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IEEE International Conference on Bioinformatics and Biomedicine (BIBM)

作者： Zhenhong Liu Xudong Ru Xingce Wang Zhongke Wu Yi-Cheng Zhu Chong Zhang Alejandro F. Frangi School of Artificial Intelligence Beijing Normal University Beijing China Department of Neurology Peking Union Medical College Hospital Beijing China Bioimage Analysis Barcelona Spain Department of Computer Science Christabel Pankhurst Institute Division of Informatics Imaging and Data Sciences School of Health Sciences School of Engineering The University of Manchester UK Department of Cardiovascular Sciences and the Department of Electrical Engineering Medical Imaging Research Centre (MIRC) KU Leuven Leuven Belgium Alan Turing Institute London UK

ISBN: (数字)9798350386226

ISBN: (纸本)9798350386233

A fast and fully automatic design of 3D cranial implants is highly desired in cranioplasty, and is key to the treatment of skull trauma. We have defined the repair of skull defects as a 3D shape completion task by proposing a two-stage diffusion model based on the representation of 3D shapes using signed distance function (SDF). Specifically, we design a diffusion model conditioned on partial shapes, we compress the 3D shape into a compact latent representation using the encoder in the vector quantized variational autoencoder (VQ-VAE) and learn the diffusion model based on this compressed discrete representation. Encoding the latent space with the autoencoder can achieve high-quality 3D cranial shape completion. In order to accurately capture local and fine-grained shape details, the training data is geometrically encoded from a compactly learned code-book. The two-stage diffusion generator with a coarse-to-fine approach possesses precise and expressive structural modeling capabilities to ensure the supplementation of detailed geometric information. Experimental results verified sufficient expressiveness of our model with generating high-fidelity results with fine-grained local details, outperforming the state-of-the-art methods.

关键词： Solid modeling Three-dimensional displays Shape Autoencoders Training data Implants Diffusion models Skull Vectors Cranial

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A Novel Augmented Reality-Based Simulator for Enhancing Orthopedic Surgical Training

SSRN

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SSRN 2024年

作者： Wu, Luohong Seibold, Matthias Cavalcanti, Nicola A. Hein, Jonas Gerth, Tatiana Lekar, Roni Hoch, Armando Vlachopoulos, Lazaros Grabner, Helmut Zingg, Patrick Farshad, Mazda Fürnstahl, Philipp Research in Orthopedic Computer Science Balgrist University Hospital University of Zurich Lengghalde 5 Zurich Zurich8008 Switzerland Department of Orthopaedics Balgrist University Hospital University of Zurich Forchstrasse 340 Zurich Zurich8008 Switzerland Computer Vision and Geometry Group ETH Zurich Ramistrasse 101 Zurich Zurich8092 Switzerland Institute of Computer Science School of Engineering Zurich University of Applied Sciences Obere Kirchgasse 2 Winterthur Zurich8401 Switzerland Institute of Data Analysis and Process Design School of Engineering Zurich University of Applied Sciences Technikumstrasse 81 Winterthur Zurich8400 Switzerland

Background: Total Hip Arthroplasty (THA) is a well-established and common orthopedic surgery. Due to the complexity involved in THA, orthopedic surgeons require rigorous training. However, the current gold standard, the tutor-guided and -evaluated apprenticeship model is time-consuming, costly, and poses risks to patients. There is a pressing need for additional training resources to enhance the efficiency and safety of the training process. In this work, we present a novel Augmented Reality (AR)-based simulator designed for THA that helps enable a new self-paced training and learning paradigm without the need for ***: The simulator reduces the need for instructors by integrating an AR guidance module and an automated performance evaluation module. Three types of AR guidance were developed: Overlay, Virtual Twin, and Sectional Views. A feasibility study was conducted with five resident surgeons and two senior surgeons to compare these guidance methods quantitatively and qualitatively. The automated performance evaluation module was assessed against manual performance evaluation using Bland-Altman analysis with limits of agreement (LoA) and Mann-Whitney U ***: The quantitative feasibility results indicate the efficacy of the developed AR guidance, characterized by mean transitional and rotational deviation errors below 3 mm and 3 degrees. Based on the qualitative results, we provide recommendations for efficient AR guidance designs. The Bland-Altman analysis results (0.22 ± 1.32 mm with LoA -2.37 to 2.81 mm for distance deviation, 0.94 ± 2.41 degrees with LoA -3.78 to 5.66 degrees for yaw deviation, -0.34 ± 1.30 degrees with LoA -2.90 to 2.22 degrees for pitch deviation) and p-values of Mann-Whitney U tests (0.64 for distance deviation, 0.12 for yaw deviation, 0.11 for pitch deviation) indicate no statistically significant differences between the automated and manual performance evaluation at a significance level of ***: This wor

关键词： Augmented reality

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Touchstone benchmark: are we on the right way for evaluating AI algorithms for medical segmentation? 24

Touchstone benchmark: are we on the right way for evaluating...

