检索结果-内蒙古大学图书馆

BigNeuron: a resource to benchmark and predict performance of algorithms for automated tracing of neurons in light microscopy datasets

引用

Nature methods 2023年第6期20卷 824-835页

作者： Linus Manubens-Gil Zhi Zhou Hanbo Chen Arvind Ramanathan Xiaoxiao Liu Yufeng Liu Alessandro Bria Todd Gillette Zongcai Ruan Jian Yang Miroslav Radojević Ting Zhao Li Cheng Lei Qu Siqi Liu Kristofer E Bouchard Lin Gu Weidong Cai Shuiwang Ji Badrinath Roysam Ching-Wei Wang Hongchuan Yu Amos Sironi Daniel Maxim Iascone Jie Zhou Erhan Bas Eduardo Conde-Sousa Paulo Aguiar Xiang Li Yujie Li Sumit Nanda Yuan Wang Leila Muresan Pascal Fua Bing Ye Hai-Yan He Jochen F Staiger Manuel Peter Daniel N Cox Michel Simonneau Marcel Oberlaender Gregory Jefferis Kei Ito Paloma Gonzalez-Bellido Jinhyun Kim Edwin Rubel Hollis T Cline Hongkui Zeng Aljoscha Nern Ann-Shyn Chiang Jianhua Yao Jane Roskams Rick Livesey Janine Stevens Tianming Liu Chinh Dang Yike Guo Ning Zhong Georgia Tourassi Sean Hill Michael Hawrylycz Christof Koch Erik Meijering Giorgio A Ascoli Hanchuan Peng Institute for Brain and Intelligence Southeast University Nanjing China. Microsoft Corporation Redmond WA USA. Tencent AI Lab Bellevue WA USA. Computing Environment and Life Sciences Directorate Argonne National Laboratory Lemont IL USA. Kaya Medical Seattle WA USA. University of Cassino and Southern Lazio Cassino Italy. Center for Neural Informatics Structures and Plasticity Krasnow Institute for Advanced Study George Mason University Fairfax VA USA. Faculty of Information Technology Beijing University of Technology Beijing China. Beijing International Collaboration Base on Brain Informatics and Wisdom Services Beijing China. Nuctech Netherlands Rotterdam the Netherlands. Janelia Research Campus Howard Hughes Medical Institute Ashburn VA USA. Department of Electrical and Computer Engineering University of Alberta Edmonton Alberta Canada. Ministry of Education Key Laboratory of Intelligent Computation and Signal Processing Anhui University Hefei China. Paige AI New York NY USA. Scientific Data Division and Biological Systems and Engineering Division Lawrence Berkeley National Lab Berkeley CA USA. Helen Wills Neuroscience Institute and Redwood Center for Theoretical Neuroscience UC Berkeley Berkeley CA USA. RIKEN AIP Tokyo Japan. Research Center for Advanced Science and Technology (RCAST) The University of Tokyo Tokyo Japan. School of Computer Science University of Sydney Sydney New South Wales Australia. Texas A&M University College Station TX USA. Cullen College of Engineering University of Houston Houston TX USA. Graduate Institute of Biomedical Engineering National Taiwan University of Science and Technology Taipei Taiwan. National Centre for Computer Animation Bournemouth University Poole UK. PROPHESEE Paris France. Department of Neuroscience Columbia University New York NY USA. Mortimer B. Zuckerman Mind Brain Behavior Institute Columbia University New York NY USA. Department of Computer Science Northern Illinois Universit

