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Corrections to "Contrastive Graph Pooling for Explainable Classification of Brain Networks"

IEEE transactions on medical imaging 2024年第11期43卷 4075页

作者： Jiaxing Xu Qingtian Bian Xinhang Li Aihu Zhang Yiping Ke Miao Qiao Wei Zhang Wei Khang Jeremy Sim Balazs Gulyas School of Computer Science and Engineering Nanyang Technological University Jurong West Singapore Department of Computer Science and Technology Tsinghua University Beijing China School of Computer Science The University of Auckland Auckland New Zealand Cognitive Neuroimaging Centre and the Lee Kong Chian School of Medicine Nanyang Technological University Jurong West Singapore Cognitive Neuroimaging Centre and IGP-Neuroscience Interdisciplinary Graduate Program Nanyang Technological University Jurong West Singapore Department of Clinical Neuroscience Karolinska Institutet Stockholm Sweden

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An Analysis of the Influence of Transfer Learning When Measuring the Tortuosity of Blood Vessels

arXiv

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arXiv 2021年

作者： da Silva, Matheus V. Ouellette, Julie Lacoste, Baptiste Comin, Cesar H. Department of Computer Science Federal University of São Carlos SP São Carlos Brazil Department of Cellular and Molecular Medicine Faculty of Medicine University of Ottawa OttawaON Canada Neuroscience Program Ottawa Hospital Research Institute OttawaON Canada

Convolutional Neural Networks (CNNs) can provide excellent results regarding the segmentation of blood vessels. One important aspect of CNNs is that they can be trained on large amounts of data and then be made available, for instance, in image processing software. The pre-trained CNNs can then be easily applied in downstream blood vessel characterization tasks, such as the calculation of the length, tortuosity, or caliber of the blood vessels. Yet, it is still unclear if pre-trained CNNs can provide robust, unbiased, results in downstream tasks when applied to datasets that they were not trained on. Here, we focus on measuring the tortuosity of blood vessels and investigate to which extent CNNs may provide biased tortuosity values even after fine-tuning the network to the new dataset under study. We show that the tortuosity values obtained by a CNN trained from scratch on a dataset may not agree with those obtained by a fine-tuned network that was pre-trained on a dataset having different tortuosity statistics. In addition, we show that the improvement in segmentation performance when fine-tuning the network does not necessarily lead to a respective improvement on the estimation of the tortuosity. To mitigate the aforementioned issues, we propose the application of data augmentation techniques even in situations where they do not improve segmentation performance. For instance, we found that the application of elastic transformations was enough to prevent an underestimation of 8% of blood vessel tortuosity when applying CNNs to different datasets. © 2021, CC BY.

关键词： Convolutional neural networks

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Inferring spatial transcriptomics markers from whole slide images to characterize metastasis-related spatial heterogeneity of colorectal tumors: A pilot study

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Journal of Pathology Informatics 2023年 14卷 100308-100308页

作者： Fatemi, Michael Feng, Eric Sharma, Cyril Azher, Zarif Goel, Tarushii Ramwala, Ojas Palisoul, Scott M. Barney, Rachael E. Perreard, Laurent Kolling, Fred W. Salas, Lucas A. Christensen, Brock C. Tsongalis, Gregory J. Vaickus, Louis J. Levy, Joshua J. Department of Computer Science University of Virginia Charlottesville VA United States Thomas Jefferson High School for Science and Technology Alexandria VA United States Department of Computer Science Purdue University West Lafayette IN United States Department of Computer Science Massachusetts Institute of Technology Cambridge MA United States Department of Biomedical Informatics and Medical Education University of Washington Seattle WA United States Emerging Diagnostic and Investigative Technologies Department of Pathology and Laboratory Medicine Dartmouth Health NH United States Dartmouth Cancer Center NH United States Department of Epidemiology Dartmouth College Geisel School of Medicine Hanover NH United States Department of Molecular and Systems Biology Dartmouth College Geisel School of Medicine Hanover NH United States Integrative Neuroscience at Dartmouth (IND) graduate program Dartmouth College Geisel School of Medicine Hanover NH United States Department of Community and Family Medicine Dartmouth College Geisel School of Medicine Hanover NH United States Department of Dermatology Dartmouth Health NH United States Program in Quantitative Biomedical Sciences Dartmouth College Geisel School of Medicine Hanover NH United States

