Publications

PAIP 2019: Liver cancer segmentation challenge

Abstract

Pathology Artificial Intelligence Platform (PAIP) is a free research platform in support of pathological artificial intelligence (AI). The main goal of the platform is to construct a high-quality pathology learning data set that will allow greater accessibility. The PAIP Liver Cancer Segmentation Challenge, organized in conjunction with the Medical Image Computing and Computer Assisted Intervention Society (MICCAI 2019), is the first image analysis challenge to apply PAIP datasets. The goal of the challenge was to evaluate new and existing algorithms for automated detection of liver cancer in whole-slide images (WSIs). Additionally, the PAIP of this year attempted to address potential future problems of AI applicability in clinical settings. In the challenge, participants were asked to use analytical data and statistical metrics to evaluate the performance of automated algorithms in two different tasks. The participants were given the two different tasks: Task 1 involved investigating Liver Cancer Segmentation and Task 2 involved investigating Viable Tumor Burden Estimation. There was a strong correlation between high performance of teams on both tasks, in which teams that performed well on Task 1 also performed well on Task 2. After evaluation, we summarized the top 11 team’s algorithms. We then gave pathological implications on the easily predicted images for cancer segmentation and the challenging images for viable tumor burden estimation. Out of the 231 participants of the PAIP challenge datasets, a total of 64 were submitted from 28 team participants. The submitted algorithms predicted the automatic segmentation on the liver cancer with WSIs to an accuracy of a score estimation of 0.78. The PAIP challenge was created in an effort to combat the lack of research that has been done to address Liver cancer using digital pathology. It remains unclear of how the applicability of AI algorithms created during the challenge can affect clinical diagnoses. However, the results of this dataset and evaluation metric provided has the potential to aid the development and benchmarking of cancer diagnosis and segmentation.

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Do not treat boundaries and regions differently: An example on heart left atrial segmentation

Abstract

Atrial fibrillation is the most common heart rhythm disease. Due to a lack of understanding in matter of underlying atrial structures, current treatments are still not satisfying. Recently, with the popularity of deep learning, many segmentation methods based on fully convolutional networks have been proposed to analyze atrial structures, especially from late gadolinium-enhanced magnetic resonance imaging. However, two problems still occur: 1) segmentation results include the atrial- like background; 2) boundaries are very hard to segment. Most segmentation approaches design a specific network that mainly focuses on the regions, to the detriment of the boundaries. Therefore, this paper proposes an attention full convolutional network framework based on the ResNet-101 architecture, which focuses on boundaries as much as on regions. The additional attention module is added to have the network pay more attention on regions and then to reduce the impact of the misleading similarity of neighboring tissues. We also use a hybrid loss composed of a region loss and a boundary loss to treat boundaries and regions at the same time. We demonstrate the efficiency of the proposed approach on the MICCAI 2018 Atrial Segmentation Challenge public dataset.

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FOANet: A focus of attention network with application to myocardium segmentation

Abstract

In myocardium segmentation of cardiac magnetic resonance images, ambiguities often appear near the boundaries of the target domains due to tissue similarities. To address this issue, we propose a new architecture, called FOANet, which can be decomposed in three main steps: a localization step, a Gaussian-based contrast enhancement step, and a segmentation step. This architecture is supplied with a hybrid loss function that guides the FOANet to study the transformation relationship between the input image and the corresponding label in a three-level hierarchy (pixel-, patch- and map-level), which is helpful to improve segmentation and recovery of the boundaries. We demonstrate the efficiency of our approach on two public datasets in terms of regional and boundary segmentations.