BigNeuron is an open community bench-testing platform with the goal of setting open standards for accurate and fast automatic neuron tracing. We gathered a diverse set of image volumes across several species that is representative of the data obtained in many neuroscience laboratories interested in neuron tracing. Here, we report generated gold standard manual annotations for a subset of the available imaging datasets and quantified tracing quality for 35 automatic tracing algorithms. The goal of generating such a hand-curated diverse dataset is to advance the development of tracing algorithms and enable generalizable benchmarking. Together with image quality features, we pooled the data in an interactive web application that enables users and developers to perform principal component analysis, t-distributed stochastic neighbor embedding, correlation and clustering, visualization of imaging and tracing data, and benchmarking of automatic tracing algorithms in user-defined data subsets. The image quality metrics explain most of the variance in the data, followed by neuromorphological features related to neuron size. We observed that diverse algorithms can provide complementary information to obtain accurate results and developed a method to iteratively combine methods and generate consensus reconstructions. The consensus trees obtained provide estimates of the neuron structure ground truth that typically outperform single algorithms in noisy datasets. However, specific algorithms may outperform the consensus tree strategy in specific imaging conditions. Finally, to aid users in predicting the most accurate automatic tracing results without manual annotations for comparison, we used support vector machine regression to predict reconstruction quality given an image volume and a set of automatic tracings.

关键词：

来源：评论

学校读者我要写书评

暂无评论

Convex optimization for non-equilibrium steady states on a hybrid quantum processor

arXiv

引用

arXiv 2022年

作者： Lau, Jonathan Wei Zhong Lim, Kian Hwee Bharti, Kishor Kwek, Leong-Chuan Vinjanampathy, Sai Centre for Quantum Technologies National University of Singapore 3 Science Drive 2 Singapore117543 Singapore Joint Center for Quantum Information and Computer Science Joint Quantum Institute NIST University of Maryland College ParkMD20742 United States 1 Fusionopolis Way #16-16 Connexis Singapore138632 Singapore MajuLab CNRS-UNS-NUS-NTU International Joint Research Unit UMI 3654 Singapore National Institute of Education Nanyang Technological University 1 Nanyang Walk 637616 Singapore School of Electrical and Electronic Engineering Block S2.1 50 Nanyang Avenue Singapore639798 Singapore Department of Physics Indian Institute of Technology-Bombay Powai Mumbai400076 India Centre of Excellence in Quantum Information Computation Science and Technology Indian Institute of Technology Bombay Powai Mumbai400076 India

Finding the transient and steady state properties of open quantum systems is a central problem in various fields of quantum technologies. Here, we present a quantum-assisted algorithm to determine the steady states of open system dynamics. By reformulating the problem of finding the fixed point of Lindblad dynamics as a feasibility semidefinite program, we bypass several well known issues with variational quantum approaches to solving for steady states. We demonstrate that our hybrid approach allows us to estimate the steady states of higher dimensional open quantum systems and discuss how our method can find multiple steady states for systems with symmetries. Copyright © 2022, The Authors. All rights reserved.

关键词： Convex optimization

来源：评论

学校读者我要写书评

暂无评论

A large-scale multicenter breast cancer DCE-MRI benchmark dataset with expert segmentations

