Call for Papers: Open Data for Discovery Science (due to July, 31, 2017)

The Journal BMC Medical Informatics and Decision Making (SCI IF (2015): 2,042)
invites to submit to a new thematic series on open data for discovery science

https://bmcmedinformdecismak.biomedcentral.com/articles/collections/odds

Note: Excellent submissions to the IFIP Cross Domain Conference on Machine Learning and Knowledge Discovery (CD-MAKE), (Submission due to May, 15, 2017) relevant to the topics described below, will be invited to expand their work into this thematic series:
The use of open data for discovery science has gained much attention recently as its full potential is unfolding and being explored in projects spanning all areas of healthcare research. A plethora of data sets are now available thanks to drives to make data universally accessible and usable for discovery science. However, with these advances come inherent challenges with the processing and management of ever expanding data sources. The computational and informatics tools and methods currently used in most investigational settings are often labor intensive and rely upon technologies that have not been designed to scale and support reasoning across multi-dimensional data resources. In addition, there are many challenges associated with the storage and responsible use of open data, particularly medical data, such as privacy, data protection, safety, information security and fair use of the data. There are therefore significant demands from the research community for the development of data management and analytic tools supporting heterogeneous analytic workflows and open data sources. Effective anonymisation tools are also of paramount importance to protect data security whilst preserving the usability of the data.

The purpose of this thematic series is to bring together articles reporting advances in the use of open data including the following:

  • The development of tools and methods targeting the reproducible and rigorous use of open data for discovery science, including but not limited to: syntactic and semantic standards, platforms for data sharing and discovery, and computational workflow orchestration technologies that enable the creation of data analytics, machine learning and knowledge extraction pipelines.
  • Practical approaches for the automated and/or semi-automated harmonization, integration, analysis, and presentation of data products to enable hypothesis discovery or testing.
  • Theoretical and practical approaches for solutions to make use of interactive machine learning to put a human-in-the-loop, answering questions including: could human intelligence lead to general heuristics that we can use to improve heuristics?
  • Frameworks for the application of open data in hypothesis generation and testing in projects spanning translational, clinical, and population health research.
  • Applied studies that demonstrate the value of using open data either as a primary or as an enriching source of information for the purposes of hypothesis generation/testing or for data-driven decision making in the research, clinical, and/or population health environments.
  • Privacy preserving machine learning and knowledge extraction algorithms that can enable the sharing of previously “privileged” data types as open data.
  • Evaluation and benchmarking methodologies, methods and tools that can be used to demonstrate the impact of results generated through the primary or secondary use of open data.
  • Socio-cultural, usability, acceptance, ethical and policy issues and frameworks relevant to the sharing, use, and dissemination of information and knowledge derived from the analysis of open data.

Submission is open to everyone, and all submitted manuscripts will be peer-reviewed through the standard BMC Medical Informatics and Decision Making review process. Manuscripts should be formatted according to the submission guidelines and submitted via the online submission system. Please indicate clearly in the covering letter that the manuscript is to be considered for the ‘Open data for discovery science’ collection. The deadline for submissions will be 31 July 2017.

For further information, please email the editors of the thematic series:
Andreas HOLZINGER a.holzinger@hci-kdd.org,
Philip PAYNE prpayne@wustl.edu ,or the BMC in-house editor
Emma COOKSON at emma.cookson@biomedcentral.com

Link to the IFIP Cross-Domain Conference on Machine Learning and Knowledge Extraction (CD-MAKE):
https://cd-make.net

Federated Collaborative Machine Learning

The Google Research Group [1] is always doing awesome stuff, the most recent one is on Federated Learning [2], which enables e.g. smart phones (of course any computational device, and maybe later all internet-of-things, intelligent sensors in either smart hospitals or in smart factories etc.) to collaboratively learn a shared representation model, whilst keeping all the training data on the local devices, decoupling the ability to do machine learning from the need to store the data centralized in the cloud. This goes beyond the use of local models that make predictions on mobile devices (like the Mobile Vision API and On-Device Smart Reply) by bringing model training to the device as well – which is great. The problem with standard approaches is that you always need centralized training data – either on your USB-stick, as the medical doctors do, or in a sophisticated centralized data center.

