FAQ: How Many Clusters Did You Use?

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 [Advanced Access]  [Previous discussion on this blog]

Coelho, Luis Pedro, Tao Peng, and Robert F. Murphy. “Quantifying the Distribution of Probes Between Subcellular Locations Using Unsupervised Pattern Unmixing.” Bioinformatics 26.12 (2010): i7–i12. DOI: 10.1093/bioinformatics/btq220  [Previous discussion on this blog]

Both of my Bioinformatics papers above use the concept of bag of visual words. The first for classification, the second for pattern unmixing.

Visual words are formed by clustering local appearance descriptors. The descriptors may have different origins (see the papers above and the references below) and the visual words are used differently, but the clustering is a common intermediate step.

A common question when I present this work is how many clusters do I use? Here’s the answer: it does not matter too much.

I used to just pick a round number like 256 or 512, but for the local features paper, I decided to look at the issue a bit closer. This is one of the panels from the paper, showing accuracy (y-axis) as a function of the number of clusters (x-axis):

profile-field-dna+-RT-widefield-gs

As you can see, if you use enough clusters, you’ll do fine. If I had extended the results rightwards, then you’d see a plateau (read the full paper & supplements for these results) and then a drop-off. The vertical line shows N/4, where N is the number of images in the study. This seems like a good heuristic across several datasets.

One very interesting result is that choosing clusters by minimising AIC can be counter-productive! Here is the killer data (remember, we would be minimizing the AIC):

accuracy-aic-rt-widefield-gs

Minimizing the AIC leads to lower accuracy! AIC was never intended to be used in this context, of course, but it is often used as a criterion to select the number of clusters. I’ve done it myself.

Punchline: If doing classification using visual words, minimsing AIC may be detrimental, try using N/4 (N=nr of images).

Other References

This paper (reviewed before on this blog) presents supporting data too:

Noa Liscovitch, Uri Shalit, & Gal Chechik (2013). FuncISH: learning a functional representation of neural ISH images Bioinformatics DOI: 10.1093/bioinformatics/btt207

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Unsupervised subcellular pattern unmixing. Part II

On Friday, I presented the pattern unmixing problem. Today, I’ll discuss how we solved it.

Coelho, Luis Pedro, Tao Peng, and Robert F. Murphy. “Quantifying the Distribution of Probes Between Subcellular Locations Using Unsupervised Pattern Unmixing.” Bioinformatics 26.12 (2010): i7–i12. DOI: 10.1093/bioinformatics/btq220

The first step is to extract objects. For this, we use a combination of global & local thresholding: this means that a pixel is on if it is both above a global threshold which identifies the cells from the background and a local threshold (which identifies subcellular objects [1]).

We then group the objects found using k-means clustering. Here is what we obtain for a lysosomal picture (different colours mean different clusters) [2].

unmixing-colours-1

and the equivalent for the mitochondrial image:

unmixing-colours-0

You will see that the mitochondrial image has many green things and less dark purple objects, but both mitochondrial and lysosomal images have all of the groups. Now (and this is an important point): we do not attempt to classify each individual object, only to estimate the mixture.

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Of course, if we had the identity of each object, the mixture would be trivially estimated. But we do not need to identify each object. In fact, to attempt to do so would be a gross violation of Vapnik’s Dictum (which says do not solve, as an intermediate step, a harder problem than the one you are trying to solve). It is easier to just estimate the mixtures [3].

In this formulation it might not even matter much that some of the objects we detect correspond to multiple biological objects!

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How do we solve the mixture problem? Latent Dirichlet allocation or basis pursuit. The details are in the paper, but I will jump to the punchline.

We tested the method using a dataset where we had manipulated the cell tagging so we know the ground truth (but the algorithm, naturally, does not see it). On the graph below, the x-axis is the (hidden) truth and the y-axis is the automated estimate. In green, the perfect diagonal; and each dot represents one condition:

unmixing_corrcoef_lda

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I will note that each individual dot in the above plot represents several images from each condition. On a single image (or single cell) level the prediction is not so accurate. Only by aggregating a large number of objects can the model predict well.

This also points out why it may be very difficult for humans to perform this task (nobody has tried to do it, actually).

[1] A global threshold did not appear to be sufficient for this because there is a lot of in-cell background light (auto-fluorescence and auto-focus light).
[2] For this picture, I used 5 clusters to get 5 different colours. The real process used a larger number, obtained by minimising BIC.
[3] Sure, we can then reverse engineer and obtain a probability distribution for each individual object, but that is not the goal.

Old Work: Unsupervised Subcellular Pattern Unmixing

Continuing down nostalgia lane, here is another old paper of mine:

Coelho, Luis Pedro, Tao Peng, and Robert F. Murphy. “Quantifying the Distribution of Probes Between Subcellular Locations Using Unsupervised Pattern Unmixing.” Bioinformatics 26.12 (2010): i7–i12. DOI: 10.1093/bioinformatics/btq220

I have already discussed the subcellular location determination problem. This is Given images of a protein, can we assign it to an organelle?

This is, however, a simplified version of the world: many proteins are present in multiple organelles. They may move between organelles in response to a stimulus or as part of the cell cycle. For example, here is an image of mitochondria in green (nuclei in red):

img17

Here is one of lysosomes:

img71

And here is a mix of both!:

img77-2

This is a dataset constructed for the purpose of this work, so we know what is happening, but it simulates the situation where a protein is present in two locations simultaneously.

Thus, we can move beyond simple assignment of a protein to an organelle to assigning it to multiple organelles. In fact, some work (both from the Murphy group and others) has looked at subcellular location classification using multiple labels per image. This, however, is still not enough: we want to quantify this.

This is the pattern unmixing problem. The goal is to go from an image (or a set of images) to something like the following: This is 30% nuclear and 70% cytoplasmic, which is very different from 70% nuclear and 30% cytoplasmic. The basic organelles can serve as the base patterns [1].

Before our paper, there was some work in approaching this problem from a supervised perspective: Given examples of different organelles (ie, of markers that locate to a single organelle), can we automatically build a system which when given images of a protein which is distributed in multiple organelles, can figure out which fraction comes from each organelle?

Our paper extended this to work to the unsupervised case: can you learn a mixture when you do not know which are the basic patterns?

References

Determining the distribution of probes between different subcellular locations through automated unmixing of subcellular patterns Tao Peng, Ghislain M. C. Bonamy, Estelle Glory-Afshar, Daniel R. Rines, Sumit K. Chanda, and Robert F. Murphy PNAS 2010 107 (7) 2944-2949; published ahead of print February 1, 2010, doi:10.1073/pnas.0912090107

Object type recognition for automated analysis of protein subcellular location T Zhao, M Velliste, MV Boland, RF Murphy Image Processing, IEEE Transactions on 14 (9), 1351-1359

[1] This is still a limited model because we are not sure even how many base patterns we should consider, but it will do for now.