arXiv

引用

arXiv 2024年

作者： Garrucho, Lidia Kushibar, Kaisar Reidel, Claire-Anne Joshi, Smriti Osuala, Richard Tsirikoglou, Apostolia Bobowicz, Maciej del Riego, Javier Catanese, Alessandro Gwoździewicz, Katarzyna Cosaka, Maria-Laura Abo-Elhoda, Pasant M. Tantawy, Sara W. Sakrana, Shorouq S. Shawky-Abdelfatah, Norhan O. Abdo-Salem, Amr Muhammad Kozana, Androniki Divjak, Eugen Ivanac, Gordana Nikiforaki, Katerina Klontzas, Michail E. García-Dosdá, Rosa Gulsun-Akpinar, Meltem Lafcı, Oğuz Mann, Ritse Martín-Isla, Carlos Prior, Fred Marias, Kostas Starmans, Martijn P.A. Strand, Fredrik Díaz, Oliver Igual, Laura Lekadir, Karim Barcelona Spain Department of Oncology-Pathology Karolinska Institutet Stockholm Sweden Institute of Machine Learning in Biomedical Imaging Helmholtz Center Munich Munich Germany School of Computation Information and Technology Technical University of Munich Munich Germany 2nd Dept. of Radiology Medical University of Gdansk Gdansk Poland Parc Taulí Hospital Universitari Sabadell Spain Hospital Germans Trias i Pujol Badalona Spain Centro Mamario Instituto Alexander Fleming Buenos Aires Argentina Department of Diagnostic & Interventional Radiology and Molecular Imaging Faculty of Medicine Ain Shams University Cairo Egypt Department of Radiology University Hospital of Heraklion Stavrakia Greece Department of Diagnostic and Interventional Radiology University Hospital Dubrava Zagreb Croatia University of Zagreb School of Medicine Zagreb Croatia Computational BioMedicine Laboratory Institute of Computer Science Foundation for Research and Technology—Hellas Heraklion Greece Department of Radiology School of Medicine University of Crete Heraklion Greece Medical Imaging and Radiology Universitary and Politechnic Hospital La Fe Valencia Spain Department of Radiology Hacettepe University Faculty of Medicine Sihhiye Ankara Turkey Department of Biomedical Imaging and Image-guided Therapy Medical University of Vienna Vienna Austria Department of Radiology and Nuclear Medicine Radboud University Medical Center Netherlands University of Arkansas for Medical Sciences Little RockAR United States Department of Electrical and Computer Engineering Hellenic Mediterranean University Heraklion Greece Heraklion Greece Department of Radiology and Nuclear Medicine Erasmus MC Cancer Institute University Medical Center Rotterdam Rotterdam Netherlands Department of Pathology Erasmus MC Cancer Institute University Medical Center Rotterdam Rotterdam Netherlands Breast Radiology Karolinska University Hospital Stockholm Sweden Passeig Lluís Companys 23 Barcelona Sp

Artificial Intelligence (AI) research in breast cancer Magnetic Resonance Imaging (MRI) faces challenges due to limited expert-labeled segmentations. To address this, we present a multicenter dataset of 1506 pretreatment T1-weighted dynamic contrast-enhanced MRI cases, including expert annotations of primary tumors and non-mass-enhanced regions. The dataset integrates imaging data from four collections in The Cancer Imaging Archive (TCIA), where only 163 cases with expert segmentations were initially available. To facilitate the annotation process, a deep learning model was trained to produce preliminary segmentations for the remaining cases. These were subsequently corrected and verified by 16 breast cancer experts (averaging 9 years of experience), creating a fully annotated dataset. Additionally, the dataset includes 49 harmonized clinical and demographic variables, as well as pre-trained weights for a baseline nnU-Net model trained on the annotated data. This resource addresses a critical gap in publicly available breast cancer datasets, enabling the development, validation, and benchmarking of advanced deep learning models, thus driving progress in breast cancer diagnostics, treatment response prediction, and personalized care. Copyright © 2024, The Authors. All rights reserved.

关键词： Dynamic contrast enhanced MRI

来源：评论

学校读者我要写书评

暂无评论

Abstracting Fairness: Oracles, Metrics, and Interpretability

arXiv

引用

arXiv 2020年

作者： Dwork, Cynthia Ilvento, Christina Rothblum, Guy N. Sur, Pragya Harvard John A. Paulson School of Engineering and Applied Sciences Radcliffe Institute for Advanced Study Microsoft Research CambridgeMA United States Harvard John A. Paulson School of Engineering and Applied Sciences CambridgeMA United States Department of Computer Science and Applied Mathematics Weizmann Institute of Science Rehovot Israel Center for Research on Computation and Society Harvard John A. Paulson School of Engineering and Applied Sciences CambridgeMA United States

It is well understood that classification algorithms, for example, for deciding on loan applications, cannot be evaluated for fairness without taking context into account. We examine what can be learned from a fairness oracle equipped with an underlying understanding of "true" fairness. The oracle takes as input a (context, classifier) pair satisfying an arbitrary fairness definition, and accepts or rejects the pair according to whether the classifier satisfies the underlying fairness truth. Our principal conceptual result is an extraction procedure that learns the underlying truth;moreover, the procedure can learn an approximation to this truth given access to a weak form of the oracle. Since every "truly fair" classifier induces a coarse metric, in which those receiving the same decision are at distance zero from one another and those receiving different decisions are at distance one, this extraction process provides the basis for ensuring a rough form of metric fairness, also known as individual fairness. Our principal technical result is a higher fidelity extractor under a mild technical constraint on the weak oracle’s conception of fairness. Our framework permits the scenario in which many classifiers, with differing outcomes, may all be considered fair. Our results have implications for interpretablity – a highly desired but poorly defined property of classification systems that endeavors to permit a human arbiter to reject classifiers deemed to be "unfair" or illegitimately derived. Copyright © 2020, The Authors. All rights reserved.

