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arXiv 2025年

作者： Hébert-Dufresne, Laurent Ahn, Yong-Yeol Allard, Antoine Crothers, Jessica W. Dodds, Peter Sheridan Galesic, Mirta Ghanbarnejad, Fakhteh Gravel, Dominique Hammond, Ross A. Lerman, Kristina Lovato, Juniper Openshaw, John J. Redner, S. Scarpino, Samuel V. St-Onge, Guillaume Tangherlini, Timothy R. Young, Jean-Gabriel Vermont Complex Systems Institute University of Vermont BurlingtonVT United States Translational Global Infectious Disease Research Center University of Vermont BurlingtonVT United States Department of Computer Science University of Vermont BurlingtonVT United States Center for Complex Networks and Systems Research Luddy School of Informatics Computing and Engineering Indiana University BloomingtonIN United States Département de physique de génie physique et d’optique Université Laval QuébecQC Canada Department of Pathology and Laboratory Medicine Robert Larner M.D. College of Medicine University of Vermont BurlingtonVT United States Santa Fe Institute Santa FeNM United States Complexity Science Hub Vienna Austria School of Technology and Architecture SRH University of Applied Sciences Heidelberg Leipzig Germany Département de biologie Université de Sherbrooke SherbrookeQC Canada Brown School Washington University in St. Louis St. LouisMO United States The Brookings Institution WashingtonDC United States Information Sciences Institute University of Southern California United States Division of Infectious Diseases and Geographic Medicine Stanford University StanfordCA United States Institute for Experiential AI Northeastern University BostonMA United States Laboratory for the Modeling of Biological and Socio-technical Systems Northeastern University BostonMA United States The Roux Institute Northeastern University PortlandME United States Department of Scandinavian School of Information University of California Berkeley BerkeleyCA United States Department of Mathematics & Statistics University of Vermont BurlingtonVT United States

From pathogens and computer viruses to genes and memes, contagion models have found widespread utility across the natural and social sciences. Despite their success and breadth of adoption, the approach and structure of these models remain surprisingly siloed by field. Given the siloed nature of their development and widespread use, one persistent assumption is that a given contagion can be studied in isolation, independently from what else might be spreading in the population. In reality, countless contagions of biological and social nature interact within hosts (interacting with existing beliefs, or the immune system) and across hosts (interacting in the environment, or affecting transmission mechanisms). Additionally, from a modeling perspective, we know that relaxing these assumptions has profound effects on the physics and translational implications of the models. Here, we review mechanisms for interactions in social and biological contagions, as well as the models and frameworks developed to include these interactions in the study of the contagions. We highlight existing problems related to the inference of interactions and to the scalability of mathematical models and identify promising avenues of future inquiries. In doing so, we highlight the need for interdisciplinary efforts under a unified science of contagions and for removing a common dichotomy between social and biological contagions. Copyright © 2025, The Authors. All rights reserved.

关键词： Histology

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Repurpose open data to discover therapeutics for covid-19 using deep learning

arXiv

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arXiv 2020年

作者： Zeng, Xiangxiang Song, Xiang Ma, Tengfei Pan, Xiaoqin Zhou, Yadi Hou, Yuan Zhang, Zheng Karypis, George Cheng, Feixiong School of Computer Science and Engineering Hunan University Changsha410012 China AWS Shanghai AI Lab Shanghai200335 China Genomic Medicine Institute Lerner Research Institute Cleveland Clinic ClevelandOH44106 United States New York University Shanghai Shanghai200122 China AWS AI East Palo AltoCA94303 United States Department of Computer Science and Engineering University of Minnesota 200 Union Street SE MinneapolisMN United States Department of Molecular Medicine Cleveland Clinic Lerner College of Medicine Case Western Reserve University ClevelandOH44195 United States Case Comprehensive Cancer Center Case Western Reserve University School of Medicine ClevelandOH44106 United States

