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Lecture Session Invitation: Machine Learning and AI in Biomedicine

Lecture Session Invitation:
Machine Learning and AI in Biomedicine

(Due to overwhelming responses, registration for the session is now closed.)

Professor Vladimir Brusic, Griffith University, Queensland, Australia

 

Date: 22 December 2017
Time: 6.00 pm – 7.00 pm
Location: Charles Babbage Room,
National Supercomputer Centre, Singapore, 1 Fusionopolis Way, #17-01 Connexis South

Abstract

The World’s total data is currently doubling every two years. This data expansion includes not only the
growth in quantity, but also in complexity and the types of data. The enormous rate of generation and online
access to data is profoundly changing the way how health business and biomedical research is
conducted. Biomedical data include R&D data, clinical data, activity and cost data, patient behavior data,
basic science data, and standards and ontologies, among others. Big Data approaches are increasingly
needed for utilization of results from various Omics studies and their translation into clinical practice.
These applications include predictive and content analytics for a variety of applications that support drug
discovery and optimization, the development of new diagnostic methods, and personalization of
medicine. Biomedical data vary in granularity, quality, dimensionality and complexity. There is a variety
of sources and data formats – web pages, publications, technical reports, images and graphs, tables, and
databases. The challenge is to make the transition from data to actionable knowledge. An emerging area
is the use of knowledge-based approaches for Big Data analytics whereby well-annotated data are
combined with specialized analytical tools and integrated into analytical workflows. A set of well-defined
workflow types with rich summarization and visualization capacity facilitates the transformation from
data to critical information and knowledge that enable understanding, decision making, and selection of
actions for solving various problems. Statistical and artificial intelligence methods are used as analytical
engines to make sense of rich datasets. The emerging Big Data requires dynamic integration of
standardized data into knowledge bases to make selected data sources accessible through integration
with the analytical tools. We will demonstrate the utilization of Big Data Analytics, mathematical
modeling, and artificial intelligence tools as well as challenges with two distinct examples: diagnosis of
endometriosis, and design of universal multivalent vaccines.

Biographical sketch

Dr. Brusic is a Professor at Menzies Health Institute Queensland, Griffith University, Australia. He is an
Adjunct Professor of Computer Science at the Metropolitan College, Boston University, USA and a Visiting
Professor at Kumamoto University, Japan. Dr Brusic holds BEng (Mechanical Engineering), MEng
(Biomedical Engineering), MAppSci (Info Tech), MBA, and PhD degrees. He holds a Honorary Doctorate in
Medicine from Semmelweis Medical University, Budapest, Hungary.
His previous positions include faculty or PI appointments at Harvard Medical School (Boston, USA),
University of Queensland (Brisbane, Australia), National University of Singapore, Nanyang Technological
University (Singapore), Institute for Infocomm Research (Singapore), and Walter and Eliza Hall Institute
for Medical Research (Melbourne, Australia). Dr Brusic is an Associate Editor of Frontiers in Immmunology
and an Editor of Briefings in Bioinformatics. He has published more than 200 scientific publications and
two patents. His work has attracted 12,000 citations and h-index of 47. The list of publications can be
found here: https://goo.gl/qRSmQe
His work is in the fields of Bioinformatics and Medical Informatics in immunology, cancer, medical
diagnostics, and modeling of biological systems. His research interests span the fields of Big Data analytics,
Biological Databases, computational modeling of biological systems, simulation of molecular interactions,
and biological discovery using simulation of laboratory experiments. He has developed knowledge-based
systems for biological data mining and knowledge discovery. Recently, Dr. Brusic has been developing a
new field of elemental metabolomics that focuses on the study of elements in biological and
environmental samples, transfer of elements along the food chain and environmental exposure, and their
effects on human health.

 

Jointly organized with:

NSCC Signs MoU with RiST

On 20 June 2016, the Research Organization for Information Science and Technology (RIST) and the National Supercomputing Centre Singapore (NSCC) signed a Memorandum of Understanding (MOU) expressing interest to conduct bilateral exchange of information.

RIST is a Japanese non-profit public-service organisation working for the development and utilisation of computational science and technology to support highly information-oriented societies. It currently oversees the awarding process of K computer general use category project proposals, High Performance Computing Infrastructure (HPCI) system project proposals and user services and technical support.

In accordance with the MOU, RIST and NSCC will schedule regular meetings for the exchange of information between both organisations on activities relating to the areas of:

  1. promotion of shared use of supercomputers,
  2. supercomputer user support and human resource development, and
  3. exploring the possibility of co-operation related to these activities.

