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arXiv 2025年

作者： Almagro-Pérez, Cristina Song, Andrew H. Weishaupt, Luca Kim, Ahrong Jaume, Guillaume Williamson, Drew F.K. Hemker, Konstantin Lu, Ming Y. Singh, Kritika Chen, Bowen Le, Long Phi Baras, Alexander S. Jiang, Sizun Bashashati, Ali Liu, Jonathan T.C. Mahmood, Faisal Department of Pathology Mass General Brigham Harvard Medical School BostonMA United States Cancer Program Broad Institute of Harvard and MIT CambridgeMA United States Data Science Program Dana-Farber Cancer Institute BostonMA United States Harvard-MIT Division of Health Sciences and Technology Massachusetts Institute of Technology CambridgeMA United States Department of Pathology Pusan National University Busan Korea Republic of Department of Pathology and Laboratory Medicine Emory University School of Medicine AtlantaGA United States Department of Computer Science & Technology University of Cambridge Cambridge United Kingdom Department of Electrical Engineering and Computer Science Massachusetts Institute of Technology CambridgeMA United States Rutgers Robert Wood Johnson Medical School New BrunswickNJ United States Department of Pathology Johns Hopkins Hospital BaltimoreMD United States Department of Biomedical Engineering Johns Hopkins Hospital BaltimoreMD United States Broad Institute of Harvard and MIT CambridgeMA United States Center for Virology and Vaccine Research Beth Israel Deaconess Medical Center Harvard Medical School BostonMA United States Department of Pathology Dana Farber Cancer Institute BostonMA United States Department of Pathology and Laboratory Medicine University of British Columbia VancouverBC Canada School of Biomedical Engineering University of British Columbia VancouverBC Canada Department of Mechanical Engineering Bioengineering Laboratory Medicine & Pathology University of Washington SeattleWA United States Harvard Data Science Initiative Harvard University CambridgeMA United States

A comprehensive three-dimensional (3D) map of tissue architecture and gene expression is crucial for illuminating the complexity and heterogeneity of tissues across diverse biomedical applications1. However, most spatial transcriptomics (ST) approaches remain limited to two-dimensional (2D) sections of tissue2–4. Although current 3D ST methods hold promise, they typically require extensive tissue sectioning, are complex, are not compatible with non-destructive 3D tissue imaging technologies, and often lack scalability5–8. Here, we present VOlumetrically Resolved Transcriptomics EXpression (VORTEX), an AI framework that leverages 3D tissue morphology and minimal 2D ST to predict volumetric 3D ST. By pretraining on diverse 3D morphology–transcriptomic pairs from heterogeneous tissue samples and then fine-tuning on minimal 2D ST data from a specific volume of interest, VORTEX learns both generic tissue-related and sample-specific morphological correlates of gene expression. This approach enables dense, high-throughput, and fast 3D ST, scaling seamlessly to large tissue volumes far beyond the reach of existing 3D ST techniques. By offering a cost-effective and minimally destructive route to obtaining volumetric molecular insights, we anticipate that VORTEX will accelerate biomarker discovery and our understanding of morphomolecular associations and cell states in complex tissues. Interactive 3D ST volumes can be viewed at https://***/. © 2025, CC BY-NC-ND.

关键词： Vortex flow

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Toward Complete Transformation of Sodium Polysulfides by Regulating the Second-Shell Coordinating Environment of Atomically Dispersed Fe

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Angewandte Chemie 2023年第26期135卷