关键词： Extraction

来源：评论

学校读者我要写书评

暂无评论

Toward a Wearable Data Assimilation Platform

Toward a Wearable Data Assimilation Platform

引用

IEEE Biomedical Circuits and Systems (BIOCAS)

作者： Philip Graybill Bruce J. Gluckman Mehdi Kiani School of Electrical Engineering and Computer Science The Pennsylvania State University PA USA Center for Neural Enginering Engineering Science and Mechanics Neurosurgery The Pennsylvania State University PA USA

Data assimilation (DA) refers to a family of methods used to synchronize a dynamical model to sparse or noisy measurements of model states. In this paper, we propose a wearable DA platform for neurological research and report our progress in translating a DA computational framework from desktop computation to embedded computation. The unscented Kalman filter (UKF) and a neural mass model (NMM) for sleep-wake regulation are introduced. Next, selection of suitable UKF parameters through MATLAB simulations is described. Finally, four variations of the DA framework are run on an embedded microprocessor in order to find the variation that minimizes computation time while maintaining state reconstruction accuracy. By reducing computational precision of the equation integrator and using a piecewise-linear approximation in place of the tanh function, we increased computational speed by a factor of 3.6 while maintaining a high level of state reconstruction fidelity.

关键词：

来源：评论

学校读者我要写书评

暂无评论

BPS2025 - Structural basis of potassium selectivity in kalium channelrhodopsins

引用

Biophysical Journal 2025年第3期124卷 64a-65a页

作者： Seiya Tajima Yoon Seok Kim YoungJu Jo Peter Y. Wang Joseph M. Paggi Charu Ramakrishnan Shunki Takaramoto Takashi Nagata Masae Konno Kota Katayama Hideki Kandori Ron O. Dror Keiichi Inoue Karl Deisseroth Hideaki Kato Research Center for Advanced Science and Technology The University of Tokyo Tokyo Japan Department of Bioengineering Stanford University Stanford CA USA Department of Computer Science Stanford University Stanford CA USA Cracking the Neural Code Program Stanford University Stanford CA USA The Institute for Solid State Physics The University of Tokyo Kashiwa Japan PRESTO Japan Science and Technology Agency Kawaguchi Japan Department of Life Science and Applied Chemistry Nagoya Institute of Technology Nagoya Japan OptoBioTechnology Research Center Nagoya Institute of Technology Nagoya Japan Institute for Computational and Mathematical Engineering Stanford University Stanford CA USA Howard Hughes Medical Institute Stanford University Stanford CA USA Graduate School of Arts and Sciences The University of Tokyo Tokyo Japan

来源：评论

学校读者我要写书评

暂无评论

Exploring explainable selection to control abstract generation

arXiv

引用

arXiv 2020年

作者： Haonan, Wang Yang, Gao Yu, Bai Lapata, Mirella Heyan, Huang School of Computer Science and Technology Beijing Institute of Technology Beijing100081 China Institute for Language Cognition and Computation School of Informatics University of Edinburgh 10 Crichton Street EdinburghEH8 9AB United Kingdom Beijing Engineering Research Center of High Volume Language Information Processing and Cloud Computing Applications

It is a big challenge to model long-range input for document summarization. In this paper, we target using a select and generate paradigm to enhance the capability of selecting explainable contents (i.e., interpret the selection given its semantics, novelty, relevance) and then guiding to control the abstract generation. Specifically, a new designed pair-wise extractor is proposed to capture the sentence pair interactions and its centrality. Furthermore, the generator is hybrid with the selected content and is jointly integrated with a pointer distribution that is derived from a sentence deployment's attention. The abstract generation can be controlled by an explainable mask matrix that determines to what extent the content can be included in the summary. Encoders are adaptable with both Transformerbased and BERT-based configurations. Overall, both results based on ROUGE metrics and human evaluation gain outperformance over several state-of-The-Art models on two benchmark CNN/DailyMail and NYT datasets. Copyright © 2020, The Authors. All rights reserved.

