Adriana Romero Soriano

Pietro Lio’

Johannes Welbl

Pontus Stenetorp

Yonghui Wu

Mike Schuster

Quoc Zhifeng Chen

Mohammad Le

Wolfgang Norouzi

Macherey

M. Krikun

Yuan Cao

Qin Gao

William W. Cohen

Jianxing Yu

Xiaojun Quan

Qinliang Su

Jian Yin

Yuyu Zhang

Hanjun Dai

Zornitsa Kozareva

Cheng Zhao

Chenyan Xiong

Corby Rosset

Xia

Paul Song

Bennett Saurabh

Tiwary

Yao Zhao

Xiaochuan Ni

Yuanyuan Ding

Qingyu Zhou

Nan Yang

Furu Wei

Chuanqi Tan

Previous research on automated question gen-001 eration has almost exclusively focused on gen-002 erating factoid questions whose answers ca… (voir plus)n 003 be extracted from a single document. How-004 ever, there is an increasing interest in develop-005 ing systems that are capable of more complex 006 multi-hop question generation (QG), where an-007 swering the question requires reasoning over 008 multiple documents. In this work, we pro-009 pose a simple and effective approach based on 010 the transformer model for multi-hop QG. Our 011 approach consists of specialized input repre-012 sentations, a supporting sentence classiﬁcation 013 objective, and training data weighting. Prior 014 work on multi-hop QG considers the simpli-015 ﬁed setting of shorter documents and also ad-016 vocates the use of entity-based graph struc-017 tures as essential ingredients in model design. 018 On the contrary, we showcase that our model 019 can scale to the challenging setting of longer 020 documents as input, does not rely on graph 021 structures, and substantially outperforms the 022 state-of-the-art approaches as measured by au-023 tomated metrics and human evaluation. 024

2021-01-01

(publié)

www.semanticscholar.org

3D Shape Reconstruction from Vision and Touch

Edward J. Smith

Roberto Calandra

Georgia Gkioxari

David Meger

Jitendra Malik

Michal Drozdzal

When a toddler is presented a new toy, their instinctual behaviour is to pick it up and inspect it with their hand and eyes in tandem, clear… (voir plus)ly searching over its surface to properly understand what they are playing with. Here, touch provides high fidelity localized information while vision provides complementary global context. However, in 3D shape reconstruction, the complementary fusion of visual and haptic modalities remains largely unexplored. In this paper, we study this problem and present an effective chart-based approach to fusing vision and touch, which leverages advances in graph convolutional networks. To do so, we introduce a dataset of simulated touch and vision signals from the interaction between a robotic hand and a large array of 3D objects. Our results show that (1) leveraging both vision and touch signals consistently improves single-modality baselines; (2) our approach outperforms alternative modality fusion methods and strongly benefits from the proposed chart-based structure; (3) the reconstruction quality increases with the number of grasps provided; and (4) the touch information not only enhances the reconstruction at the touch site but also extrapolates to its local neighborhood.

Automated segmentation of cortical layers in BigBrain reveals divergent cortical and laminar thickness gradients in sensory and motor cortices.

Konrad Wagstyl

Stéphanie Larocque

Guillem Cucurull

Claude Lepage

Joseph Paul Cohen

Sebastian Bludau

Nicola Palomero-Gallagher

L. Lewis

Thomas Funck

Hannah Spitzer

Timo Dicksheid

Paul C Fletcher

Karl Zilles

Katrin Amunts

Alan C. Evans

Abstract Large-scale in vivo neuroimaging datasets offer new possibilities for reliable, well-powered measures of interregional structural d… (voir plus)ifferences and biomarkers of pathological changes in a wide variety of neurological and psychiatric diseases. However, so far studies have been structurally and functionally imprecise, being unable to relate pathological changes to specific cortical layers or neurobiological processes. We developed artificial neural networks to segment cortical and laminar surfaces in the BigBrain, a 3D histological model of the human brain. We sought to test whether previously-reported thickness gradients, as measured by MRI, in sensory and motor processing cortices, were present in a histological atlas of cortical thickness, and which cortical layers were contributing to these gradients. Identifying common gradients of cortical organisation enables us to meaningfully relate microstructural, macrostructural and functional cortical parameters. Analysis of thickness gradients across sensory cortices, using our fully segmented six-layered model, was consistent with MRI findings, showing increasing thickness moving up the processing hierarchy. In contrast, fronto-motor cortices showed the opposite pattern with changes in thickness of layers III, V and VI being the primary drivers of these gradients. As well as identifying key differences between sensory and motor gradients, our findings show how the use of this laminar atlas offers insights that will be key to linking single-neuron morphological changes, mesoscale cortical layers and macroscale cortical thickness.