作者： Ruilin Bai Qiaosong Lin Xinyu Li Fangxin Ling Huijuan Wang Sha Tan Lingxiang Hu Mingze Ma Prof. Xiaojun Wu Yu Shao Xianhong Rui Prof. Enyuan Hu Dr. Yu Yao Prof. Yan Yu Hefei National Research Center for Physical Sciences at the Microscale Department of Materials Science and Engineering CAS Key Laboratory of Materials for Energy Conversion University of Science and Technology of China Hefei Anhui 230026 China Contribution: Conceptualization (lead) Writing - original draft (lead) State Key Laboratory of Molecular Reaction Dynamics Dalian Institute of Chemical Physics Chinese Academy of Sciences Dalian 116023 Liaoning China University of Chinese Academy of Sciences Beijing 100049 China Contribution: Data curation (lead) Contribution: Formal analysis (equal) Contribution: Investigation (lead) Experimental Center of Engineering and Material Science University of Science and Technology of China Hefei 230026 China Contribution: Methodology (equal) Chemistry Division Brookhaven National Laboratory Upton NY USA Contribution: Resources (equal) Department of Electrical Engineering and Computer Science Institut Polytechnique de Paris 91120 Palaiseau Île-de-France France Contribution: Software (equal) Contribution: Data curation (equal) Jiujiang DeFu Technology Co. Ltd. Jiujiang Jiangxi 332000 (P. R. China School of Materials and Energy Guangdong University of Technology Guangzhou 510006 China Contribution: Validation (lead) Contribution: Methodology (lead) Contribution: Writing - review & editing (lead) National Synchrotron Radiation Laboratory Hefei Anhui 230026 China Contribution: Project administration (lead) Writing - review & editing (lead)

Room temperature sodium-sulfur (RT Na-S) batteries are highly competitive as potential energy storage devices. Nevertheless, their actually achieved reversible capacities are far below the theoretical value due to incomplete transformation of polysulfides. Herein, atomically dispersed Fe-N/S active center by regulating the second-shell coordinating environment of Fe single atom is proposed. The Fe−N 4 S 2 coordination structure with enhanced local electronic concentration around the Fermi level is revealed via synchrotron radiation X-ray absorption spectroscopy (XAS) and theoretical calculations, which can not only significantly promote the transformation kinetics of polysulfides, but induce uniform Na deposition for dendrite-free Na anode. As a result, the obtained S cathode delivers a high initial reversible capacity of 1590 mAh g −1 , nearly the theoretical value. This work opens up a new avenue to facilitate the complete transformation of polysulfides for RT Na-S batteries.

关键词： Catalysis Coordinating Environment Fe Single Atom RT Na-S Batteries Transformation Kinetics

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Multimodal Whole Slide Foundation Model for Pathology

arXiv

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arXiv 2024年

作者： Ding, Tong Wagner, Sophia J. Song, Andrew H. Chen, Richard J. Lu, Ming Y. Zhang, Andrew Vaidya, Anurag J. Jaume, Guillaume Shaban, Muhammad Kim, Ahrong Williamson, Drew F.K. Chen, Bowen Almagro-Perez, Cristina Doucet, Paul Sahai, Sharifa Chen, Chengkuan Komura, Daisuke Kawabe, Akihiro Ishikawa, Shumpei Gerber, Georg Peng, Tingying Le, Long Phi Mahmood, Faisal Department of Pathology Mass General Brigham Harvard Medical School BostonMA United States Data Science Program Dana-Farber Cancer Institute BostonMA United States Cancer Program Broad Institute of Harvard and MIT CambridgeMA United States John A. Paulson School of Engineering and Applied Sciences Harvard University CambridgeMA United States Helmholtz Munich German Research Center for Environment and Health Munich Germany School of Computation Information and Technology Technical University of Munich Munich Germany Department of Electrical Engineering and Computer Science Massachusetts Institute of Technology CambridgeMA United States Harvard-MIT Division of Health Sciences and Technology Massachusetts Institute of Technology CambridgeMA United States Department of Pathology Pusan National University Busan Korea Republic of Department of Pathology and Laboratory Medicine Emory University School of Medicine AtlantaGA United States Harvard Data Science Initiative Harvard University CambridgeMA United States Department of Systems Biology Harvard Medical School BostonMA United States Department of Preventive Medicine Graduate School of Medicine The University of Tokyo Tokyo Japan Division of Pathology National Cancer Center Exploratory Oncology Research & Clinical Trial Center Chiba Japan

