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Computational analysis of laminar structure of the human cortex based on local neuron features

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arXiv 2019年

作者： Stajduhar, Andrija Lipic, Tomislav Sedmak, Goran Loncaric, Sven Judaš, Milos Croatian Institute for Brain Research University of Zagreb School of Medicine Šalata 12 Zagreb10000 Croatia Laboratory for Machine Learning and Knowledge Representation Rud-er Boškovic Institute Faculty of Electrical Engineering and Computing University of Zagreb

In this paper, we present a novel method for analysis and segmentation of laminar structure of the cortex based on tissue characteristics whose change across the gray matter facilitates distinction between cortical layers. We develop and analyze features of individual neurons to investigate changes in architectonic differentiation and present a novel high-performance, automated tree-ensemble method trained on data manually labeled by three human investigators. From the location and basic measures of neurons, more complex features are developed and used in machine learning models for automatic segmentation of cortical layers. Tree ensembles are used on data manually labeled by three human experts. The most accurate classification results were obtained by training three models separately and creating another ensemble by combining probability outputs for final neuron layer classification. Measurement of importances of developed neuron features on both global model level and individual prediction level are obtained. Copyright © 2019, The Authors. All rights reserved.

关键词： Neurons

ContinUNet: fast deep radio image segmentation in the Square Kilometre Array era with U-Net

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RAS Techniques and Instruments 2024年第1期3卷 315-332页

作者： Stewart, Hattie Birkinshaw, Mark Yeung, Siu-Lun Maddox, Natasha Maughan, Ben Thiyagalingam, Jeyan School of Physics University of Bristol HH Wills Physics Laboratory SciML Scientific Computing Department Research Complex at Harwell Rutherford Appleton Laboratory UKRI Centre for Doctoral Training in Artificial Intelligence Machine Learning & Advanced Computing Department of Physics Vivian Tower Swansea University

We present a new machine learning (ML)-driven source-finding tool for next-generation radio surveys that performs fast source extraction on a range of source morphologies at large dynamic ranges with minimal parameter tuning and post-processing. The construction of the Square Kilometre Array (SKA) radio telescope will revolutionize the field of radio astronomy. However, accurate and automated source-finding techniques are required to reach SKA science goals. We have developed a novel source-finding method, ContinUNet, powered by an ML segmentation algorithm, U-Net, that has proven highly effective and efficient when tested on SKA precursor data sets. Our model was trained and tested on simulated radio continuum data from SKA Science Data Challenge 1 and proved comparable with the state-of-the-art source-finding methods, PyBDSF and ProFound. ContinUNet was then tested on the MeerKAT International GHz Tiered Extragalactic Exploration Early Science data without retraining and was able to extract point-like and extended sources with equal ease;processing a 1.6 deg² field in <13 s on a supercomputer and ≈2 min on a personal laptop. We were able to associate components of extended sources without manual intervention with the powerful inference capabilities learnt within the network, making ContinUNet a promising tool for enabling science in the upcoming SKA era. © 2024 The Author(s).

关键词： Data Methods Evolution Galaxies Galaxies machine learning Radio Continuum Software

Improving generative model-based unfolding with Schrödinger bridges

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Physical Review D 2024年第7期109卷 076011-076011页

作者： Sascha Diefenbacher Guan-Horng Liu Vinicius Mikuni Benjamin Nachman Weili Nie Physics Division Lawrence Berkeley National Laboratory Berkeley California 94720 USA Autonomous Control and Decision Systems Laboratory Georgia Institute of Technology Atlanta Georgia 30332 USA National Energy Research Scientific Computing Center Berkeley Lab Berkeley California 94720 USA Berkeley Institute for Data Science University of California Berkeley California 94720 USA Machine Learning Research Group NVIDIA Research

machine learning-based unfolding has enabled unbinned and high-dimensional differential cross section measurements. Two main approaches have emerged in this research area; one based on discriminative models and one based on generative models. The main advantage of discriminative models is that they learn a small correction to a starting simulation while generative models scale better to regions of phase space with little data. We propose to use Schrödinger bridges and diffusion models to create sbunfold, an unfolding approach that combines the strengths of both discriminative and generative models. The key feature of sbunfold is that its generative model maps one set of events into another without having to go through a known probability density as is the case for normalizing flows and standard diffusion models. We show that sbunfold achieves excellent performance compared to state of the art methods on a synthetic Z+jets dataset.