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Proceedings of the 38th International Conference on Neural Information Processing Systems

作者： Pedro R. A. S. Bassi Wenxuan Li Yucheng Tang Fabian Isensee Zifu Wang Jieneng Chen Yu-Cheng Chou Saikat Roy Yannick Kirchhoff Maximilian Rokuss Ziyan Huang Jin Ye Junjun He Tassilo Wald Constantin Ulrich Michael Baumgartner Klaus H. Maier-Hein Paul Jaeger Yiwen Ye Yutong Xie Jianpeng Zhang Ziyang Chen Yong Xia Zhaohu Xing Lei Zhu Yousef Sadegheih Afshin Bozorgpour Pratibha Kumari Reza Azad Dorit Merhof Pengcheng Shi Ting Ma Yuxin Du Fan Bai Tiejun Huang Bo Zhao Haonan Wang Xiaomeng Li Hanxue Gu Haoyu Dong Jichen Yang Maciej A. Mazurowski Saumya Gupta Linshan Wu Jiaxin Zhuang Hao Chen Holger Roth Daguang Xu Matthew B. Blaschko Sergio Decherchi Andrea Cavalli Alan L. Yuille Zongwei Zhou Department of Computer Science Johns Hopkins University and Department of Pharmacy and Biotechnology University of Bologna and Center for Biomolecular Nanotechnologies Istituto Italiano di Tecnologia Department of Computer Science Johns Hopkins University NVIDIA Division of Medical Image Computing German Cancer Research Center (DKFZ) and Helmholtz Imaging German Cancer Research Center (DKFZ) ESAT-PSI KU Leuven Division of Medical Image Computing German Cancer Research Center (DKFZ) and Faculty of Mathematics and Computer Science Heidelberg University Division of Medical Image Computing German Cancer Research Center (DKFZ) and Faculty of Mathematics and Computer Science Heidelberg University and HIDSS4Health - Helmholtz Information and Data Science School for Health Shanghai Jiao Tong University Shanghai Artificial Intelligence Laboratory Division of Medical Image Computing German Cancer Research Center (DKFZ) Division of Medical Image Computing German Cancer Research Center (DKFZ) and Pattern Analysis and Learning Group Department of Radiation Oncology Heidelberg University Hospital Helmholtz Imaging German Cancer Research Center (DKFZ) and Interactive Machine Learning Group (IML) DKFZ School of Computer Science and Engineering Northwestern Polytechnical University Australian Institute for Machine Learning The University of Adelaide College of Computer Science and Technology Zhejiang University Hong Kong University of Science and Technology (Guangzhou) Hong Kong University of Science and Technology (Guangzhou) and Hong Kong University of Science and Technology Faculty of Informatics and Data Science University of Regensburg Faculty of Electrical Engineering and Information Technology RWTH Aachen University Faculty of Informatics and Data Science University of Regensburg and Fraunhofer Institute for Digital Medicine MEVIS Electronic & Information Engineering School Harbin Institute of Technology (Shenzhen) Shanghai Jiao Tong University and Beijing Academy of Artificial Intelligence (BAAI) S

ISBN: (纸本)9798331314385

How can we test AI performance? This question seems trivial, but it isn't. Standard benchmarks often have problems such as in-distribution and small-size test sets, oversimplified metrics, unfair comparisons, and short-term outcome pressure. As a consequence, good performance on standard benchmarks does not guarantee success in real-world scenarios. To address these problems, we present Touchstone, a large-scale collaborative segmentation benchmark of 9 types of abdominal organs. This benchmark is based on 5,195 training CT scans from 76 hospitals around the world and 5,903 testing CT scans from 11 additional hospitals. This diverse test set enhances the statistical significance of benchmark results and rigorously evaluates AI algorithms across out-of-distribution scenarios. We invited 14 inventors of 19 AI algorithms to train their algorithms, while our team, as a third party, independently evaluated these algorithms. In addition, we also evaluated pre-existing AI frameworks—which, differing from algorithms, are more flexible and can support different algorithms—including MONAI from NVIDIA, nnU-Net from DKFZ, and numerous other open-source frameworks. We are committed to expanding this benchmark to encourage more innovation of AI algorithms for the medical domain.