The field of computational pathology has been transformed with recent advances in foundation models that encode histopathology region-of-interests (ROIs) into versatile and transferable feature representations via self-supervised learning (SSL). However, translating these advancements to address complex clinical challenges at the patient and slide level remains constrained by limited clinical data in disease-specific cohorts, especially for rare clinical conditions. We propose TITAN, a multimodal whole slide foundation model pretrained using 335,645 WSIs via visual self-supervised learning and vision-language alignment with corresponding pathology reports and 423,122 synthetic captions generated from a multimodal generative AI copilot for pathology. Without any finetuning or requiring clinical labels, TITAN can extract general-purpose slide representations and generate pathology reports that generalize to resource-limited clinical scenarios such as rare disease retrieval and cancer prognosis. We evaluate TITAN on diverse clinical tasks and find that TITAN outperforms both ROI and slide foundation models across machine learning settings such as linear probing, few-shot and zero-shot classification, rare cancer retrieval and cross-modal retrieval, and pathology report generation. The model is publicly accessible at https://***/mahmoodlab/TITAN © 2024, CC BY-NC-ND.

关键词： Self-supervised learning

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Interpretable Symbolic Regression for Data Science: Analysis of the 2022 Competition

arXiv

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arXiv 2023年

作者： de Franca, F.O. Virgolin, M. Kommenda, M. Majumder, M.S. Cranmer, M. Espada, G. Ingelse, L. Fonseca, A. Landajuela, M. Petersen, B. Glatt, R. Mundhenk, N. Lee, C.S. Hochhalter, J.D. Randall, D.L. Kamienny, P. Zhang, H. Dick, G. Simon, A. Burlacu, B. Kasak, Jaan Machado, Meera Wilstrup, Casper La Cava, W.G. Federal University of ABC Santo Andre Brazil Evolutionary Intelligence Group Centrum Wiskunde & Informatica Science Park 123 Amsterdam Netherlands Computational Health Informatics Program Boston Children's Hospital Harvard Medical School Boston United States University of Applied Sciences Upper Austria Hagenberg Austria Center for Computational Astrophysics Flatiron Institute Department of Astrophysical Sciences Princeton University United States LASIGE Faculdade de Ciências Universidade de Lisboa Lisboa Portugal Computational Engineering Division Lawrence Livermore National Laboratory Livermore United States University of Utah Department of Mechanical Engineering Utah United States Meta FAIR France Victoria University of Wellington School of Engineering and Computer Science New Zealand University of otago Department of Information Science New Zealand Institut für Angewandte Physik Universität Tübingen Max Planck Institute for Intelligent Systems Tübingen Germany Abzu AI Orient Plads 1 Nordhavn 2150 Denmark

Symbolic regression searches for analytic expressions that accurately describe studied phenomena. The main attraction of this approach is that it returns an interpretable model that can be insightful to users. Historically, the majority of algorithms for symbolic regression have been based on evolutionary algorithms. However, there has been a recent surge of new proposals that instead utilize approaches such as enumeration algorithms, mixed linear integer programming, neural networks, and Bayesian optimization. In order to assess how well these new approaches behave on a set of common challenges often faced in real-world data, we hosted a competition at the 2022 Genetic and Evolutionary Computation Conference consisting of different synthetic and real-world datasets which were blind to entrants. For the real-world track, we assessed interpretability in a realistic way by using a domain expert to judge the trustworthiness of candidate models. We present an in-depth analysis of the results obtained in this competition, discuss current challenges of symbolic regression algorithms and highlight possible improvements for future competitions. Copyright © 2023, The Authors. All rights reserved.

关键词： Machine learning

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An objective measure of signal quality for pediatric lung auscultations

An objective measure of signal quality for pediatric lung au...