The basic idea is that the mobile device downloads the current modela and subsequently improves it by learning from data on the respective device, and then summarizes the changes as a small focused update. The remarkable detail is that only this update to the model is sent to the cloud (yes, here privacy, data protection safety and security is challenged see e.g. [3] – but this is much easier to do with this small data – as when you would do it with the raw data – think for example on patient data), where it is immediately averaged with other devicer updates to improve the shared model. All the training data remains on the local devices, and no individual updates are stored in the cloud.

The Google Group recently solved a lot of algorithmic and technical challenges. In a typical machine learning system, an optimization algorithm e.g. Stochastic Gradient Descent (SGD) [4] runs on a large dataset partitioned homogeneously across servers in the cloud. Such highly iterative algorithms require low-latency, high-throughput connections to the training data. But in the Federated Learning setting, the data is distributed across millions of devices in a highly uneven fashion. In addition, these devices have significantly higher-latency, lower-throughput connections and are only intermittently available for training.

This calls for a lot of further investigations with interactive Machine Learning (iML) bringing the human-into-the loop, i.e. making use of human cognitive abilities. This can be of particular interest to solve problems, where learning algorithms suffer due to insufficient training samples (rare events, single events), where we deal with complex data and/or computationally hard problems. For example, “doctors-in-the-loop” can help with their long-term experience and heursitic knowledge to solve problems which otherwise would remain NP-hard [5, 6]. A further step is with many humans-in-the-loop: Such collaborative interactive Machine Learning (ciML) can help in many application areas and domains, e.g. in in health informatics (smart hospital) or in industrial applications (smart factory) [7].

Read the original article, posted on April, 6, 2017,  here:
https://research.googleblog.com/2017/04/federated-learning-collaborative.html

[1] https://research.googleblog.com

[2] NIPS Workshop on Private Multi-Party Machine Learning, Barcelona, December, 9, 2016, https://pmpml.github.io/PMPML16/

[3] Bonawitz, K., Ivanov, V., Kreuter, B., Marcedone, A., Mcmahan, H. B., Patel, S., Ramage, D., Segal, A. & Seth, K. 2016. Practical Secure Aggregation for Federated Learning on User-Held Data. arXiv preprint arXiv:1611.04482.

[4] Bottou, L. 2010. Large-scale machine learning with stochastic gradient descent. Proceedings of COMPSTAT’2010. Springer, pp. 177-186. doi:10.1007/978-3-7908-2604-3_16  (N.B.: 836 citations as of 08.04.2017)

[5] Holzinger, A. 2016. Interactive Machine Learning for Health Informatics: When do we need the human-in-the-loop? Brain Informatics, 3, (2), 119-131, doi:10.1007/s40708-016-0042-6

[6] Holzinger, A., Plass, M., Holzinger, K., Crisan, G., Pintea, C. & Palade, V. 2016. Towards interactive Machine Learning (iML): Applying Ant Colony Algorithms to solve the Traveling Salesman Problem with the Human-in-the-Loop approach. In: Springer Lecture Notes in Computer Science LNCS 9817. Heidelberg, Berlin, New York: Springer, pp. 81-95, [pdf]

[7] Robert, S., Büttner, S., Röcker, C. & Holzinger, A. 2016. Reasoning Under Uncertainty: Towards Collaborative Interactive Machine Learning. In: Machine Learning for Health Informatics: Lecture Notes in Artifical Intelligence LNAI 9605. Springer, pp. 357-376, [pdf]

Image source: https://research.googleblog.com/2017/04/federated-learning-collaborative.html

 

Integrated interactomes and pathways in precision medicine by Igor Jurisica, Toronto

Machine learning is the fastest growing field in computer science, and Health Informatics is amongst the greatest application challenges, providing benefits in improved medical diagnoses, disease analyses, and pharmaceutical development – towards future precision medicine.

