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The project has received funding from the European Union’s Horizon 2020 research and innovation programme under grant agreement No 825111.The project has received funding from the European Union’s Horizon 2020 research and innovation programme under grant agreement No 825111.
DeepHealth Needs & Requirements for
Benchmarking
Jon Ander Gómez (Technical Manager) - jon@upv.es
DataBench BenchLearning webinar
July 8th 2020
Deep-Learning and HPC to Boost Biomedical Applications for Health
2
The project has received funding from the European Union’s Horizon 2020 research and innovation programme under grant agreement No 825111.
A Little bit of context
• Healthcare: key sector in the global economy
• Public health systems generate large datasets of biomedical images
• Large unexploited knowledge database
• Interpretation of the clinical expert manually
• R & D on applying Artificial Intelligence (AI) to analyze biomedical images but . .
.
• Need for advanced skills in AI and different technologies and tools
• Expensive processes in time and resources
• Needs of high-quality data and take care of ethics
• HPC and BigData technologies (Big Data, HPC) sufficiently mature and
available.
3
The project has received funding from the European Union’s Horizon 2020 research and innovation programme under grant agreement No 825111.
The scenario
SOFTWARE
PLATFORM
BIOMEDICAL
APPLICATION
Variety of
current libs
tools
Medical image
(CT , MRI , X-Ray,…)
Health professionals
(Doctors & Medical staff)
ICT Expert users
Prediction
Score and/or highlighted
RoI returned to the
doctor
Data used to train
models
Images labelled by doctors
Add validated
images
Production environment Training environment
Samples to be pre-processed and validated
Images pending to
be pre-processed
and validated
4
The project has received funding from the European Union’s Horizon 2020 research and innovation programme under grant agreement No 825111.
About DeepHealth
Aim & Goals
• Put HPC computing power at the service of biomedical applications with DL needs and apply DL
techniques on large and complex image biomedical datasets to support new and more efficient ways of
diagnosis, monitoring and treatment of diseases.
• Facilitate the daily work and increase the productivity of medical personnel and IT professionals in
terms of image processing and the use and training of predictive models without the need of combining
numerous tools.
• Offer a unified framework adapted to exploit underlying heterogeneous HPC and Cloud architectures
supporting state-of-the-art and next-generation Deep Learning (AI) and Computer Vision algorithms to
enhance European-based medical software platforms.
Duration: 36 months
Starting date: Jan 2019
Budget 14.642.366 €
EU funding 12.774.824 €
22 partners from 9 countries:
Research centers, Health organizations,
large industries and SMEs
Research Organisations Health Organisations Large Industries SMEs
Key facts
5
The project has received funding from the European Union’s Horizon 2020 research and innovation programme under grant agreement No 825111.
Developments & Expected Results
• The DeepHealth toolkit
• Free and open-source software: 2 libraries + front-end.
• EDDLL: The European Distributed Deep Learning Library
• ECVL: the European Computer Vision Library
• Ready to run algorithms on Hybrid HPC + Cloud architectures with heterogeneous hardware (Distributed
versions of the training algorithms)
• Ready to be integrated into end-user software platforms or applications
• HPC infrastructure for an efficient execution of the training algorithms which are computational intensive
by making use of heterogeneous hardware in a transparent way
• Seven enhanced biomedical and AI software platforms provided by EVERIS, PHILIPS, THALES,
UNITO, WINGS, CRS4 and CEA that integrate the DeepHealth libraries to improve their potential
• Proposal for a structure for anonymised and pseudonymised data lakes
• Validation in 14 use cases (Neurological diseases, Tumor detection and early cancer prediction, Digital
pathology and automated image annotation).
EU libraries
6
The project has received funding from the European Union’s Horizon 2020 research and innovation programme under grant agreement No 825111.
