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densratio-0.3.0
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مشاهده بیشترتوضیحات
A Python Package for Density Ratio Estimation
| ویژگی | مقدار |
|---|---|
| سیستم عامل | - |
| نام فایل | densratio-0.3.0 |
| نام | densratio |
| نسخه کتابخانه | 0.3.0 |
| نگهدارنده | [] |
| ایمیل نگهدارنده | [] |
| نویسنده | Koji Makiyama, Ameya Daigavane, Krzysztof Mierzejewski |
| ایمیل نویسنده | hoxo.smile@gmail.com |
| آدرس صفحه اصلی | https://github.com/hoxo-m/densratio_py |
| آدرس اینترنتی | https://pypi.org/project/densratio/ |
| مجوز | MIT + file LICENSE |
A Python Package for Density Ratio Estimation
================
Koji Makiyama (@hoxo-m), Ameya Daigavane (@ameya98), and Krzysztof
Mierzejewski (@mierzejk)
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## 1. Overview
**Density ratio estimation** is described as follows: for given two data
samples `x1` and `x2` from unknown distributions `p(x)` and `q(x)`
respectively, estimate `w(x) = p(x) / q(x)`, where `x1` and `x2` are
d-dimensional real numbers.
The estimated density ratio function `w(x)` can be used in many
applications such as the inlier-based outlier detection \[1\] and
covariate shift adaptation \[2\]. Other useful applications for density
ratio estimation were summarized by Sugiyama et al.ﾂ(2012) in \[3\].
The package **densratio** provides a function `densratio()` that returns
an object with a method to estimate density ratio as
`compute_density_ratio()`.
Further, the alpha-relative density ratio
`p(x)/(alpha * p(x) + (1 - alpha) * q(x))` (where alpha is in the range
\[0, 1\]) can also be estimated. When alpha is 0, this reduces to the
ordinary density ratio `w(x)`. The alpha-relative PE-divergence and
KL-divergence between `p(x)` and `q(x)` are also computed.
<!-- -->
For example,
``` python
import numpy as np
from scipy.stats import norm
from densratio import densratio
np.random.seed(1)
x = norm.rvs(size=500, loc=0, scale=1./8)
y = norm.rvs(size=500, loc=0, scale=1./2)
alpha = 0.1
densratio_obj = densratio(x, y, alpha=alpha)
print(densratio_obj)
```
gives the following output:
#> Method: RuLSIF
#>
#> Alpha: 0.1
#>
#> Kernel Information:
#> Kernel type: Gaussian
#> Number of kernels: 100
#> Bandwidth(sigma): 0.1
#> Centers: array([[-0.09591373],..
#>
#> Kernel Weights (theta):
#> array([0.04990797, 0.0550548 , 0.04784736, 0.04951904, 0.04840418,..
#>
#> Regularization Parameter (lambda): 0.1
#>
#> Alpha-Relative PE-Divergence: 0.618794133598705
#>
#> Alpha-Relative KL-Divergence: 0.7037648129307483
#>
#> Function to Estimate Density Ratio:
#> compute_density_ratio(x)
#>
In this case, the true density ratio `w(x)` is known, so we can compare
`w(x)` with the estimated density ratio `w-hat(x)`. The code below gives
the plot shown above.
``` python
from matplotlib import pyplot as plt
from numpy import linspace
def true_alpha_density_ratio(sample):
return norm.pdf(sample, 0, 1./8) / (alpha * norm.pdf(sample, 0, 1./8) + (1 - alpha) * norm.pdf(sample, 0, 1./2))
def estimated_alpha_density_ratio(sample):
return densratio_obj.compute_density_ratio(sample)
sample_points = np.linspace(-1, 3, 400)
plt.plot(sample_points, true_alpha_density_ratio(sample_points), 'b-', label='True Alpha-Relative Density Ratio')
plt.plot(sample_points, estimated_alpha_density_ratio(sample_points), 'r-', label='Estimated Alpha-Relative Density Ratio')
plt.title("Alpha-Relative Density Ratio - Normal Random Variables (alpha={:03.2f})".format(alpha))
plt.legend()
plt.show()
```
## 2. Installation
You can install the package from
[PyPI](https://pypi.org/project/densratio/).
