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. 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.
    6. 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.
    7. 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.
    8. 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.
    9. Taneja, Anu & Arora, Anuja, 2019. "Modeling user preferences using neural networks and tensor factorization model," International Journal of Information Management, Elsevier, vol. 45(C), pages 132-148.
    10. Hanning Ying & Xiaoqing Liu & Min Zhang & Yiyue Ren & Shihui Zhen & Xiaojie Wang & Bo Liu & Peng Hu & Lian Duan & Mingzhi Cai & Ming Jiang & Xiangdong Cheng & Xiangyang Gong & Haitao Jiang & Jianshuai, 2024. "A multicenter clinical AI system study for detection and diagnosis of focal liver lesions," Nature Communications, Nature, vol. 15(1), pages 1-16, December.
    11. Cristian Simionescu & Adrian Iftene, 2022. "Deep Learning Research Directions in Medical Imaging," Mathematics, MDPI, vol. 10(23), pages 1-25, November.
    12. Jingui Zhang & Chuangji Meng & Cunlu Xu & Jingyong Ma & Wei Su, 2022. "Deep Transfer Learning Method Based on Automatic Domain Alignment and Moment Matching," Mathematics, MDPI, vol. 10(14), pages 1-14, July.
    13. Yuming Jiang & Zhicheng Zhang & Wei Wang & Weicai Huang & Chuanli Chen & Sujuan Xi & M. Usman Ahmad & Yulan Ren & Shengtian Sang & Jingjing Xie & Jen-Yeu Wang & Wenjun Xiong & Tuanjie Li & Zhen Han & , 2023. "Biology-guided deep learning predicts prognosis and cancer immunotherapy response," Nature Communications, Nature, vol. 14(1), pages 1-16, December.
    14. Marta Mazur & Artnora Ndokaj & Divyambika Catakapatri Venugopal & Michela Roberto & Cristina Albu & Maciej Jedliński & Silverio Tomao & Iole Vozza & Grzegorz Trybek & Livia Ottolenghi & Fabrizio Guerr, 2021. "In Vivo Imaging-Based Techniques for Early Diagnosis of Oral Potentially Malignant Disorders—Systematic Review and Meta-Analysis," IJERPH, MDPI, vol. 18(22), pages 1-22, November.
    15. Khalid A. Ibrahim & Kristin S. Grußmayer & Nathan Riguet & Lely Feletti & Hilal A. Lashuel & Aleksandra Radenovic, 2023. "Label-free identification of protein aggregates using deep learning," Nature Communications, Nature, vol. 14(1), pages 1-11, December.
    16. 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.
    17. Songhee Cheon & Jungyoon Kim & Jihye Lim, 2019. "The Use of Deep Learning to Predict Stroke Patient Mortality," IJERPH, MDPI, vol. 16(11), pages 1-12, May.
    18. Hailong He & Christine Schönmann & Mathias Schwarz & Benedikt Hindelang & Andrei Berezhnoi & Susanne Annette Steimle-Grauer & Ulf Darsow & Juan Aguirre & Vasilis Ntziachristos, 2022. "Fast raster-scan optoacoustic mesoscopy enables assessment of human melanoma microvasculature in vivo," Nature Communications, Nature, vol. 13(1), pages 1-10, December.
    19. Zilong Zhou & Hang Yuan & Xin Cai, 2023. "Rock Thin Section Image Identification Based on Convolutional Neural Networks of Adaptive and Second-Order Pooling Methods," Mathematics, MDPI, vol. 11(5), pages 1-27, March.
    20. Dani Kiyasseh & Aaron Cohen & Chengsheng Jiang & Nicholas Altieri, 2024. "A framework for evaluating clinical artificial intelligence systems without ground-truth annotations," Nature Communications, Nature, vol. 15(1), pages 1-14, December.

    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.