关键词： machine learning Particle detectors Probability theory

A Neurobehavioral Evaluation of the Efficacy of 1mA Longitudinal, Anodal TDCS on Multitasking and Transfer Performance

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A Neurobehavioral Evaluation of the Efficacy of 1mA Longitud...

IEEE International Conference on Systems, Man and Cybernetics

作者： Akash K Rao Shashank Uttrani Darshil Shah Vishnu K Menon Arnav Bhavsar Shubhajit Roy Chowdhury Ramsingh Negi Varun Dutt Manipal Academy of Higher Education Applied Cognitive Science Laboratory Indian Institute of Technology Mandi School of Computing and Electrical Engineering Indian Institute of Technology Mandi Cognitive Control and Machine Learning Group at the Institute of Nuclear Medicine and Allied Sciences Defence Research and Development Organization

ISBN: (数字)9781665410205

ISBN: (纸本)9781665410212

Multitasking requires rapid switching of attention and cognitive resources between different tasks in a dynamic environment, relying on cognitive processes, such as working memory, executive control, and selective attention. Although studies have investigated the efficacy of various neurobehavioral interventions in improving multitasking capabilities, the effects of longitudinal anodal transcranial direct current stimulation (tDCS) in enhancing multitasking performance have not been investigated. This research investigated the efficacy of 1mA anodal tDCS administered longitudinally on multitasking performance. 42 participants were randomly and equally divided into the experimental and placebo control conditions in this study conducted for 10 days. All participants executed two multitasking tasks on day 1 and received 1mA anodal/placebo tDCS during task training from day 2 to day 8. Various behavioral and neurophysiological measures have been measured. The findings revealed that tDCS had the propensity to augment multitasking capabilities in the trained task but had limited transfer capabilities. EEG-based brain connectivity analysis also revealed the formation of network hubs in the prefrontal and frontal regions, indicating enhanced cortical activation in the beta band. We intend to use these findings to design interventional frameworks to enhance multitasking performance using tDCS.

关键词： Training Atmospheric measurements Memory management Switches Multitasking Particle measurements Dynamic scheduling Control systems Transcranial direct current stimulation Cybernetics

Multi-Scale Clinical-Guided Binocular Fusion Framework for Predicting New-Onset Hypertension Over a Four-Year Period

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Multi-Scale Clinical-Guided Binocular Fusion Framework for P...

IEEE International Symposium on Biomedical Imaging

作者： Haoshen Li Zifan Chen Jie Zhao Heyun Chen Hexin Dong Mingze Yuan Bin Dong Li Zhang Center for Data Science Peking University China National Engineering Laboratory for Big Data Analysis and Applications Peking University China Peking University Changsha Institute for Computing and Digital Economy China Beijing International Center for Mathematical Research Peking University China Center for Machine Learning Research Peking University China

ISBN: (数字)9798350313338

ISBN: (纸本)9798350313345

Hypertension is a major global health concern, linked to various cardiovascular diseases and associated with distinct ocular manifestations. While recent advances in artificial intelligence have enabled accurate diagnosis of current hypertension through fundus images, predicting the future onset of hypertension remains an uncharted domain. In this study, we introduce the multi-scale clinical-guided binocular fusion framework (MCBO), designed to predict the likelihood of developing hypertension within the next four years. MCBO uniquely integrates left and right fundus images and clinical data, utilizing a shared-weight multi-stage Transformer-based encoder. Our multi-scale clinical-guided module (MCM) ensures image feature extraction is clinically contextualized based on clinical information, and our binocular fusion module (BFM) fuses binocular information. Comparative performance against seven baseline models establishes MCBO’s supremacy, with improvements of 6.7% in Area Under Curve (AUC), 6.9% in Accuracy (ACC), 5.1% in Sensitivity (SEN) and 5.5% in Specificity (SPE). This approach offers a promising avenue for proactive hypertension management, underscoring the potential of integrating Deep learning with clinical data for enhanced healthcare outcomes. Our code is available at https://***/HaoshenLi/MCBO.

