MPBA PREDICTIVE MODELS

FOR BIOMEDICINE AND ENVIRONMENT

Cesare Furlanello

FBK-ICT /

Complex Data Analytics

Assembling Information:

dynamic dashboards for actionable data analytics

Ack: E. Arbitrio, A. Gobbi, C. Dolci, G. Jurman

NTTS2015 – Special Session on Visualization for Data Dissemination- Bruxelles March 10

MPBA: a Data Science Lab

SCIENTIFIC & TECHNICAL ASSETS • Predictive Models for solving complex problems

on very high-dimensionality/throughput data • Machine learning, Network Analysis

Spatial data and time series, WebGIS, Data Analytics platforms

Complex Data Analytics Research Line (CODA)

Predictive Models (MPBA)

Dynamic processes in complex societies (DPCA)

Mobile and Social Computing (MobS)

Remote Sensing for the Digital Earth (RSDE)

Neuroinformatics Laboratory (NILab)

C. Furlanello – MPBA Mar 2015

Outline

1. Dissemination of data within organizations

2. Platforms for public access and strategic decisions

C. Furlanello – MPBA Mar 2015

Interactive Visualization (experience)

From Graphs to Models

Transfer Learning & Autonomy

3. Personalized data analytics

e.g. Personal Proteomics for Nutrition/Food Quality Crowdsourcing

Data Analytics in strategic marketing

Statistics for Environmental Risk

ACTIONABLE GRAPHICS FOR STRATEGIC MARKETING

FLEXIBLE MULTI-SCALE PLATFORMS

4

DataExpress - Central Strategic Analysis

+ Internal Fidelity Programme Unilife

A SINGLE INTERACTIVE DASHBOARD

for central strategic decision ( > 600 ML

Eur/y)

+ associates’ network (2-15 ML Euro / y)

Predictive Models for marginality

Seasonality / Geographic Analysis / Network

PRODUCT:

CONCEPT:

C. Furlanello – MPBA Mar 2015

C. Furlanello – MPBA Mar 2015

Interactive Biclustering (from bioinformatics)

Samples

Categories Covariates

Interactive target function on selected samples and categories

Interactive list of selected samples

Interactive WebGIS panel

C. Furlanello – MPBA Mar 2015

support data exploration: • Dendrogram structures: click on nodes to select subsamples • Here: cluster on sales, target indicator is incidence

C. Furlanello – MPBA Mar 2015

Integration of several solutions • Javascript: D3js, highcharts, highstock,

sigma.js, heatmap.js, leaflet, inchlib, • R: RJSONIO + ad hoc scripts • PostgreSQL: PLR, PostGIS

C. Furlanello – MPBA Mar 2015

From genomics: managing big taxonomies • “Sunburst” plots • Integrated with time series

C. Furlanello – MPBA Mar 2015

Add-ons for taxonomies • Visualize cascades • Each node can be rooted • Absolute/Relative importance

C. Furlanello – MPBA Mar 2015

Where should interaction features be added?

UXB-Trentino: WebGIS & UXO Risk Map of WWII - Unexploded Aerial Bombs (Civil Defense PAT)

MITRIS-FVG: High res mapping and surveillance of Traffic Risk (

(Reg. Friuli Venezia Giulia)

2002-2014: MPBA WEBGIS PLATFORMS

FAUNATN: Wildlife management & deer crash

monitoring (Forest Dept PAT)

ENVIROCHANGE: Modeling impacts of Climate Change on Alpine Agriculture

(research, dissemination, decision)

CancerAtlas-TN: Oncology Risk associated to environmental factors

MITRIS: High res mapping and surveillance of Traffic Risk (PAT)

IET , 2008-2013

Interface to Economics & Territorial data: a complete integration of the asset of statistical and environmental data of the autonomous province • Serving the reorganization of municipalities • 200 technical users/decision makers trained • System fully transferred to PAT

Official Statistics

Tools for public studies and shared decisions

URBAN PLANNING ENVIRONMENT

PROTEZIONE CIVILE

INDUSTRY ENERGY

Statistical service

ISTAT

HUB-1: Geo data

HUB-2: statistical data

WebGIS IET

IET: Harmonization + Tools

Metadata Geo

Catalogue SLD

Metadata

New data from user

session

Reporting

Graphics

Indicators

SISVSP2012 - Rome

67 indicators • society (22) • economy (21) • environment (4) • Landscape (20)

120 thematisms • Plans current

cartography • Reference to

province or township levels

THE INTERSOS HR-WEBGIS

15

A pilot Open-Source WebGIS platform developed by INTERSOS, with the technical support of FBK and its spin-off MPA Solutions, to support returnee monitoring in West Darfur (Sudan) for the United Nations High Commissioner for Refugees (UNHCR). Similar infrastructures: Chad and Yemen