关键词： Abstracting

来源：评论

学校读者我要写书评

暂无评论

Spectroscopic signatures of edge states in hexagonal boron nitride

引用

Nano Research 2019年第7期12卷 1663-1667页

作者： Chuang Gao Lei Tao Yu-Yang Zhang Shixuan Du Sokrates T. Pantelides Juan Carlos Idrobo Wu Zhou Hong-Jun Gao School of Physical Sciences and CAS Key Laboratory of Vacuum Physics University of Chinese Academy of SciencesBeijing 100049China Institute of Physics Chinese Academy of SciencesBeijing 100190China Department of Physics and Astronomy and Department of Electrical Engineering and Computer Science Vanderbilt UniversityNashvilleTN 37235USA CAS Centre for Excellence in Topological Quantum Computation University of Chinese Academy of SciencesBeijing 100049China Center for Nanophase Materials Sciences Oak Ridge National LaboratoryOak RidgeTN 37831USA

We use Z-contrast imaging and atomically resolved electron energy-loss spectroscopy on an aberration-corrected scanning transmission electron microscope to investigate the local electronic states of boron atoms at different edge structures in monolayer and bilayer *** find that edges with bonding unsaturated sp2 boron atoms have a unique spectroscopic signature with a prominent pre-peak at - 190.2 eV in the B K-edge fine ***-principles calculations reveal that the observed pre-peak arises from excitations to the in-plane lowest-energy empty sp2 boron dangling bonds at the B-terminated *** spectroscopic signature can serve as a fingerprint to explore new edge structures in h-BN.

关键词： h-BN edge structure spectroscopic signatures electron energy-loss near edge structure

来源：评论

学校读者我要写书评

暂无评论

Conditionally-additive-noise models for structure learning

arXiv

引用

arXiv 2019年

作者： Chicharro, Daniel Panzeri, Stefano Shpitser, Ilya Neural Computation Laboratory Center for Neuroscience and Cognitive Systems@UniTn Istituto Italiano di Tecnologia Rovereto38068 Department of Neurobiology Harvard Medical School BostonMA02115 United States Department of Computer Science Whiting School of Engineering Johns Hopkins University

Constraint-based structure learning algorithms infer the causal structure of multi-variate systems from observational data by determining an equivalent class of causal structures compatible with the conditional independencies in the data. Methods based on additive-noise (AN) models have been proposed to further discriminate between causal structures that are equivalent in terms of conditional independencies. These methods rely on a particular form of the generative functional equations, with an additive noise structure, which allows inferring the directionality of causation by testing the independence between the residuals of a nonlinear regression and the predictors (nrr-independencies). Full causal structure identifiability has been proven for systems that contain only additive-noise equations and have no hidden variables. We extend the AN framework in several ways. We introduce alternative regression-free tests of independence based on conditional variances (cv-independencies). We consider conditionally-additive-noise (CAN) models, in which the equations may have the AN form only after conditioning. We exploit asymmetries in nrr-independencies or cv-independencies resulting from the CAN form to derive a criterion that infers the causal relation between a pair of variables in a multivariate system without any assumption about the form of the equations or the presence of hidden *** Codes 62-07 62-09 Copyright © 2019, The Authors. All rights reserved.