Talk announcement: Friday, 12th May, 2017, 10:00, Seminaraum 137, Parterre, Inffeldgasse 16c

Integrated interactomes and pathways in precision medicine

by Igor Jurisica, University of Toronto and Princess Margaret Cancer Center Toronto

Abstract: Fathoming cancer and other complex disease development processes requires systematically integrating diverse types of information, including multiple high-throughput datasets and diverse annotations. This comprehensive and integrative analysis will lead to data-driven precision medicine, and in turn will help us to develop new hypotheses, and answer complex questions such as what factors cause disease; which patients are at high risk; will patients respond to a given treatment; how to rationally select a combination therapy to individual patient, etc.
Thousands of potentially important proteins remain poorly characterized. Computational biology methods, including machine learning, knowledge extraction, data mining and visualization, can help to fill this gap with accurate predictions, making disease modeling more comprehensive. Intertwining computational prediction and modeling with biological experiments will lead to more useful findings faster and more economically.

Short Bio: Igor Jurisica is Tier I Canada Research Chair in Integrative Cancer Informatics, Senior Scientist at Princess Margaret Cancer Centre, Professor at University of Toronto and Visiting Scientist at IBM CAS. He is also an Adjunct Professor at the School of Computing, Pathology and Molecular Medicine at Queen’s University, Computer Science at York University, scientist at the Institute of Neuroimmunology, Slovak Academy of Sciences and an Honorary Professor at Shanghai Jiao Tong University in China. Since 2015, he has also served as Chief Scientist at the Creative Destruction Lab, Rotman School of Management. Igor has published extensively on data mining, visualization and cancer informatics, including multiple papers in Science, Nature, Nature Medicine, Nature Methods, Journal of Clinical Oncology, and received over 9,960 citations since 2012. He has been included in Thomson Reuters 2016, 2015 & 2014 list of Highly Cited Researchers, and The World’s Most Influential Scientific Minds: 2015 & 2014 Reports.

Jurisica Lab, IBM Life Sciences Discovery Center: http://www.cs.toronto.edu/~juris/

Canada Tier I Research Chair: http://www.chairs-chaires.gc.ca/chairholders-titulaires/profile-eng.aspx?profileId=2347

On Nutrigenomics [1]: http://www.uhn.ca/corporate/News/Pages/Igor_Jurisica_talks_nutrigenomics.aspx

[1] Nutrigenomics tries to define the causality or relationship between specific nutrients and specific nutrient regimes (diets) on human health. The underlying idea is in personalized nutrition based on the *omics background, which may help to foster personal dietrary recommendations. Ultimately, nutrigenomics will allow effective dietary-intervention strategies to recover normal homeostasis and to prevent diet-related diseases, see: Muller, M. & Kersten, S. 2003. Nutrigenomics: goals and strategies. Nature Reviews Genetics, 4, (4), 315-322.

What is machine learning?

Many services of our every day life rely meanwhile on machine learning – a field of science and a powerful technology that allows machines to learn from data; a very nice info graphic by the Royal Society – interactive with a quiz – can be found here:

Royal Society Infographic “What is machine learning?”

This is part of a info campaign about machine learning from the Royal Society:

https://royalsociety.org/topics-policy/projects/machine-learning/

The Royal Society was formed by a group of natural scientists influenced by Francis Bacon (1561-1626).  The first ‘learned society’ meeting on 28 November 1660 followed a lecture at Gresham College by Christopher Wren. Joined by Robert Boyle and John Wilkins and others, the group received royal approval by King Charles II (1630-1685) in 1663 and was known since as ‘The Royal Society of London for Improving Natural Knowledge’.

Machine Learning Guide

An excellent podcast which I can fully recommend to my students is the Machine Learning Guide by Tyler RENELLE (Tensor Flow). This series aims to teach the high level fundamentals of machine learning with a focus on algorithms and some underlying mathematics, which is really great.

http://ocdevel.com/podcasts/machine-learning

 

 

 

CD-MAKE machine learning and knowledge extraction

Cross Domain Conference for Machine Learning & Knowledge Extraction

cd-make.net

Call for Papers – due to May, 15, 2017

http://www.wikicfp.com/cfp/servlet/event.showcfp?eventid=61244&copyownerid=17803

Call for Papers due to May, 15, 2017

International IFIP Cross Domain Conference for Machine Learning & Knowledge Extraction CD-MAKE
in Reggio di Calabria (Italy) August 29 – September 1, 2017

https://cd-make.net

CD stands for Cross-Domain and means the integration and appraisal of different fields and application domains (e.g. Health, Industry 4.0, etc.) to provide an atmosphere to foster different perspectives and opinions. The conference is dedicated to offer an international platform for novel ideas and a fresh look on the methodologies to put crazy ideas into Business for the benefit of the human. Serendipity is a desired effect, and shall cross-fertilize methodologies and transfer of algorithmic developments.

