optimize_graph_layout: Optimize Graph Layout

View source: R/uwot.R

optimize_graph_layoutR Documentation

Optimize Graph Layout


Carry out dimensionality reduction on an input graph, where the distances in the low dimensional space attempt to reproduce the neighbor relations in the input data. By default, the cost function used to optimize the output coordinates use the Uniform Manifold Approximation and Projection (UMAP) method (McInnes et al., 2018), but the approach from LargeVis (Tang et al., 2016) can also be used. This function can be used to produce a low dimensional representation of the graph produced by similarity_graph.


  X = NULL,
  n_components = 2,
  n_epochs = NULL,
  learning_rate = 1,
  init = "spectral",
  init_sdev = NULL,
  spread = 1,
  min_dist = 0.01,
  repulsion_strength = 1,
  negative_sample_rate = 5,
  a = NULL,
  b = NULL,
  method = "umap",
  approx_pow = FALSE,
  pcg_rand = TRUE,
  fast_sgd = FALSE,
  n_sgd_threads = 0,
  grain_size = 1,
  verbose = getOption("verbose", TRUE),
  batch = FALSE,
  opt_args = NULL,
  epoch_callback = NULL,
  pca_method = NULL,
  binary_edge_weights = FALSE



A sparse, symmetric N x N weighted adjacency matrix representing a graph. Non-zero entries indicate an edge between two nodes with a given edge weight. There can be a varying number of non-zero entries in each row/column.


Optional input data. Used only for PCA-based initialization.


The dimension of the space to embed into. This defaults to 2 to provide easy visualization, but can reasonably be set to any integer value in the range 2 to 100.


Number of epochs to use during the optimization of the embedded coordinates. By default, this value is set to 500 for datasets containing 10,000 vertices or less, and 200 otherwise. If n_epochs = 0, then coordinates determined by "init" will be returned. For UMAP, the default is "none".


Initial learning rate used in optimization of the coordinates.


Type of initialization for the coordinates. Options are:

  • "spectral" Spectral embedding using the normalized Laplacian of the fuzzy 1-skeleton, with Gaussian noise added.

  • "normlaplacian". Spectral embedding using the normalized Laplacian of the fuzzy 1-skeleton, without noise.

  • "random". Coordinates assigned using a uniform random distribution between -10 and 10.

  • "lvrandom". Coordinates assigned using a Gaussian distribution with standard deviation 1e-4, as used in LargeVis (Tang et al., 2016) and t-SNE.

  • "laplacian". Spectral embedding using the Laplacian Eigenmap.

  • "pca". The first two principal components from PCA of X if X is a data frame, and from a 2-dimensional classical MDS if X is of class "dist".

  • "spca". Like "pca", but each dimension is then scaled so the standard deviation is 1e-4, to give a distribution similar to that used in t-SNE. This is an alias for init = "pca", init_sdev = 1e-4.

  • "agspectral" An "approximate global" modification of "spectral" which all edges in the graph to a value of 1, and then sets a random number of edges (negative_sample_rate edges per vertex) to 0.1, to approximate the effect of non-local affinities.

  • A matrix of initial coordinates.

For spectral initializations, ("spectral", "normlaplacian", "laplacian", "agspectral"), if more than one connected component is identified, no spectral initialization is attempted. Instead a PCA-based initialization is attempted. If verbose = TRUE the number of connected components are logged to the console. The existence of multiple connected components implies that a global view of the data cannot be attained with this initialization. Increasing the value of n_neighbors may help.


If non-NULL, scales each dimension of the initialized coordinates (including any user-supplied matrix) to this standard deviation. By default no scaling is carried out, except when init = "spca", in which case the value is 0.0001. Scaling the input may help if the unscaled versions result in initial coordinates with large inter-point distances or outliers. This usually results in small gradients during optimization and very little progress being made to the layout. Shrinking the initial embedding by rescaling can help under these circumstances. Scaling the result of init = "pca" is usually recommended and init = "spca" as an alias for init = "pca", init_sdev = 1e-4 but for the spectral initializations the scaled versions usually aren't necessary unless you are using a large value of n_neighbors (e.g. n_neighbors = 150 or higher). For compatibility with recent versions of the Python UMAP package, if you are using init = "spectral", then you should also set init_sdev = "range", which will range scale each of the columns containing the initial data between 0-10. This is not set by default to maintain backwards compatibility with previous versions of uwot.


The effective scale of embedded points. In combination with min_dist, this determines how clustered/clumped the embedded points are.


The effective minimum distance between embedded points. Smaller values will result in a more clustered/clumped embedding where nearby points on the manifold are drawn closer together, while larger values will result on a more even dispersal of points. The value should be set relative to the spread value, which determines the scale at which embedded points will be spread out.


Weighting applied to negative samples in low dimensional embedding optimization. Values higher than one will result in greater weight being given to negative samples.


The number of negative edge/1-simplex samples to use per positive edge/1-simplex sample in optimizing the low dimensional embedding.


More specific parameters controlling the embedding. If NULL these values are set automatically as determined by min_dist and spread.


More specific parameters controlling the embedding. If NULL these values are set automatically as determined by min_dist and spread.


Cost function to optimize. One of:

  • "umap". The UMAP method of McInnes and co-workers (2018).

  • "tumap". UMAP with the a and b parameters fixed to 1.

  • "largevis". The LargeVis method Tang and co-workers (2016).


If TRUE, use an approximation to the power function in the UMAP gradient, from https://martin.ankerl.com/2012/01/25/optimized-approximative-pow-in-c-and-cpp/.