There have been more than 850,000 confirmed cases and over 48,000 deaths from the human coronavirus disease 2019 (COVID-19) pandemic, caused by novel severe acute respiratory syndrome coronavirus (SARS-CoV-2), in the United States alone. However, there are currently no proven effective medications against COVID-19. Drug repurposing offers a promising way for the development of prevention and treatment strategies for COVID-19. This study reports an integrative, network-based deep learning methodology to identify repurposable drugs for COVID-19 (termed CoV-KGE). Specifically, we built a comprehensive knowledge graph that includes 15 million edges across 39 types of relationships connecting drugs, diseases, genes, pathways, and expressions, from a large scientific corpus of 24 million PubMed publications. Using Amazon's AWS computing resources, we identified 41 repurposable drugs (including indomethacin, toremifene and niclosamide) whose therapeutic association with COVID-19 were validated by transcriptomic and proteomic data in SARS-CoV-2 infected human cells and data from ongoing clinical trials. While this study, by no means recommends specific drugs, it demonstrates a powerful deep learning methodology to prioritize existing drugs for further investigation, which holds the potential of accelerating therapeutic development for *** Codes I.2.1 Copyright © 2020, The Authors. All rights reserved.

关键词： Coronavirus

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Dependency and span, cross-style semantic role labeling on PropBank and NomBank

arXiv

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arXiv 2019年

作者： Li, Zuchao Zhao, Hai Zhou, Junru Parnow, Kevin He, Shexia Department of Computer Science and Engineering Key Laboratory of Shanghai Education Commission for Intelligent Interaction and Cognitive Engineering MoE Key Lab of Artificial Intelligence AI Institute Shanghai Jiao Tong University China

The latest developments in neural semantic role labeling (SRL) have shown great performance improvements with both the dependency and span formalisms/styles. Although the two styles share many similarities in linguistic meaning and computation, most previous studies focus on a single style. In this paper, we define a new cross-style semantic role label convention and propose a new cross-style joint optimization model designed around the most basic linguistic meaning of a semantic role, providing a solution to make the results of the two styles more comparable and allowing both formalisms of SRL to benefit from their natural connections in both linguistics and computation. Our model learns a general semantic argument structure and is capable of outputting in either style. Additionally, we propose a syntax-aided method to uniformly enhance the learning of both dependency and span representations. Experiments show that the proposed methods are effective on both span and dependency SRL benchmarks. Copyright © 2019, The Authors. All rights reserved.

关键词： Syntactics

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Soft yet Effective Robots via Holistic Co-Design

arXiv

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arXiv 2025年

作者： Stölzle, Maximilian Pagliarani, Niccolò Stella, Francesco Hughes, Josie Laschi, Cecilia Rus, Daniela Cianchetti, Matteo Santina, Cosimo Della Zardini, Gioele Laboratory for Information & Decision Systems Massachusetts Institute of Technology CambridgeMA02139 United States Cognitive Robotics Delft University of Technology Mekelweg 2 CD Delft2628 Netherlands The BioRobotics Institute Scuola Superiore Sant’Anna Pisa56025 Italy Embodied AI AG Lausanne1015 Switzerland CREATE Lab EPFL Lausanne1015 Switzerland Advanced Robotics Centre Department of Mechanical Engineering National University of Singapore 117575 Singapore Computer Science and Artificial Intelligence Laboratory Massachusetts Institute of Technology CambridgeMA02139 United States

