Source code for datasets.dna

# Copyright 2011 Hugo Larochelle. All rights reserved.
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"""
Module ``datasets.dna`` gives access to the DNA dataset.

| **Reference:** 
| Tractable Multivariate Binary Density Estimation and the Restricted Boltzmann Forest
| Larochelle, Bengio and Turian
| http://www.cs.toronto.edu/~larocheh/publications/NECO-10-09-1100R2-PDF.pdf

"""

import mlpython.misc.io as mlio
import numpy as np
import os

[docs]def load(dir_path,load_to_memory=False): """ Loads the DNA dataset. The data is given by a dictionary mapping from strings ``'train'``, ``'valid'`` and ``'test'`` to the associated pair of data and metadata. **Defined metadata:** * ``'input_size'`` * ``'targets'`` * ``'length'`` """ input_size=180 dir_path = os.path.expanduser(dir_path) targets = set([0,1,2]) target_mapping = {'1':0,'2':1,'3':2} def convert_target(target): return target_mapping[target] def load_line(line): return mlio.libsvm_load_line(line,convert_target=convert_target,sparse=False,input_size=input_size) train_file,valid_file,test_file = [os.path.join(dir_path, 'dna_scale_' + ds + '.libsvm') for ds in ['train','valid','test']] # Get data train,valid,test = [mlio.load_from_file(f,load_line) for f in [train_file,valid_file,test_file]] lengths = [1400,600,1186] if load_to_memory: train,valid,test = [mlio.MemoryDataset(d,[(input_size,),(1,)],[np.float64,int],l) for d,l in zip([train,valid,test],lengths)] # Get metadata train_meta,valid_meta,test_meta = [{'input_size':input_size, 'length':l,'targets':targets} for l in lengths] return {'train':(train,train_meta),'valid':(valid,valid_meta),'test':(test,test_meta)}
[docs]def obtain(dir_path): """ Downloads the dataset to ``dir_path``. """ dir_path = os.path.expanduser(dir_path) print 'Downloading the dataset' import urllib urllib.urlretrieve('http://www.cs.toronto.edu/~larocheh/public/datasets/dna/dna_scale_train.libsvm',os.path.join(dir_path,'dna_scale_train.libsvm')) urllib.urlretrieve('http://www.cs.toronto.edu/~larocheh/public/datasets/dna/dna_scale_valid.libsvm',os.path.join(dir_path,'dna_scale_valid.libsvm')) urllib.urlretrieve('http://www.cs.toronto.edu/~larocheh/public/datasets/dna/dna_scale_test.libsvm',os.path.join(dir_path,'dna_scale_test.libsvm')) print 'Done '