates neural networks of potentially disparate architectures, trained for different individual acquisition platforms, into a larger architecture that is refined in unison. The MSP utilizes high-level features of single networks for individual tasks, as inputs of additional neural networks to inform the final prediction, therefore exploiting redundancy across tasks to make the most of limited training data. We validate our methods on a dMRI harmonization challenge dataset, where we predict three modern platform types, from one obtained from an old scanner. We show how MTL architectures, such as the MSP, produce around 20% improvement of patch-based mean-squared error over current state-of-the-art methods and that our MSP outperforms off-the-shelf MTL networks. Our code is availabl

Stochastic Filter Groups for Multi-Task CNNs: Learning Specialist and Generalist Convolution Kernels

The performance of multi-task learning in Convolutional Neural Networks (CNNs) hinges on the design of feature sharing between tasks within the architecture. The number of possible sharing patterns are combinatorial in the depth of the network and the number of tasks, and thus hand-crafting an architecture, purely based on the human intuitions of task relationships can be time-consuming and suboptimal. In this paper, we present a probabilistic approach to learning task-specific and shared representations in CNNs for multi-task learning. Specifically, we propose "stochastic filter groups'' (SFG), a mechanism to assign convolution kernels in each layer to "specialist'' or "generalist'' groups, which are specific to or shared across different tasks, respectively. The SFG modules determine the connectivity between layers and the structures of task-specific and shared representations in the network. We employ variational inference to learn the posterior distribution over the possible grouping of kernels and network parameters. Experiments demonstrate that the proposed method generalises across multiple tasks and shows improved performance over baseline methods.Comment: Accepted for oral presentation at ICCV 201

(Re)constructing Dimensions

Compactifying a higher-dimensional theory defined in R^{1,3+n} on an n-dimensional manifold {\cal M} results in a spectrum of four-dimensional (bosonic) fields with masses m^2_i = \lambda_i, where - \lambda_i are the eigenvalues of the Laplacian on the compact manifold. The question we address in this paper is the inverse: given the masses of the Kaluza-Klein fields in four dimensions, what can we say about the size and shape (i.e. the topology and the metric) of the compact manifold? We present some examples of isospectral manifolds (i.e., different manifolds which give rise to the same Kaluza-Klein mass spectrum). Some of these examples are Ricci-flat, complex and K\"{a}hler and so they are isospectral backgrounds for string theory. Utilizing results from finite spectral geometry, we also discuss the accuracy of reconstructing the properties of the compact manifold (e.g., its dimension, volume, and curvature etc) from measuring the masses of only a finite number of Kaluza-Klein modes.Comment: 23 pages, 3 figures, 2 references adde

Gallot-Tanno Theorem for closed incomplete pseudo-Riemannian manifolds and applications

We extend the Gallot-Tanno Theorem to closed pseudo-Riemannian manifolds. It is done by showing that if the cone over a manifold admits a parallel symmetric $(0,2)-$tensor then it is Riemannian. Applications of this result to the existence of metrics with distinct Levi-Civita connections but having the same unparametrized geodesics and to the projective Obata conjecture are given. We also apply our result to show that the holonomy group of a closed $(O(p+1,q),S^{p,q})$-manifold does not preserve any nondegenerate splitting of $\R^{p+1,q}$.Comment: minor correction

Food-induced fatal anaphylaxis: from epidemiological data to general prevention strategies

BACKGROUND: Anaphylaxis hospitalisations are increasing in many countries, in particular for medication and food triggers in young children. Food-related anaphylaxis remains an uncommon cause of death, but a significant proportion of these are preventable. AIM: To review published epidemiological data relating to food-induced anaphylaxis and potential risk factors of fatal and/or near-fatal anaphylaxis cases, in order to provide strategies to reduce the risk of severe adverse outcomes in food anaphylaxis. METHODS: We identified 32 published studies available in MEDLINE (1966-2017), EMBASE (1980-2017), CINAHL (1982-2017), using known terms and synonyms suggested by librarians and allergy specialists. RESULTS: Young adults with a history of asthma, previously known food allergy particularly to peanut/tree nuts are at higher risk of fatal anaphylaxis reactions. In some countries, cow's milk and seafood/fish are also becoming common triggers of fatal reactions. Delayed adrenaline injection is associated with fatal outcomes, but timely adrenaline alone may be insufficient. There is still a lack of evidence regarding the real impact of these risk factors and co-factors (medications and/or alcohol consumption, physical activities, and mast cell disorders). CONCLUSIONS: General strategies should include optimization of the classification and coding for anaphylaxis (new ICD 11 anaphylaxis codes), dissemination of international recommendations on the treatment of anaphylaxis, improvement of the prevention in food and catering areas and, dissemination of specific policies for allergic children in schools. Implementation of these strategies will involve national and international support for ongoing local efforts in relationship with networks of centres of excellence to provide personalized management (which might include immunotherapy) for the most at-risk patients. This article is protected by copyright. All rights reserved

Energy properness and Sasakian-Einstein metrics

In this paper, we show that the existence of Sasakian-Einstein metrics is closely related to the properness of corresponding energy functionals. Under the condition that admitting no nontrivial Hamiltonian holomorphic vector field, we prove that the existence of Sasakian-Einstein metric implies a Moser-Trudinger type inequality. At the end of this paper, we also obtain a Miyaoka-Yau type inequality in Sasakian geometry.Comment: 27 page