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arXiv 2023年

作者： Zhang, Kai Zhou, Rong Adhikarla, Eashan Yan, Zhiling Liu, Yixin Yu, Jun Liu, Zhengliang Chen, Xun Davison, Brian D. Ren, Hui Huang, Jing Chen, Chen Zhou, Yuyin Fu, Sunyang Liu, Wei Liu, Tianming Li, Xiang Chen, Yong He, Lifang Zou, James Li, Quanzheng Liu, Hongfang Sun, Lichao Department of Computer Science and Engineering Lehigh University PA United States School of Computing University of Georgia GA United States Samsung Research America CA United States Department of Radiology Massachusetts General Hospital Harvard Medical School MA United States Department of Biostatistics Epidemiology and Informatics University of Pennsylvania PA United States PolicyLab Children’s Hospital of Philadelphia PA United States Center for Research in Computer Vision University of Central Florida FL United States Department of Computer Science and Engineering University of California Santa CruzCA United States McWilliams School of Biomedical Informatics UTHealth HoustonTX United States Department of Radiation Oncology Mayo Clinic AZ United States University of Pennsylvania PA United States PA United States Leonard Davis Institute of Health Economics PA United States Department of Biomedical Data Science Stanford University School of Medicine CA United States Department of Computer Science Stanford University CA United States

Traditional biomedical artificial intelligence (ai) models, designed for specific tasks or modalities, often exhibit limited flexibility in real-world deployment and struggle to utilize holistic information. Generalist ai holds the potential to address these limitations due to its versatility in interpreting different data types and generating tailored outputs for diverse needs. However, existing biomedical generalist ai solutions are typically heavyweight and closed source to researchers, practitioners, and patients. Here, we propose BiomedGPT, the first open-source and lightweight vision-language foundation model, designed as a generalist capable of performing various biomedical tasks. BiomedGPT achieved state-of-the-art results in 16 out of 25 experiments while maintaining a computing-friendly model scale. We also conducted human evaluations to assess the capabilities of BiomedGPT in radiology visual question answering, report generation, and summarization. BiomedGPT exhibits robust prediction ability with a low error rate of 3.8% in question answering, satisfactory performance with an error rate of 8.3% in writing complex radiology reports, and competitive summarization ability with a nearly equivalent preference score to human experts. Our method demonstrates that effective training with diverse data can lead to more practical biomedical ai for improving diagnosis and workflow efficiency. © 2023, CC BY.

关键词： Visual languages

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Retrospective for the dynamic sensorium competition for predicting large-scale mouse primary visual cortex activity from videos 24

Retrospective for the dynamic sensorium competition for pred...

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

作者： Polina Turishcheva Paul G. Fahey Michaela Vystrčilová Laura Hansel Rachel Froebe Kayla Ponder Yongrong Qiu Konstantin F. Willeke Mohammad Bashiri Ruslan Baikulov Yu Zhu Lei Ma Shan Yu Tiejun Huang Bryan M. Li Wolf De Wulf Nina Kudryashova Matthias H. Hennig Nathalie L. Rochefort Arno Onken Eric Wang Zhiwei Ding Andreas S. Tolias Fabian H. Sinz Alexander S. Ecker Institute of Computer Science and Campus Institute Data Science University of Göttingen Germany Department of Neuroscience & Center for Neuroscience and Artificial Intelligence Baylor College of Medicine Houston Texas and Department of Ophthalmology Byers Eye Institute Stanford University School of Medicine Stanford CA and Stanford Bio-X Stanford University Stanford CA and Wu Tsai Neurosciences Institute Stanford University Stanford CA Department of Neuroscience & Center for Neuroscience and Artificial Intelligence Baylor College of Medicine Houston Texas Institute of Computer Science and Campus Institute Data Science University of Göttingen Germany and Department of Ophthalmology Byers Eye Institute Stanford University School of Medicine Stanford CA and Stanford Bio-X Stanford University Stanford CA and Wu Tsai Neurosciences Institute Stanford University Stanford CA Institute of Computer Science and Campus Institute Data Science University of Göttingen Germany and International Max Planck Research School for Intelligent Systems Tübingen Germany and Institute for Bioinformatics and Medical Informatics Tübingen University Germany lRomul Russia Institute of Automation Chinese Academy of Sciences China and Beijing Academy of Artificial Intelligence China Beijing Academy of Artificial Intelligence China Institute of Automation Chinese Academy of Sciences China The Alan Turing Institute UK and School of Informatics University of Edinburgh UK School of Informatics University of Edinburgh UK Centre for Discovery Brain Sciences University of Edinburgh UK and Simons Initiative for the Developing Brain University of Edinburgh UK Department of Neuroscience & Center for Neuroscience and Artificial Intelligence Baylor College of Medicine Houston Texas and Department of Ophthalmology Byers Eye Institute Stanford University School of Medicine Stanford CA and Stanford Bio-X Stanford University Stanford CA and Wu Tsai Neurosciences Institute Stanford University Stanf

