Recognition of an Organelle Marker is not the Same as Recognition of the Organelle

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, Determining the subcellular location of new proteins from microscope images using local features in Bioinformatics, 2013 [DOI]

As I wrote on Wednesday, this paper has two main ideas: (1) traditional subcellular location determination systems do not generalize very well and (2) local features do better. I will now try to explain the first point in depth.


Here are the first two sentences of the abstract (added emphasis):

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.

To expand on this: the typical evaluation model is the following:

  1. Define the classes of interest (e.g., the major organelles: nucleusmitochondria, …).
  2. For each class, choose a representative. It could be a protein which was fluorescently tagged or another fluorescent marker (like DAPI for DNA). In our work, we only used fluoresencent proteins, but the same logic applies to small molecular markers.
  3. Collect multiple images of cells tagged with this marker.
  4. Split up the set of images into training and testing groups. Learn a classifier on the training set, evaluate it on the testing sets.
  5. Report the results.

The techniques were, almost always, feature based [1]. A feature is a function which computes a number from the image. By computing numbers which represent the properties of interest, we can hope that images from the same class will have similar results. The following image illustrates this [2]:

Images of known proteins (left and right) are projected into a low dimensional space of features. Then an image of unknown label can be predicted by looking in this low dimensional space as well.


We can get very high accuracies, above 95% in some cases, with this family of systems, which have been interpreted as meaning that automated system can determine the location of proteins at high accuracies. There is a big hidden assumption in the reasoning, however!

There are two hypothesis that are consistent with the data:

  1. The system is very good at recognizing this location.
  2. The system is very good at recognizing this protein.

Under the second hypothesis, the system is very good at recognizing the marker you used for DNA (say DAPI), but may fail miserably when presented with another nuclear marker.


Fundamentally, to test between the two hypothesis above, we need datasets with multiple proteins per location. This is what we collected. And, when we tested the generalization ability of traditional methods, they fell short.

While a traditional approach was able to get 84% accuracy when it only needed to recognize the proteins it had been trained on (10 classes), it fell to 62% when it needed to recognize locations of new proteins. However, this is the important problem: to determine the location of new proteins, not the ones the system was trained on.

As the title says: Recognition of an Organelle Marker is not the Same as Recognition of the Organelle


Over the next few posts I will explain how we tested this & then, finally, how we got some better results on this harder problem.

[1] There is an exception that I know of, from the beginning of the field: Danckaert et al. 2003 in Traffic. They used a neural network directly on the pixels with a single hidden layer. It would be very interesting to re-attempt this approach for cell images with the new technology in deep learning that was developed in the meanwhile (I don’t have enough time to do it myself, so feel free to take this idea and run with it; or get in touch if you want to do it together).
[2] This image is in Wikipedia, but I put it there, so I don’t need to credit it.

2 thoughts on “Recognition of an Organelle Marker is not the Same as Recognition of the Organelle

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