The Concept
SOFTWARE
PLATFORM
BIOMEDICAL
APPLICATION
Medical image
(CT , MRI , X-Ray,…)
Health professionals
(Doctors & Medical staff)
ICT Expert users
Prediction
Score and/or highlighted
RoI returned to the
doctor
Data used to train
models
Platform uses
the toolkit to
train models
(optional)
Images labelled by doctors
Add validated
images
Production environment Training environment
Using loaded/trained predictive
models
Samples to be pre-processed and validated
Images pending to
be pre-processed
and validated
HPC infrastructure
TOOLKIT
7
The project has received funding from the European Union’s Horizon 2020 research and innovation programme under grant agreement No 825111.
Data & Model Pipelines
Dataset
design
Data
Acquisition
Data
Curation
Persistent
Data
Storage
Data
Partitioning
Data
Augmentation
AI/ML/DL
Model
training
AI/ML/DL
Model
evaluation
Solution
Deployment
Data Pipeline
AI/ML/DL Model Pipeline
Model Pipeline is considered part of the Data Pipeline
Both pipelines are suitable for business and research applications
The whole Data Pipeline is applicable to any sector. Our project is focused on the Health sector
8
The project has received funding from the European Union’s Horizon 2020 research and innovation programme under grant agreement No 825111.
Data & Model Pipelines – Dataset Design
Dataset
design
Data
Acquisition
Data
Curation
Persistent
Data
Storage
Data
Partitioning
Data
Augmentation
AI/ML/DL
Model
training
AI/ML/DL
Model
evaluation
Solution
Deployment
Data Pipeline
AI/ML/DL Model Pipeline
• Data types and formats –identification and definition
• Metadata definition
• Data Lake structure definition
• Guidelines / HOW-TOs
• Etc.
9
The project has received funding from the European Union’s Horizon 2020 research and innovation programme under grant agreement No 825111.
Data & Model Pipelines – Acquisition + Curation + Storage
Dataset
design
Data
Acquisition
Data
Curation
Persistent
Data
Storage
Data
Partitioning
Data
Augmentation
AI/ML/DL
Model
training
AI/ML/DL
Model
evaluation
Solution
Deployment
Data Pipeline
AI/ML/DL Model Pipeline
• Data acquisition continuum
• Data cleansing/cleaning/wrangling/crunching
• Aggregated data/values computation
• Implementation of the data-lake definition
• Creation of users and permissions or make data public
10
The project has received funding from the European Union’s Horizon 2020 research and innovation programme under grant agreement No 825111.
Data & Model Pipelines – Model Pipeline
Dataset
design
Data
Acquisition
Data
Curation
Persistent
Data
Storage
Data
Partitioning
Data
Augmentation
AI/ML/DL
Model
training
AI/ML/DL
Model
evaluation
Solution
Deployment
Data Pipeline
AI/ML/DL Model Pipeline
Model training loop:
• Partitioning in training/validation/test subsets
• Data augmentation on-the-fly
• Training and evaluation of models
• Cloud & High Performance Computing requirements
11
The project has received funding from the European Union’s Horizon 2020 research and innovation programme under grant agreement No 825111.
Needs & Requirements
Evaluate datasets in terms of
1. Findability – where should a data scientist search for the dataset?
2. Availability – how long does a data scientist need to start the initial
exploratory data analysis?
3. Interoperability – how long does a data scientist need to start training
AI/ML/DL models with a dataset?
4. Reusability – are previously obtained results with a dataset public and
available to other researchers / data scientists?
5. Privacy / Anonymisation – can the dataset be made public without
compromising the identity of individuals?
6. Quality – is the dataset biased or unbalanced? What procedure has been
followed to validate annotations?
12
The project has received funding from the European Union’s Horizon 2020 research and innovation programme under grant agreement No 825111.
Needs & Requirements
Evaluate Deep Learning libraries in terms of
1. Speed-up – is distributed learning really efficient?
2. Convergence – does the distributed learning reach the same model
accuracy in less time?
3. Usability – how long does a developer need to use the libraries effectively?
4. Integrability – how difficult is it to integrate the libraries as part of solutions
to deploy?