ISBN: (纸本)9798331314385

Understanding how biological visual systems process information is challenging because of the nonlinear relationship between visual input and neuronal responses. Artificial neural networks allow computational neuroscientists to create predictive models that connect biological and machine vision. Machine learning has benefited tremendously from benchmarks that compare different models on the same task under standardized conditions. However, there was no standardized benchmark to identify state-of-the-art dynamic models of the mouse visual system. To address this gap, we established the SENSORIUM 2023 Benchmark Competition with dynamic input, featuring a new large-scale dataset from the primary visual cortex of ten mice. This dataset includes responses from 78,853 neurons to 2 hours of dynamic stimuli per neuron, together with behavioral measurements such as running speed, pupil dilation, and eye movements. The competition ranked models in two tracks based on predictive performance for neuronal responses on a held-out test set: one focusing on predicting in-domain natural stimuli and another on out-of-distribution (OOD) stimuli to assess model generalization. As part of the NeurIPS 2023 Competition Track, we received more than 160 model submissions from 22 teams. Several new architectures for predictive models were proposed, and the winning teams improved the previous state-of-the-art model by 50%. Access to the dataset as well as the benchmarking infrastructure will remain online at ***.

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A Text Multi-label Classification Scheme Based on Resampling and Ensemble Learning 8th

A Text Multi-label Classification Scheme Based on Resampling...

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8th International Conference on Artificial Intelligence and Security , ICaiS 2022

作者： Wang, Tianhao Weng, Tianrang Ji, Jiacheng Zhong, Mingjun Zhang, Baili School of Computer Science and Engineering Southeast University Nanjing211189 China Key Laboratory of Computer Network and Information Integration in Southeast University Ministry of Education Nanjing211189 China Research Center for Judicial Big Data Supreme Count of China Nanjing211189 China Department of Computing Science University of Aberdeen AberdeenAB24 3UE United Kingdom

ISBN: (纸本)9783031067600

The medical dispute cases are professional and closely related to medicine. Therefore, the mediation of cases in practice depends heavily on similar historical cases. Multi-label classification of legal documents can efficiently filter irrelevant historical cases, which helps to recommend the similar historical cases faster and better. However, the imbalance and label symbiosis of the data set directly affect multi-label classification of legal documents. Therefore, a multi-label classification scheme based on resampling and ensemble learning is presented in this paper The scheme includes two parts: in the first part, in order to reduce the impact of label symbiosis on resampling, a resampling algorithm based on the average sparsity of the label set is proposed improve the imbalance of the data set;in the second one, a multi-label classification algorithm based on ensemble learning is proposed to train multiple base classifiers and combine each base classifier with a voting strategy of one vote. It can effectively improve the effect of multi-label classification. The experimental results show that the scheme proposed in this paper can improve the effect of multi-label classification and is not only suitable for legal documents but also applicable for other text data sets with imbalanced classes and label symbiosis problems. © 2022, The Author(s), under exclusive license to Springer Nature Switzerland AG.

关键词： Learning algorithms

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The Utility of Voided Urine Samples as a Proxy for the Vaginal Microbiome and for the Prediction of Bacterial Vaginosis

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Infectious Microbes & Diseases 2022年第4期4卷 149-156页

作者： Bin Zhu Christopher Diachok Laahirie Edupuganti David J.Edwards Jeffrey R.Donowitz Katherine Tossas Andrey Matveyev Katherine M.Spaine Vladimir Lee Myrna G.Serrano Gregory A.Buck Department of Microbiology and Immunology School of MedicineVirginia Commonwealth UniversityRichmondVirginiaUSA Center for Microbiome Engineering and Data Analysis Virginia Commonwealth UniversityRichmondVirginiaUSA Department of Statistical Sciences and Operations Research College of Humanities and SciencesVirginia Commonwealth UniversityRichmondVirginiaUSA Department of Pediatric Infectious Diseases Children's Hospital of Richmond at Virginia Commonwealth UniversityRichmondVirginiaUSA Department of Infectious Diseases and International Health University of VirginiaCharlottesvilleVirginiaUSA Department of Health Behavior and Policy School of MedicineVirginia Commonwealth UniversityRichmondVirginiaUSA Department of Family Medicine and Population Health School of MedicineVirginia Commonwealth UniversityRichmondVirginiaUSA Computer Science Department College of EngineeringVirginia Commonwealth UniversityRichmondVirginiaUSA Genomics Core Virginia Commonwealth UniversityRichmondVirginiaUSA