Soft robots promise inherent safety via their material compliance for seamless interactions with humans or delicate environments. Yet, their development is challenging because it requires integrating materials, geometry, actuation, and autonomy into complex mechatronic systems. Despite progress, the field struggles to balance task-specific performance with broader factors like durability and manufacturability—a difficulty that we find is compounded by traditional sequential design processes with their lack of feedback loops. In this perspective, we review emerging co-design approaches that simultaneously optimize the body and brain, enabling the discovery of unconventional designs highly tailored to the given tasks. We then identify three key shortcomings that limit the broader adoption of such co-design methods within the soft robotics domain. First, many rely on simulation-based evaluations focusing on a single metric, while real-world designs must satisfy diverse criteria. Second, current methods emphasize computational modeling without ensuring feasible realization, risking sim-to-real performance gaps. Third, high computational demands limit the exploration of the complete design space. Finally, we propose a holistic co-design framework that addresses these challenges by incorporating a broader range of design values, integrating real-world prototyping to refine evaluations, and boosting efficiency through surrogate metrics and model-based control strategies. This holistic framework, by simultaneously optimizing functionality, durability, and manufacturability, has the potential to enhance reliability and foster broader acceptance of soft robotics, transforming human-robot interactions. © 2025, CC BY.

关键词： Intellectual property core

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Accelerated Parallel Based Distance Calculations for Live-Cell Time-Lapse Images 23rd

Accelerated Parallel Based Distance Calculations for Live-Ce...

引用

23rd International computer Symposium, ICS 2018

作者： Cheng, Hui-Jun Lin, Chun-Yuan Mao, Chun-Chien AI Innovation Research Center Chang Gung University Taoyuan33302 Taiwan Department of Computer Science and Information Engineering Chang Gung University Taoyuan33302 Taiwan Division of Rheumatology Allergy and Immunology Chang Gung Memorial Hospital Taoyuan33305 Taiwan Brain Research Center National Tsing Hua University Hsinchu30013 Taiwan

ISBN: (纸本)9789811391897

Live-cell time-lapse images with particles generated by experiments are useful for observing results, even for proposing novel hypotheses. By identifying particles and cells as objects from these images and then calculating measures from them, such as the distances, they can be quantized for the relationship of particles and cells. However, this work is very time-consuming when calculating the distances among a large number of images. Hence, a very important issue will be presented here in order to accelerate the calculations. In this paper, we will propose parallel algorithms for calculating particle-cell distances, abbreviate to a PCD problem. Two parallel PCD algorithms, called PPCDOMP and PPCDCUDA, will be developed by using OpenMP and CUDA. After the experimental tests, the PPCDOMP with 16 CPU threads achieves 11.7 times by comparing with the PCD algorithm in a single thread;however, the PPCDCUDA with 256 GPU threads per thread block only achieves 3.2 times. Therefore, the PPCDOMP algorithm is suitable for analyzing live-cell time-lapse images with particles based on the shared memory environments. © Springer Nature Singapore Pte Ltd. 2019.

关键词： Cells

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Learning programmatic idioms for scalable semantic parsing

arXiv

引用

arXiv 2019年

作者： Iyer, Srinivasan Cheung, Alvin Zettlemoyer, Luke Paul G. Allen School of Computer Science and Engineering Univ. of Washington SeattleWA United States Department of Electrical Engineering and Computer Sciences UC Berkeley BerkeleyCA United States Facebook AI Research Seattle

Programmers typically organize executable source code using high-level coding patterns or idiomatic structures such as nested loops, exception handlers and recursive blocks, rather than as individual code tokens. In contrast, state of the art (SOTA) semantic parsers still map natural language instructions to source code by building the code syntax tree one node at a time. In this paper, we introduce an iterative method to extract code idioms from large source code corpora by repeatedly collapsing most-frequent depth-2 subtrees of their syntax trees, and train semantic parsers to apply these idioms during decoding. Applying idiom-based decoding on a recent contextdependent semantic parsing task improves the SOTA by 2.2% BLEU score while reducing training time by more than 50%. This improved speed enables us to scale up the model by training on an extended training set that is 5× larger, to further move up the SOTA by an additional 2.3% BLEU and 0.9% exact match. Finally, idioms also significantly improve accuracy of semantic parsing to SQL on the ATIS-SQL dataset, when training data is limited. Copyright © 2019, The Authors. All rights reserved.