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Annual International Conference of the IEEE engineering in Medicine and Biology Society (EMBC)

作者： Annapurna Kala Amyna Husain Eric D McCollum Mounya Elhilali Department of Electrical and Computer Engineering Johns Hopkins University Department of Pediatrics Johns Hopkins University Johns Hopkins School of Medicine Global Program of Pediatric Respiratory Sciences Eudowood Division of Pediatric Respiratory Sciences

ISBN: (数字)9781728119908

ISBN: (纸本)9781728119915

A stethoscope is a ubiquitous tool used to 'listen' to sounds from the chest in order to assess lung and heart conditions. With advances in health technologies including digital devices and new wearable sensors, access to these sounds is becoming easier and abundant; yet proper measures of signal quality do not exist. In this work, we develop an objective quality metric of lung sounds based on low-level and high-level features in order to independently assess the integrity of the signal in presence of interference from ambient sounds and other distortions. The proposed metric outlines a mapping of auscultation signals onto rich low-level features extracted directly from the signal which capture spectral and temporal characteristics of the signal. Complementing these signal-derived attributes, we propose high-level learnt embedding features extracted from a generative auto-encoder trained to map auscultation signals onto a representative space that best captures the inherent statistics of lung sounds. Integrating both low-level (signal-derived) and high-level (embedding) features yields a robust correlation of 0.85 to infer the signal-to-noise ratio of recordings with varying quality levels. The method is validated on a large dataset of lung auscultation recorded in various clinical settings with controlled varying degrees of noise interference. The proposed metric is also validated against opinions of expert physicians in a blind listening test to further corroborate the efficacy of this method for quality assessment.

关键词： Lung Feature extraction Signal to noise ratio Medical services Spectrogram Noise measurement

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Publisher Correction: Deciphering DNA variant-associated aberrant splicing with the aid of RNA sequencing

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Nature genetics 2023年第7期55卷 1251页

作者： Bin Zhang Xin Gao Computer Science Program Computer Electrical and Mathematical Sciences and Engineering Division King Abdullah University of Science and Technology (KAUST) Thuwal Saudi Arabia. KAUST Computational Bioscience Research Center King Abdullah University of Science and Technology Thuwal Saudi Arabia. Computer Science Program Computer Electrical and Mathematical Sciences and Engineering Division King Abdullah University of Science and Technology (KAUST) Thuwal Saudi Arabia. xin.gao@kaust.edu.sa. KAUST Computational Bioscience Research Center King Abdullah University of Science and Technology Thuwal Saudi Arabia. xin.gao@kaust.edu.sa.

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Mind the performance gap: Examining dataset shift during prospective validation

arXiv

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arXiv 2021年

作者： Ötles, Erkin Oh, Jeeheh Li, Benjamin Bochinski, Michelle Joo, Hyeon Ortwine, Justin Shenoy, Erica Washer, Laraine Young, Vincent B. Rao, Krishna Wiens, Jenna Department of Industrial & Operations Engineering University of Michigan Medical Scientist Training Program University of Michigan Medical School Division of Computer Science & Engineering University of Michigan Nursing Informatics Michigan Medicine Department of Anesthesiology University of Michigan Medical School Department of Learning Health Sciences University of Michigan Medical School Infection Control Unit Division of Infectious Diseases Massachusetts General Hospital Harvard Medical School Department of Internal Medicine Division of Infectious Diseases University of Michigan Medical School Department of Microbiology & Immunology University of Michigan Medical School

Once integrated into clinical care, patient risk stratification models may perform worse compared to their retrospective performance. To date, it is widely accepted that performance will degrade over time due to changes in care processes and patient populations. However, the extent to which this occurs is poorly understood, in part because few researchers report prospective validation performance. In this study, we compare the 2020-2021 (’20-’21) prospective performance of a patient risk stratification model for predicting healthcare-associated infections to a 2019-2020 (’19-’20) retrospective validation of the same model. We define the difference in retrospective and prospective performance as the performance gap. We estimate how i) "temporal shift", i.e., changes in clinical workflows and patient populations, and ii) "infrastructure shift", i.e., changes in access, extraction and transformation of data, both contribute to the performance gap. Applied prospectively to 26,864 hospital encounters during a twelve-month period from July 2020 to June 2021, the model achieved an area under the receiver operating characteristic curve (AUROC) of 0.767 (95% confidence interval (CI): 0.737, 0.801) and a Brier score of 0.189 (95% CI: 0.186, 0.191). Prospective performance decreased slightly compared to’19-’20 retrospective performance, in which the model achieved an AUROC of 0.778 (95% CI: 0.744, 0.815) and a Brier score of 0.163 (95% CI: 0.161, 0.165). The resulting performance gap was primarily due to infrastructure shift and not temporal shift. So long as we continue to develop and validate models using data stored in large research data warehouses, we must consider differences in how and when data are accessed, measure how these differences may negatively affect prospective performance, and work to mitigate those differences. Copyright © 2021, The Authors. All rights reserved.

