Orientation in Informatics

Dr Katy Wolstencroft

LIACS, Sept 13 2016

Orientation

Studying computer science

Studying computer science @ LIACS

Studying computer science as a science

Computer science in industry and business

Computer science in society

Course content

Classes

Lectures, guest lectures, workshops

13:45-15:30 Tuesday

Class website for details of each class

http://liacs.leidenuniv.nl/~wolstencroftkj/orientation.html

Completing the course

Attendance at lectures/workshops *

Successful completion of assignments

Scientific writing practical and assignment

Report on computer science jobs

Computer science in society – class debate

* Attendance is mandatory

Date Title Class Notes

06-09-2016 No lecture

13-09-2016 Intro to Orientation Lecture

20-09-2016 Scientific Communication Lecture

27-09-2016 Scientific Writing Computer practical

04-10-2016 Computer Science and Biology Lecture Date TBC

11-10-2016 Social Network Analysis Lecture Date TBC

18-10-2016 Computer Science in Society Lecture Date TBC

25-10-2016 No lecture

01-11-2016 Computer Science in Business Lecture LIACS alumni

experiences

08-11-2016 Multimedia Research Lecture

15-11-2016 Data Science: Sports Analytics Lecture

22-11-2016 Computer Science in Healthcare Lecture Date TBC

29-11-2016 Computer Science in Business Lecture Academia/TNO

06-12-2016 Computer Science in Society Class debate Interactive

13-12-2016 No lecture

Timetable

Scientific Writing

Scientific writing workshop

Experience in the conventions and styles of scientific writing

Interpreting results

Visualising results

Assignment 1:

Conduct an experiment and report your findings as a scientific report

Careers in Computer Science

LIACS alumnus returns to share experiences

Lecture from Prof in academia and industry

Assignment 2: comparing CS job opportunities

Computer Science in Society

Lecture from Chair in Computing for Society

Using CS techniques to solve real world problems

Assignment 3:

Where do you stand on topical computer science issues?

Give your opinions and reasons for them

Class discussion on the issue

Outline

Why computer science?

Computer science @LIACS

Leiden

Research areas and topics

Why study computer science?

Problem solving

Identify the problem

Define the context

Explore potential strategies

Take action – select the best strategy

Reflect and evaluate

Did you solve the problem?

If not, why not?

If you did, was it the best way?

Computers are ubiquitous

Source: International Telecommunications Union https://en.wikipedia.org/wiki/History_of_the_Internet CC BY-SA 3.0

Jobs and careers

Out of all STEM jobs, 60% are computing jobs

Out of all STEM students, only 2% are computer scientists

This gap is getting bigger

https://code.org/promote

Creative opportunities

Worth $100 billion in the next 3 years

Computer science in:

Movie production

Sound

Games design

Computational infrastructure for multi-player and real time games

New and Changing Fast

Almost all computer science pioneers did their work in the last 100 years

Many pioneers are still alive and doing research

New and Changing Fast

Almost all computer science pioneers did their work in the last 100 years

Some pioneers are still alive and doing research

Sir Tim Berners-Lee • Internet pioneer • HTTP protocol • World Wide Web

• Director of the W3C – World Wide Web

Consortium and WWW foundation • University of Southampton • MIT

• Favours Net Neutrality • Linked Data/Semantic web - data.gov.uk

What Happens in an Internet Minute

http://blogs.worldbank.org/category/tags/intel

30 hours of video uploaded to YouTube

More than 2 million Google searches

6 million Facebook views

…and much more

Gamification

Reverse the Odds – Cancer Research Game

http://www.cancerresearchuk.org

Help annotate tumour images as part of the game

Data from patients who have already been treated

Data intended for learning

What you need for Citizen Science

1. A critical mass of volunteers

2. A task that is easy to learn and repeat

3. Not too much specialist knowledge

Citizen Science Galaxy Zoo (http://www.galaxyzoo.org) To understand how galaxies formed we need your help to

classify them according to their shapes. If you're quick, you may even be the first person to see the galaxies you're asked to classify