Recent work has shown that the vaginal microbiome exerts a strong impact on women's gynecological ***,collection of vaginal specimens is invasive and requires previous clinical training or the involvement of a trained *** contrast,urine sample collection is routine and noninvasive and does not require involvement of a *** sought to compare the vaginal and urogenital microbiomes to assess the utility of voided urine samples as a proxy for the vaginal *** urogenital and vaginal samples were collected from pregnant women and characterized by 16S rRNA taxonomic *** examined diversities and compositions of paired urogenital and vaginal microbiomes using five discrete strategies to explore the similarity between the vaginal and urogenital microbiomes.A strategy comparing the paired urogenital and vaginal microbiomes in which taxa were assigned using the STIRRUPS database and urine-specific taxa were removed showed no significant difference in diversity and composition between the paired urogenital and vaginal ***,the relative abundances of common vaginal taxa were linearly correlated with those in the paired *** similarities suggest that voided urine samples could represent a noninvasive protocol for accurate profiling of the vaginalmicrobiome with likely clinical ***,a machine learning model was established in which the voided urine microbiome was compared favorably to the vaginal microbiome in predicting bacterial vaginosis.

关键词： 16S rRNA vaginal microbiome urine microbiome bacterial vaginosis reproductive and gynecologic health

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Cavity approach for the approximation of spectral density of graphs with heterogeneous structures

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Physical Review E 2024年第3期109卷 034303-034303页

作者： Grover E. C. Guzman Peter F. Stadler Andre Fujita Department of Computer Science Institute of Mathematics and Statistics University of São Paulo Rua do Matão 1010 São Paulo - SP 05508-090 Brazil. Bioinformatics Group Department of Computer Science Interdisciplinary Center for Bioinformatics School of Excellence in Embedded Composite AI Dresden/Leipzig (SECAI) Leipzig University Härtelstraße 16-18 D-04107 Leipzig Germany German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig Puschstraße 4 04103 Leipzig Germany Competence Center for Scalable Data Services and Solutions Dresden-Leipzig Humboldtstraße 25 04105 Leipzig Germany Leipzig University Härtelstraße 16-18 D-04107 Leipzig Germany Max Planck Institute for Mathematics in the Sciences Inselstraße 22 D-04103 Leipzig Germany Institute for Theoretical Chemistry University of Vienna Währingerstraße 17 A-1090 Wien Austria Facultad de Ciencias Universidad Nacional de Colombia Sede Bogotá 111321 Colombia and The Santa Fe Institute 1399 Hyde Park Road Santa Fe New Mexico 87501 USA. Department of Computer Science Institute of Mathematics and Statistics University of São Paulo Rua do Matão 1010 São Paulo - SP 05508-090 Brazil and Division of Network AI Statistics Medical Institute of Bioregulation Kyushu University Fukuoka 812-8582 Japan.

Graphs have become widely used to represent and study social, biological, and technological systems. Statistical methods to analyze empirical graphs were proposed based on the graph's spectral density. However, their running time is cubic in the number of vertices, precluding direct application to large instances. Thus, efficient algorithms to calculate the spectral density become necessary. For sparse graphs, the cavity method can efficiently approximate the spectral density of locally treelike undirected and directed graphs. However, it does not apply to most empirical graphs because they have heterogeneous structures. Thus, we propose methods for undirected and directed graphs with heterogeneous structures using a new vertex's neighborhood definition and the cavity approach. Our methods' time and space complexities are O(|E|hmax3t) and O(|E|hmax2t), respectively, where |E| is the number of edges, hmax is the size of the largest local neighborhood of a vertex, and t is the number of iterations required for convergence. We demonstrate the practical efficacy by estimating the spectral density of simulated and real-world undirected and directed graphs.

关键词： Network structure Directed networks Monte Carlo methods Network Models Topological tools

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Federated Learning-Based Intelligent Indoor Smoke and Fire Detection System for Smart Buildings

Federated Learning-Based Intelligent Indoor Smoke and Fire D...

