|
[1]
|
Tenenbaum, J.B., Silva, V.d. and Langford, J.C. (2000) A Global Geometric Framework for Nonlinear Dimensionality Reduction. Science, 290, 2319-2323. [Google Scholar] [CrossRef] [PubMed]
|
|
[2]
|
Roweis, S.T. and Saul, L.K. (2000) Nonlinear Dimensionality Reduction by Locally Linear Embedding. Science, 290, 2323-2326. [Google Scholar] [CrossRef] [PubMed]
|
|
[3]
|
Shlens, J. (2014) A Tutorial on Principal Component Analysis.
|
|
[4]
|
Balakrishnama, S. and Ganapathiraju, A. (1998) Linear Discriminant Analysis—A Brief Tutorial. Institute for Signal and Information Processing, 1-8.
|
|
[5]
|
Van der Maaten, L. and Hinton, G. (2008) Visualizing Data Using t-SNE. Journal of Machine Learning Research, 9, 2579-2605.
|
|
[6]
|
Wang, Y., Huang, H., Rudin, C., Shaposhnik, Y., et al. (2021) Understanding How Dimension Reduction Tools Work: An Empirical Approach to Deciphering t-SNE, UMAP, TriMAP, and PaCMAP for Data Visualization. Journal of Machine Learning Research, 22, 1-73.
|
|
[7]
|
Belkina, A.C., Ciccolella, C.O., Anno, R., Halpert, R., Spidlen, J. and Snyder-Cappione, J.E. (2019) Automated Optimized Parameters for T-Distributed Stochastic Neighbor Embedding Improve Visualization and Analysis of Large Datasets. Nature Communications, 10, Article No. 5415. [Google Scholar] [CrossRef] [PubMed]
|
|
[8]
|
McInnes, L., Healy, J., Melville, J., et al. (2018) UMAP: Uniform Manifold Approximation and Projection for Dimension Reduction.
|
|
[9]
|
Ghojogh, B., Ghodsi, A., Karray, F., Crowley, M., et al. (2021) Uniform Manifold Approximation and Projection (UMAP) and Its Variants: Tutorial and Survey.
|
|
[10]
|
Amid, E. and Warmuth, M.K. (2019) TriMap: Large-Scale Dimensionality Reduction Using Triplets.
|
|
[11]
|
Wattenberg, M., Viégas, F. and Johnson, I. (2016) How to Use T-Sne Effectively. Distill. [Google Scholar] [CrossRef]
|
|
[12]
|
Dorrity, M.W., Saunders, L.M., Queitsch, C., et al. (2020) Dimensionality Reduction by UMAP to Visualize Physical and Genetic Interactions. Nature Communications, 11, Article No. 1537. [Google Scholar] [CrossRef] [PubMed]
|
|
[13]
|
Amid, E. and Warmuth, M.K. (2018) A More Globally Accurate Dimensionality Reduction Method Using Triplets.
|
|
[14]
|
Kobak, D. and Linderman, G.C. (2021) Initialization Is Critical for Preserving Global Data Structure in Both t-SNE and UMAP. Nature Biotechnology, 39, 156-157. [Google Scholar] [CrossRef] [PubMed]
|
|
[15]
|
Cao, H. and Wang, L. (2017) Advancing t-SNE’s Efficiency with Distance Metric Learning. Pattern Recognition Letters, 94, 62-67.
|
|
[16]
|
Nguyen, L.H. and Holmes, S. (2019) Ten Quick Tips for Effective Dimensionality Reduction. PLOS Computational Biology, 15, e1006907. 7 [Google Scholar] [CrossRef]
|
|
[17]
|
Belkina, A.C. (2019) Automated Optimization of t-SNE. Bioinformatics.
|
|
[18]
|
Van der Maaten, L. (2009) Learning a Parametric Embedding by Preserving Local Structure. The 12th International Conference on. Artificial Intelligence and Statistics, Clearwater Beach, 16-18 April 2009, 384-391.
|
|
[19]
|
Sainburg, T., McInnes, L. and Gentner, T.Q. (2021) Parametric UMAP Embeddings for Representation and Semisupervised Learning. Neural Computation, 33, 2881-2907. [Google Scholar] [CrossRef] [PubMed]
|
|
[20]
|
Szubert, B., Cole, J.E., Monaco, C. and Drozdov, I. (2019) Structure-Preserving Visualisation of High Dimensional Single-Cell Datasets. Scientific Reports, 9, Article No. 8914. [Google Scholar] [CrossRef] [PubMed]
|
|
[21]
|
Koch, G., Zemel, R. and Salakhutdinov, R. (2015) Siamese Neural Networks for One-Shot Image Recognition. In: ICML Deep Learning Workshop, Volume 2, 1-30.