Public domain image https://commons.wikimedia.org/wiki/File:Galaxies_Gone_Wild!.jpg

Computer simulations enable a new kind of science

Computer simulations allow scientists to mathematically model working systems and compute outcomes based on input parameter sets

Public domain image: https://en.wikipedia.org/wiki/Wikipedia:WikiProject_Tropical_cyclones/Tracks

You can make a difference

https://en.wikipedia.org/wiki/Medical_image_computing CC BY-SA 3.0

https://en.wikipedia.org/wiki/Cardiac_monitoring CC BY-SA 2.5

Public domain: https://commons.wikimedia.org/wiki/File:Mapping_Reads.png

Public domain image: https://en.wikipedia.org/wiki/Wikipedia:WikiProject_Tropical_cyclones/Tracks

Studying Computer Science @ LIACS

Leiden University

Leiden University

Oldest in the Netherlands

Founded in February 1575

A gift from William of Orange to the citizens of Leiden who had withstood a long siege by the Spaniards

3 October festival

Commemorates the end of the siege of Leiden 1574

Leiden university holiday

League of European Research Universities

Leiden University

Three Full Professor Nobel prize winners

Many more famous alumni

Leiden University

Three Full Professor Nobel prize winners

1902 Prof.dr. H.A. Lorentz, Physics the influence of magnetism upon radiation phenomena

1913 Prof. dr. H. Kamerlingh Onnes, Physics the properties of matter at low temperatures

1924 Prof. dr. W.H. Einthoven, Medicine for his discovery of the mechanism of the electrocardiogram

Many more famous alumni

1920, Albert Einstein appointed "Bijzonder Hoogleraar" (special professor)

LIACS

Leiden Institute of Advanced Computer Science

Part of the Natural Science Faculty Mathematics, Physics, Astronomy, Chemistry, Biology, Bio-

Pharmaceutical Sciences and Computer Science

Science Faculty Mission

……to carry out excellent research and to provide outstanding undergraduate and postgraduate education

Science Faculty

Faculty head (Dean)

Prof Geert de Snoo

Faculty

Faculty Board

Faculty Council

Institutes:

Management Team (Scientific Director, Director of Education)

Institute Council

LIACS Management Team

Scientific Director Prof Aske Plaat

Professor of Data Science

Education Director Prof Marcello Bonsangue

Theoretical Computing

Managing Director

Annemart Berendse

LIACS Research

Algorithms and Software technology

Data Mining

Natural Computing

Software technology

Software Engineering

Technology and Innovation Management

Theoretical Computer Science

Computer Systems, Imagery and Media

High Performance Computing

Embedded Research Centre

Imaging and Bioinformatics

Media Research

Media Technology

Leiden Centre of Data Science

Algorithms and software technology

Methods and techniques for algorithm design and analysis, with an emphasis on algorithms and architectures for large data volumes as well as on natural computing.

Development of formalisms, methods, techniques and tools to design, analyze, and construct software systems and components.

Data Mining

Natural Computing

Software technology

Software Engineering

Technology and Innovation Management

Theoretical Computer Science

Algorithms and software technology

Data Mining

Finding patterns in data

Secondary analysis of data – data reuse

Algorithms to process and manage large quantities of data

Typical Data Mining Results

Identifying patterns in interaction networks

Identifying events that are likely to occur together

Identification of indicators of future events weather, economics etc

Clustering or classifying things based on their attributes

Patients in healthy or disease state

Social demographics

Studying Networks

http://www.martingrandjean.ch/wp-content/uploads/2013/10/Graphe3.png CC BY-SA 3.0

Studying Networks

http://www.martingrandjean.ch/wp-content/uploads/2013/10/Graphe3.png CC BY-SA 3.0

•Network analysis • The way information spreads • Modelling and Prediction • Privacy

Six Degrees of Separation

Everyone is connected to everyone else by 6 or fewer steps

Friend of a friend chains

Katy Wolstencroft -> Barack Obama

2013 - 3rd Friend of a friend of a friend

2015 – 2nd Friend of a friend!