关键词： Semantics

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The medical segmentation decathlon

arXiv

引用

arXiv 2021年

作者： Antonelli, Michela Reinke, Annika Bakas, Spyridon Farahani, Keyvan Kopp-Schneider, Annette Landman, Bennett A. Litjens, Geert Menze, Bjoern Ronneberger, Olaf Summers, Ronald M. van Ginneken, Bram Bilello, Michel Bilic, Patrick Christ, Patrick F. Do, Richard K.G. Gollub, Marc J. Heckers, Stephan H. Huisman, Henkjan Jarnagin, William R. McHugo, Maureen K. Napel, Sandy Golia Pernicka, Jennifer S. Rhode, Kawal Tobon-Gomez, Catalina Vorontsov, Eugene Hulsmon, Hankan Meakin, James A. Ourselin, Sebastien Wiesenfarth, Manuel Arbeláez, Pablo Bae, Byeonguk Chen, Sihong Daza, Laura Feng, Jianjiang He, Baochun Isensee, Fabian Ji, Yuanfeng Jia, Fucang Kim, Namkug Kim, Ildoo Merhof, Dorit Pai, Akshay Park, Beomhee Perslev, Mathias Rezaiifar, Ramin Rippel, Oliver Sarasua, Ignacio Shen, Wei Son, Jaemin Wachinger, Christian Wang, Liansheng Wang, Yan Xia, Yingda Xu, Daguang Xu, Zhanwei Zheng, Yefeng Simpson, Amber L. Maier-Hein, Lena Cardoso, M. Jorge School of Biomedical Engineering & Imaging Sciences King’s College London London United Kingdom Heidelberg Germany Heidelberg Germany Faculty of Mathematics and Computer Science University of Heidelberg Heidelberg Germany University of Pennsylvania PhiladelphiaPA United States BethesdaMD United States Heidelberg Germany Electrical Engineering and Computer Science Vanderbilt University NashvilleTN United States Radboud University Medical Center Radboud Institute for Health Sciences Nijmegen Netherlands Quantitative Biomedicine University of Zurich Zurich Switzerland DeepMind London United Kingdom School of Computing Department of Biomedical and Molecular Sciences Queen’s University KingstonON Canada Department of Surgery Memorial Sloan Kettering Cancer Center New YorkNY United States BethesdaMD United States Department of Informatics Technische Universität München Germany Department of Radiology Memorial Sloan Kettering Cancer Center New YorkNY United States Department of Psychiatry & Behavioral Sciences Vanderbilt University Medical Center NashvilleTN United States Department of Radiology Stanford University StanfordCA United States Department of Computer Science and Software Engineering École Polytechnique de Montréal Department of Radiology Perelman School of Medicine University of Pennsylvania PhiladelphiaPA United States Department of Pathology and Laboratory Medicine Perelman School of Medicine University of Pennsylvania PhiladelphiaPA United States Medical Faculty University of Heidelberg Heidelberg Germany VUNO Inc. Seoul Korea Republic of Universidad de los Andes Colombia Department of Automation Tsinghua University Beijing China Heidelberg Germany Department of Computer Science Xiamen University Xiamen361005 China Shenzhen Institute of Advanced Technology Chinese Academy of Sciences Shenzhen China Kakao Brain Korea Republic of Institute of Imaging & Computer Vision RWTH Aachen University Aachen Germany Cere

International challenges have become the de facto standard for comparative assessment of image analysis algorithms given a specific task. Segmentation is so far the most widely investigated medical image processing task, but the various segmentation challenges have typically been organized in isolation, such that algorithm development was driven by the need to tackle a single specific clinical problem. We hypothesized that a method capable of performing well on multiple tasks will generalize well to a previously unseen task and potentially outperform a custom-designed solution. To investigate the hypothesis, we organized the Medical Segmentation Decathlon (MSD)—a biomedical image analysis challenge, in which algorithms compete in a multitude of both tasks and modalities. The underlying data set was designed to explore the axis of difficulties typically encountered when dealing with medical images, such as small data sets, unbalanced labels, multi-site data and small objects. The MSD challenge confirmed that algorithms with a consistent good performance on a set of tasks preserved their good average performance on a different set of previously unseen tasks. Moreover, by monitoring the MSD winner for two years, we found that this algorithm continued generalizing well to a wide range of other clinical problems, further confirming our hypothesis. Three main conclusions can be drawn from this study: (1) state-of-the-art image segmentation algorithms are mature, accurate, and generalize well when retrained on unseen tasks;(2) consistent algorithmic performance across multiple tasks is a strong surrogate of algorithmic generalizability;(3) the training of accurate ai segmentation models is now commoditized to non ai *** Codes 68T07. © 2021, CC BY-NC-SA.