|
|
[22]
|
Chicco, D. (2020) Siamese Neural Networks: An Overview. In: Cartwright, H., Ed., Artificial Neural Networks, Springer, 73-94. [Google Scholar] [CrossRef] [PubMed]
|
|
[23]
|
Zhang, Z.J. (2018) Improved Adam Optimizer for Deep Neural Networks. 2018 IEEE/ACM 26th International Symposium on Quality of Service (IWQoS), Banff, 4-6 June 2018, 1-2. [Google Scholar] [CrossRef]
|
|
[24]
|
Maas, A.L., Hannun, A.Y. and Ng, A.Y. (2013) Rectifier Nonlinearities Improve Neural Network Acoustic Models. In: Proc. Icml, Vol. 30, p. 3.
|
|
[25]
|
Xu, B., Wang, N., Chen, T., Li, M., et al. (2015) Empirical Evaluation of Rectified Activations in Convolutional Network.
|
|
[26]
|
Borg, I. and Groenen, P.J.F. (2007) Modern Multidimensional Scaling: Theory and Applications. Springer Science & Business Media.
|
|
[27]
|
Belkin, M. and Niyogi, P. (2002) Laplacian Eigenmaps and Spectral Techniques for Embedding and Clustering. In: Dietterich, T.G., Becker, S. and Ghahramani, Z., Eds., Advances in Neural Information Processing Systems 14, The MIT Press, 585-592. [Google Scholar] [CrossRef]
|
|
[28]
|
Tang, J., Liu, J., Zhang, M. and Mei, Q. (2016) Visualizing Large-Scale and High-Dimensional Data. Proceedings of the 25th International Conference on World Wide Web, Montréal, 11-15 April 2016, 287-297. [Google Scholar] [CrossRef]
|
|
[29]
|
Tang, J., Qu, M., Wang, M., Zhang, M., Yan, J. and Mei, Q. (2015) LINE: Large-Scale Information Network Embedding. Proceedings of the 24th International Conference on World Wide Web, Florence, 18-22 May 2015, 1067-1077. [Google Scholar] [CrossRef]
|
|
[30]
|
Hinton, G.E. and Roweis, S. (2002) Stochastic Neighbor Embedding. Proceedings of the 16th International Conference on Neural Information Processing Systems, 1 January 2002, 857-864.
|
|
[31]
|
Lai, C., Kuo, M., Lien, Y., Su, K. and Wang, Y. (2022) Parametric Dimension Reduction by Preserving Local Structure. 2022 IEEE Visualization and Visual Analytics (VIS), Oklahoma City, 16-21 October 2022, 75-79. [Google Scholar] [CrossRef]
|
|
[32]
|
Fischer, A. and Igel, C. (2014) Training Restricted Boltzmann Machines: An Introduction. Pattern Recognition, 47, 25-39. [Google Scholar] [CrossRef]
|
|
[33]
|
van der Maaten, L. and Weinberger, K. (2012) Stochastic Triplet Embedding. 2012 IEEE International Workshop on Machine Learning for Signal Processing, Santander, 23-26 September 2012, 1-6.
|
|
[34]
|
Wilber, M.J., Kwak, I.S., Kriegman, D. and Belongie, S. (2015) Learning Concept Embeddings with Combined Human-Machine Expertise. 2015 IEEE International Conference on Computer Vision (ICCV), Santiago, 7-13 December 2015, 981-989. [Google Scholar] [CrossRef]
|
|
[35]
|
Zelnik-Manor, L. and Perona, P. (2004) Self-Tuning Spectral Clustering. Proceedings of the 18th International Conference on Neural Information Processing Systems, Vancouver, 1 December 2004, 1601-1608.
|
|
[36]
|
Hoffer, E. and Ailon, N. (2015) Deep Metric Learning Using Triplet Network. In: Feragen, A., Pelillo, M. and Loog, M., Eds., Similarity-Based Pattern Recognition, Springer International Publishing, 84-92. [Google Scholar] [CrossRef]
|
|
[37]
|
Bromley, J., Bentz, J.W., Bottou, L., Guyon, I., Lecun, Y., Moore, C., et al. (1994) Signature Verification Using a “Siamese” Time Delay Neural Network. In: Guyon, I. and Wang, P.S.P., Eds., Advances in Pattern Recognition Systems Using Neural Network Technologies, World Scientific, 25-44. [Google Scholar] [CrossRef]
|
|
[38]
|
Hermans, A., Beyer, L. and Leibe, B. (2017) In Defense of the Triplet Loss for Person Re-Identification.
|
|
[39]
|
Wang, B., Zhu, J., Pierson, E., Ramazzotti, D. and Batzoglou, S. (2017) Visualization and Analysis of Single-Cell RNA-seq Data by Kernel-Based Similarity Learning. Nature Methods, 14, 414-416. [Google Scholar] [CrossRef] [PubMed]
|