5. KPIs: time-of-training-models (totm), performance/power/accuracy trade-
off, etc.
6. Others – can you help us to evaluate other aspects?
13
The project has received funding from the European Union’s Horizon 2020 research and innovation programme under grant agreement No 825111.
Needs & Requirements
Evaluate Software Platforms in terms of
1. Usability – how long does a domain application expert need to manage the
software tool effectively?
2. Completeness – does the application platform provide all the
algorithms/procedures/functions to allow domain application experts to
easily define the sequences of steps to implement the data and/or model
pipelines?
3. Compatibility – how many data formats does the platform admits to
import/export data and models from/to other frameworks?
4. KPIs: time-to-model-in-production (ttmip), time-of-pre-processing-images
(toppi), etc.
5. Others – can you help us to evaluate other aspects?
14
The project has received funding from the European Union’s Horizon 2020 research and innovation programme under grant agreement No 825111.The project has received funding from the European Union’s Horizon 2020 research and innovation programme under grant agreement No 825111.
Questions?
@DeepHealthEU
https://deephealth-project.eu
Technical Manager: Jon Ander Gómez jon@upv.es

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Virtual BenchLearning - DeepHealth - Needs & Requirements for Benchmarking

  • 1. 1 The project has received funding from the European Union’s Horizon 2020 research and innovation programme under grant agreement No 825111.The project has received funding from the European Union’s Horizon 2020 research and innovation programme under grant agreement No 825111. DeepHealth Needs & Requirements for Benchmarking Jon Ander Gómez (Technical Manager) - jon@upv.es DataBench BenchLearning webinar July 8th 2020 Deep-Learning and HPC to Boost Biomedical Applications for Health
  • 2. 2 The project has received funding from the European Union’s Horizon 2020 research and innovation programme under grant agreement No 825111. A Little bit of context • Healthcare: key sector in the global economy • Public health systems generate large datasets of biomedical images • Large unexploited knowledge database • Interpretation of the clinical expert manually • R & D on applying Artificial Intelligence (AI) to analyze biomedical images but . . . • Need for advanced skills in AI and different technologies and tools • Expensive processes in time and resources • Needs of high-quality data and take care of ethics • HPC and BigData technologies (Big Data, HPC) sufficiently mature and available.
  • 3. 3 The project has received funding from the European Union’s Horizon 2020 research and innovation programme under grant agreement No 825111. The scenario SOFTWARE PLATFORM BIOMEDICAL APPLICATION Variety of current libs tools Medical image (CT , MRI , X-Ray,…) Health professionals (Doctors & Medical staff) ICT Expert users Prediction Score and/or highlighted RoI returned to the doctor Data used to train models Images labelled by doctors Add validated images Production environment Training environment Samples to be pre-processed and validated Images pending to be pre-processed and validated
  • 4. 4 The project has received funding from the European Union’s Horizon 2020 research and innovation programme under grant agreement No 825111. About DeepHealth Aim & Goals • Put HPC computing power at the service of biomedical applications with DL needs and apply DL techniques on large and complex image biomedical datasets to support new and more efficient ways of diagnosis, monitoring and treatment of diseases. • Facilitate the daily work and increase the productivity of medical personnel and IT professionals in terms of image processing and the use and training of predictive models without the need of combining numerous tools. • Offer a unified framework adapted to exploit underlying heterogeneous HPC and Cloud architectures supporting state-of-the-art and next-generation Deep Learning (AI) and Computer Vision algorithms to enhance European-based medical software platforms. Duration: 36 months Starting date: Jan 2019 Budget 14.642.366 € EU funding 12.774.824 € 22 partners from 9 countries: Research centers, Health organizations, large industries and SMEs Research Organisations Health Organisations Large Industries SMEs Key facts