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Equivalence between digital well-composedness and well-composedness in the sense of Alexandrov on $n$-D cubical grids

Abstract

Among the different flavors of well-composednesses on cubical grids, two of them, called respectively Digital Well-Composedness (DWCness) and Well-Composedness in the sens of Alexandrov (AWCness), are known to be equivalent in 2D and in 3D. The former means that a cubical set does not contain critical configurations when the latter means that the boundary of a cubical set is made of a disjoint union of discrete surfaces. In this paper, we prove that this equivalence holds in $n$-D, which is of interest because today images are not only 2D or 3D but also 4D and beyond. The main benefit of this proof is that the topological properties available for AWC sets, mainly their separation properties, are also true for DWC sets, and the properties of DWC sets are also true for AWC sets: an Euler number locally computable, equivalent connectivities from a local or global point of view… This result is also true for gray-level images thanks to cross-section topology, which means that the sets of shapes of DWC gray-level images make a tree like the ones of AWC gray-level images.

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Topological properties of the first non-local digitally well-composed interpolation on $n$-D cubical grids

Abstract

In discrete topology, we like digitally well-composed (shortly DWC) interpolations because they remove pinches in cubical images. Usual well-composed interpolations are local and sometimes self-dual (they treat in a same way dark and bright components in the image). In our case, we are particularly interested in $n$-D self-dual DWC interpolations to obtain a purely self-dual tree of shapes. However, it has been proved that we cannot have an $n$-D interpolation which is at the same time local, self-dual, and well-composed. By removing the locality constraint, we have obtained an $n$-D interpolation with many properties in practice: it is self-dual, DWC, and in-between (this last property means that it preserves the contours). Since we did not published the proofs of these results before, we propose to provide in a first time the proofs of the two last properties here (DWCness and in-betweeness) and a sketch of the proof of self-duality (the complete proof of self-duality requires more material and will come later). Some theoretical and practical results are given.

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Two stages CNN-based segmentation of gliomas, uncertainty quantification and prediction of overall patient survival

Abstract

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3BI-ECC: A decentralized identity framework based on blockchain technology and elliptic curve cryptography

Abstract

Most of the authentication protocols assume the existence of a Trusted Third Party (TTP) in the form of a Certificate Authority or as an authentication server. The main objective of this research is to present an autonomous solution where users could store their credentials, without depending on TTPs. For this, the use of an autonomous network is imperative, where users could use their uniqueness in order to identify themselves. We propose the framework “Three Blockchains Identity Management with Elliptic Curve Cryptography (3BI-ECC)”. Our proposed framework is a decentralize identity management system where users’ identities are self-generated.

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On the usefulness of clause strengthening in parallel SAT solving

Abstract

In the context of parallel SATisfiability solving, this paper presents an implementation and evaluation of a clause strengthening algorithm. The developed component can be easily combined with (virtually) any CDCL-like SAT solver. Our implementation is integrated as a part of Painless, a generic and modular framework for building parallel SAT solvers.

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A 4D counter-example showing that DWCness does not imply CWCness in $n$-D

Abstract

In this paper, we prove that the two flavours of well-composedness called Continuous Well-Composedness (shortly CWCness), stating that the boundary of the continuous analog of a discrete set is a manifold, and Digital Well-Composedness (shortly DWCness), stating that a discrete set does not contain any critical configuration, are not equivalent in dimension 4. To prove this, we exhibit the example of a configuration of 8 tesseracts (4D cubes) sharing a common corner (vertex), which is DWC but not CWC. This result is surprising since we know that CWCness and DWCness are equivalent in 2D and 3D. To reach our goal, we use local homology.

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Euler well-composedness

Abstract

In this paper, we define a new flavour of well-composedness, called Euler well-composedness, in the general setting of regular cell complexes: A regular cell complex is Euler well-composed if the Euler characteristic of the link of each boundary vertex is $1$. A cell decomposition of a picture $I$ is a pair of regular cell complexes $\big(K(I),K(\bar{I})\big)$ such that $K(I)$ (resp. $K(\bar{I})$) is a topological and geometrical model representing $I$ (resp. its complementary, $\bar{I}$). Then, a cell decomposition of a picture $I$ is self-dual Euler well-composed if both $K(I)$ and $K(\bar{I})$ are Euler well-composed. We prove in this paper that, first, self-dual Euler well-composedness is equivalent to digital well-composedness in dimension 2 and 3, and second, in dimension 4, self-dual Euler well-composedness implies digital well-composedness, though the converse is not true.

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