Over 150 000 Americans are diagnosed with colorectal cancer (CRC) every year, and annually over 50 000 individuals will die from CRC, necessitating improvements in screening, prognostication, disease management, and therapeutic options. Tumor metastasis is the primary factor related to the risk of recurrence and mortality. Yet, screening for nodal and distant metastasis is costly, and invasive and incomplete resection may hamper adequate assessment. Signatures of the tumor-immune microenvironment (TIME) at the primary site can provide valuable insights into the aggressiveness of the tumor and the effectiveness of various treatment options. Spatially resolved transcriptomics technologies offer an unprecedented characterization of TIME through high multiplexing, yet their scope is constrained by cost. Meanwhile, it has long been suspected that histological, cytological, and macroarchitectural tissue characteristics correlate well with molecular information (e.g., gene expression). Thus, a method for predicting transcriptomics data through inference of RNA patterns from whole slide images (WSI) is a key step in studying metastasis at scale. In this work, we collected tissue from 4 stage-III (pT3) matched colorectal cancer patients for spatial transcriptomics profiling. The Visium spatial transcriptomics (ST) assay was used to measure transcript abundance for 17 943 genes at up to 5000 55-micron (i.e., 1–10 cells) spots per patient sampled in a honeycomb pattern, co-registered with hematoxylin and eosin (H&E) stained WSI. The Visium ST assay can measure expression at these spots through tissue permeabilization of mRNAs, which are captured through spatially (i.e., x–y positional coordinates) barcoded, gene specific oligo probes. WSI subimages were extracted around each co-registered Visium spot and were used to predict the expression at these spots using machine learning models. We prototyped and compared several convolutional, transformer, and graph convolutional neural

关键词： Colorectal cancer Deep learning Graph neural network Histomorphology Spatial transcriptomics Transformers

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3D-Printed electrochemical sensor-integrated transwell systems

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Microsystems & Nanoengineering 2020年第1期6卷 357-368页

作者： Pradeep Ramiah Rajasekaran Ashley Augustiny Chapin David N.Quan Jens Herberholz William E.Bentley Reza Ghodssi Institute for Systems Research University of MarylandCollege ParkMDUSA Fischell Department of Bioengineering University of MarylandCollege ParkMDUSA Department of Psychology and Neuroscience and Cognitive Science Program University of MarylandCollege ParkMDUSA Institute for Bioscience and Biotechnology Research University of MarylandCollege ParkMDUSA Robert E.Fischell Institute for Biomedical Devices University of MarylandCollege ParkMDUSA Department of Electrical and Computer Engineering University of MarylandCollege ParkMDUSA

This work presents a 3D-printed,modular,electrochemical sensor-integrated transwell system for monitoring cellular and molecular events in situ without sample extraction or microfluidics-assisted downstream *** additive manufacturing techniques such as 3D printing,shadow masking,and molding are used to fabricate this modular system,which is autoclavable,biocompatible,and designed to operate following standard operating protocols(SOPs)of cellular *** to the platform is a flexible porous membrane,which is used as a cell culture substrate similarly to a commercial transwell *** electrochemical sensors fabricated on the membrane allow direct access to cells and their products.A pair of gold electrodes on the top side of the membrane measures impedance over the course of cell attachment and growth,characterized by an exponential decrease(~160%at 10Hz)due to an increase in the double layer capacitance from secreted extracellular matrix(ECM)*** voltammetry(CV)sensor electrodes,fabricated on the bottom side of the membrane,enable sensing of molecular release at the site of cell culture without the need for downstream ***-time detection of ferrocene dimethanol injection across the membrane showed a three order-of-magnitude higher signal at the membrane than in the bulk media after reaching *** modular sensor-integrated transwell system allows unprecedented direct,real-time,and noninvasive access to physical and biochemical information,which cannot be obtained in a conventional transwell system.