• Standardization of movement information from the tables (PHP) • Calculation of nearest border points for movt. to Chad border (SQL) • PostGreSQL query [RdbiPgSQL] • >2500 movt. in 2002-2007; total population involved: >1 M

2008-2010

WEBGIS: GAP ANALYTICS

+

PL/R: integration of R functions within

PostgreSQL/PostGIS

Rdbi PgSQL

spatstat

sp grass6

Gap analysis • maps • graphs • indicators • shapefiles

Data

THE PLATFORM

The MITRIS client-server architecture & internal engine + geostatistical indicator functions

Prototype Gap Analysis module: compute and display space-time indicators about gaps

16

access to safe water resources by UNICEF standards

SICURSKIWEB from SKI RESCUE reports

A web/mobile architecture for alpine ski safety

Esecurity EU-SEC project 2013-15

(with eCrime UNITN & Questura di Trento)

A “predictive policing” framework to model the risk of crimes (real and perceived) in Trento.

Framework: WebGIS + database

Support the right to safety

First a FBK project: now funded as a regional infrastructure for 25 Ski-Areas, Ski-School association (1500)

Enabled for Personal Wearable Sensors

Data Analytics for Safety and Security

eSecGIS Structure

eSecDB Criminology in GeoDB

eSecGIS Spatial Data Infrastructure with smart city Big Data

Moduli di data mining predittivo

Algoritmi criminologici

Identification of

Emerging patterns

Predictive Policing

Maps

Report

05

e-0

61

e-0

51

.5e

-05

2e

-05

2.5

e-0

5

with eCrime UNITN & Questura di Trento

C. Furlanello – MPBA Mar 2015

COMPARING CRIMES AND VICTIMIZATION

ENVIRONMENT

Assess the impact of climate change on plant and pathogens dynamic in agriculture at the regional scale (short-term biological, environmental and economic); spatialization and clustering of time series on HPC.

1-3

5-10

10-25

3-5

> 25

Breast cancer

incidence,

RT1999/2002

CANCER ATLAS TRENTINO Georeferenced version of Cancer Registry, in a

WebGIS interface, complete of statistical functions

(e.g. small area analysis) for epidemiology

NanoWebGIS: an open source GeoICT platform for cell image analysis based on spatial features

ENVIRO an innovative web mapping tool to monitor and forecast plant and pests dynamics based on climate data

MPBA Agroecosistemi Sostenibili e Biorisorse

Future IPM in Europe Riva del Garda , 19 Marzo 2013

ENVIRO an innovative web mapping tool to monitor and forecast plant and pests dynamics based on climate data

Some example of questions ENVIRO can answer:

1. What will be the effect of climate on the phenology of the chardonnay?

2. What is the dynamics of risk powdery mildew?

3. What is the influence of climate on copper treatments in organic agriculture and how they will change?

4. How to optimize the monitoring of the territory according risk of new diseases?

5. How to optimize lab analysis in case of risk of mycotoxin contamination of grape?

Model used: (Development and evaluation of a warning model for the optimal use of copper in organic viticulture. Pellegrini et al, 2010)

1. EU normative and restrictions

2. How will it change in the future?

Need for Interactive simulation

Long term decisions R

How will the use of copper change in organic agriculture in the future?

2003

2008

R

2021/2050

2071/2099

R Based on climate change models: how will the use of copper change in organic agriculture in the future?

NEW FRONTIER: BIG DATA FROM PERSONAL PROTEOMICS

27

NEAR INFRARED SPECTROMETRY (NIRS) • Pocket molecular sensor by

Consumer Physics (20g)

• Pledged: $2.7 M of $200K goal

• DLP4500NIR TI MEMS technology also available to open use of NIR for mobile use

Consumer Physics, Israel

Start: 2015

• Partner: OPBG Rome Children Hospital excellence center in clinical proteomics and metabolomics

CROWD-SOURCING IN HEALTH – WELL BEING

QUALITY & SAFETY OF NUTRITION

SCIENTIFIC VALIDATION

Engaging the new colleagues

• WebValley is the FBK summer school for dissemination of interdisciplinary scientific research

• The WebValley formula, since 2001, is to create a team of enthusiast and motivated high school students (18 y) tutored by experienced researchers. The project activities are developed mostly working in groups, in a high-tech lab located in a small Alpine town. ~ 300 students – international from 2011.

• The team accepts a challenge by a top scientist collaborator from Ecology, Biology or Social Sciences, and develops in three weeks a new web-based prototype for data analysis and management.

Young People

Innovative ICT tools

C. Furlanello – MPBA Feb 2015