Major classes are
HDBSCAN(min_cluster_size=5, min_samples=None, metric='euclidean', alpha=1.0, p=None, algorithm='best', leaf_size=40, memory=Memory(cachedir=None), approx_min_span_tree=True, gen_min_span_tree=False, core_dist_n_jobs=4, cluster_selection_method='eom', allow_single_cluster=False, prediction_data=False, match_reference_implementation=False, **kwargs)¶
Perform HDBSCAN clustering from vector array or distance matrix.
HDBSCAN - Hierarchical Density-Based Spatial Clustering of Applications with Noise. Performs DBSCAN over varying epsilon values and integrates the result to find a clustering that gives the best stability over epsilon. This allows HDBSCAN to find clusters of varying densities (unlike DBSCAN), and be more robust to parameter selection.
- min_cluster_size : int, optional (default=5)
- The minimum size of clusters; single linkage splits that contain fewer points than this will be considered points “falling out” of a cluster rather than a cluster splitting into two new clusters.
- min_samples : int, optional (default=None)
- The number of samples in a neighbourhood for a point to be considered a core point.
- metric : string, or callable, optional (default=’euclidean’)
- The metric to use when calculating distance between instances in a feature array. If metric is a string or callable, it must be one of the options allowed by metrics.pairwise.pairwise_distances for its metric parameter. If metric is “precomputed”, X is assumed to be a distance matrix and must be square.
- p : int, optional (default=None)
- p value to use if using the minkowski metric.
- alpha : float, optional (default=1.0)
- A distance scaling parameter as used in robust single linkage. See  for more information.
- algorithm : string, optional (default=’best’)
Exactly which algorithm to use; hdbscan has variants specialised for different characteristics of the data. By default this is set to
bestwhich chooses the “best” algorithm given the nature of the data. You can force other options if you believe you know better. Options are:
- leaf_size: int, optional (default=40)
- If using a space tree algorithm (kdtree, or balltree) the number of points ina leaf node of the tree. This does not alter the resulting clustering, but may have an effect on the runtime of the algorithm.
- memory : Instance of joblib.Memory or string (optional)
- Used to cache the output of the computation of the tree. By default, no caching is done. If a string is given, it is the path to the caching directory.
- approx_min_span_tree : bool, optional (default=True)
- Whether to accept an only approximate minimum spanning tree. For some algorithms this can provide a significant speedup, but the resulting clustering may be of marginally lower quality. If you are willing to sacrifice speed for correctness you may want to explore this; in general this should be left at the default True.
- gen_min_span_tree: bool, optional (default=False)
- Whether to generate the minimum spanning tree with regard to mutual reachability distance for later analysis.
- core_dist_n_jobs : int, optional (default=4)
- Number of parallel jobs to run in core distance computations (if
supported by the specific algorithm). For
core_dist_n_jobsbelow -1, (n_cpus + 1 + core_dist_n_jobs) are used.
- cluster_selection_method : string, optional (default=’eom’)
The method used to select clusters from the condensed tree. The standard approach for HDBSCAN* is to use an Excess of Mass algorithm to find the most persistent clusters. Alternatively you can instead select the clusters at the leaves of the tree – this provides the most fine grained and homogeneous clusters. Options are:
- allow_single_cluster : bool, optional (default=False)
- By default HDBSCAN* will not produce a single cluster, setting this to True will override this and allow single cluster results in the case that you feel this is a valid result for your dataset.
- prediction_data : boolean, optional
- Whether to generate extra cached data for predicting labels or membership vectors few new unseen points later. If you wish to persist the clustering object for later re-use you probably want to set this to True. (default False)
- match_reference_implementation : bool, optional (default=False)
- There exist some interpretational differences between this HDBSCAN* implementation and the original authors reference implementation in Java. This can result in very minor differences in clustering results. Setting this flag to True will, at a some performance cost, ensure that the clustering results match the reference implementation.
- **kwargs : optional
- Arguments passed to the distance metric
- labels_ : ndarray, shape (n_samples, )
- Cluster labels for each point in the dataset given to fit(). Noisy samples are given the label -1.
- probabilities_ : ndarray, shape (n_samples, )
- The strength with which each sample is a member of its assigned cluster. Noise points have probability zero; points in clusters have values assigned proportional to the degree that they persist as part of the cluster.
- cluster_persistence_ : ndarray, shape (n_clusters, )
- A score of how persistent each cluster is. A score of 1.0 represents a perfectly stable cluster that persists over all distance scales, while a score of 0.0 represents a perfectly ephemeral cluster. These scores can be guage the relative coherence of the clusters output by the algorithm.
- condensed_tree_ : CondensedTree object
- The condensed tree produced by HDBSCAN. The object has methods for converting to pandas, networkx, and plotting.
- single_linkage_tree_ : SingleLinkageTree object
- The single linkage tree produced by HDBSCAN. The object has methods for converting to pandas, networkx, and plotting.
- minimum_spanning_tree_ : MinimumSpanningTree object
- The minimum spanning tree of the mutual reachability graph generated by HDBSCAN. Note that this is not generated by default and will only be available if gen_min_span_tree was set to True on object creation. Even then in some optimized cases a tre may not be generated.
- outlier_scores_ : ndarray, shape (n_samples, )
- Outlier scores for clustered points; the larger the score the more outlier-like the point. Useful as an outlier detection technique. Based on the GLOSH algorithm by Campello, Moulavi, Zimek and Sander.
- prediction_data_ : PredictionData object
- Cached data used for predicting the cluster labels of new or
unseen points. Necessary only if you are using functions from
 Campello, R. J., Moulavi, D., & Sander, J. (2013, April). Density-based clustering based on hierarchical density estimates. In Pacific-Asia Conference on Knowledge Discovery and Data Mining (pp. 160-172). Springer Berlin Heidelberg.  Campello, R. J., Moulavi, D., Zimek, A., & Sander, J. (2015). Hierarchical density estimates for data clustering, visualization, and outlier detection. ACM Transactions on Knowledge Discovery from Data (TKDD), 10(1), 5.  Chaudhuri, K., & Dasgupta, S. (2010). Rates of convergence for the cluster tree. In Advances in Neural Information Processing Systems (pp. 343-351).
Perform HDBSCAN clustering from features or distance matrix.
- X : array or sparse (CSR) matrix of shape (n_samples, n_features), or array of shape (n_samples, n_samples)
- A feature array, or array of distances between samples if
- self : object
- Returns self
Performs clustering on X and returns cluster labels.
- A feature array, or array of distances between samples if
- y : ndarray, shape (n_samples, )
- cluster labels
Create data that caches intermediate results used for predicting the label of new/unseen points. This data is only useful if you are intending to use functions from