关键词： transwell electrochemical culture

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CellBiAge: Improved single-cell age classification using data binarization

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Cell Reports 2023年第12期42卷 113500页

作者： Yu, Doudou Li, Manlin Linghu, Guanjie Hu, Yihuan Hajdarovic, Kaitlyn H. Wang, An Singh, Ritambhara Webb, Ashley E. Molecular Biology Cell Biology and Biochemistry Graduate Program Brown University Providence 02912 RI United States Data Science Institute Brown University Providence 02912 RI United States Neuroscience Graduate Program Brown University Providence 02912 RI United States Department of Applied Mathematics & Statistics Johns Hopkins University Baltimore 21218 MD United States Department of Computer Science Brown University Providence 02912 RI United States Center for Computational Molecular Biology Brown University Providence 02912 RI United States Department of Molecular Biology Cell Biology and Biochemistry Brown University Providence 02912 RI United States Center on the Biology of Aging Brown University Providence 02912 RI United States Carney Institute for Brain Science Brown University Providence 02912 RI United States Center for Translational Neuroscience Brown University Providence 02912 RI United States

Aging is a major risk factor for many diseases. Accurate methods for predicting age in specific cell types are essential to understand the heterogeneity of aging and to assess rejuvenation strategies. However, classifying organismal age at single-cell resolution using transcriptomics is challenging due to sparsity and noise. Here, we developed CellBiAge, a robust and easy-to-implement machine learning pipeline, to classify the age of single cells in the mouse brain using single-cell transcriptomics. We show that binarization of gene expression values for the top highly variable genes significantly improved test performance across different models, techniques, sexes, and brain regions, with potential age-related genes identified for model prediction. Additionally, we demonstrate CellBiAge's ability to capture exercise-induced rejuvenation in neural stem cells. This study provides a broadly applicable approach for robust classification of organismal age of single cells in the mouse brain, which may aid in understanding the aging process and evaluating rejuvenation methods. © 2023 The Authors

关键词： aging brain CP: Cell biology hypothalamus machine learning single-cell RNA-seq

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Fast, accurate, and versatile data analysis platform for the quantification of molecular spatiotemporal signals

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Cell 2025年第10期188卷 2794-2809.e21页

作者： Mi, Xuelong Chen, Alex Bo-Yuan Duarte, Daniela Carey, Erin Taylor, Charlotte R. Braaker, Philipp N. Bright, Mark Almeida, Rafael G. Lim, Jing-Xuan Ruetten, Virginia M.S. Wang, Yizhi Wang, Mengfan Zhang, Weizhan Zheng, Wei Reitman, Michael E. Huang, Yongkang Wang, Xiaoyu Li, Lei Deng, HanFei Shi, Song-Hai Poskanzer, Kira E. Lyons, David A. Nimmerjahn, Axel Ahrens, Misha B. Yu, Guoqiang Bradley Department of Electrical and Computer Engineering Virginia Polytechnic Institute and State University Arlington 22203 VA United States Janelia Research Campus Howard Hughes Medical Institute Ashburn 20147 VA United States Department of Molecular and Cellular Biology Harvard University Cambridge 02138 MA United States Graduate Program in Neuroscience Harvard Medical School Boston 02115 MA United States Waitt Advanced Biophotonics Center The Salk Institute for Biological Studies La Jolla 92037 CA United States Department of Biochemistry & Biophysics University of California San Francisco San Francisco CA United States Neuroscience Graduate Program University of California San Francisco San Francisco CA United States Centre for Discovery Brain Sciences University of Edinburgh Edinburgh BioQuarter Edinburgh EH16 4SB United Kingdom Gatsby Computational Neuroscience Unit UCL London W1T 4JG United Kingdom Kavli Institute for Fundamental Neuroscience San Francisco CA United States Department of Automation Tsinghua University Beijing 100084 China IDG/McGovern Institute for Brain Research Tsinghua University Beijing 100084 China New Cornerstone Science Laboratory Tsinghua-Peking Center for Life Sciences Beijing Frontier Research Center for Biological Structure School of Life Sciences Tsinghua University Beijing 100084 China State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science Institutes of Brain Science Fudan University Shanghai 200032 China Beijing National Research Center for Information Science and Technology Beijing 100084 China

