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For the reading assignment you first have to select a recent journal publication and then write a short review.

Paper selection

You are free to select the paper that you will review (in consultations with the course instructors and teaching assistants). Use the following selection criteria for the paper:

  • Describes an application of Machine Learning to a Medical Imaging or Computational Biology problem
  • Recently published (after and including 2019)
  • Published in a high-quality journal (see the reference list and examples below)
  • On a topic that you find interesting and want to learn more about

Here is a non-extensive list of journals that you can use as a reference:

Medical Imaging:

  • Medical Image Analysis
  • IEEE Transactions on Medical Imaging
  • IEEE Transactions on Biomedical Engineering
  • IEEE Transactions on Pattern Analysis and Machine Intelligence
  • Computer Vision and Image Understanding
  • Computerized Medical Imaging and Graphics
  • Magnetic Resonance in Medicine
  • Neuroimage
  • Radiology: Artificial Intelligence

Computational Biology:

  • Bioinformatics
  • PloS Computational Biology
  • Molecular Systems Biology
  • Cell Systems
  • Cancer Research
  • Nature Biotechnology
  • Frontiers in Oncology
  • Frontiers in Immunoloty
  • Cell Reports

Some specialised publications also publish Medical Imaging or Computational Biology research. For example, the Modern Pathology journal often publishes papers on image analysis for histopathology. You can also find such papers in interdisciplinary/wides scope journals such as Nature Methods, Nature Communications, Nature Medicine, Scientific Reports, PlosONE etc.

An example paper on the use of machine learning in Computational Biology: Ali, M., Khan, S. A., Wennerberg, K., & Aittokallio, T. (2017). Global proteomics profiling improves drug sensitivity prediction: results from a multi-omics, pan-cancer modeling approach. Bioinformatics, (November 2017), 1–10.

An example paper on the use of machine learning in Medical Imaging: Campanella, G., Hanna, M. G., Geneslaw, L., Miraflor, A., Silva, V. W. K., Busam, K. J., ... & Fuchs, T. J. (2019). Clinical-grade computational pathology using weakly supervised deep learning on whole slide images. Nature Medicine, 25(8), 1301-1309.

Paper review

Once you have selected the paper, you have to write a short 800 word review that:

  • Gives a summary of the application domain of the paper
  • Gives a summary of the used (Machine Learning) methodology and evaluation metrics
  • Discusses the strong and weak points of the methodology and evaluation metrics
  • Suggests alternative methodology, evaluation metrics and ideas for improvement

Deliverables

In Canvas you will find two assignments grouped under "Reading assignment".

The first one is "Paper selection". You have to use this assignment to discuss your paper selection with the course instructors and teaching assistants. It is best if you suggest a few papers and order them by preference. One of the instructors or teaching assistants has to approve the paper selection.

The second assignment "Paper Review" is for submitting the paper review as a PDF document.

Note that there are deadlines for both assignments.