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Telecommunications and Intelligent Systems (ICTIS), International Conference on

作者： Mohamed Rafik Aymene Berkani Ammar Chouchane Yassine Himeur Anes Abdennebi Seref Sagiroglu Abbes Amira Research Laboratory in Advanced Electronics Systems (LSEA) University Yahia Fares of Medea Medea Algeria Laboratory of LI3C University Biskra University Center of Barika Barika Algeria College of Engineering and Information Technology University of Dubai Dubai United Arab Emirates Software and Information Technology Engineering École de Technologie Supérieure Montréal Canada Artificial Intelligence and Big Data Analytics Security R&D Center Gazi University Ankara Turkey Department of Computer Science University of Sharjah Sharjah United Arab Emirates

ISBN: (数字)9798331527396

ISBN: (纸本)9798331527402

Ensuring safety in smart buildings is crucial due to the increasing prevalence of smoke and fire hazards in modern environments. This paper introduces a novel privacy-preserving FL approach based on a CNN1D for smoke and fire detection in smart buildings. Our system integrates data from wearable environmental sensors to train a lightweight, edge-deployable DL-CNN1D model, ensuring data privacy while enabling collaborative learning across distributed clients using Federated Averaging (FedAvg) aggregation. Experiments conducted on a comprehensive air measurement dataset for smoke and fire detection demonstrate exceptional performance, with the global model achieving 99.97% accuracy, 99.96% precision, in smoke and fire recognition. Our model demonstrates a low communication cost of 0.4 MB, underscoring its efficiency for real-time applications. Our FL-based approach represents a significant step towards balancing the need for robust safety systems with growing privacy concerns in smart building environments.

关键词： Privacy Smart buildings Costs Federated learning Atmospheric modeling data models Convolutional neural networks Wearable sensors Monitoring Intelligent sensors

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Improving efficiency of the path optimization method for a gauge theory

arXiv

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arXiv 2022年

作者： Namekawa, Yusuke Kashiwa, Kouji Matsuda, Hidefumi Ohnishi, Akira Takase, Hayato Education and Research Center for Artificial Intelligence and Data Innovation Hiroshima University Hiroshima730-0053 Japan Department of Physics Faculty of Science Kyoto University Kyoto606-8502 Japan Yukawa Institute for Theoretical Physics Kyoto University Kyoto606-8502 Japan Department of Computer Science and Engineering Faculty of Information Engineering Fukuoka Institute of Technology Fukuoka811-0295 Japan Department of Physics Center for Field Theory and Particle Physics Fudan University Shanghai200433 China

We investigate efficiency of a gauge-covariant neural network and an approximation of the Jacobian in optimizing the complexified integration path toward evading the sign problem in lattice field theories. For the construction of the complexified integration path, we employ the path optimization method. The 2-dimensional U(1) gauge theory with the complex gauge coupling constant is used as a laboratory to evaluate the efficiency. It is found that the gauge-covariant neural network, which is composed of the Stout-like smearing, can enhance the average phase factor, as the gauge-invariant input does. For the approximation of the Jacobian, we test the most drastic case in which we perfectly drop the Jacobian during the learning process. It reduces the numerical cost of the Jacobian calculation from O(N3) to O(1), where N means the number of degrees of freedom of the theory. The path optimization using this Jacobian approximation still enhances the average phase factor at expense of a slight increase of the statistical error. Copyright © 2022, The Authors. All rights reserved.

关键词： Efficiency

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Advances in artificial intelligence techniques drive the application of radiomics in the clinical research of hepatocellular carcinoma

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iLIVER 2022年第1期1卷 49-54页

作者： Jingwei Wei Meng Niu Ouyang Yabo Yu Zhou Xiaoke Ma Xue Yang Hanyu Jiang Hui Hui Hongyi Cao Binwei Duan Hongjun Li Dawei Ding Jie Tian Key Laboratory of Molecular Imaging Institute of AutomationChinese Academy of SciencesBeijing 100190China Beijing Key Laboratory of Molecular Imaging Beijing 100190China Department of Interventional Radiology The First Affiliated Hospital of China Medical UniversityShenyangLiaoning110000China Beijing YouAn Hospital Capital Medical UniversityBeijing Institute of HepatologyBeijing100069China School of Life Science and Technology Xidian UniversityXi'anChina School of Computer Science and Technology Xidian UniversityXi'anShaanxiChina Department of Radiology Beijing Youan HospitalCapital Medical UniverstiyBeijing100069China Department of Radiology West China HospitalSichuan UniversityChengduSichuan 610041China Department of Pathology College of Basic Medical ScienceChina Medical UniversityShenyangLiaoning110000China The Department of General Surgery Center Beijing YouAn HospitalCapital Medical UniversityChina School of Bioengineering Beihang UniversityBeijing100191China School of Automation and Electrical Engineering University of Science and Technology BeijingBeijing 100083China Beijing Advanced Innovation Center for Big Data-Based Precision Medicine School of Medicine Beihang UniversityBeijing100191China Engineering Research Center of Molecular and Neuro Imaging of Ministry of Education School of Life Science and TechnologyXidian UniversityXi'anShaanxi710126China