  • 5. 5 The project has received funding from the European Union’s Horizon 2020 research and innovation programme under grant agreement No 825111. Developments & Expected Results • The DeepHealth toolkit • Free and open-source software: 2 libraries + front-end. • EDDLL: The European Distributed Deep Learning Library • ECVL: the European Computer Vision Library • Ready to run algorithms on Hybrid HPC + Cloud architectures with heterogeneous hardware (Distributed versions of the training algorithms) • Ready to be integrated into end-user software platforms or applications • HPC infrastructure for an efficient execution of the training algorithms which are computational intensive by making use of heterogeneous hardware in a transparent way • Seven enhanced biomedical and AI software platforms provided by EVERIS, PHILIPS, THALES, UNITO, WINGS, CRS4 and CEA that integrate the DeepHealth libraries to improve their potential • Proposal for a structure for anonymised and pseudonymised data lakes • Validation in 14 use cases (Neurological diseases, Tumor detection and early cancer prediction, Digital pathology and automated image annotation). EU libraries
  • 6. 6 The project has received funding from the European Union’s Horizon 2020 research and innovation programme under grant agreement No 825111. The Concept SOFTWARE PLATFORM BIOMEDICAL APPLICATION Medical image (CT , MRI , X-Ray,…) Health professionals (Doctors & Medical staff) ICT Expert users Prediction Score and/or highlighted RoI returned to the doctor Data used to train models Platform uses the toolkit to train models (optional) Images labelled by doctors Add validated images Production environment Training environment Using loaded/trained predictive models Samples to be pre-processed and validated Images pending to be pre-processed and validated HPC infrastructure TOOLKIT
  • 7. 7 The project has received funding from the European Union’s Horizon 2020 research and innovation programme under grant agreement No 825111. Data & Model Pipelines Dataset design Data Acquisition Data Curation Persistent Data Storage Data Partitioning Data Augmentation AI/ML/DL Model training AI/ML/DL Model evaluation Solution Deployment Data Pipeline AI/ML/DL Model Pipeline Model Pipeline is considered part of the Data Pipeline Both pipelines are suitable for business and research applications The whole Data Pipeline is applicable to any sector. Our project is focused on the Health sector
  • 8. 8 The project has received funding from the European Union’s Horizon 2020 research and innovation programme under grant agreement No 825111. Data & Model Pipelines – Dataset Design Dataset design Data Acquisition Data Curation Persistent Data Storage Data Partitioning Data Augmentation AI/ML/DL Model training AI/ML/DL Model evaluation Solution Deployment Data Pipeline AI/ML/DL Model Pipeline • Data types and formats –identification and definition • Metadata definition • Data Lake structure definition • Guidelines / HOW-TOs • Etc.
  • 9. 9 The project has received funding from the European Union’s Horizon 2020 research and innovation programme under grant agreement No 825111. Data & Model Pipelines – Acquisition + Curation + Storage Dataset design Data Acquisition Data Curation Persistent Data Storage Data Partitioning Data Augmentation AI/ML/DL Model training AI/ML/DL Model evaluation Solution Deployment Data Pipeline AI/ML/DL Model Pipeline • Data acquisition continuum • Data cleansing/cleaning/wrangling/crunching • Aggregated data/values computation • Implementation of the data-lake definition • Creation of users and permissions or make data public
  • 10. 10 The project has received funding from the European Union’s Horizon 2020 research and innovation programme under grant agreement No 825111. Data & Model Pipelines – Model Pipeline Dataset design Data Acquisition Data Curation Persistent Data Storage Data Partitioning Data Augmentation AI/ML/DL Model training AI/ML/DL Model evaluation Solution Deployment Data Pipeline AI/ML/DL Model Pipeline Model training loop: • Partitioning in training/validation/test subsets • Data augmentation on-the-fly • Training and evaluation of models • Cloud & High Performance Computing requirements
  • 11. 11 The project has received funding from the European Union’s Horizon 2020 research and innovation programme under grant agreement No 825111. Needs & Requirements Evaluate datasets in terms of 1. Findability – where should a data scientist search for the dataset? 2. Availability – how long does a data scientist need to start the initial exploratory data analysis? 3. Interoperability – how long does a data scientist need to start training AI/ML/DL models with a dataset? 4. Reusability – are previously obtained results with a dataset public and available to other researchers / data scientists? 5. Privacy / Anonymisation – can the dataset be made public without compromising the identity of individuals? 6. Quality – is the dataset biased or unbalanced? What procedure has been followed to validate annotations?