MAKE stands for MAchine Learning & Knowledge Extraction.

CD-MAKE is a joint effort of IFIP TC 5, IFIP WG 8.4, IFIP WG 8.9 and IFIP WG 12.9 and is held in conjunction with the International Conference on Availability, Reliability and Security (ARES).
Keynote Speakers are Neil D. LAWRENCE (Amazon) and Marta MILO (University of Sheffield).

IFIP is the International Federation for Information Processing and the leading multi-national, non-governmental, apolitical organization in Information & Communications Technologies and Computer Sciences, is recognized by the United Nations and was established in the year 1960 under the auspices of the UNESCO as an outcome of the first World Computer Congress held in Paris in 1959.

Papers are sought from the following seven topical areas (see image below). Papers which deal with fundamental questions and theoretical aspects in machine learning are very welcome.

❶ Data science (data fusion, preprocessing, data mapping, knowledge representation),
❷ Machine learning (both automatic ML and interactive ML with the human-in-the-loop),
❸ Graphs/network science (i.e. graph-based data mining),
❹ Topological data analysis (i.e. topology data mining),
❺ Time/entropy (i.e. entropy-based data mining),
❻ Data visualization (i.e. visual analytics), and last but not least
❼ Privacy, data protection, safety and security (i.e. privacy aware machine learning).

Proposals for Workshops, Special Sessions, Tutorials: April, 19, 2017
Submission Deadline: May, 15, 2017
Author Notification: June, 14, 2017
Camera Ready Deadline: July, 07, 2017

 

 https://cd-make.net/call-for-papers

 

Stan: A probabilistic programming language

A long time ago submitted paper from the Stan developers
http://mc-stan.org/
has finally been appeared at the Journal of statistical software:
https://www.jstatsoft.org

Carpenter, B., Gelman, A., Hoffman, M., Lee, D., Goodrich, B., Betancourt, M., Brubaker, M. A., Guo, J., Li, P. & Riddell, A. 2017. Stan: A probabilistic programming language. Journal of Statistical Software, 76, (1), 1-32, doi:10.18637/jss.v076.i01

Also the Python package can be downloaded from the site!

Stan is a probabilistic programming language for specifying statistical models. A Stan program imperatively defines a log probability function over parameters conditioned on specified data and constants. Stan provides full Bayesian inference
for continuous-variable models through Markov chain Monte Carlo methods such as the No-U-Turn sampler, an adaptive form of Hamiltonian Monte Carlo sampling. Penalized maximum likelihood estimates are calculated using optimization methods such as the limited memory Broyden-Fletcher-Goldfarb-Shanno algorithm. Stan is also a platform for computing log densities and their gradients and Hessians, which can be used in alternative algorithms such as variational Bayes, expectation propagation, and marginal inference using approximate integration. To this end, Stan is set up so that the densities, gradients, and Hessians, along with intermediate quantities of the algorithm such as acceptance probabilities, are easily accessible. Stan can be called from the command line using the cmdstan package, through R using the rstan package, and through Python using the pystan package. All three interfaces support sampling and optimization-based inference with diagnostics and posterior analysis. rstan and pystan also provide access to log probabilities, gradients, Hessians, parameter transforms, and specialized plotting.

Congratulations from the Holzinger Group to the authors!

Machine Learning Podcast: Data Skeptic (recommendable)

Data Skeptic is a weekly podcast that is skeptical of and with data. They explain methods and algorithms that power our world in an accessible manner through short mini-episode discussions and longer interviews with experts in the field, see:

http://dataskeptic.com

 

Call for Papers – Privacy Aware Machine Learning PAML due to April, 1, 2017

Privacy Aware Machine Learning (PAML)
for Health Data Science

Special Session on September, 1, 2017, organized by Andreas HOLZINGER, Peter KIESEBERG, Edgar WEIPPL and A Min TJOA in the context of the 12th International Conference on Availability, Reliability and Security (ARES and CD-ARES), Reggio di Calabria, Italy, August 29 – September, 2, 2017

Session Homepage

supported by the International Federation of Information Processing IFIP >  TC5 and WG 8.4 and WG 8.9
http://cd-ares-conference.eu
http://www.ares-conference.eu

Keynote Talk by Neil D. LAWRENCE, University of Sheffield and Amazon

With the new European data protection and privacy regulations coming into effect with January, 1, 2018 issues having been nice to have so far are becoming a must have. Privacy aware machine learning will be one of the most important fields for the European research community and the IT business in particular. Most affected is the whole area of biology, medicine and health, partiuclarly driven by the fact that health sciences are becoming a more and more data intensive science.

