trendfilter 0.3.2
Useful trendfilter algorithm
License: MIT
Keywords: cvxpy, trendfilter

# trendfilter: 

Trend filtering is about building a model for a 1D function
(could be a time series) that has some nice properties such as 
smoothness or sparse changes in slopes (piecewise linear). It can
also incorporate other features such as seasonality and can be 
made very robust to outliers and other data corruption features.

Here's a visual example

![](https://raw.githubusercontent.com/dave31415/trendfilter/master/plots/bokeh_plot_l1_trend_filter_mono.png)


The objective to be minimized is, in our case, Huber loss with
regularization on 1st and 2nd derivative plus some constraints. 
Can be either L1 or L2 norms for regularization.

This library provides a flexible and powerful python function to 
do trend filtering and is built on top of the 
convex optimization library cvxpy.

Trend filtering is very useful on typical data science problems we
that we commonly run into in the business world. These types of 
data series are typically not very large and low signal-to-noise. An
example might be monthly sales of one type of product. 

Unlike high signal-to-noise data, that is 
often treated with other time-series techniques, thee main desire
is finding the most recent trend and extrapolating forward a bit. The
biggest problem is data quality issues. So we want to do this as 
robustly as possible. It's also quite useful when we want to include
the data corruption as part of the model and extract it at the same 
time instead of requiring a pre-processing step with some arbitrary 
rules.

This is what this technique is best utilized for.
Larger, richer data sets (e.g. medical EKG data) with thousands 
or millions of points, low noise and no outliers, might be
better approached with other techniques that focus most of all on 
extracting the full complexity of the signal from a small amount of
noise.

# Install

pip install trendfilter

or clone the repo. 

# Examples:

Contruct some x, y data where there is noise as well as few 
outliers. See 
[test file](https://github.com/dave31415/trendfilter/blob/master/test/test_tf.py)
for prep_data code and plotting code.

First build the base model with no regularization. This is essentially
just an overly complex way of constructing an interpolation function. 

```
from trendfilter import trend_filter, get_example_data, plot_model

x, y_noisy = get_example_data()
result = trend_filter(x, y_noisy)
title = 'Base model, no regularization'
plot_model(result, title=title)
```

![](https://raw.githubusercontent.com/dave31415/trendfilter/master/plots/bokeh_plot_base_model_no_reg.png)

This has no real use by itself. It's just saying the model is the
same as the data points.

You'll always want to give it some key-words to
apply some kind of regularization or constraint so that the model
is not simply the same as the noisy data.

Let's do something more useful. Don't do any regularization yet. Just
force the model to be monotonically increasing. So basically, it 
is looking for the model which has minimal Huber loss but is 
constrained to be monotonically increasing. 

We use Huber loss because it is robust to outliers while still
looking like quadratic loss for small values.

```
result = trend_filter(x, y_noisy, monotonic=True)
plot_model(result, show_extrap=True, extrap_max=3)
```

![](https://raw.githubusercontent.com/dave31415/trendfilter/master/plots/bokeh_plot_best_mono.png)

The green line, by the way, just shows that the function can be extrapolated 
which is a very useful thing, for example, if you want to make predictions
about the future.

Ok, now let's do an L1 trend filter model. So we are going to 
penalize any non-zero second derivative with an L1 norm. As we 
probably know, L1 norms induce sparseness. So the second dervative at 
most of the points will be exactly zero but will probably be non-zero
at a few of them. Thus, we expect piecewise linear trends that 
occasionally have sudden slope changes.

```
result = trend_filter(x, y_noisy, l_norm=1, alpha_2=0.2)
plot_model(result, show_extrap=True, extrap_max=3)
```

![](https://raw.githubusercontent.com/dave31415/trendfilter/master/plots/bokeh_plot_l1_trend_filter.png)

Let's do the same thing but enforce it to be monotonic.

```
result = trend_filter(x, y_noisy, l_norm=1, alpha_2=0.2, monotonic=True)
plot_model(result, show_extrap=True, extrap_max=3)
```

![](https://raw.githubusercontent.com/dave31415/trendfilter/master/plots/bokeh_plot_l1_trend_filter_mono.png)


Now let's increase the regularization parameter to give a higher
penalty to slope changes. It results in longer trends. Fewer slope
changes. Overall, less complexity.

```
result = trend_filter(x, y_noisy, l_norm=1, alpha_2=2.0)
plot_model(result, show_extrap=True, extrap_max=3)
```

![](https://raw.githubusercontent.com/dave31415/trendfilter/master/plots/bokeh_plot_l1_trend_filter_more_reg.png)


Did you like the stair steps? Let's do that again. But now
we will not force it to be monotonic. We are going to put an
L1 norm on the first derivative. This produces a similar 
output but it could actually decrease if the data actually
did so. Let's also constrain the curve to go through the origin, 
(0,0).

```
result = trend_filter(x, y_noisy, l_norm=1, alpha_1=1.0, constrain_zero=True)
plot_model(result, show_extrap=True, extrap_max=3)
```

![](https://raw.githubusercontent.com/dave31415/trendfilter/master/plots/bokeh_plot_stair_steps.png)