Hepatocellular carcinoma(HCC)remains the most common malignancy to threaten public health *** advances in artificial intelligence techniques,radiomics for HCC management provides a novel perspective to solve unmet needs in clinical settings,and reveals pixel-level radiological information for medical imaging big data,correlating the radiological phenotype with targeted clinical *** radiomics pipelines depend on handcrafted engineering features,and further deep learning-based radiomics pipelines are supplemented with deep features calculated via self-learning *** the past decade,radiomics has been widely applied in accurate diagnoses and pathological or biological behavior evaluation,as well as in prognosis *** this review,we systematically introduce the main pipelines of artificial intelligence-based radiomics and their efficacy in the clinical studies of HCC.

关键词： Artificial intelligence Diagnosis Hepatocellular carcinoma Prognosis Radiomics

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Nonequilibrium transport and the fluctuation theorem in the thermodynamic behaviors of nonlinear photonic systems

arXiv

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arXiv 2024年

作者： Liu, Yang Lu, Jincheng Xiong, Zhongfei Wu, Fan O. Christodoulides, Demetrios Chen, Yuntian Jiang, Jian-Hua School of Physical Science and Technology Collaborative Innovation Center of Suzhou Nano Science and Technology Soochow University 1 Shizi Street Suzhou215006 China Jiangsu Key Laboratory of Micro and Nano Heat Fluid Flow Technology and Energy Application School of Physical Science and Technology Suzhou University of Science and Technology Suzhou215009 China School of Optical and Electronic Information Huazhong University of Science and Technology Wuhan430074 China CREOL College of Optics and Photonics University of Central Florida OrlandoFL32816-2700 United States Ming Hsieh Department of Electrical and Computer Engineering University of Southern California Los AngelesCA90089 United States School of Biomedical Engineering Suzhou Institute for Advanced Research University of Science and Technology of China Suzhou215123 China School of Physics University of Science and Technology of China Hefei230026 China

Nonlinear multimode optical systems have attracted substantial attention due to their rich physical properties. Complex interplay between the nonlinear effects and mode couplings makes it difficult to understand the collective dynamics of photons. Recent studies show that such collective phenomena can be effectively described by a Rayleigh–Jeans thermodynamics theory which is a powerful tool for the study of nonlinear multimode photonic systems. These systems, in turn, offer a compelling platform for investigating fundamental issues in statistical physics, attributed to their tunability and the ability to access negative temperature regimes. However, to date, a theory for the nonequilibrium transport and fluctuations is yet to be established. Here, we employ the full counting statistics theory to study the nonequilibrium transport of particle and energy in nonlinear multimode photonic systems in both positive and negative temperature regimes. Furthermore, we discover that in situations involving two reservoirs of opposite temperatures and chemical potentials, an intriguing phenomenon known as the loop current effect can arise, wherein the current in the positive energy sector runs counter to that in the negative energy sector. In addition, we numerically confirm that the fluctuation theorem remains applicable in optical thermodynamics systems across all regimes, from positive temperature to negative ones. Our findings closely align with numerical simulations based on first-principles nonlinear wave equations. Our work seeks to deepen the understanding of irreversible non-equilibrium processes and statistical fluctuations in nonlinear many-body photonic systems which will enhance our grasp of collective phenomena of photons and foster a fruitful intersection between optics and statistical physics. © 2024, CC BY-NC-ND.

关键词： Temperature

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Path optimization method for the sign problem caused by the fermion determinant

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Physical Review D 2025年第9期111卷 094503-094503页

作者： Kazuki Hisayoshi Kouji Kashiwa Yusuke Namekawa Hayato Takase Department of Computer Science and Engineering Faculty of Information Engineering Fukuoka Institute of Technology Fukuoka 811-0295 Japan Education and Research Center for Artificial Intelligence and Data Innovation Hiroshima University Hiroshima 730-0053 Japan

The path optimization method with machine learning is applied to the one-dimensional massive lattice Thirring model, which has the sign problem caused by the fermion determinant. This study aims to investigate how the path optimization method works for the sign problem. We show that the path optimization method successfully reduces statistical errors and reproduces the analytic results. We also examine an approximation of the Jacobian calculation in the learning process and show that it gives consistent results with those without an approximation.

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