关键词： Image segmentation

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Deep spectral clustering using dual autoencoder network

arXiv

引用

arXiv 2019年

作者： Yang, Xu Deng, Cheng Zheng, Feng Yan, Junchi Liu, Wei School of Electronic Engineering Xidian University Xian710071 China Department of Computer Science and Engineering Southern University of Science and Technology Department of CSE MoE Key Lab of Artificial Intelligence Shanghai Jiao Tong University Tencent AI Lab Shenzhen China

The clustering methods have recently absorbed evenincreasing attention in learning and vision. Deep clustering combines embedding and clustering together to obtain optimal embedding subspace for clustering, which can be more effective compared with conventional clustering methods. In this paper, we propose a joint learning framework for discriminative embedding and spectral clustering. We first devise a dual autoencoder network, which enforces the reconstruction constraint for the latent representations and their noisy versions, to embed the inputs into a latent space for clustering. As such the learned latent representations can be more robust to noise. Then the mutual information estimation is utilized to provide more discriminative information from the inputs. Furthermore, a deep spectral clustering method is applied to embed the latent representations into the eigenspace and subsequently clusters them, which can fully exploit the relationship between inputs to achieve optimal clustering results. Experimental results on benchmark datasets show that our method can significantly outperform state-of-the-art clustering approaches. Copyright © 2019, The Authors. All rights reserved.

关键词： Clustering algorithms

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Meta-learning techniques to analyze the raman data for optical diagnosis of oral cancer detection

Meta-learning techniques to analyze the raman data for optic...

引用

2019 IEEE International Conferences on Ubiquitous Computing and Communications and Data science and Computational Intelligence and Smart Computing, Networking and Services, IUCC/DSCI/SmartCNS 2019

作者： Sharma, Mukta Sharma, Lokesh Jeng, Ming-Jer Chang, Liann-Be Huang, Shiang-Fu Wu, Shih-Lin Department of Electronic Engineering Chang Gung University Taoyuan333 Taiwan Department of Otolaryngology-Head and Neck Surgery Chang Gung Memorial Hospital Linkou244 Taiwan Department of Public Health Chang Gung University Taoyuan 333 Taiwan AI Innovation Research Center Chang Gung University Taoyuan333 Taiwan Department of Cardiology Chang Gung Memorial Hospital Taoyuan333 Taiwan Department of Electrical Engineering Ming Chi University of Technology New Taipei City24301 Taiwan Department of Computer Science and Information Engineering Chang Gung University Taoyuan333 Taiwan

ISBN: (纸本)9781728152097

Recently, Machine Learning methods have shown great improvement while analyzing the biomedical data. Raman Spectroscopy (RS), a non-invasive technique, and widely used in screening to diagnose the oral cancer. In order to spot cancer in a smarter and faster way, we have employed Meta-Learning (ml) techniques to learn such as Bagging and Boosting on RS data. Further, we employed normal and tumor tissue class classification by Linear Discriminant Analysis (LDA), Quadratic Discriminant Analysis (QDA) and Adaptive Boosting (AdaBoost) classifiers. The present study aims at examining the RS data with total 110 samples, including 57 tumor and 53 normal ones. To evaluate the performance, we have used the training samples to optimize, and testing samples to generalize the model parameters. The results show that the AdaBoost classifier with Bagging techniques showed the significant changes in accuracy. © 2019 IEEE.