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Cross Prompting Consistency with Segment Anything Model for Semi-supervised Medical Image Segmentation

arXiv

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arXiv 2024年

作者： Miao, Juzheng Chen, Cheng Zhang, Keli Chuai, Jie Li, Quanzheng Heng, Pheng-Ann Department of Computer Science and Engineering The Chinese University of Hong Kong Hong Kong Center for Advanced Medical Computing and Analysis Massachusetts General Hospital Harvard Medical School BostonMA United States Huawei Noah’s Ark Lab. Shenzhen China Data Science Office Massachusetts General Brigham BostonMA United States Institute of Medical Intelligence and XR The Chinese University of Hong Kong Hong Kong

Semi-supervised learning (SSL) has achieved notable progress in medical image segmentation. To achieve effective SSL, a model needs to be able to efficiently learn from limited labeled data and effectively exploit knowledge from abundant unlabeled data. Recent developments in visual foundation models, such as the Segment Anything Model (SAM), have demonstrated remarkable adaptability with improved sample efficiency. To harness the power of foundation models for application in SSL, we propose a cross prompting consistency method with segment anything model (CPC-SAM) for semi-supervised medical image segmentation. Our method employs SAM’s unique prompt design and innovates a cross-prompting strategy within a dual-branch framework to automatically generate prompts and supervisions across two decoder branches, enabling effectively learning from both scarce labeled and valuable unlabeled data. We further design a novel prompt consistency regularization, to reduce the prompt position sensitivity and to enhance the output invariance under different prompts. We validate our method on two medical image segmentation tasks. The extensive experiments with different labeled-data ratios and modalities demonstrate the superiority of our proposed method over the state-of-the-art SSL methods, with more than 9% Dice improvement on the breast cancer segmentation task. Code is available at: https://***/JuzhengMiao/CPC-SAM. © 2024, CC BY.

关键词： Image segmentation

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An explainable probabilistic classifier for categorical data inspired to quantum physics

arXiv

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arXiv 2021年

作者： Guidotti, Emanuele Ferrara, Alfio Institute of Financial Analysis Université de Neuchâtel Switzerland Department of Computer Science Data Science Research Center Università degli Studi di Milano Italy

This paper presents Sparse Tensor Classifier (STC), a supervised classification algorithm for categorical data inspired by the notion of superposition of states in quantum physics. By regarding an observation as a superposition of features, we introduce the concept of wave-particle duality in machine learning and propose a generalized framework that unifies the classical and the quantum probability. We show that STC possesses a wide range of desirable properties not available in most other machine learning methods but it is at the same time exceptionally easy to comprehend and use. Empirical evaluation of STC on structured data and text classification demonstrates that our methodology achieves state-of-the-art performances compared to both standard classifiers and deep learning, at the additional benefit of requiring minimal data pre-processing and hyper-parameter tuning. Moreover, STC provides a native explanation of its predictions both for single instances and for each target label globally. All the code is released at https://*** Codes 68Txx, 81Pxx © 2021, CC BY.

关键词： Clustering algorithms

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An elementary approach based on variational inequalities for modelling a friction-based locomotion problem

arXiv

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arXiv 2024年

作者： Chen, Panyu González, Álvaro Mateos Mertz, Laurent Department of Computer Science Duke University United States University of Michigan-Shanghai Jiao Tong University Joint Institute Shanghai Jiao Tong University Shanghai200240 China Modeling Data Analysis & Computational Tools for Biology Research Group Biomathematics Unit Department of Biodiversity Ecology & Evolution Faculty of Biological Sciences Complutense University of Madrid Madrid28040 Spain Department of Mathematics City University of Hong Kong Kowloon Hong Kong

We propose an elementary proof based on a penalization technique to show the existence and uniqueness of the solution to a system of variational inequalities modelling the friction-based motion of a two-body crawling ... 详细信息

关键词： Friction

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DAE-Former: Dual Attention-guided Efficient Transformer for Medical Image Segmentation

arXiv

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arXiv 2022年

作者： Azad, Reza Arimond, René Aghdam, Ehsan Khodapanah Kazerouni, Amirhossein Merhof, Dorit Institute of Imaging and Computer Vision RWTH Aachen University Aachen Germany Department of Electrical Engineering Shahid Beheshti University Tehran Iran School of Electrical Engineering Iran University of Science and Technology Tehran Iran Institute of Image Analysis and Computer Vision Faculty of Informatics and Data Science University of Regensburg Regensburg Germany Fraunhofer Institute for Digital Medicine MEVIS Bremen Germany

Transformers have recently gained attention in the computer vision domain due to their ability to model long-range dependencies. However, the self-attention mechanism, which is the core part of the Transformer model, usually suffers from quadratic computational complexity with respect to the number of tokens. Many architectures attempt to reduce model complexity by limiting the self-attention mechanism to local regions or by redesigning the tokenization process. In this paper, we propose DAE-Former, a novel method that seeks to provide an alternative perspective by efficiently designing the self-attention mechanism. More specifically, we reformulate the self-attention mechanism to capture both spatial and channel relations across the whole feature dimension while staying computationally efficient. Furthermore, we redesign the skip connection path by including the cross-attention module to ensure the feature reusability and enhance the localization power. Our method outperforms state-of-the-art methods on multi-organ cardiac and skin lesion segmentation datasets without requiring pre-training weights. The code is publicly available at GitHub. © 2022, CC BY.

