Mike's Page

Informatics, Development, Cycling, Data, Travel ...

Kampala Air Pollution

When I lived in Uganda, I used to cycle to work every day, and was aware of the pollution building as I cycled down the hill into the city centre.

Air pollution monitor and example output. The vertical lines mark when we lit a match in the same room as the sensor.

Air pollution monitor and example output. The vertical lines mark when we lit a match in the same room as the sensor.

I wanted to measure this pollution, so using the (very cheap) shinyei sensor and a mobile phone investigated what we could measure, and with what accuracy. I’ve not got very far yet, but this funding app gives and idea about what we’ve done and what we hope to achieve.

Air pollution monitoring in Kampala

Trilateration Part 2

Example of trilateration on the output areas of Sheffield

Example of trilateration on the output areas of Sheffield

In the last post, we looked at methods to find the optimum landmark. In this post we look at how to find one’s location given a set of landmarks.

Previously I’ve naively found the probability of each location on a grid, given the reported distances to the landmarks, then sampled from this grid to find the probability for each output area.

In this notebook we approach the problem differently, and look for the probability of the set of distances to the landmarks given the output area. By swapping the order, we are able to use the node in the Bayesian network.

Read more (ipynb)

Trilateration

Combining two estimated distances to find your location.

Combining two estimated distances to find your location.

Trilateration is like triangulation, but uses the distances to landmarks, rather than their angles, to determine one’s location. GPS is probably the most common example of trilateration in use at the moment.

In our problem we have a set of landmarks. We know the distance (with some uncertainty) to one, and we want to know which of the remaining landmarks we should select next to maximise the amount of information we gain about our location.

For our particular example, we ask people to estimate the distance of various landmarks from their house.

We look at how to find a good landmark quickly, by using Bayes’ rule to rearrange the expression for the entropy in the probability distribution.

Read more.

Some tools for using MVPA

During my PhD I used the Multivariate Pattern Analysis Toolbox (www.pni.princeton.edu/mvpa), a Matlab-based toolbox to facilitate multi-voxel pattern analysis of neuroimaging data. I’ve made several alterations/additions to the tool, which others might find useful:

Data preprocessing

Multiclass SVM Classification

Just a note, as lots of people have asked:

The MVPA toolbox contains a two class SVM classifier (train_svm). Ryan Mruczek wrote a wrapper for the Chih-Chung Chang and Chih-Jen Lin’s svm library, and posted it on the MVPA group. We’ve hosted the train and test files here for ease of use. To use it, you will also need to download libSVM from the download section of Chang and Lin’s SVM website.

Boltzmann Machine pattern classifier for fMRI using the MVPA toolbox

The MVPA toolbox contains several classifiers such as linear regression, support vector machines etc. To supplement these, we have worked on a generative classifier which uses Restricted Boltzmann Machines (RBM). The general principle behind an individual RBM is that one alters the weights to make the visible nodes activity similar to one of the classes of training data. This can be used as a generative classifier by seeing which of a set of RBMs has the lowest free energy when the test data is applied. The one with the lowest has been trained (probably) on data most similar to the test data. It is based on work by Tanya Schmah, Geoffrey Hinton, et al.
The training and test scripts are available here:

train_rbm.m, test_rbm.m [to add, needs to be recovered from archive]

Psychophysics

One of the great contributions of psychophysics to psychology is the notion of measuring threshold, i.e. the signal strength required for a criterion level of response by the observer. Watson and Pelli (1983) described a maximum likelihood procedure, which they called QUEST, for estimating threshold. The Quest algorithm is an adaptive staircase method, you can think of it as a Bayesian toolbox for testing observers and estimating their thresholds. We have written Python implementations of the Quest algorithm that you can download here:

files: quest.py, test_quest.py [to add, need to be recovered from archive]

Other useful hints

Structural Equation Modelling. The link from the SPM site to the SEM extension is dead. Douglas Steele kindly linked me to this tutorial. But some of the links were dead and I had trouble getting the code to compile. So I’ve produced a step-by-step summary describing how to get it working.

Failing to install the online psychic

The online psychic is running happily on my local machine, but I needed to get it onto this webserver.

Unfortunately the server doesn’t have pandas, numpy, etc installed.

I tried downloading virtualenv, which when untarred and run generates its own module collection. But I found its version of pip didn’t work, “shared host SystemError: Cannot compile ‘Python.h’. “.

So the next option: Anaconda? (I’ve only 1Gb of space, turns out that’s not enough).

Back to virtualenv:

Install my own version of python: https://my.justhost.com/cgi/help/python-install

Then following the instructions here: http://stackoverflow.com/questions/24748084/installing-numpy-without-sudo

Combined with the help here:

http://docs.python-guide.org/en/latest/dev/virtualenvs/

(download virtualenv here: https://pypi.python.org/pypi/virtualenv#downloads )

It still didn’t work – there’s a problem with the configuration of virtualenv’s python. It might be better to scrap virtualenv and download all the modules etc that I’ll need and compile them. The only advantage of virtualenv was that it would provide pip etc.

New python executable in venv/bin/python
ERROR: The executable venv/bin/python is not functioning
ERROR: It thinks sys.prefix is u'/home/.sites/81/site18/.users/89/mts-michael/python' (should be u'/home/.sites/81/site18/.users/89/mts-michael/venv')

Lessons in Matrix Factorisation, Bayes and Collaborative Filtering

These ‘lessons’ are really notes for myself, as I become familiar with python, pandas, matrix factorisation methods, etc. I’ll add a bit of an introduction at some point, and organise them nicely, but for now you can read them in my ipython folder.

Gibbs sampling a 2d multivariate gaussian

Gibbs sampling a 2d multivariate Gaussian

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