On June, 6, 2019, 10:00-16:00 we organize in Graz/Austria a small Symposium on AI/Machine Learning for Digital Pathology
Open and Collaborative Digital Pathology using Cytomine
In this talk Raphael Maree will present the past, present, and future of Cytomine.
Cytomine ,  is an open-source software, continuously developed since 2010. It is based on modern web and distributed software development methodologies and machine learning, i.e. deep learning. It provides remote and collaborative features so that users can readily and securely share their large-scale imaging data worldwide. It relies on data models that allow to easily organize and semantically annotate imaging datasets in a standardized way (e.g. to build pathology atlases for training courses or ground-truth datasets for machine learning). It efficiently supports digital slides produced by most scanner vendors. It provides mechanisms to proofread and share image quantifications produced by machine/deep learning-based algorithms. Cytomine can be used free of charge and it is distributed under a permissive license. It has been installed at various institutes worldwide and it is used by thousands of users in research and educational settings.
Recent research and developments will be presented such as our new web user interfaces and new modules for multimodal and multispectral data (Proteomics Clin Appl, 2019), object recognition in histology and cytology using deep transfer learning (CVMI 2018), user behavior analytics in educational settings (ECDP 2018), as well as our new reproducible architecture to benchmark bioimage analysis workflows.
Raphaël Marée received the PhD degree in computer science in 2005 from the University of Liège, Belgium, where he is now working at the Montefiore EE&CS Institute (http://www.montefiore.ulg.ac.be/~maree/). In 2010 he initiated the CYTOMINE research project (http://uliege.cytomine.org/), and since 2017 he is also co-founder of the not-for-profit Cytomine cooperative (http://cytomine.coop). His research interests are in the broad area of machine learning, computer vision techniques, and web-based software development, with specific focus on their applications on big imaging data such as in digital pathology and life science research, while following open science principles.
 Raphaël Marée, Loïc Rollus, Benjamin Stévens, Renaud Hoyoux, Gilles Louppe, Rémy Vandaele, Jean-Michel Begon, Philipp Kainz, Pierre Geurts & Louis Wehenkel 2016. Collaborative analysis of multi-gigapixel imaging data using Cytomine. Bioinformatics, 32, (9), 1395-1401, doi:10.1093/bioinformatics/btw013.
Google Scholar Profile of Raphael Maree:
Homepage of Raphael Maree:
An awesome question stated in an article by Michael BEREKET and Thao NGUYEN (Febuary 7, 2018) brings it straight to the point: Deep learning has revolutionized the field of computer vision. So why are pathologists still spending their time looking at cells through microscopes?
The most famous machine learning experiments have been done with recognizing cats (see the video by Peter Norvig) – and the question is relevant, how different are these cats from the cells in histopathology?
Machine Learning, and in particular deep learning, has reached a human-level in certain tasks, particularly in image classification. Interestingly, in the field of pathology these methods are not so ubiqutiously used currently. A valid question indeed is: Why do human pathologists spend so much time with visual inspection? Of course we restrict this debate on routine tasks!
This excellent article is worthwhile giving a read:
Stanford AI for healthcare: How different are cats from cells
Source of the animated gif above:
Yoshua BENGIO from the Canadian Institute for Advanced Research (CIFAR) emphasized during his workshop talk entitled “towards disentangling underlying explanatory factors” (cool title) at the ICML 2018 in Stockholm, that the key for success in AI/machine learning is to understand the explanatory/causal factors and mechanisms. This means generalizing beyond identical independent data (i.i.d.); current machine learning theories are strongly dependent on this iid assumption, but applications in the real-world (we see this in the medical domain!) often require learning and generalizing in areas simply not seen during the training epoch. Humans interestingly are able to protect themselves in such situations, even in situations which they have never seen before. See Yoshua BENGIO’s awesome talk here:
and here a longer talk (1:17:04) at Microsoft Research Redmond on January, 22, 2018 – awesome – enjoy the talk, I recommend it cordially to all my students!
We just had our keynote by Randy GOEBEL from the Alberta Machine Intelligence Institute (Amii), working on enhnancing understanding and innovation in artificial intelligence:
You can see his slides with friendly permission of Randy here (pdf, 2,680 kB):
Here you can read a preprint of our joint paper of our explainable ai session (pdf, 835 kB):
GOEBEL et al (2018) Explainable-AI-the-new-42
Randy Goebel, Ajay Chander, Katharina Holzinger, Freddy Lecue, Zeynep Akata, Simone Stumpf, Peter Kieseberg & Andreas Holzinger. Explainable AI: the new 42? Springer Lecture Notes in Computer Science LNCS 11015, 2018 Cham. Springer, 295-303, doi:10.1007/978-3-319-99740-7_21.
Here is the link to our session homepage:
amii is part of the Pan-Canadian AI Strategy, and conducts leading-edge research to push the bounds of academic knowledge, and forging business collaborations both locally and internationally to create innovative, adaptive solutions to the toughest problems facing Alberta and the world in Artificial Intelligence/Machine Learning.
Here some snapshots:
R.G. (Randy) Goebel is Professor of Computing Science at the University of Alberta, in Edmonton, Alberta, Canada, and concurrently holds the positions of Associate Vice President Research, and Associate Vice President Academic. He is also co-founder and principle investigator in the Alberta Innovates Centre for Machine Learning. He holds B.Sc., M.Sc. and Ph.D. degrees in computer science from the University of Regina, Alberta, and British Columbia, and has held faculty appointments at the University of Waterloo, University of Tokyo, Multimedia University (Malaysia), Hokkaido University, and has worked at a variety of research institutes around the world, including DFKI (Germany), NICTA (Australia), and NII (Tokyo), was most recently Chief Scientist at Alberta Innovates Technology Futures. His research interests include applications of machine learning to systems biology, visualization, and web mining, as well as work on natural language processing, web semantics, and belief revision. He has experience working on industrial research projects in scheduling, optimization, and natural language technology applications.
Here is Randy’s homepage at the University of Alberta:
The University of Alberta at Edmonton hosts approximately 39k students from all around the world and is among the five top universities in Canada and togehter with Toronto and Montreal THE center in Artificial Intelligence and Machine Learning.
In a recent interview Been KIM from the Google Brain team emphasizes the significance of research in explainable AI. Particularly, she emphasized the importance of Human-Computer Interaction (HCI) for Artificial Intelligence generally and Machine Learning specifically (see the differences between AI and ML here), and the urgent need of an research framework around the field of interpretability. Listen to the episode six of season four of Talking Machines by Katherine GORMAN and Neil LAWRENCE here (Start at approx. 26:00): https://www.thetalkingmachines.com/episodes/explainability-and-inexplicable
Been KIM is a research scientist at the Google Brain team and is interested in designing machine learning methods that make sense to humans. Her current focus is building interpretability methods for already-trained models (e.g., high performance neural networks). In particular, she believes that the language of explanations should include higher-level, human-friendly concepts. Been gave a tutorial on explainable AI at ICML 2017 and recently the group published the paper: Menaka Narayanan, Emily Chen, Jeffrey He, Been Kim, Sam Gershman & Finale Doshi-Velez 2018. How do Humans Understand Explanations from Machine Learning Systems? An Evaluation of the Human-Interpretability of Explanation. arXiv:1802.00682.