``` :sh
$ pip install densratio
```
Also, you can install the package from
[GitHub](https://github.com/hoxo-m/densratio_py).
``` :sh
$ pip install git+https://github.com/hoxo-m/densratio_py.git
```
The source code for **densratio** package is available on GitHub at
<https://github.com/hoxo-m/densratio_py>.
## 3. Details
### 3.1. Basics
The package provides `densratio()`. The function returns an object that
has a function to compute estimated density ratio.
For data samples `x` and `y`,
``` python
from scipy.stats import norm
from densratio import densratio
x = norm.rvs(size = 200, loc = 1, scale = 1./8)
y = norm.rvs(size = 200, loc = 1, scale = 1./2)
result = densratio(x, y)
```
In this case, `result.compute_density_ratio()` can compute estimated
density ratio.
``` python
from matplotlib import pyplot as plt
density_ratio = result.compute_density_ratio(y)
plt.plot(y, density_ratio, "o")
plt.xlabel("x")
plt.ylabel("Density Ratio")
plt.show()
```
<!-- -->
### 3.2. The Method
The package estimates density ratio by the RuLSIF method.
**RuLSIF** (Relative unconstrained Least-Squares Importance Fitting)
estimates the alpha-relative density ratio by minimizing the squared
loss between the true and estimated alpha-relative ratios. You can find
more information in Hido et al.ﾂ(2011) \[1\] and Liu et al (2013) \[4\].
The method assumes that the alpha-relative density ratio is represented
by a linear kernel model:
`w(x) = theta1 * K(x, c1) + theta2 * K(x, c2) + ... + thetab * K(x, cb)`
where `K(x, c) = exp(- ||x - c||^2 / (2 * sigma ^ 2))` is the Gaussian
RBF kernel.
`densratio()` performs the following: - Decides kernel parameter `sigma`
by cross-validation. - Optimizes for kernel weights `theta`. - Computes
the alpha-relative PE-divergence and KL-divergence from the learned
alpha-relative ratio.
As the result, you can obtain `compute_density_ratio()`, which will
compute the alpha-relative density ratio at the passed coordinates.
### 3.3. Result and Parameter Settings
`densratio()` outputs the result like as follows:
#> Method: RuLSIF
#>
#> Alpha: 0
#>
#> Kernel Information:
#> Kernel type: Gaussian
#> Number of kernels: 100
#> Bandwidth(sigma): 0.1
#> Centers: array([[0.92113356],..
#>
#> Kernel Weights (theta):
#> array([0.08848922, 0.03377533, 0.0753727 , 0.06141277, 0.02543963,..
#>
#> Regularization Parameter (lambda): 1.0
#>
#> Alpha-Relative PE-Divergence: 0.9635169300831041
#>
#> Alpha-Relative KL-Divergence: 0.838826626547327
#>
#> Function to Estimate Density Ratio:
#> compute_density_ratio(x)
#>
- **Method** is fixed as RuLSIF.
- **Kernel type** is fixed as Gaussian RBF.
- **Number of kernels** is the number of kernels in the linear model.
You can change by setting `kernel_num` parameter. In default,
`kernel_num = 100`.
- **Bandwidth(sigma)** is the Gaussian kernel bandwidth. In default,
`sigma = "auto"`, the algorithm automatically select an optimal
value by cross validation. If you set `sigma` a number, that will be
used. If you set `sigma` a numeric array, the algorithm select an
optimal value in them by cross validation.
- **Centers** are centers of Gaussian kernels in the linear model.
These are selected at random from the data sample `x` underlying a
numerator distribution `p(x)`. You can find the whole values in
`result.kernel_info.centers`.
- **Kernel weights(theta)** are theta parameters in the linear kernel
model. You can find these values in `result.theta`.
- **The function to estimate the alpha-relative density ratio** is
named `compute_density_ratio()`.
## 4. Multi Dimensional Data Samples
So far, we have deal with one-dimensional data samples `x` and `y`.
`densratio()` allows to input multidimensional data samples as
`numpy.ndarray` or `numpy.matrix`, as long as their dimensions are the
same.