This special session will bring together scientists with diverse background, interested in both the underlying theoretical principles as well as the application of such methods for practical use in the biomedical, life sciences and health care domain. The cross-domain integration and appraisal of different fields will provide an atmosphere to foster different perspectives and opinions; it will offer a platform for novel crazy ideas and a fresh look on the methodologies to put these ideas into business.

All paper will be peer-reviewed by three members of the international PAML-commitee. Paper acceptance rate of the last session was 35 %. Accepted papers will be published in a Springer Lecture Notes in Computer Science (LNCS) Volume and excellent contributions will be invited to be extented in a special issue of a journal (planned Springer MACH and/or BMC MIDM).

Research topics covered by this special session include but are not limited to the following topics:

– Production of Open Data Sets
– Synthetic data sets for learning algorithm testing
– Privacy preserving machine learning, data mining and knowledge discovery
– Data leak detection
– Data citation
– Differential privacy
– Anonymization and pseudonymization
– Securing expert-in-the-loop machine learning systems
– Evaluation and benchmarking

This picture was taken by our local host, Francesco Buccafurri on January, 3, 2017: from the conference venue you have a direct view to the Aetna volcano:

Picture taken by Francesco Buccafurri on January, 3, 2017

Picture taken by Francesco Buccafurri on January, 3, 2017

3,2 Trillion USD on health per year

The U.S. spends more on health care than any other country

Dieleman et al. (2016) just (Dec, 27, 2016) published a paper [1] which discusses data from the National Health Expenditure Accounts to estimate US spending on personal health care and public health, according to condition, age and sex group, and type of care. This paper was mentioned in the Washington Post by Carolyn Y. Johnson on December 27 at 11:00 AM

Here a link to the original paper:

[1] Dieleman JL, Baral R, Birger M, Bui AL, Bulchis A, Chapin A, Hamavid H, Horst C, Johnson EK, Joseph J, Lavado R, Lomsadze L, Reynolds A, Squires E, Campbell M, DeCenso B, Dicker D, Flaxman AD, Gabert R, Highfill T, Naghavi M, Nightingale N, Templin T, Tobias MI, Vos T, Murray CJL. US Spending on Personal Health Care and Public Health, 1996-2013. JAMA. 2016;316(24):2627-2646. doi:10.1001/jama.2016.16885

Here the article (shortened) from the Washington Post:

American health-care spending, measured in trillions of dollars, boggles the mind. Last year, we spent $3.2 trillion on health care  a number so large that it can be difficult to grasp its scale.

A new study published in the Journal of the American Medical Association reveals what patients and their insurers are spending that money on, breaking it down by 155 diseases, patient age and category — such as pharmaceuticals or hospitalizations. Among its findings:

  • Chronic — and often preventable — diseases are a huge driver of personal health spending. The three most expensive diseases in 2013: diabetes ($101 billion), the most common form of heart disease ($88 billion) and back and neck pain ($88 billion).
  • Yearly spending increases aren’t uniform: Over a nearly two-decade period, diabetes and low back and neck pain grew at more than 6 percent per year — much faster than overall spending. Meanwhile, heart disease spending grew at 0.2 percent.
  • Medical spending increases with age — with the exception of newborns. About 38 percent of personal health spending in 2013 was for people over age 65. Annual spending for girls between 1 and 4 years old averaged $2,000 per person; older women 70 to 74 years old averaged $16,000.

Here the link to the original article:
https://www.washingtonpost.com/news/wonk/wp/2016/12/27/the-u-s-spends-more-on-health-care-than-any-other-country-heres-what-were-buying/?tid=pm_business_pop&utm_term=.71fc517cdc11