IDEAS home Printed from https://ideas.repec.org/a/nat/natcom/v14y2023i1d10.1038_s41467-023-43958-w.html
   My bibliography  Save this article

Revealing hidden patterns in deep neural network feature space continuum via manifold learning

Author

Listed:
  • Md Tauhidul Islam

    (Stanford University)

  • Zixia Zhou

    (Stanford University)

  • Hongyi Ren

    (Stanford University)

  • Masoud Badiei Khuzani

    (Stanford University)

  • Daniel Kapp

    (Stanford University)

  • James Zou

    (Stanford University)

  • Lu Tian

    (Stanford University)

  • Joseph C. Liao

    (Stanford University)

  • Lei Xing

    (Stanford University)

Abstract

Deep neural networks (DNNs) extract thousands to millions of task-specific features during model training for inference and decision-making. While visualizing these features is critical for comprehending the learning process and improving the performance of the DNNs, existing visualization techniques work only for classification tasks. For regressions, the feature points lie on a high dimensional continuum having an inherently complex shape, making a meaningful visualization of the features intractable. Given that the majority of deep learning applications are regression-oriented, developing a conceptual framework and computational method to reliably visualize the regression features is of great significance. Here, we introduce a manifold discovery and analysis (MDA) method for DNN feature visualization, which involves learning the manifold topology associated with the output and target labels of a DNN. MDA leverages the acquired topological information to preserve the local geometry of the feature space manifold and provides insightful visualizations of the DNN features, highlighting the appropriateness, generalizability, and adversarial robustness of a DNN. The performance and advantages of the MDA approach compared to the existing methods are demonstrated in different deep learning applications.

Suggested Citation

  • Md Tauhidul Islam & Zixia Zhou & Hongyi Ren & Masoud Badiei Khuzani & Daniel Kapp & James Zou & Lu Tian & Joseph C. Liao & Lei Xing, 2023. "Revealing hidden patterns in deep neural network feature space continuum via manifold learning," Nature Communications, Nature, vol. 14(1), pages 1-20, December.
  • Handle: RePEc:nat:natcom:v:14:y:2023:i:1:d:10.1038_s41467-023-43958-w
    DOI: 10.1038/s41467-023-43958-w
    as

    Download full text from publisher

    File URL: https://www.nature.com/articles/s41467-023-43958-w
    File Function: Abstract
    Download Restriction: no

    File URL: https://libkey.io/10.1038/s41467-023-43958-w?utm_source=ideas
    LibKey link: if access is restricted and if your library uses this service, LibKey will redirect you to where you can use your library subscription to access this item
    ---><---

    References listed on IDEAS

    as
    1. Andre Esteva & Brett Kuprel & Roberto A. Novoa & Justin Ko & Susan M. Swetter & Helen M. Blau & Sebastian Thrun, 2017. "Correction: Corrigendum: Dermatologist-level classification of skin cancer with deep neural networks," Nature, Nature, vol. 546(7660), pages 686-686, June.
    2. Yicong Wu & Xiaofei Han & Yijun Su & Melissa Glidewell & Jonathan S. Daniels & Jiamin Liu & Titas Sengupta & Ivan Rey-Suarez & Robert Fischer & Akshay Patel & Christian Combs & Junhui Sun & Xufeng Wu , 2021. "Multiview confocal super-resolution microscopy," Nature, Nature, vol. 600(7888), pages 279-284, December.
    3. Sarah Webb, 2018. "Deep learning for biology," Nature, Nature, vol. 554(7693), pages 555-557, February.
    4. David Ouyang & Bryan He & Amirata Ghorbani & Neal Yuan & Joseph Ebinger & Curtis P. Langlotz & Paul A. Heidenreich & Robert A. Harrington & David H. Liang & Euan A. Ashley & James Y. Zou, 2020. "Video-based AI for beat-to-beat assessment of cardiac function," Nature, Nature, vol. 580(7802), pages 252-256, April.
    5. Andrew W. Senior & Richard Evans & John Jumper & James Kirkpatrick & Laurent Sifre & Tim Green & Chongli Qin & Augustin Žídek & Alexander W. R. Nelson & Alex Bridgland & Hugo Penedones & Stig Petersen, 2020. "Improved protein structure prediction using potentials from deep learning," Nature, Nature, vol. 577(7792), pages 706-710, January.
    6. Andre Esteva & Brett Kuprel & Roberto A. Novoa & Justin Ko & Susan M. Swetter & Helen M. Blau & Sebastian Thrun, 2017. "Dermatologist-level classification of skin cancer with deep neural networks," Nature, Nature, vol. 542(7639), pages 115-118, February.
    7. Haitham A. Elmarakeby & Justin Hwang & Rand Arafeh & Jett Crowdis & Sydney Gang & David Liu & Saud H. AlDubayan & Keyan Salari & Steven Kregel & Camden Richter & Taylor E. Arnoff & Jihye Park & Willia, 2021. "Biologically informed deep neural network for prostate cancer discovery," Nature, Nature, vol. 598(7880), pages 348-352, October.
    8. Logan G. Wright & Tatsuhiro Onodera & Martin M. Stein & Tianyu Wang & Darren T. Schachter & Zoey Hu & Peter L. McMahon, 2022. "Deep physical neural networks trained with backpropagation," Nature, Nature, vol. 601(7894), pages 549-555, January.
    9. Ivan Anishchenko & Samuel J. Pellock & Tamuka M. Chidyausiku & Theresa A. Ramelot & Sergey Ovchinnikov & Jingzhou Hao & Khushboo Bafna & Christoffer Norn & Alex Kang & Asim K. Bera & Frank DiMaio & La, 2021. "De novo protein design by deep network hallucination," Nature, Nature, vol. 600(7889), pages 547-552, December.
    10. Ming Y. Lu & Tiffany Y. Chen & Drew F. K. Williamson & Melissa Zhao & Maha Shady & Jana Lipkova & Faisal Mahmood, 2021. "AI-based pathology predicts origins for cancers of unknown primary," Nature, Nature, vol. 594(7861), pages 106-110, June.
    11. Bo Zhu & Jeremiah Z. Liu & Stephen F. Cauley & Bruce R. Rosen & Matthew S. Rosen, 2018. "Image reconstruction by domain-transform manifold learning," Nature, Nature, vol. 555(7697), pages 487-492, March.
    12. Md Tauhidul Islam & Lei Xing, 2023. "Cartography of Genomic Interactions Enables Deep Analysis of Single-Cell Expression Data," Nature Communications, Nature, vol. 14(1), pages 1-17, December.
    Full references (including those not matched with items on IDEAS)