For example,
``` python
from scipy.stats import multivariate_normal
from densratio import densratio
np.random.seed(1)
x = multivariate_normal.rvs(size=3000, mean=[1, 1], cov=[[1. / 8, 0], [0, 1. / 8]])
y = multivariate_normal.rvs(size=3000, mean=[1, 1], cov=[[1. / 2, 0], [0, 1. / 2]])
alpha = 0
densratio_obj = densratio(x, y, alpha=alpha, sigma_range=[0.1, 0.3, 0.5, 0.7, 1], lambda_range=[0.01, 0.02, 0.03, 0.04, 0.05])
print(densratio_obj)
```
gives the following output:
#> Method: RuLSIF
#>
#> Alpha: 0
#>
#> Kernel Information:
#> Kernel type: Gaussian
#> Number of kernels: 100
#> Bandwidth(sigma): 0.3
#> Centers: array([[1.01477443, 1.38864061],..
#>
#> Kernel Weights (theta):
#> array([0.06151164, 0.08012094, 0.10467369, 0.13868176, 0.14917063,..
#>
#> Regularization Parameter (lambda): 0.04
#>
#> Alpha-Relative PE-Divergence: 0.653615870855595
#>
#> Alpha-Relative KL-Divergence: 0.6214285743087565
#>
#> Function to Estimate Density Ratio:
#> compute_density_ratio(x)
#>
In this case, as well, we can compare the true density ratio with the
estimated density ratio.
``` python
from matplotlib import pyplot as plt
from numpy import linspace, dstack, meshgrid, concatenate
def true_alpha_density_ratio(x):
return multivariate_normal.pdf(x, [1., 1.], [[1. / 8, 0], [0, 1. / 8]]) / \
(alpha * multivariate_normal.pdf(x, [1., 1.], [[1. / 8, 0], [0, 1. / 8]]) + (1 - alpha) * multivariate_normal.pdf(x, [1., 1.], [[1. / 2, 0], [0, 1. / 2]]))
def estimated_alpha_density_ratio(x):
return densratio_obj.compute_density_ratio(x)
range_ = np.linspace(0, 2, 200)
grid = np.concatenate(np.dstack(np.meshgrid(range_, range_)))
levels = [0, 0.5, 1, 1.5, 2, 2.5, 3, 3.5, 4.5]
plt.figure(figsize=(10, 4))
plt.subplot(1, 2, 1)
plt.contourf(range_, range_, true_alpha_density_ratio(grid).reshape(200, 200), levels)
#> <matplotlib.contour.QuadContourSet object at 0x0000022E950202E0>
plt.colorbar()
#> <matplotlib.colorbar.Colorbar object at 0x0000022E9500DA80>
plt.title("True Alpha-Relative Density Ratio")
plt.subplot(1, 2, 2)
plt.contourf(range_, range_, estimated_alpha_density_ratio(grid).reshape(200, 200), levels)
#> <matplotlib.contour.QuadContourSet object at 0x0000022E942C8EE0>
plt.colorbar()
#> <matplotlib.colorbar.Colorbar object at 0x0000022E95095150>
plt.title("Estimated Alpha-Relative Density Ratio")
plt.show()
```
<!-- -->
## 5. References
\[1\] Hido, S., Tsuboi, Y., Kashima, H., Sugiyama, M., & Kanamori, T.
**Statistical outlier detection using direct density ratio estimation.**
Knowledge and Information Systems 2011.
\[2\] Sugiyama, M., Nakajima, S., Kashima, H., von Bﾃｼnau, P. & Kawanabe,
M. **Direct importance estimation with model selection and its
application to covariate shift adaptation.** NIPS 2007.
\[3\] Sugiyama, M., Suzuki, T. & Kanamori, T. **Density Ratio Estimation
in Machine Learning.** Cambridge University Press 2012.
\[4\] Liu, S., Yamada, M., Collier, N., & Sugiyama, M. **Change-Point
Detection in Time-Series Data by Relative Density-Ratio Estimation**
Neural Networks, 2013.
## 6. Related Work
- densratio for R <https://github.com/hoxo-m/densratio>
- pykliep <https://github.com/srome/pykliep>
نیازمندی
| مقدار | نام |
|---|---|
| - | numpy |
نحوه نصب
نصب پکیج whl densratio-0.3.0:
pip install densratio-0.3.0.whl
نصب پکیج tar.gz densratio-0.3.0:
pip install densratio-0.3.0.tar.gz