Deep Learning with labeled and Unlabeled data: application to Imaging

Mass Spectrometry Data

Introduction:
Imaging mass spectrometry (MSI) enables visualization of the spatial distribution of a wide
range of biomolecules, making it a prime tool for exploratory tissue research in biological
systems. A typical IMS experiment consists of a grid of measurement locations or pixels
covering the tissue section, with an individual mass spectrum attached to each pixel. The
generated data structure can be considered as a three-dimensional array with two spatial
dimensions (x,y) and one mass-over-charge (m/z) dimension.

Classification of partially labeled data:

By examining the tissue section, the pathologist can often
provide only a partial labeling of the cell types that it contains.
Based on staining methods certain regions can be clearly
labeled as diseased or healthy. However the tissue will
contains a large amount of intermediate tissue of unknown
labeling, beside that some regions cannot be labeled as
diseased or healthy as a consequence of the complexity of the
structure of the cell types.
The main objective of the thesis would be to train deep neural
networks in a semi-supervised setting to automatically label
the tissue sections. Deep learning architectures like deep
convolutional networks can be pre-trained unsupervised on
unlabeled data [1,2].

After this pre-training the network can be fine tuned with the labeled data that is available.
These techniques have already been used successfully in image recognition, and are the
current state of the art.
Work Description:
1. Literature study on MSI and Deep Neural Networks.
2. Create an artificial MSI dataset suited for benchmarking the classification method.
3. Recreate and adjust a Deep Neural Network in Python (Theano, Pylearn2) or Lua
(Torch7).
4. Pre-train the deep network in an unsupervised setting.
5. Fine tune the network with the labelled data.
6. Test the trained network on the MSI dataset.
Literature (40 %), Programming (30%), Writing (30%)
Profile:
Basic Python (or Lua) knowledge.
Courses in Machine Learning, Artificial Neural Networks or Computer Vision are a plus
Promotor:
Prof. Bart De Moor (bart.demoor@esat.kuleuven.be )
Department of Electrical Engineering (ESAT)
STADIUS
Daily supervisors:
Yousef El Aalamat (yousef.elaalamat@esat.kuleuven.be)
Nico Verbeeck (nico.verbeeck@esat.kuleuven.be)
Peter Roelants (peter.roelants@esat.kuleuven.be)
Number of students: 1
Suitable for: Bioi, WIT, AI, CS
References:
[1] Why Does Unsupervised Pre-training Help Deep Learning? Dumitru Erhan, Yoshua Bengio,
Aaron Courville, Pierre-Antoine Manzagol, Pascal Vincent, Samy Bengio; 11(Feb):625660,
2010.
[2] Convolutional deep belief networks for scalable unsupervised learning of hierarchical
representations. Honglak Lee, Roger Grosse, Rajesh Ranganath, and Andrew Y. Ng. In
Proceedings of the 26th Annual International Conference on Machine Learning, ICML 09, pages
609616, New York, NY, USA, 2009. ACM.