关键词： Data warehouses

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Observation of the dual quantum spin Hall insulator by density-tuned correlations in a van der Waals monolayer

arXiv

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arXiv 2024年

作者： Tang, Jian Ding, Thomas Siyuan Chen, Hongyu Gao, Anyuan Qian, Tiema Huang, Zumeng Sun, Zhe Han, Xin Strasser, Alex Li, Jiangxu Geiwitz, Michael Shehabeldin, Mohamed Belosevich, Vsevolod Wang, Zihan Wang, Yiping Watanabe, Kenji Taniguchi, Takashi Bell, David C. Wang, Ziqiang Fu, Liang Zhang, Yang Qian, Xiaofeng Burch, Kenneth S. Shi, Youguo Ni, Ni Chang, Guoqing Xu, Su-Yang Ma, Qiong Department of Physics Boston College Chestnut HillMA United States Division of Physics and Applied Physics School of Physical and Mathematical Sciences Nanyang Technological University Singapore Singapore Department of Chemistry and Chemical Biology Harvard University CambridgeMA United States Department of Physics and Astronomy and California NanoSystems Institute University of California Los Angeles Los AngelesCA United States Beijing National Laboratory for Condensed Matter Physics Institute of Physics Chinese Academy of Sciences Beijing China Department of Materials Science and Engineering Texas A&M University College StationTX United States Department of Physics and Astronomy University of Tennessee KnoxvilleTN United States Min H. Kao Department of Electrical Engineering and Computer Science University of Tennessee KnoxvilleTN United States Research Center for Electronic and Optical Materials National Institute for Materials Science Tsukuba Japan Research Center for Materials Nanoarchitectonics National Institute for Materials Science Tsukuba Japan Harvard John A. Paulson School of Engineering and Applied Sciences The Center for Nanoscale system Harvard University CambridgeMA United States Department of Physics Massachusetts Institute of Technology CambridgeMA United States CIFAR Azrieli Global Scholars program CIFAR Toronto Canada

The convergence of topology and correlations represents a highly coveted realm in the pursuit of novel quantum states of matter [1, 2]. Introducing electron correlations to a quantum spin Hall (QSH) insulator can lead to the emergence of a fractional topological insulator and other exotic time-reversal-symmetric topological order [3- 10], not possible in quantum Hall and Chern insulator systems. However, the QSH insulator with quantized edge conductance remains rare, let alone that with significant correlations. In this work, we report a novel dual QSH insulator within the intrinsic monolayer crystal of TaIrTe4, arising from the interplay of its single-particle topology and density-tuned electron correlations. At charge neutrality, monolayer TaIrTe4 demonstrates the QSH insulator that aligns with single-particle band structure calculations, manifesting enhanced nonlocal transport and quantized helical edge conductance. Interestingly, upon introducing electrons from charge neutrality, TaIrTe4 only shows metallic behavior in a small range of charge densities but quickly goes into a new insulating state, entirely unexpected based on TaIrTe4's single-particle band structure. This insulating state could arise from a strong electronic instability near the van Hove singularities (VHS), likely leading to a charge density wave (CDW). Remarkably, within this correlated insulating gap, we observe a resurgence of the QSH state, marked by the revival of nonlocal transport and quantized helical edge conduction. Our observation of helical edge conduction in a CDW gap could bridge spin physics and charge orders. The discovery of a dual QSH insulator introduces a new method for creating topological flat minibands via CDW superlattices, which offer a promising platform for exploring time-reversal-symmetric fractional phases and electromagnetism [3-5, 11, 12]. Copyright © 2024, The Authors. All rights reserved.