Let's do L2 norms for regularization on the second 
derivative. L2 norms don't care very much about small values. 
They don't force them all the way to zero to create sparse 
solution. They care more about big values. This results is a 
smooth continuous curve. This is a nice way of doing robust 
smoothing. 

```
result = trend_filter(x, y_noisy, l_norm=2, alpha_2=2.0)
plot_model(result, show_extrap=True, extrap_max=3)
```

![](https://raw.githubusercontent.com/dave31415/trendfilter/master/plots/bokeh_plot_l2_smooth.png)


Here is the full function signature.

```
def trend_filter(x, y, y_err=None, alpha_1=0.0,
                 alpha_2=0.0, l_norm=2,
                 constrain_zero=False, monotonic=False,
                 positive=False,
                 linear_deviations=None):
```

So you see there are alpha key-words for regularization parameters. 
The number n, tells you the derivative is being penalized.
You can use any, all or none of them. The key-word
l_norm gives you the choice of 1 or 2. Monotonic and 
constrain_zero, we've explained already. positive forces the 
base model to be positive. linear_deviations will be explained in a bit.

The data structure returned by trend_filter is a dictionary with various
pieces of information about the model. The most import are 
'y_fit' which is an array of best fit model values corresponding to 
each point x. The 'function' element is a function mapping any x to the
model value, including points outside the initial range. These external 
points will be extrapolated linearly. In the case that the data is a 
time-series, this function can provide forecasts for the future.

We didn't discuss y_err. That's the uncertainty on y. The
default is 1. The Huber loss is actually applied to (data-model)/y_err.
So, you can weight points differently if you have a good reason to,
such as knowing the actual error values or knowing that some points 
are dubious or if some points are known exactly. That would be the limit
as y_err goes towards zero and it will make the curve go through those
points.

All in all, these keywords give you a huge amount of freedom in
what you want your model to look like.

# Linear model deviations and seasonality:

Any time series library should include ways of modeling seasonality and 
this one does as well. In fact, it includes something more general which is
the ability to add in any linear features to the model. 
This linearity preserves convexity and so we can still use 
convex optimization. 
By linear deviation we means any addition to the model that is a specified
matrix multiplied by a variable vector. That variable vector can be solved
for as well. 

To do this you create a data structure called linear deviations

```
linear_deviation = {'mapping': lambda x: int(x) % 12,
                    'name': 'seasonal_term',
                    'n_vars': 12,
                    'alpha': 0.1}
```

This assumes the matrix above is an assignment matrix. You can also create
a matrix yourself and include that as 'matrix' instead of 'mapping'. 

This provides a mapping from x to some set of integer indices. You tell
it there are 12 of them. One for each month of the year. We can give it a 
name 'seasonal_term' and a regularization parameter. Evidently, we are
going to use this on a monthly time series. 

Now just call it like this.

```
linear_deviations = [linear_deviation]
result = trend_filter(x, y_noisy, l_norm=1, alpha_2=4.0, linear_deviations=linear_deviations)
```

Note that you input it as a list if linear deviations. You can include
multiple. Perhaps for example, you have one that marks months for which
the kids are in school or months where there was a convention 
in town.

Let's see it in action.

We've created another data set with some seasonal pattern added.
This is how it looks when the model is run without seasonality.

```
from trendfilter import get_example_data_seasonal()

x, y_noisy = get_example_data_seasonal()
result = trend_filter(x, y_noisy,  l_norm=1, alpha_2=4.0)
plot_model(result, show_extrap=True, extrap_max=40)
```

![](https://raw.githubusercontent.com/dave31415/trendfilter/master/plots/bokeh_plot_without_seasonal.png)

In this case the model is just trying to model all the wiggles
with a changing trend. This doesn't produce a very 
convincing looking forecast. We can improve that some and iron
out the wiggles by using a higher alpha_2.

But if we notice there is some periodicity to it, we can 
actually model it using the structure we created above.

```
result = trend_filter(x, y_noisy, l_norm=1, alpha_2=4.0, linear_deviations=linear_deviations)
plot_model(result, show_extrap=True, extrap_max=40, show_base=True)
```

![](https://raw.githubusercontent.com/dave31415/trendfilter/master/plots/bokeh_plot_with_seasonal.png)

Now, we can see that there is indeed a prominant seasonal
pattern on top of a rather smooth base model. The forecast 
now will include that same seasonal pattern which should 
lead to a more accurate forecast.

The 'alpha' regularization determines the amount of evidence required
to make use of the seasonal component. For a larger alpha and the same 
pattern here, it will take more cycles before it will overcome the barrier.
At this point the total objective is lower than trying to model the 
wiggles with slope changes or tolerating a difference between model and 
data.


First pypi version April 12, 2021

0.1.4 
Added more examples with more documentation and plots in the Readme

0.1.5
Mostly a refactor but changed API slightly.

0.2.0
Includes seasonality and linear deviations.

0.2.1
Switched to ECOS solver

0.3.0 
Switched to Claribel solver which is the new built in solver
Inputs now converted to numpy arrays so list inputs should work

0.3.2 Fixing PyPi to show plots, use full URLs