关键词： Equivalence classes

来源：评论

学校读者我要写书评

暂无评论

MetaSleepLearner: A pilot study on fast adaptation of bio-signals-based sleep stage classifier to new individual subject using Meta-Learning

arXiv

引用

arXiv 2020年

作者： Banluesombatkul, Nannapas Ouppaphan, Pichayoot Leelaarporn, Pitshaporn Lakhan, Payongkit Chaitusaney, Busarakum Jaimchariyatam, Nattapong Chuangsuwanich, Ekapol Chen, Wei Phan, Huy Dilokthanakul, Nat Wilaiprasitporn, Theerawit Bio-inspired Robotics and Neural Engineering Lab School of Information Science and Technology Vidyasirimedhi Institute of Science & Technology Rayong Thailand Department of Otolaryngology Faculty of Medicine Chulalongkorn University Thailand Excellence Center for Sleep Disorders King Chulalongkorn Memorial Hospital Thai Red Cross Society Bangkok Thailand Division of Pulmonary and Critical Care Medicine Faculty of Medicine Chulalongkorn University Thailand Head of Excellence Center for Sleep Disorders King Chulalongkorn Memorial Hospital Thai Red Cross Society Bangkok Thailand The Computer Engineering Department Chulalongkorn University Bangkok Thailand The Center for Intelligent Medical Electronics Department of Electronic Engineering School of Information Science and Technology Fudan University Shanghai200433 China The School of Electronic Engineering and Computer Science Queen Mary University of London United Kingdom

Identifying bio-signals based-sleep stages requires time-consuming and tedious labor of skilled clinicians. Deep learning approaches have been introduced in order to challenge the automatic sleep stage classification conundrum. However, the difficulties can be posed in replacing the clinicians with the automatic system due to the differences in many aspects found in individual bio-signals, causing the inconsistency in the performance of the model on every incoming individual. Thus, we aim to explore the feasibility of using a novel approach, capable of assisting the clinicians and lessening the workload. We propose the transfer learning framework, entitled MetaSleepLearner, based on Model Agnostic Meta-Learning (MAML), in order to transfer the acquired sleep staging knowledge from a large dataset to new individual subjects (source code is available at https://***/IoBTVISTEC/MetaSleepLearner). The framework was demonstrated to require the labelling of only a few sleep epochs by the clinicians and allow the remainder to be handled by the system. Layer-wise Relevance Propagation (LRP) was also applied to understand the learning course of our approach. In all acquired datasets, in comparison to the conventional approach, MetaSleepLearner achieved a range of 5.4% to 17.7% improvement with statistical difference in the mean of both approaches. The illustration of the model interpretation after the adaptation to each subject also confirmed that the performance was directed towards reasonable learning. MetaSleepLearner outperformed the conventional approaches as a result from the fine-tuning using the recordings of both healthy subjects and patients. This is the first work that investigated a non-conventional pre-training method, MAML, resulting in a possibility for human-machine collaboration in sleep stage classification and easing the burden of the clinicians in labelling the sleep stages through only several epochs rather than an entire recording. © 2020, CC BY-N

关键词： Convolutional neural networks

来源：评论

学校读者我要写书评

暂无评论

建议与咨询留下您的常用邮箱和电话号码，以便我们向您反馈解决方案和替代方法

时间限定

文献类型

馆藏选择

核心期刊

语言

文献类型

帮助

文字说明：

检索规则说明：

检索范例：

分类表

所选分类

限定检索结果

文献类型

馆藏范围

日期分布

学科分类号

主题

机构

作者

语言

请选择保存的检索档案：

请选择收藏分类：

通借通还

建议与咨询 留下您的常用邮箱和电话号码，以便我们向您反馈解决方案和替代方法

时间限定

文献类型

馆藏选择

核心期刊

语言

文献类型

帮助

文字说明：

检索规则说明：

检索范例：

分类表

所选分类

限定检索结果

文献类型

馆藏范围

日期分布

学科分类号

主题

机构

作者

语言

请选择保存的检索档案： 新增检索档案 确定 取消

请选择收藏分类： 新增自定义分类 确定 取消

通借通还

建议与咨询留下您的常用邮箱和电话号码，以便我们向您反馈解决方案和替代方法

请选择保存的检索档案：

请选择收藏分类：