Through these activities, both organisations aim to contribute to the HPC community in each country as well as collaboration between two communities.

NSCC-RIST

20 June 2016

At ISC2016 Supercomputing Conference in Frankfurt

A/Prof. Tan Tin Wee, Director, NSCC (left)

Dr. Motoi Okuda, Deputy Head of Kobe center, RIST (right)

Post-Alpha Testbed Town Hall Meetings

CAD-IT ANSYS Convergence 2016DSC_0177NSCC is organising a series of town hall meetings as a follow-up to the Alpha Testbed. We will update the users of the status and explain the changes to be implemented post Alpha Testbed. We will also seek input from our users based on their experience with the Alpha Testbed. All users are encouraged to participate in the meeting near you.

Date/Time Location
Tue Jun14 10:00 AM Fusionopolis, MPH 2, Level 1, Tower A, Innovis
Tue Jun14 2:00 PM NTU, SPMS COMP LAB 1 (SPMS-MAS-03-02)
Wed Jun15 10:00 AM Biopolis, Creation Theatre, Level 4, Matrix
Wed Jun15 2:00 PM NUS, CIT Auditorium, L2 Computer Centre

Workshop: Optimisation Techniques, May 25, A*STAR

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Optimisation Techniques

Part 1. General Overview

  • Optimization process: guidance, tips and tricks
  • How to decide which optimization techniques to focus on
  • Performance characteristics of the Haswell architecture

Part 2. Compiler optimization

  • Optimization Flags
  • OpenMP compilation
  • Optimized libraries
  • Precision and reproducibility
  • Options for correctness checking and debugging
  • Options for source code optimization reports (Intel compiler)
  • Hands-on session

Part 3. MPI optimization

  • Gathering communication statistics
  • Improving MPI communication
  • Process & Thread placement
  • Hands-on session

Part 4. Advanced topics

  • Profile guided optimization (Intel compiler)
  • Auto-parallelization (Intel compiler)
  • Hands-on session

This workshop is fully subscribed. Details can be found on the Workshop website.

Workshop: Introductory Class, May 16, 2016, A*STAR

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Introductory Class

Part 1. Introduction

  • Introduction to NSCC
  • About HPC
  • More about NSCC HPC cluster
  • PBS Pro (Scheduler)
  • Compilers and Libraries
  • Developer Tools
  • Co-processor / Accelerators
  • Environment Modules
  • Applications
  • NSCC helpdesk/support
  • Q&A

Part 2. Understanding basic operation (Hands-on)

  • User Enrollment
  • Login to NSCC Login nodes
  • Using Compute manager interface
  • Transfer files
  • Creating PBS Job submission script
  • Load environment module
  • Compiling simple C Program
  • Create job submission script and submit job
  • Create job submission script for MPI
  • Submit pre-compiled application job

Please visit Workshop website for more details and registration. 

Singapore GPU Users Group Meeting (May 2016)

[vc_row][vc_column][vc_single_image image=”15611″ img_size=”full”][vc_column_text]Singapore GPU Users Group Meeting (May 2016)

When: Tuesday, May 17, 2016 17:30 to 19:15
Where: Fusionopolis, Connexis South Tower, 1 Fusionopolis Way 138632
ACRC/NSCC headquarter, Level 17, Charles Babbage Room

We have the pleasure to invite you at our regular GPU meeting. We will keep the same informal atmosphere and allow you to interact and exchange ideas with colleagues from different fields.

To register: http://www.meetup.com/Singapore-GPU-Users/events/230511460/

Provisional agenda:

• 17:30 – 18:15  Jianxiong Yin (ROSE Lab, NTU) – Hardware Architecture Considerations for Building Efficient GPU Cluster for Accelerated CNN Training
18:15 – 18:45 Gabriel Noaje (ACRC) – GPU Technology Conference 2016 Review
18:45 – 19:05 Your name  – Your presentation
• 19:05 – 19:15 Q&A, Discussions, Announcements, …

We encourage an open discussion environment, so any input from the members is most welcome. If you would like to share how you are using GPUs in your domain, please contact the organizers to arrange presentation slot for the next meeting. We hope to meet you soon.
For further details, please contact Singapore GPU Users Group Organizer GABRIEL NOAJE.[/vc_column_text][/vc_column][/vc_row]

InnovFest Unbound

[vc_row][vc_column][vc_single_image image=”15601″ img_size=”full” alignment=”center” onclick=”custom_link” link=”https://docs.google.com/forms/d/1Y_C_2yF5oCb-4GAe7GouK9Lgk59JsHydBo6TuiEP-C0/viewform?c=0&w=1″][/vc_column][/vc_row]

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