关键词： Reusability

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Asymptotics of Bayesian Uncertainty Estimation in Random Features Regression

arXiv

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arXiv 2023年

作者： Baek, Youngsoo Berchuck, Samuel I. Mukherjee, Sayan Department of Statistical Science Duke University DurhamNC27705 United States Department of Biostatistics & Bioinformatics Duke University DurhamNC27705 United States Center for Scalable Data Analysis and Artificial Intelligence Universität Leipzig Leipzig04105 Germany Deparments of Mathematics Computer Science Biostatistics & Bioinformatics Duke University NC United States Max Planck Institute for Mathematics in the Sciences Leipzig Germany

In this paper, we compare and contrast the behavior of the posterior predictive distribution to the risk of the maximum a posteriori (MAP) estimator for the random features regression model in the overparameterized regime. We will focus on the variance of the posterior predictive distribution (Bayesian model average) and compare its asymptotics to that of the risk of the MAP estimator. In the regime where the model dimensions grow faster than any constant multiple of the number of samples, asymptotic agreement between these two quantities is governed by the phase transition in the signal-to-noise ratio. They also asymptotically agree with each other when the number of samples grows faster than any constant multiple of model dimensions. Numerical simulations illustrate finer distributional properties of the two quantities for finite dimensions. We conjecture they have Gaussian fluctuations and exhibit similar properties as found by previous authors in a Gaussian sequence model, which is of independent theoretical interest. © 2023, CC BY.

关键词： Signal to noise ratio

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Cognitive modelling with multilayer networks: Insights, advancements and future challenges

arXiv

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arXiv 2022年

作者： Stella, Massimo Citraro, Salvatore Rossetti, Giulio Marinazzo, Daniele Kenett, Yoed N. Vitevitch, Michael S. CogNosco Lab Department of Computer Science University of Exeter Exeter United Kingdom Department of Computer Science University of Pisa Pisa Italy Institute of Information Science and Technologies National Research Council Pisa Italy Faculty of Psychology and Educational Sciences Department of Data Analysis University of Ghent Ghent Belgium Cognitive Complexity Lab Faculty of Industrial Engineering and Management Technion Israel Institute of Technology Israel Department of Psychology University of Kansas LawrenceKS United States

The mental lexicon is a complex cognitive system representing information about the words/concepts that one knows. Decades of psychological experiments have shown that conceptual associations across multiple, interactive cognitive levels can greatly influence word acquisition, storage, and processing. How can semantic, phonological, syntactic, and other types of conceptual associations be mapped within a coherent mathematical framework to study how the mental lexicon works? We here review cognitive multilayer networks as a promising quantitative and interpretative framework for investigating the mental lexicon. Cognitive multilayer networks can map multiple types of information at once, thus capturing how different layers of associations might co-exist within the mental lexicon and influence cognitive processing. This review starts with a gentle introduction to the structure and formalism of multilayer networks. We then discuss quantitative mechanisms of psychological phenomena that could not be observed in single-layer networks and were only unveiled by combining multiple layers of the lexicon: (i) multiplex viability highlights language kernels and facilitative effects of knowledge processing in healthy and clinical populations;(ii) multilayer community detection enables contextual meaning reconstruction depending on psycholinguistic features;(iii) layer analysis can mediate latent interactions of mediation, suppression and facilitation for lexical access. By outlining novel quantitative perspectives where multilayer networks can shed light on cognitive knowledge representations, also in next-generation brain/mind models, we discuss key limitations and promising directions for cutting-edge future research. © 2022, CC BY.

关键词： Network layers

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Landscape analysis for shallow neural networks: complete classification of critical points for affine target functions

arXiv

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arXiv 2021年

作者： Cheridito, Patrick Jentzen, Arnulf Rossmannek, Florian Department of Mathematics ETH Zurich Switzerland School of Data Science Shenzhen Research Institute of Big Data The Chinese University of Hong Kong Shenzhen China Institute for Analysis and Numerics Faculty of Mathematics and Computer Science University of Münster Germany

In this paper, we analyze the landscape of the true loss of neural networks with one hidden layer and ReLU, leaky ReLU, or quadratic activation. In all three cases, we provide a complete classification of the critical points in the case where the target function is affine and one-dimensional. In particular, we show that there exist no local maxima and clarify the structure of saddle points. Moreover, we prove that non-global local minima can only be caused by ‘dead’ ReLU neurons. In particular, they do not appear in the case of leaky ReLU or quadratic activation. Our approach is of a combinatorial nature and builds on a careful analysis of the different types of hidden neurons that can *** Codes 68T07 Copyright © 2021, The Authors. All rights reserved.

关键词： Chemical activation

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