Natural computing

Natural computing focuses on computational methods inspired by nature and natural systems

Theory and application of evolutionary algorithms - adaptive optimization methods gleaned from the model of organic evolution

Natural Computing Examples

Self-organisation

CC BY 2.0 https://en.wikipedia.org/wiki/Bait_ball

Theoretical Computing

Functional verification and proof of algorithms

E.g. proving that the TimSort algorithm (used in Android, Java and Python) is broken

.....and showing how to fix it

Major bug in TimSort that could crash programs and compromise security

S. de Gouw, F. de Boer, J. Rot: “Proof Pearl: The KeY to Correct and Stable Sorting”, Journal of Autom. Reasoning 53(2), 129-139, 2014

Computer Systems, Imagery and Media

Methods and techniques for the design, implementation and application of advanced computer systems, in particular parallel, distributed and embedded computer systems

Research on methods and techniques for the analysis and synthesis of images, pattern recognition, image fusion, 3D reconstruction and visualization, computer vision, imaging systems, image search, media technology

Research on methods and techniques in bioinformatics for semantic data integration and omics analyses

Computer Systems, Imagery and Media

High Performance Computing

Embedded Research Centre

Imaging and Bioinformatics

Media Research

Media Technology

Embedded Research Centre

Embedded Systems

Computation in devices – printers, cars, medical imaging machines, coffee machines etc

A computer system that exists as part of a larger electronic or mechanical device and often has to manage real-time computing

Low power consumption crucial

Small, robust, cheap

Media Research and Media Technology

Multimedia analysis/understanding, artificial intelligence, deep learning, human computer interaction and internet technologies

Embedding of humans in the computerised world

Human Computer Interaction

Augmented reality

Automatic visual machine learning

Automatically identify objects in images

Deep learning

Michael Lew – Media Lab

http://goliath.liacs.nl:2016/

Imaging and Bioinformatics

3D imaging data

Integration of different types of microscopy data 2D/3D

Image recognition

Automation Sophisticated analysis

pipelines

A set of services to analyse or manage data (either local or remote*, GRID or Cloud)

Data flow through services

Control of service invocation

Iteration

Provenance

* Remote Services = Web services (WSDL/SOAP or REST)

http://taverna.org.uk

Bioinformatics – Semantic Data Integration and Analysis

Bioinformatics – Semantic Data Integration and Analysis

Data Science

Data science

Focus is on extracting added value from data

Understanding the possibilities, limitations and presentation of data

“the sexiest job in the 21st century”

The Digital Age

21st Century = century of information

We have generated more data in the last 2 years than in the whole of human history

http://www.datasciencecentral.com/forum/topics/the-3vs-that-define-big-data

The Three V’s

Volume

Velocity

Variety

Volume

Large Hadron Collider

the collider, 4 detectors and the GRID

15 Petabytes per year, 2 million jobs run every day,

8000 physicists, 40 countries, 170 computing centres, 250000 CPU cores,

Variety

Example: Translational Research IT project

Infrastructure for personalised diagnostics and treatment http://www.esciencecenter.nl/project/trait

Many data types: Clinical research data, biomedical imaging, Biobank samples, gene sequences, gene expression, proteomics, microscopy data

Issues: multimedia, some big data, some small data, heterogeneity, time of validity

Velocity

Recording and analysing sensor data

Continuous information in real-time

Requires real-time analysis to benefit

Infrawatch- Hollandse Brug

Velocity

Infrawatch project – LU and TU Delft

Monitoring the Hollandse Brug

Sensor network: 145 sensors: 5GB/day,8TB/4years

Strain, vibration and temperature sensors

LIACS Research

Algorithms and Software technology

Data Mining

Natural Computing

Software technology

Software Engineering

Technology and Innovation Management

Theoretical Computer Science

Computer Systems, Imagery and Media

High Performance Computing

Embedded Research Centre

Imaging and Bioinformatics

Media Research

Media Technology

Leiden Centre of Data Science Focus on fundamental and Life Science research

What we will discover

Computer science is a broad subject

Computer science is a SCIENCE

Computer science plays a vital role in business and society

Next Week

Lecture: Working in science and scientific communication