Generalisable Subcellular Location Classification

See the video abstract for the highlights.

Most of subcellular location analysis in the past has been pursued using datasets that contain multiple copies of the same representative protein (i.e., a specific protein is selected to serve as a nuclear protein, another to serve as a microtubular protein).

Algorithms are then evaluated by measuring their ability to recognise this protein. It has then been inferred that the algorithm is thus capable of recognizing location patterns. Unfortunately, this is a leap of judgement that has not been tested. We tested this using a new dataset with multiple proteins standing in the same location group.

The algorithms we were using previously performed significantly worse in this new dataset and we thus employed new methods to achieve better results.

The paper describing this work has been published in Bioinformatics:

Determining the subcellular location of new proteins from microscope images using local features by Luis Pedro Coelho, Joshua D. Kangas, Armaghan Naik, Elvira Osuna-Highley, Estelle Glory-Afshar, Margaret Fuhrman, Ramanuja Simha, Peter B. Berget, Jonathan W. Jarvik, and Robert F. Murphy (2013). Bioinformatics, [DOI] [open access version]

(For the BibTeX citation, see below.)

Download the data from Data Dryad

Local Features for Bioimage Analysis

We also show that using SURF (a form of local features) achieves excellent results in subcellular classification and we recommend it for bioimage analysis.

Open source code is available as part of my computer vision package, mahotas, to implement these features.

We have a step-by-step tutorial on how to apply SURF to your own research. Feel free to email me if you run into trouble.

We also made available the code to reproduce the paper exactly.

You can also read several blog posts related to this paper.

Citation

Here is the full bibtex citation:

@article{Coelho08072013,
author = {Coelho, Luis Pedro and Kangas, Joshua D. and Naik, Armaghan W.
    and Osuna-Highley, Elvira and Glory-Afshar, Estelle and Fuhrman, Margaret
    and Simha, Ramanuja and Berget, Peter B. and Jarvik, Jonathan W. and
    Murphy, Robert F.},
title = {Determining the subcellular location of new proteins from
    microscope images using local features},
doi = {10.1093/bioinformatics/btt392},
volume = {29},
number = {18},
pages = {2343-2349},
year = {2013},
journal = {Bioinformatics},

abstract = {Motivation: Evaluation of previous systems for automated
    determination of subcellular location from microscope images has been done
    using datasets in which each location class consisted of multiple images of
    the same representative protein. Here, we frame a more challenging and
    useful problem where previously unseen proteins are to be classified.

    Results: Using CD-tagging, we generated two new image datasets for
    evaluation of this problem, which contain several different proteins
    for each location class. Evaluation of previous methods on these new
    datasets showed that it is much harder to train a classifier that
    generalizes across different proteins than one that simply recognizes a
    protein it was trained on. We therefore developed and evaluated
    additional approaches, incorporating novel modifications of local
    features techniques. These extended the notion of local features to
    exploit both the protein image and any reference markers that were
    imaged in parallel. With these, we obtained a large accuracy
    improvement in our new datasets over existing methods. Additionally,
    these features help achieve classification improvements for other
    previously studied datasets.

    Availability: The datasets are available for download at
    https://murphylab.cbd.cmu.edu/data/. The software was written in Python
    and C++ and is available under an open-source license at
    https://murphylab.cbd.cmu.edu/software/. The code is split into a
    library which can be easily reused for other data and a small driver
    script for reproducing all results presented here. A step-by-step
    tutorial on applying the methods to new datasets is also available at
    that address.

    Contact: murphy@cmu.edu}
}