2019-03-17

bioRxiv (prépublication)

BigBrain 3D atlas of cortical layers: Cortical and laminar thickness gradients diverge in sensory and motor cortices

Konrad Wagstyl

Stéphanie Larocque

Guillem Cucurull

Claude Lepage

Joseph Paul Cohen

Sebastian Bludau

Nicola Palomero-Gallagher

L. Lewis

Thomas Funck

Hannah Spitzer

Timo Dicksheid

Paul C Fletcher

Karl Zilles

Katrin Amunts

Alan C. Evans

Histological atlases of the cerebral cortex, such as those made famous by Brodmann and von Economo, are invaluable for understanding human b… (voir plus)rain microstructure and its relationship with functional organization in the brain. However, these existing atlases are limited to small numbers of manually annotated samples from a single cerebral hemisphere, measured from 2D histological sections. We present the first whole-brain quantitative 3D laminar atlas of the human cerebral cortex. This atlas was derived from a 3D histological model of the human brain at 20 micron isotropic resolution (BigBrain), using a convolutional neural network to segment, automatically, the cortical layers in both hemispheres. Our approach overcomes many of the historical challenges with measurement of histological thickness in 2D and the resultant laminar atlas provides an unprecedented level of precision and detail. We utilized this BigBrain cortical atlas to test whether previously reported thickness gradients, as measured by MRI in sensory and motor processing cortices, were present in a histological atlas of cortical thickness, and which cortical layers were contributing to these gradients. Cortical thickness increased across sensory processing hierarchies, primarily driven by layers III, V and VI. In contrast, fronto-motor cortices showed the opposite pattern, with decreases in total and pyramidal layer thickness. These findings illustrate how this laminar atlas will provide a link between single-neuron morphology, mesoscale cortical layering, macroscopic cortical thickness and, ultimately, functional neuroanatomy.

2019-03-17

bioRxiv (prépublication)

BigBrain 3D atlas of cortical layers: Cortical and laminar thickness gradients diverge in sensory and motor cortices

Konrad Wagstyl

Stéphanie Larocque

Guillem Cucurull

Claude Lepage

Joseph Paul Cohen

Sebastian Bludau

Nicola Palomero-Gallagher

L. Lewis

Thomas Funck

Hannah Spitzer

Timo Dicksheid

Paul C Fletcher

Karl Zilles

Katrin Amunts

Alan C. Evans

Histological atlases of the cerebral cortex, such as those made famous by Brodmann and von Economo, are invaluable for understanding human b… (voir plus)rain microstructure and its relationship with functional organization in the brain. However, these existing atlases are limited to small numbers of manually annotated samples from a single cerebral hemisphere, measured from 2D histological sections. We present the first whole-brain quantitative 3D laminar atlas of the human cerebral cortex. This atlas was derived from a 3D histological model of the human brain at 20 micron isotropic resolution (BigBrain), using a convolutional neural network to segment, automatically, the cortical layers in both hemispheres. Our approach overcomes many of the historical challenges with measurement of histological thickness in 2D and the resultant laminar atlas provides an unprecedented level of precision and detail. We utilized this BigBrain cortical atlas to test whether previously reported thickness gradients, as measured by MRI in sensory and motor processing cortices, were present in a histological atlas of cortical thickness, and which cortical layers were contributing to these gradients. Cortical thickness increased across sensory processing hierarchies, primarily driven by layers III, V and VI. In contrast, fronto-motor cortices showed the opposite pattern, with decreases in total and pyramidal layer thickness. These findings illustrate how this laminar atlas will provide a link between single-neuron morphology, mesoscale cortical layering, macroscopic cortical thickness and, ultimately, functional neuroanatomy.

