Faster Serialization in Python

TLDR; Pickle is slow, cPickle is faster, JSON is surprisingly fast, Marshal is fastest, but when using PyPy all fall before a humble text file parser.


I’ve been working on the Yandex Personalized Web Search challenge on kaggle, which requires me to read in a large amount of data stored as multi-line, tab-separated, records. The data is ragged, each record has sub-fields of variable length, and there are 34.5 million of them. There are too many records to load in memory, and starting out, I’m not quite sure what features will end up being important. To reduce the bottle-neck of reading the files from disk, I wanted to pre-process the data, and store it in some format which afforded me faster reading and writing off the disk, without going to a full blown database solution. I ended up testing the following formats:

  1. pickle (using both the pickle and cPickle modules), a module which can serialize just about any datas structure, but is only available for python. I’ve used this extensively to persistify derived data for work.
  2. JSON, which only supports a basic set of data-types (fine for this use case), but can be handled by a larger number of languages (irrelevant for this use case).
  3. Marshal, which is not really meant for general serialization, but I was curious about it’s internals. This is not really a recommended format, the documentation clearly warns “Details of the format are undocumented on purpose; it may change between Python versions.”

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A (brief?) shining moment

 TL;DR: We’re kicking butts over at!


A colleague and I recently joined a competition in which, given a set of measurements of two variables, the point is to determine whether one is causally linked to the other. Conceptually, this is an interesting problem, and we’ve only just started hacking away at it, but we’ve already had some success. Our latest submission netted us 6th place!

I feel all warm and fuzzy inside. Now, time to step up our game and move up higher!


Samsung Motion Analysis

TLDR; A write up of an assignment from Coursera’s Data Analysis course aiming to identify patterns of activity from accelerometer data using SVD and Randrom Forests in R.

I’ve been following Coursera’s “Data Analysis” course, taught by Jeff Leek (straight outta Hopkins!). It’s been interesting, having spent 7 years doing particle physics, most of the techniques are not new, but the jargon is. It has also highlighted some important differences in the methodology of Particle Physics and Bio-statistics, driven by our reliance on synthetic data (or conversely, driven by their lack of reliable Monte Carlo). Since the second assignment is over and done with, I thought I’d post a little write-up here.

The aim was to study the predictive power of data collected by the accelerometer and gyroscope of Samsung Galaxy S II smartphones, carried by a group of individuals performing various activities (walking, walking upstairs, walking downstairs, sitting, standing, and laying down). The dataset consists of 7352 samples (pre-processed by applying noise filters and by sampling the values in fixed time windows) of 562 features collected from 21 individuals. Of these 21 individuals, I randomly set aside three as a testing sample, and another four as a validation sample.

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TL;DR: I talk about some text frequency analysis I did on the corpus using python, mysql, and R to identify trends and spot interesting new physics results.


In one of my previous posts, I mentioned some optimization I had done on a word-frequency anlysis tool. I thought I’d say a bit more here about the tool (buzzArxiv), which I’ve put together using Python and R to find articles that are creating a lot of ‘buzz’.

For those who don’t know, is an online repository of scientific papers, categorized by field (experimental particle physics, astrophysics, condensed matter, etc…). Most of the pre-print articles posted to the arxiv eventually also get submitted to journals, but it’s usually on the arxiv that the word about new work gets disseminated in the community. The thing is, there’s just gobs of new material on there every day. The experimental, pheonomonolgy, and theory particle physics mailings can each have a dozen or so articles per day.

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