    Most related items

    These are the items that most often cite the same works as this one and are cited by the same works as this one.
    1. Jasper Tromp & David Bauer & Brian L. Claggett & Matthew Frost & Mathias Bøtcher Iversen & Narayana Prasad & Mark C. Petrie & Martin G. Larson & Justin A. Ezekowitz & Scott D. Solomon, 2022. "A formal validation of a deep learning-based automated workflow for the interpretation of the echocardiogram," Nature Communications, Nature, vol. 13(1), pages 1-9, December.
    2. Lin Lu & Laurent Dercle & Binsheng Zhao & Lawrence H. Schwartz, 2021. "Deep learning for the prediction of early on-treatment response in metastatic colorectal cancer from serial medical imaging," Nature Communications, Nature, vol. 12(1), pages 1-11, December.
    3. Zheng Yan & Wenqian Robertson & Yaosheng Lou & Tom W. Robertson & Sung Yong Park, 2021. "Finding leading scholars in mobile phone behavior: a mixed-method analysis of an emerging interdisciplinary field," Scientometrics, Springer;Akadémiai Kiadó, vol. 126(12), pages 9499-9517, December.
    4. Freddy Gabbay & Rotem Lev Aharoni & Ori Schweitzer, 2022. "Deep Neural Network Memory Performance and Throughput Modeling and Simulation Framework," Mathematics, MDPI, vol. 10(21), pages 1-20, November.
    5. Jungyoon Kim & Jihye Lim, 2021. "A Deep Neural Network-Based Method for Prediction of Dementia Using Big Data," IJERPH, MDPI, vol. 18(10), pages 1-13, May.
    6. Gang Yu & Kai Sun & Chao Xu & Xing-Hua Shi & Chong Wu & Ting Xie & Run-Qi Meng & Xiang-He Meng & Kuan-Song Wang & Hong-Mei Xiao & Hong-Wen Deng, 2021. "Accurate recognition of colorectal cancer with semi-supervised deep learning on pathological images," Nature Communications, Nature, vol. 12(1), pages 1-13, December.
    7. DonHee Lee & Seong No Yoon, 2021. "Application of Artificial Intelligence-Based Technologies in the Healthcare Industry: Opportunities and Challenges," IJERPH, MDPI, vol. 18(1), pages 1-18, January.
    8. Claus Zippel & Sabine Bohnet-Joschko, 2021. "Rise of Clinical Studies in the Field of Machine Learning: A Review of Data Registered in ClinicalTrials.gov," IJERPH, MDPI, vol. 18(10), pages 1-14, May.
    9. Dario Sipari & Betsy D. M. Chaparro-Rico & Daniele Cafolla, 2022. "SANE (Easy Gait Analysis System): Towards an AI-Assisted Automatic Gait-Analysis," IJERPH, MDPI, vol. 19(16), pages 1-27, August.
    10. Jamil Ahmad & Abdul Khader Jilani Saudagar & Khalid Mahmood Malik & Waseem Ahmad & Muhammad Badruddin Khan & Mozaherul Hoque Abul Hasanat & Abdullah AlTameem & Mohammed AlKhathami & Muhammad Sajjad, 2022. "Disease Progression Detection via Deep Sequence Learning of Successive Radiographic Scans," IJERPH, MDPI, vol. 19(1), pages 1-16, January.
    11. Rasheed Omobolaji Alabi & Alhadi Almangush & Mohammed Elmusrati & Ilmo Leivo & Antti Mäkitie, 2022. "Measuring the Usability and Quality of Explanations of a Machine Learning Web-Based Tool for Oral Tongue Cancer Prognostication," IJERPH, MDPI, vol. 19(14), pages 1-13, July.
    12. Andreas Fügener & Jörn Grahl & Alok Gupta & Wolfgang Ketter, 2022. "Cognitive Challenges in Human–Artificial Intelligence Collaboration: Investigating the Path Toward Productive Delegation," Information Systems Research, INFORMS, vol. 33(2), pages 678-696, June.
    13. Vidhya V. & Anjan Gudigar & U. Raghavendra & Ajay Hegde & Girish R. Menon & Filippo Molinari & Edward J. Ciaccio & U. Rajendra Acharya, 2021. "Automated Detection and Screening of Traumatic Brain Injury (TBI) Using Computed Tomography Images: A Comprehensive Review and Future Perspectives," IJERPH, MDPI, vol. 18(12), pages 1-29, June.