If TRUE, use the PCG random number generator (O'Neill, 2014) during optimization. Otherwise, use the faster (but probably less statistically good) Tausworthe "taus88" generator. The default is TRUE.


If TRUE, then the following combination of parameters is set: pcg_rand = TRUE, n_sgd_threads = "auto" and approx_pow = TRUE. The default is FALSE. Setting this to TRUE will speed up the stochastic optimization phase, but give a potentially less accurate embedding, and which will not be exactly reproducible even with a fixed seed. For visualization, fast_sgd = TRUE will give perfectly good results. For more generic dimensionality reduction, it's safer to leave fast_sgd = FALSE. If fast_sgd = TRUE, then user-supplied values of pcg_rand, n_sgd_threads, and approx_pow are ignored.


Number of threads to use during stochastic gradient descent. If set to > 1, then be aware that if batch = FALSE, results will not be reproducible, even if set.seed is called with a fixed seed before running. If set to "auto" then half the number of concurrent threads supported by the system will be used.


The minimum amount of work to do on each thread. If this value is set high enough, then less than n_threads or n_sgd_threads will be used for processing, which might give a performance improvement if the overhead of thread management and context switching was outweighing the improvement due to concurrent processing. This should be left at default (1) and work will be spread evenly over all the threads specified.


If TRUE, log details to the console.


If TRUE, then embedding coordinates are updated at the end of each epoch rather than during the epoch. In batch mode, results are reproducible with a fixed random seed even with n_sgd_threads > 1, at the cost of a slightly higher memory use. You may also have to modify learning_rate and increase n_epochs, so whether this provides a speed increase over the single-threaded optimization is likely to be dataset and hardware-dependent.


A list of optimizer parameters, used when batch = TRUE. The default optimization method used is Adam (Kingma and Ba, 2014).

  • method The optimization method to use. Either "adam" or "sgd" (stochastic gradient descent). Default: "adam".

  • beta1 (Adam only). The weighting parameter for the exponential moving average of the first moment estimator. Effectively the momentum parameter. Should be a floating point value between 0 and 1. Higher values can smooth oscillatory updates in poorly-conditioned situations and may allow for a larger learning_rate to be specified, but too high can cause divergence. Default: 0.5.

  • beta2 (Adam only). The weighting parameter for the exponential moving average of the uncentered second moment estimator. Should be a floating point value between 0 and 1. Controls the degree of adaptivity in the step-size. Higher values put more weight on previous time steps. Default: 0.9.

  • eps (Adam only). Intended to be a small value to prevent division by zero, but in practice can also affect convergence due to its interaction with beta2. Higher values reduce the effect of the step-size adaptivity and bring the behavior closer to stochastic gradient descent with momentum. Typical values are between 1e-8 and 1e-3. Default: 1e-7.

  • alpha The initial learning rate. Default: the value of the learning_rate parameter.


A function which will be invoked at the end of every epoch. Its signature should be: (epoch, n_epochs, coords), where:

  • epoch The current epoch number (between 1 and n_epochs).

  • n_epochs Number of epochs to use during the optimization of the embedded coordinates.

  • coords The embedded coordinates as of the end of the current epoch, as a matrix with dimensions (N, n_components).


Method to carry out any PCA dimensionality reduction when the pca parameter is specified. Allowed values are:

  • "irlba". Uses prcomp_irlba from the irlba package.

  • "rsvd". Uses 5 iterations of svdr from the irlba package. This is likely to give much faster but potentially less accurate results than using "irlba". For the purposes of nearest neighbor calculation and coordinates initialization, any loss of accuracy doesn't seem to matter much.

  • "bigstatsr". Uses big_randomSVD from the bigstatsr package. The SVD methods used in bigstatsr may be faster on systems without access to efficient linear algebra libraries (e.g. Windows). Note: bigstatsr is not a dependency of uwot: if you choose to use this package for PCA, you must install it yourself.

  • "svd". Uses svd for the SVD. This is likely to be slow for all but the smallest datasets.

  • "auto" (the default). Uses "irlba", unless more than 50 case "svd" is used.


If TRUE then edge weights in the input graph are treated as binary (0/1) rather than real valued.


A matrix of optimized coordinates.


Kingma, D. P., & Ba, J. (2014). Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980. https://arxiv.org/abs/1412.6980

McInnes, L., Healy, J., & Melville, J. (2018). UMAP: Uniform Manifold Approximation and Projection for Dimension Reduction arXiv preprint arXiv:1802.03426. https://arxiv.org/abs/1802.03426

O’Neill, M. E. (2014). PCG: A family of simple fast space-efficient statistically good algorithms for random number generation (Report No. HMC-CS-2014-0905). Harvey Mudd College.

Tang, J., Liu, J., Zhang, M., & Mei, Q. (2016, April). Visualizing large-scale and high-dimensional data. In Proceedings of the 25th International Conference on World Wide Web (pp. 287-297). International World Wide Web Conferences Steering Committee. https://arxiv.org/abs/1602.00370


iris30 <- iris[c(1:10, 51:60, 101:110), ]

# return a 30 x 30 sparse matrix with similarity data based on 10 nearest
# neighbors per item
iris30_sim_graph <- similarity_graph(iris30, n_neighbors = 10)
# produce 2D coordinates replicating the neighbor relations in the similarity
# graph
iris30_opt <- optimize_graph_layout(iris30_sim_graph, X = iris30)

# the above two steps are the same as:
# set.seed(42); iris_umap <- umap(iris30, n_neighbors = 10)

jlmelville/uwot documentation built on May 20, 2024, 1:29 a.m.