2019-03-17

bioRxiv (prépublication)

On the Iterative Refinement of Densely Connected Representation Levels for Semantic Segmentation

Arantxa Casanova

Guillem Cucurull

Michal Drozdzal

State-of-the-art semantic segmentation approaches increase the receptive field of their models by using either a downsampling path composed … (voir plus)of poolings/strided convolutions or successive dilated convolutions. However, it is not clear which operation leads to best results. In this paper, we systematically study the differences introduced by distinct receptive field enlargement methods and their impact on the performance of a novel architecture, called Fully Convolutional DenseResNet (FC-DRN). FC-DRN has a densely connected backbone composed of residual networks. Following standard image segmentation architectures, receptive field enlargement operations that change the representation level are interleaved among residual networks. This allows the model to exploit the benefits of both residual and dense connectivity patterns, namely: gradient flow, iterative refinement of representations, multi-scale feature combination and deep supervision. In order to highlight the potential of our model, we test it on the challenging CamVid urban scene understanding benchmark and make the following observations: 1) downsampling operations outperform dilations when the model is trained from scratch, 2) dilations are useful during the finetuning step of the model, 3) coarser representations require less refinement steps, and 4) ResNets (by model construction) are good regularizers, since they can reduce the model capacity when needed. Finally, we compare our architecture to alternative methods and report state-of-the-art result on the Camvid dataset, with at least twice fewer parameters.

2018-06-18

2018 IEEE/CVF Conference on Computer Vision and Pattern Recognition Workshops (CVPRW) (publié)

BigBrain: 1D convolutional neural networks for automated sementation of cortical layers

Konrad Wagstyl

Claude Lepage

Karl Zilles

Sebastian Bludau

G. Cucurul

Alan C. Evans

Paul C Fletcher

Joseph Paul Cohen

Stéphanie Larocque

Thomas Funck

Katrin Amunts

Convolutional neural networks for mesh-based parcellation of the cerebral cortex

Guillem Cucurull

Konrad Wagstyl

Arantxa Casanova

Petar Veličković

Estrid Jakobsen

Michal Drozdzal

Alan C. Evans

In order to understand the organization of the cerebral cortex, it is necessary to create a map or parcellation of cortical areas. Reconstru… (voir plus)ctions of the cortical surface created from structural MRI scans, are frequently used in neuroimaging as a common coordinate space for representing multimodal neuroimaging data. These meshes are used to investigate healthy brain organization as well as abnormalities in neurological and psychiatric conditions. We frame cerebral cortex parcellation as a mesh segmentation task, and address it by taking advantage of recent advances in generalizing convolutions to the graph domain. In particular, we propose to assess graph convolutional networks and graph attention networks, which, in contrast to previous mesh parcellation models, exploit the underlying structure of the data to make predictions. We show experimentally on the Human Connectome Project dataset that the proposed graph convolutional models outperform current state-of-the-art and baselines, highlighting the potential and applicability of these methods to tackle neuroimaging challenges, paving the road towards a better characterization of brain diseases.

2018-01-01

MIDL.amsterdam/2018/Conference (présentation orale)

openreview.net

Graph Attention Networks

Petar Veličković

Guillem Cucurull

Arantxa Casanova

Pietro Lio

2018-01-01

ICLR.cc/2018/Conference (poster)

openreview.net

Graph Attention Networks

Petar Veličković

Guillem Cucurull

Arantxa Casanova

Pietro Lio

2017-10-30

ArXiv (prépublication)

Graph Attention Networks

Petar Veličković

Guillem Cucurull

Arantxa Casanova

Pietro Lio

2017-10-30

ArXiv (prépublication)

A Benchmark for Endoluminal Scene Segmentation of Colonoscopy Images

David Vázquez

Jorge Bernal

F. Javier Sánchez

Gloria Fernández-Esparrach

Antonio M. López

Michal Drozdzal

Aaron Courville

Colorectal cancer (CRC) is the third cause of cancer death worldwide. Currently, the standard approach to reduce CRC-related mortality is to… (voir plus) perform regular screening in search for polyps and colonoscopy is the screening tool of choice. The main limitations of this screening procedure are polyp miss rate and the inability to perform visual assessment of polyp malignancy. These drawbacks can be reduced by designing decision support systems (DSS) aiming to help clinicians in the different stages of the procedure by providing endoluminal scene segmentation. Thus, in this paper, we introduce an extended benchmark of colonoscopy image segmentation, with the hope of establishing a new strong benchmark for colonoscopy image analysis research. The proposed dataset consists of 4 relevant classes to inspect the endoluminal scene, targeting different clinical needs. Together with the dataset and taking advantage of advances in semantic segmentation literature, we provide new baselines by training standard fully convolutional networks (FCNs). We perform a comparative study to show that FCNs significantly outperform, without any further postprocessing, prior results in endoluminal scene segmentation, especially with respect to polyp segmentation and localization.

2017-07-26

Journal of Healthcare Engineering (publié)