关键词： Charge density waves

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Regularity and numerical approximation of fractional elliptic differential equations on compact metric graphs

arXiv

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arXiv 2023年

作者： Bolin, David Kovács, Mihály Kumar, Vivek Simas, Alexandre B. Statistics Program Computer Electrical and Mathematical Sciences and Engineering Division King Abdullah University of Science and Technology Thuwal23955-6900 Saudi Arabia Department of Mathematical Sciences Chalmers University of Technology University of Gothenburg GothenburgSE-41296 Sweden Department of Differential Equations Budapest University of Technology and Economics Mauegyetem rkp. 3. BudapestH-1111 Hungary Faculty of Information Technology and Bionics Pázmány Péter Catholic University Práter utca 50/a. BudapestH-1083 Hungary Theoretical Statistics and Mathematics Unit Indian Statistical Institute Bangalore Centre 8th Mile Mysore Road Karnataka Bangalore560059 India

The fractional differential equation Lβu = f posed on a compact metric graph is considered, where β > 0 and L = κ2 − ∇(a∇) is a second-order elliptic operator equipped with certain vertex conditions and sufficiently smooth and positive coefficients κ, a. We demonstrate the existence of a unique solution for a general class of vertex conditions and derive the regularity of the solution in the specific case of Kirchhoff vertex conditions. These results are extended to the stochastic setting when f is replaced by Gaussian white noise. For the deterministic and stochastic settings under generalized Kirchhoff vertex conditions, we propose a numerical solution based on a finite element approximation combined with a rational approximation of the fractional power L−β. For the resulting approximation, the strong error is analyzed in the deterministic case, and the strong mean squared error as well as the L2(Γ×Γ)error of the covariance function of the solution are analyzed in the stochastic setting. Explicit rates of convergences are derived for all cases. Numerical experiments for L = κ2 − ∆, κ > 0 are performed to illustrate the *** Codes 35R02, 35A01, 35A02, 60H15, 60H40 Copyright © 2023, The Authors. All rights reserved.

关键词： Errors

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Deep-Strong Coupling between Cavity Photons and Terahertz TO Phonons in PbTe

Deep-Strong Coupling between Cavity Photons and Terahertz TO...

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2023 Conference on Lasers and Electro-Optics, CLEO 2023

作者： Baydin, Andrey Manjappa, Manukumara Mishra, Sobhan Subhra Xu, Hongjing Tay, Fuyang Kim, Dasom Hernandez, Felix G.G. Rappl, Paulo H.O. Abramof, Eduardo Singh, Ranjan Kono, Junichiro Department of Electrical and Computer Engineering Rice University HoustonTX77005 United States Smalley-Curl Institute Rice University HoustonTX77005 United States Instrumentation and Applied Physics Department Indian Institute of Science Bangalore560012 India Center for Disruptive Photonic Technologies The Photonics Institute Nanyang Technological University 639798 Singapore Department of Physics and Astronomy Rice University HoustonTX77005 United States Applied Physics Graduate Program Smalley-Curl Institute Rice University HoustonTX77005 United States Instituto de Física Universidade de Sao Paulo SP Sao Paulo05508-090 Brazil Laboratorio Associado de Sensores e Materiais Instituto Nacional de Pesquisas Espaciais SP Sao Jose dos Campos12201-970 Brazil Division of Physics and Applied Physics School of Physical and Mathematical Sciences Nanyang Technological University 637371 Singapore Department of Material Science and NanoEngineering Rice University HoustonTX77005 United States

We have investigated the resonant coupling of photons with TO phonons in lead telluride in small-mode-volume terahertz cavities, observing a giant vacuum Rabi splitting on the order of the bare cavity-phonon frequency... 详细信息

ISBN: (纸本)9781957171258

关键词： Photons

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