Optical recording of intricate molecular dynamics is becoming an indispensable technique for biological studies, accelerated by the development of new or improved biosensors and microscopy technology. This creates major computational challenges to extract and quantify biologically meaningful spatiotemporal patterns embedded within complex and rich data sources, many of which cannot be captured with existing methods. Here, we introduce activity quantification and analysis (AQuA2), a fast, accurate, and versatile data analysis platform built upon advanced machine-learning techniques. It decomposes complex live-imaging-based datasets into elementary signaling events, allowing accurate and unbiased quantification of molecular activities and identification of consensus functional units. We demonstrate applications across a wide range of biosensors, cell types, organs, animal models, microscopy techniques, and imaging approaches. As exemplar findings, we show how AQuA2 identified drug-dependent interactions between neurons and astroglia, as well as distinct sensorimotor signal propagation patterns in the mouse spinal cord. © 2025 The Author(s)

关键词： AQuA2 astrocytes cell interaction analysis functional units glial cells image analysis machine learning molecular spatiotemporal signals neurons time-lapse imaging

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Plug-and-Play Stability for Intracortical Brain-computer Interfaces: A One-Year Demonstration of Seamless Brain-to-Text Communication

arXiv

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arXiv 2023年

作者： Fan, Chaofei Hahn, Nick Kamdar, Foram Avansino, Donald Wilson, Guy H. Hochberg, Leigh Shenoy, Krishna V. Henderson, Jaimie M. Willett, Francis R. Bio-X Program Stanford University United States Department of Neuroscience Stanford University United States Department of Neurosurgery Stanford University United States Department of Neurobiology Stanford University United States Department of Bioengineering Stanford University United States Department of Computer Science Stanford University United States Wu Tsai Neurosciences Institute Stanford University United States Howard Hughes Medical Institute Stanford University United States Department of Electrical Engineering Stanford University United States School of Engineering Carney Institute for Brain Science Brown University United States VA RR&D Center for Neurorestoration and Neurotechnology VA Providence Healthcare System United States Center for Neurotechnology and Neurorecovery Department of Neurology Massachusetts General Hospital Harvard Medical School United States

Intracortical brain-computer interfaces (iBCIs) have shown promise for restoring rapid communication to people with neurological disorders such as amyotrophic lateral sclerosis (ALS). However, to maintain high performance over time, iBCIs typically need frequent recalibration to combat changes in the neural recordings that accrue over days. This requires iBCI users to stop using the iBCI and engage in supervised data collection, making the iBCI system hard to use. In this paper, we propose a method that enables self-recalibration of communication iBCIs without interrupting the user. Our method leverages large language models (LMs) to automatically correct errors in iBCI outputs. The self-recalibration process uses these corrected outputs ("pseudo-labels") to continually update the iBCI decoder online. Over a period of more than one year (403 days), we evaluated our Continual Online Recalibration with Pseudo-labels (CORP) framework with one clinical trial participant. CORP achieved a stable decoding accuracy of 93.84% in an online handwriting iBCI task, significantly outperforming other baseline methods. Notably, this is the longest-running iBCI stability demonstration involving a human participant. Our results provide the first evidence for long-term stabilization of a plug-and-play, high-performance communication iBCI, addressing a major barrier for the clinical translation of iBCIs. Copyright © 2023, The Authors. All rights reserved.

关键词： Brain computer interface

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A Systematic Review of Extended Reality (XR) for Understanding and Augmenting Vision Loss

arXiv

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arXiv 2021年

作者： Kasowski, Justin Johnson, Byron A. Neydavood, Ryan Akkaraju, Anvitha Beyeler, Michael Graduate Program in Dynamical Neuroscience University of California Santa BarbaraCA93106 United States Department of Psychological & Brain Sciences University of California Santa BarbaraCA93106 United States Department of Computer Science University of California Santa BarbaraCA93106 United States

