NeuralMap is new Python implementation of the well-known self organized artificial neural network, Self-Organizing Map (SOM), with the Relative Position (RP) Visualization method. The RP is a node-adaptive attribute that moves in a two dimensional space mimicking, at training stage, the movements of the SOM's codebook vectors in the input space.
In this way NeuralMap results in a powerfull data analysis tool that generates both a low-dimensional representation of the input data as tSNE or UMAP tools and placing codebook vectors in the input space providing a smoother version of the input space. In addition, it maps data similarity into both codebook vectors and RP neighborness, thus allowing clear identification of similarity in the two dimensional space, with the added advantage of precessing new inputs without retraining needs.
This tool supports a wide range of configurations:
- Custom distance metric
- Hexagonal or square arrangement
- Toroidal or flat topology
- Custom radius or learning rate decay functions
- Custom neighbourhood functions
After training a NeuralMap instance, you will be able to get useful information about your data, by mapping observations to the SOM, watching the features distribution over the map, analysing a dataset to get the quantization error, activation frequency and mean distance for each node, and evaluating the SOM.
Since the use of SOM for clustering is very spread, NeuralMap also includes several highly customizable visualization methods, some of them based on the Relative Positions technique to improve the interpretability of results and clusters recognition.
For instance, we have implemented some common clustering algorithms to search clusters into the SOM configuration, speeding up the search of clusters in the smoothed space representation achieved by the SOM codebook vectors or RP rather than in the, possible, high dimensional imput space:
NeuralMap has the following requirements:
- python >= 3.6
- numpy 1.18.3
- numba 0.50.1
- scikit_learn_extra 0.1.0b2
- matplotlib 3.2.1
- scipy 1.4.1
- hdbscan 0.8.26
- scikit_learn 0.23.2
To install NeuralMap use:
pip install neural-mapAfter installing NeuralMap, obtain and prepare your dataset. For this example we will create a dataset with 10 blobs in a five dimensional space and scale it to fit the observations to the range [0, 1]:
from sklearn import datasets, preprocessing
blobs = datasets.make_blobs(n_samples=1000, n_features=5, centers=10, random_state=1)
scaler = preprocessing.MinMaxScaler()
data = scaler.fit_transform(blobs[0])Then, we have to create a NeuralMap instance and train it with the data:
from neural_map import NeuralMap
nm = NeuralMap(5, 'euclidean', columns=10, rows=10)
nm.train(data, n_epochs=20)Now we can obtain a discrete representation using the HB-SCAN over the codebook vectors and represented in the two dimensional space mapped trhough the Relative Positions:
nm.plot_analysis(data)
NeuralMap was able to successfully discover and cluster all the original blobs.
It's also possible to get the U-matrix:
nm.plot_unified_distance_matrix()
Here is also possible to recognize the 10 original blobs.
For more details, see the NeuralMap documentation.
If you have a question, please open an issue.
- Elmer Andrés Fernández - Original Idea - Profile - [CIDIE]- CONICET - UCC
- Franco Bobadilla - Developer - Universidad Católica de Córdoba
- Pablo Pastore - Advice - Universidad Católica de Córdoba
To contribute, do the following:
- Open an issue to discuss possible changes or ask questions
- Create a fork of the project
- Create a new branch and push your changes
- Create a pull request
NeuralMap is licensed under MIT license.
