Held in conjunction with ECML-PKDD 2016
September 19–23, 2016 - Riva del Garda, Italy

1st International Workshop on
Deep Learning for Precision Medicine
Friday, September 23, 2016

Introduction

Deep Learning is expected to have a disruptive impact for functional genomics, with applications of high industrial and ethical relevance in pharmacogenomics and toxicogenomics. Examples in miRNA prediction already demonstrated the potential for deriving implicit features with high predictive accuracy. Following the emerging thread of interest emerged at the NIPS MLCB 2016 workshop, we wish to discuss about the best options for the adoption of deep learning models, both for improved accuracy as well as for better biomedical understanding from identification of patterns from internal features. Questions such as end­to­end modeling from structure to functionality and biological impact as well as architectures for integration of genotype, expression and epigenetics would be of immediate interest for the workshop.

This event is intended to be a one­day workshop within ECML­PKDD 2016 including lectures and discussions on this very timely, pressing and active subject. We aim to create a connection between machine learning experts and leaders in the Precision Medicine initiatives in Europe and the USA. In particular, the workshop aims to link experts from the FDA SEQC2 initiative on Precision Medicine, which will pave the way for defining optimal procedures for the development of actionable drugs that can target phenotype­selected patient groups. We wish to discuss also technical challenges such as working with very large cohorts (e.g. from 60K to 300K subjects In molecular psychiatry studies) that are now amenable for modeling with deep learning. Further, family cohorts will challenge machine learning and bioinformatics experts for new efficient solutions. In summary, both methodological aspects from deep learning, machine learning, information technology, statistics as well as actual applications, pitfalls and (medical) needs are to be featured.

Confirmed Speakers

More speakers will be announced soon!

 
 
Sir Munir Pirmohamed

Sir Munir Pirmohamed

Professor
University of Liverpool

Precision Medicine – current state and urgent needs
 
 
 

Joshua Xu

Joshua Xu

FDA SEQC Core Member
US Food and Drug Administration

Sequencing data quality control project phase 2 (SEQC2): a new FDA-led consortium effort to advance precision medicine
 

 
 
Djork-Arne' Clevert

Djork−Arné Clevert

Bayer HealthCare AG​ (Pharmacogenomics applications)

Rectified Factor Networks for Learning Sparse Representations in Pharmacogenomics
 

Abraham Heifets

Abraham Heifets

Atomwise, Inc.
 

AtomNet: A Deep Convolutional Neural Network for Bioactivity Prediction in Structure-based Drug Discovery
 

Workshop Time Table

Morning Sessions: 10:00 – 13:45
10:00 Cesare Furlanello – DLPM2016 OpeningFBK Trento
10:10 Bertram Müller–Myhsok – Machine Learning, Deep Learning and Precision MedicineMax Planck Institute of Psychiatry and University of Liverpool
10:40 Invited talk: Munir Pirmohamed – Precision Medicine – current state and urgent needsUniversity of Liverpool
11:20 Coffee Break
11:40 Invited talk: Joshua Xu – Sequencing data quality control project phase 2 (SEQC2): a new FDA-led consortium effort to advance precision medicineUS Food and Drug Administration
12:20 Invited talk: Abraham Heifets – AtomNet: A Deep Convolutional Neural Network for Bioactivity Prediction in Structure–based Drug DiscoveryAtomwise Inc [abstract]
13:00 Poster talk 1: Gurpreet Ghattaoraya – Opportunities to Implement Deep Learning within the Field of Immune–Mediated Adverse Drug ReactionsUniversity of Liverpool [abstract]
13:10 Contributed talk: Pavel Kisilev – Medical image captioning: learning to describe medical image findings using multi–task–loss CNNIBM Haifa [paper]
13:30 Lunch Break
Afternoon Sessions: 14:40 – 18.20
14:40 Invited talk: Djork–Arné Clevert – Rectified Factor Networks for Learning Sparse Representations in PharmacogenomicsBayer HealthCare AG​
15:20 Invited talk: Kristel van Steen – Steering between holistic and reductionist approaches to tackle modern problems in the omics eraGIGA–R Medical Genomics, University of Liège, Liège, Belgium [abstract]
16:00 Contributed talk: Cristóbal Esteban – Combining Static and Dynamic Information for Clinical Event PredictionSiemens München
16:20 Coffee Break
16:40 Poster talk 2: Calogero Zarbo – Integrating Deep Learning with the SEQC Data Analysis Plan for predictive biomarkers of Clinical Endpoints in NeuroblastomaFBK Trento [abstract]
16:50 Invited Talk: Gunnar Raetsch – Drugs, Patients and Mutations: Data Science Approaches for OncologyDept. of Computer Science, ETH Zürich, Zürich,Switzerland and Memorial Sloan Kettering Cancer Center, New York, USA
17:30 Closing discussion – Coordinators: Enrico DomeniciCentre for Integrative Biology, Trento & C. FurlanelloFBK Trento & Bertram Müller−Myhsok​University of Liverpool, Liverpool, UK / Max Planck Institute of Psychiatry, Munich, Germany
  Wine & Cheese
18:25 End
 

COMMITTEE

 
 
 
  • Kristel van Steen, GIGA, ​Liege, Belgium
  • Andrew Morris,​ University of Liverpool, Liverpool, UK
  • Ana Alfirevic,​ University of Liverpool, Liverpool, UK
  • Fabian Theis, Institute of Computational Biology, Helmholtz Centre Munich, Germany
  • Nico Pfeifer,​ Max­Planck Institute for Informatics, Saarbrücken, Germany
  • Enza Colonna, Istituto ​ di Genetica e Biofisica "Adriano Buzzati­Traverso", CNR, Naples, Italy
  • Erik Garrison,​ Wellcome Trust Sanger Institute, UK
  • Djork−Arné Clevert, Bayer HealthCare AG
  • Leming Shi, School of Pharmacy and School of Life Sciences, Fudan University, Shanghai, China
  • Sepp Hochreiter, Johannes Kepler University Linz, Linz, Austria
  • Sir Munir Pirmohamed,​ University of Liverpool, Liverpool, UK
  • Elisabetta Manduchi, Institute for Biomedical Informatics (IBI), Computational Genetics Laboratory (CGL), UPenn









Workshop Organizers

 
 
 
 
Cesare Furlanello

Cesare Furlanello

Fondazione Bruno Kessler
Trento, Italy

Bertram Müller­Myhsok

Bertram Müller−Myhsok​

​University of Liverpool
Liverpool, UK
Max Planck Institute of Psychiatry
Munich, Germany

 
 
 
 
Giuseppe Jurman

Giuseppe Jurman

Fondazione Bruno Kessler
Trento, Italy

Marco Chierici

Marco Chierici

Fondazione Bruno Kessler
Trento, Italy

Djork­Arné Clevert

Djork−Arné Clevert

Bayer HealthCare AG​ (Pharmacogenomics applications)