Purpose: Over the past decade, extended reality (XR) has emerged as an assistive technology not only to augment residual vision of people losing their sight but also to study the rudimentary vision restored to blind people by a visual neuroprosthesis. To make the best use of these emerging technologies, it is valuable and timely to understand the state of this research and identify any shortcomings that are present. Methods: Here we present a systematic literature review of 227 publications from 106 different venues assessing the potential of XR technology to further visual accessibility. In contrast to other reviews, we sample studies from multiple scientific disciplines, focus on augmentation of a person's residual vision, and require studies to feature a quantitative evaluation with appropriate end users. Results: We summarize prominent findings from different XR research areas, show how the landscape has changed over the last decade, and identify scientific gaps in the literature. Specifically, we highlight the need for real-world validation, the broadening of end-user participation, and a more nuanced understanding of the suitability and usability of different XR-based accessibility aids. Translational Relevance: By broadening end-user participation to early stages of the design process and shifting the focus from behavioral performance to qualitative assessments of usability, future research has the potential to develop XR technologies that may not only allow for studying vision loss, but also enable novel visual accessibility aids with the potential to impact the lives of millions of people living with vision loss. © 2021, CC BY.

关键词： Augmented reality

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Optically-generated focused ultrasound for noninvasive brain stimulation with ultrahigh precision

arXiv

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arXiv 2022年

作者： Li, Yueming Jiang, Ying Lan, Lu Ge, Xiaowei Cheng, Ran Zhan, Yuewei Chen, Guo Shi, Linli Wang, Runyu Zheng, Nan Yang, Chen Cheng, Ji-Xin Department of Mechanical Engineering Boston University BostonMA02215 United States Graduate Program for Neuroscience Boston University BostonMA02215 United States Department of Electrical and Computer Engineering Boston University BostonMA02215 United States Department of Chemistry Boston University BostonMA02215 United States Department of Biomedical Engineering Boston University BostonMA02215 United States Division of Materials Science and Engineering Boston University BostonMA02215 United States

High precision neuromodulation is a powerful tool to decipher neurocircuits and treat neurological diseases. Current non-invasive neuromodulation methods offer limited precision at the millimeter-level. Here, we report optically-generated focused ultrasound (OFUS) for non-invasive brain stimulation with ultrahigh precision. OFUS is generated by a soft optoacoustic pad (SOAP) fabricated through embedding candle soot nanoparticles in a curved polydimethylsiloxane film. SOAP generates a transcranial ultrasound focus at 15 MHz with an ultrahigh lateral resolution of 83 µm, which is two orders of magnitude smaller than that of conventional transcranial focused ultrasound (tFUS). Here, we show effective OFUS neurostimulation in vitro with a single ultrasound cycle. We demonstrate submillimeter transcranial stimulation of the mouse motor cortex in vivo. An acoustic energy of 0.6 mJ/cm2, four orders of magnitude less than that of tFUS, is sufficient for successful OFUS neurostimulation. OFUS offers new capabilities for neuroscience studies and disease treatments by delivering a focus with ultrahigh precision non-invasively. Copyright © 2022, The Authors. All rights reserved.

关键词： Silicones

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Conscious Intelligence Requires Lifelong Autonomous programming For General Purposes

arXiv

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arXiv 2020年

作者： Weng, Juyang Department of Computer Science and Engineering Cognitive Science Program Neuroscience Program Michigan State University East LansingMI48824 United States GENISAMA LLC East LansingMI48824 United States

Universal Turing Machines [29, 10, 18] are well known in computer science but they are about manual programming for general purposes. Although human children perform conscious learning (learning while being conscious) from infancy [24, 23, 14, 4], it is unknown that Universal Turing Machiness can facilitate not only our understanding of Autonomous programming For General Purposes (APFGP) by machines, but also enable early-age conscious learning. This work reports a new kind of AI—conscious learning AI from a machine’s "baby" time. Instead of arguing what static tasks a conscious machine should be able to do during its "adulthood", this work suggests that APFGP is a computationally clearer and necessary criterion for us to judge whether a machine is capable of conscious learning so that it can autonomously acquire skills along its "career path". The results here report new concepts and experimental studies for early vision, audition, natural language understanding, and emotion, with conscious learning capabilities that are absent from traditional AI systems. Copyright © 2020, The Authors. All rights reserved.

关键词： Turing machines

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