    14. Pujin Wang & Jianzhuang Xiao & Ken’ichi Kawaguchi & Lichen Wang, 2022. "Automatic Ceiling Damage Detection in Large-Span Structures Based on Computer Vision and Deep Learning," Sustainability, MDPI, vol. 14(6), pages 1-24, March.
    15. Xu Gong & Keqin Guan & Qiyang Chen, 2022. "The role of textual analysis in oil futures price forecasting based on machine learning approach," Journal of Futures Markets, John Wiley & Sons, Ltd., vol. 42(10), pages 1987-2017, October.
    16. Julian Schiele & Thomas Koperna & Jens O. Brunner, 2021. "Predicting intensive care unit bed occupancy for integrated operating room scheduling via neural networks," Naval Research Logistics (NRL), John Wiley & Sons, vol. 68(1), pages 65-88, February.
    17. Kai Feng & Han Hong & Ke Tang & Jingyuan Wang, 2023. "Statistical Tests for Replacing Human Decision Makers with Algorithms," Papers 2306.11689, arXiv.org.
    18. Zhiming Cui & Yu Fang & Lanzhuju Mei & Bojun Zhang & Bo Yu & Jiameng Liu & Caiwen Jiang & Yuhang Sun & Lei Ma & Jiawei Huang & Yang Liu & Yue Zhao & Chunfeng Lian & Zhongxiang Ding & Min Zhu & Dinggan, 2022. "A fully automatic AI system for tooth and alveolar bone segmentation from cone-beam CT images," Nature Communications, Nature, vol. 13(1), pages 1-11, December.
    19. Chowdhury, Emon Kalyan, 2019. "Use of Artificial Intelligence in Stock Trading," MPRA Paper 118175, University Library of Munich, Germany, revised 18 Apr 2019.
    20. Victor Olsavszky & Mihnea Dosius & Cristian Vladescu & Johannes Benecke, 2020. "Time Series Analysis and Forecasting with Automated Machine Learning on a National ICD-10 Database," IJERPH, MDPI, vol. 17(14), pages 1-17, July.

    More about this item

    Statistics

    Access and download statistics

    Corrections

    All material on this site has been provided by the respective publishers and authors. You can help correct errors and omissions. When requesting a correction, please mention this item's handle: RePEc:nat:natcom:v:14:y:2023:i:1:d:10.1038_s41467-023-43958-w. See general information about how to correct material in RePEc.

    If you have authored this item and are not yet registered with RePEc, we encourage you to do it here. This allows to link your profile to this item. It also allows you to accept potential citations to this item that we are uncertain about.

    If CitEc recognized a bibliographic reference but did not link an item in RePEc to it, you can help with this form .

    If you know of missing items citing this one, you can help us creating those links by adding the relevant references in the same way as above, for each refering item. If you are a registered author of this item, you may also want to check the "citations" tab in your RePEc Author Service profile, as there may be some citations waiting for confirmation.

    For technical questions regarding this item, or to correct its authors, title, abstract, bibliographic or download information, contact: Sonal Shukla or Springer Nature Abstracting and Indexing (email available below). General contact details of provider: http://www.nature.com .

    Please note that corrections may take a couple of weeks to filter through the various RePEc services.

    IDEAS is a RePEc service. RePEc uses bibliographic data supplied by the respective publishers.