cwidmer’s gists

cwidmer / pylab_external_legend.py

Last active December 30, 2015 08:39

snippet to create matplotlib plot with title, grid and externally located legend

	import pylab

	data1 = [1,2,3,4]
	data2 = [2,3,4,5]

	pylab.plot(data1, "-o", label="meh")
	pylab.plot(data2, "-o", label="arr")

	pylab.title("example")
	pylab.grid(True)

cwidmer / auc.py

Last active December 30, 2015 09:59

code snippet to calculate the common performance measures, area under the precision-recall curve and area under the receiver operator characteristic curve

	import pylab


	def plot_roc(y, out, label="", out_fn=None):
	"""
	show or save ROC curve
	"""

	pylab.figure()
	plot_roc_noshow(y, out, label=label)

cwidmer / compressed_pickle.py

Last active August 22, 2021 06:19

save/load compressed pickled objects in python

	import cPickle
	import bz2


	def save(filename, myobj):
	"""
	save object to file using pickle

	@param filename: name of destination file
	@type filename: str

cwidmer / random_sequence.py

Created December 5, 2013 20:35

generates a random sequence of length over alphabet

	def rand_seq(alphabet, length):
	"""
	generates a random sequence of length over alphabet

	@param alphabet: alphabet from which to choose characters
	@type alphabet: list<str>
	@param length: length of random string
	@type length: int
	"""

cwidmer / powerset.py

Last active December 30, 2015 10:08

Create power-set (the set of all possible subsets) from a python list

	def power_set(orignal_list):
	'''
	PowerSet of a List

	@param orignal_list: list from which to construct a powerset
	'''
	list_size = len(orignal_list)
	num_sets = 2**list_size
	powerset = []
	# Don't include empty set

cwidmer / coshuffle.py

Created December 5, 2013 20:46

Shuffle several iterables the same way

	import random


	def coshuffle(*args):
	"""
	will shuffle target_list and apply
	same permutation to other lists

	>>> helper.coshuffle([2, 1, 3], [4, 2, 8], [6, 3, 12])
	([5, 3, 2, 1, 4], [5, 3, 2, 1, 4], [5, 3, 2, 1, 4])

cwidmer / viz_seq.py

Created December 5, 2013 20:49

Visualize a list of sequences (of same length, assuming DNA encoding) as a color coded matrix

	import pylab
	import numpy


	def show_seqs(seqs):
	"""
	plot color coded training sequences
	"""

cwidmer / shogun_string_factory.py

Created December 5, 2013 21:08

python module to create shogun objects for dealing with string kernels and string data withing the COFFIN framework

	#!/usr/bin/env python2.5
	# This program is free software; you can redistribute it and/or modify
	# it under the terms of the GNU General Public License as published by
	# the Free Software Foundation; either version 2 of the License, or
	# (at your option) any later version.
	#
	# Written (W) 2010-2013 Christian Widmer
	# Copyright (C) 2010-2013 Max-Planck-Society, TU-Berlin, MSKCC

	"""

cwidmer / dendogram.py

Created January 30, 2014 09:15

plot matrix with dendogram

	import numpy as np
	import copy
	import random
	import pylab
	import scipy.cluster.hierarchy as sch


	def create_linkage_matrix(num_tasks):
	"""
	create stack of matrices for

cwidmer / experiment_toy_hmtmkl.py

Last active August 29, 2015 13:55

toy example for learning the similarity

	#!/usr/bin/env python2.6
	# This program is free software; you can redistribute it and/or modify
	# it under the terms of the GNU General Public License as published by
	# the Free Software Foundation; either version 2 of the License, or
	# (at your option) any later version.
	#
	# Written (W) 2013 Christian Widmer
	# Copyright (C) 2013 Max-Planck-Society, MSKCC, TU-Berlin

	"""

Christian Widmer cwidmer