关键词： Adaptive boosting

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DPA-2: a large atomic model as a multi-task learner

arXiv

引用

arXiv 2023年

作者： Zhang, Duo Liu, Xinzijian Zhang, Xiangyu Zhang, Chengqian Cai, Chun Bi, Hangrui Du, Yiming Qin, Xuejian Peng, Anyang Huang, Jiameng Li, Bowen Shan, Yifan Zeng, Jinzhe Zhang, Yuzhi Liu, Siyuan Li, Yifan Chang, Junhan Wang, Xinyan Zhou, Shuo Liu, Jianchuan Luo, Xiaoshan Wang, Zhenyu Jiang, Wanrun Wu, Jing Yang, Yudi Yang, Jiyuan Yang, Manyi Gong, Fu-Qiang Zhang, Linshuang Shi, Mengchao Dai, Fu-Zhi York, Darrin M. Liu, Shi Zhu, Tong Zhong, Zhicheng Lv, Jian Cheng, Jun Jia, Weile Chen, Mohan Ke, Guolin Weinan, E. Zhang, Linfeng Wang, Han AI for Science Institute Beijing100080 China DP Technology Beijing100080 China Academy for Advanced Interdisciplinary Studies Peking University Beijing100871 China State Key Lab of Processors Institute of Computing Technology Chinese Academy of Sciences Beijing100871 China University of Chinese Academy of Sciences Beijing100871 China HEDPS CAPT College of Engineering Peking University Beijing100871 China Ningbo Institute of Materials Technology and Engineering Chinese Academy of Sciences Ningbo315201 China CAS Key Laboratory of Magnetic Materials and Devices Zhejiang Province Key Laboratory of Magnetic Materials and Application Technology Chinese Academy of Sciences Ningbo315201 China School of Electronics Engineering and Computer Science Peking University Beijing100871 China Shanghai Engineering Research Center of Molecular Therapeutics & New Drug Development School of Chemistry and Molecular Engineering East China Normal University Shanghai200062 China Laboratory for Biomolecular Simulation Research Institute for Quantitative Biomedicine Department of Chemistry and Chemical Biology Rutgers University PiscatawayNJ08854 United States Department of Chemistry Princeton University PrincetonNJ08540 United States College of Chemistry and Molecular Engineering Peking University Beijing100871 China Yuanpei College Peking University Beijing100871 China School of Electrical Engineering and Electronic Information Xihua University Chengdu610039 China State Key Laboratory of Superhard Materials College of Physics Jilin University Changchun130012 China Key Laboratory of Material Simulation Methods & Software of Ministry of Education College of Physics Jilin University Changchun130012 China International Center of Future Science Jilin University Changchun130012 China Key Laboratory for Quantum Materials of Zhejiang Province Department of Physics School of Science Westlake University Zhejiang Hangzhou310030 China Atomistic Simulations Italia

The rapid advancements in artificial intelligence (ai) are catalyzing transformative changes in atomic modeling, simulation, and design. ai-driven potential energy models have demonstrated the capability to conduct large-scale, long-duration simulations with the accuracy of ab initio electronic structure methods. However, the model generation process remains a bottleneck for large-scale applications. We propose a shift towards a model-centric ecosystem, wherein a large atomic model (LAM), pre-trained across multiple disciplines, can be efficiently fine-tuned and distilled for various downstream tasks, thereby establishing a new framework for molecular modeling. In this study, we introduce the DPA-2 architecture as a prototype for LAMs. Pre-trained on a diverse array of chemical and materials systems using a multi-task approach, DPA-2 demonstrates superior generalization capabilities across multiple downstream tasks compared to the traditional single-task pre-training and fine-tuning methodologies. Our approach sets the stage for the development and broad application of LAMs in molecular and materials simulation research. Copyright © 2023, The Authors. All rights reserved.

关键词： Multi-task learning

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