关键词： Hypertension Deep learning Accuracy Sensitivity Codes Fuses Feature extraction

Entropy-based Active learning of Graph Neural Network Surrogate Models for Materials Properties

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arXiv 2021年

作者： Allotey, Johannes Butler, Keith T. Thiyagalingam, Jeyan School of Physics University of Bristol BS8 1TL United Kingdom Scientific Machine Learning Research Group Scientific Computing Department Rutherford Appleton Laboratory Science and Technology Facilities Council DidcotOX11 0DQ United Kingdom

Graph neural networks, trained on experimental or calculated data are becoming an increasingly important tool in computational materials science. Networks, once trained, are able to make highly accurate predictions at a fraction of the cost of experiments or first-principles calculations of comparable accuracy. However these networks typically rely on large databases of labelled experiments to train the model. In scenarios where data is scarce or expensive to obtain this can be prohibitive. By building a neural network that provides a confidence on the predicted properties, we are able to develop an active learning scheme that can reduce the amount of labelled data required, by identifying the areas of chemical space where the model is most uncertain. We present a scheme for coupling a graph neural network with a Gaussian process to featurise solid-state materials and predict properties including a measure of confidence in the prediction. We then demonstrate that this scheme can be used in an active learning context to speed up the training of the model, by selecting the optimal next experiment for obtaining a data label. Our active learning scheme can double the rate at which the performance of the model on a test data set improves with additional data compared to choosing the next sample at random. This type of uncertainty quantification and active learning has the potential to open up new areas of materials science, where data are scarce and expensive to obtain, to the transformative power of graph neural networks. © 2021, CC BY.

关键词： Forecasting

On Error Bounds of Inequalities in Asplund Spaces

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arXiv 2023年

作者： Wei, Zhou Théra, Michel Yao, Jen-Chih Hebei Key Laboratory of Machine Learning and Computational Intelligence College of Mathematics and Information Science Hebei University Baoding071002 China XLIM UMR CNRS 7252 Université de Limoges Limoges France Research Center for Interneural Computing China Medical University Hospital China Medical University Taichung Taiwan

Error bounds are central objects in optimization theory and its applications. They were for a long time restricted only to the theory before becoming over the course of time a field of itself. This paper is devoted to the study of error bounds of a general inequality defined by a proper lower semicontinuous function on an Asplund space. Even though the results of the dual characterization on the error bounds of a general inequality (if one drops the convexity assumption) may not be valid, several necessary dual conditions are still obtained in terms of Fréchet/Mordukhovich subdifferentials of the concerned function at points in the solution set. Moreover, for an inequality defined by a composite-convex function that is to say by a function which is the composition of a convex function with a smooth mapping, such dual conditions also turn out to be sufficient to have the error bound property. Our work is an extension of results on dual characterizations of convex inequalities to the possibly non-convex case. © 2023, CC0.

关键词： Site selection

Strategic priorities for transformative progress in advancing biology with proteomics and artificial intelligence

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arXiv 2025年

作者： Sun, Yingying Jun, A. Liu, Zhiwei Sun, Rui Qian, Liujia Payne, Samuel H. Bittremieux, Wout Ralser, Markus Li, Chen Chen, Yi Dong, Zhen Perez-Riverol, Yasset Khan, Asif Sander, Chris Aebersold, Ruedi Vizcaíno, Juan Antonio Krieger, Jonathan R. Yao, Jianhua Wen, Han Zhang, Linfeng Zhu, Yunping Xuan, Yue Sun, Benjamin Boyang Qiao, Liang Hermjakob, Henning Tang, Haixu Gao, Huanhuan Deng, Yamin Zhong, Qing Chang, Cheng Bandeira, Nuno Li, Ming Weinan, E. Sun, Siqi Yang, Yuedong Omenn, Gilbert S. Zhang, Yue Xu, Ping Fu, Yan Liu, Xiaowen Overall, Christopher M. Wang, Yu Deutsch, Eric W. Chen, Luonan Cox, Jürgen Demichev, Vadim He, Fuchu Huang, Jiaxing Jin, Huilin Liu, Chao Li, Nan Luan, Zhongzhi Song, Jiangning Yu, Kaicheng Wan, Wanggen Wang, Tai Zhang, Kang Zhang, Le Bell, Peter A. Mann, Matthias Zhang, Bing Guo, Tiannan Affiliated Hangzhou First People’s Hospital State Key Laboratory of Medical Proteomics School of Medicine Westlake University Zhejiang Province Hangzhou China Westlake Center for Intelligent Proteomics Westlake Laboratory of Life Sciences and Biomedicine Zhejiang Province Hangzhou China Biology Department Brigham Young University ProvoUT84602 United States Department of Computer Science University of Antwerp Antwerp2020 Belgium Department of Biochemistry CharitéUniversitätsmedizin Berlin Berlin Germany Biomedicine Discovery Institute Department of Biochemistry and Molecular Biology Monash University MelbourneVICVIC 3800 Australia Wellcome Genome Campus Hinxton CambridgeCB10 1SD United Kingdom Harvard Medical School Ludwig Center at Harvard United States Harvard Medical School Broad Institute Ludwig Center at Harvard Dana-Farber Cancer Institute United States Department of Biology Institute of Molecular Systems Biology ETH Zürich Zürich Switzerland Bruker Ltd. MiltonONL9T 6P4 Canada AI for Life Sciences Lab Tencent Shenzhen518057 China State Key Laboratory of Medical Proteomics AI for Science Institute Beijing100080 China Beijing Institute of Lifeomics Beijing102206 China Thermo Fisher Scientific GmbH Hanna-Kunath Str. 11 Bremen28199 Germany Informatics and Predictive Sciences Research Bristol Myers Squibb United States Department of Chemistry Fudan University Songhu Road 2005 Shanghai200438 China Department of Computer Science Luddy School of Informatics Computing and Engineering Indiana University IN47408 United States ProCan® Children’s Medical Research Institute Faculty of Medicine and Health The University of Sydney WestmeadNSW Australia La Jolla CA United States Central China Institute of Artificial Intelligence University of Waterloo Canada AI for Science Institute Center for Machine Learning Research School of Mathematical Sciences Peking University China Research Institute of Intelligent Complex Systems Fudan U

Artificial intelligence (AI) is transforming scientific research, including proteomics. Advances in mass spectrometry (MS)-based proteomics data quality, diversity, and scale, combined with groundbreaking AI techniques, are unlocking new challenges and opportunities in biological discovery. Here, we highlight key areas where AI is driving innovation, from data analysis to new biological insights. These include developing an AI-friendly ecosystem for proteomics data generation, sharing, and analysis;improving peptide and protein identification and quantification;characterizing protein-protein interactions and protein complexes;advancing spatial and perturbation proteomics;integrating multi-omics data;and ultimately enabling AI-empowered virtual cells. © 2025, CC BY.

关键词： Biotic

MSI-UNet: A Flexible UNet-Based Multi-Scale Interactive Framework for 3D Gastric Tumor Segmentation on CT Scans

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MSI-UNet: A Flexible UNet-Based Multi-Scale Interactive Fram...

IEEE International Symposium on Biomedical Imaging

作者： Heyun Chen Zifan Chen Jie Zhao Haoshen Li Jiazheng Li Yiting Liu Mingze Yuan Peng Bao Xinyu Nan Bin Dong Lei Tang Li Zhang Center for Data Science Peking University China National Engineering Laboratory for Big Data Analysis and Applications Peking University China Peking University Changsha Institute for Computing and Digital Economy China Peking University Cancer Hospital&Institute China Beijing International Center for Mathematical Research Peking University China Center for Machine Learning Research Peking University China

ISBN: (数字)9798350313338

ISBN: (纸本)9798350313345

Accurate segmentation of gastric tumors is critical yet presents a formidable challenge in medical imaging, where conventional UNet-based frameworks, despite their prevalence, falter on intricate tumor samples due to their limited interactive capacities. The SAM-based segmentation methods address this shortcoming yet with insufficient accuracy. By ingeniously blending images with mask inputs, our MSI-UNet leverages a U-shaped design to deliver pixel-perfect segmentation accuracy, while a novel multi-scale attention module adeptly harnesses interaction points for refined information extraction. When benchmarked on gastric tumor segmentation tasks, MSI-UNet surpasses existing state-of-the-art methods, elevating the Dice Similarity Coefficient (DSC) from 74.82% to 79.3% and minimizing Average Surface Distance (ASD) from 6.46 to 1.98, achieving a comparable accuracy with inter-radiologist consistency of 79.7% DSC. Furthermore, our framework demonstrates superior predictive prowess in survival analysis, enhancing the C-index from 61.7% to 68.68%. Ample experimental comparisons have substantiated that MSI-UNet holds the potential to offer considerable assistance to healthcare professionals in managing and decoding subsequent medical procedures.

关键词： Image segmentation Accuracy Three-dimensional displays Medical services Predictive models Information retrieval Decoding