  • 12. 12 The project has received funding from the European Union’s Horizon 2020 research and innovation programme under grant agreement No 825111. Needs & Requirements Evaluate Deep Learning libraries in terms of 1. Speed-up – is distributed learning really efficient? 2. Convergence – does the distributed learning reach the same model accuracy in less time? 3. Usability – how long does a developer need to use the libraries effectively? 4. Integrability – how difficult is it to integrate the libraries as part of solutions to deploy? 5. KPIs: time-of-training-models (totm), performance/power/accuracy trade- off, etc. 6. Others – can you help us to evaluate other aspects?
  • 13. 13 The project has received funding from the European Union’s Horizon 2020 research and innovation programme under grant agreement No 825111. Needs & Requirements Evaluate Software Platforms in terms of 1. Usability – how long does a domain application expert need to manage the software tool effectively? 2. Completeness – does the application platform provide all the algorithms/procedures/functions to allow domain application experts to easily define the sequences of steps to implement the data and/or model pipelines? 3. Compatibility – how many data formats does the platform admits to import/export data and models from/to other frameworks? 4. KPIs: time-to-model-in-production (ttmip), time-of-pre-processing-images (toppi), etc. 5. Others – can you help us to evaluate other aspects?
  • 14. 14 The project has received funding from the European Union’s Horizon 2020 research and innovation programme under grant agreement No 825111.The project has received funding from the European Union’s Horizon 2020 research and innovation programme under grant agreement No 825111. Questions? @DeepHealthEU https://deephealth-project.eu Technical Manager: Jon Ander Gómez jon@upv.es

Notas del editor

  1. Healthcare is one of the key sectors of the global economy, making any improvement in healthcare systems to have a high impact on the welfare society. European public health systems are generating large datasets of biomedical data, in particular images that constitute a large unexploited knowledge database, since most of its value comes from the interpretations of the experts. Nowadays, this process is still performed manually in most cases. The use of technologies, such as the recent trend on bringing together High Performance Computing (HPC) with Big Data technologies, as well as the application of Deep Learning (DL) and Artificial Intelligence (AI) techniques can overcome this issue and foster innovative solutions, in a clear path to more efficient healthcare, benefitting to people and public budgets
  2. The DeepHealth concept (depicted in the Figure) focuses on scenarios where image processing is needed for diagnosis. The training environment represents where IT expert users work with datasets of images for training predictive models. The production environment is where the medical personnel ingest an image coming from a scan into a software platform or biomedical application that uses predictive models to get clues that can help them to make decisions during diagnosis. Doctors have the knowledge to label images, define objectives and provide related metadata. IT staff are in charge of processing the labelled images, organize the datasets, perform image transformations when required, train the predictive models and load them in the software platform. The DeepHealth toolkit will allow the IT staff to train models and run the training algorithms over Hybrid HPC + Big Data architectures without a profound knowledge of Deep Learning, HPC or Big Data, and increase their productivity reducing the required time to do it. This process is transparent to doctors, they just provide images to the system and get predictions such as indicators, biomarkers or the segmentation of an image for identifying tissues, bones, nerves, blood vessels, etc.
  3. The DeepHealth concept (depicted in the Figure) focuses on scenarios where image processing is needed for diagnosis. The training environment represents where IT expert users work with datasets of images for training predictive models. The production environment is where the medical personnel ingest an image coming from a scan into a software platform or biomedical application that uses predictive models to get clues that can help them to make decisions during diagnosis. Doctors have the knowledge to label images, define objectives and provide related metadata. IT staff are in charge of processing the labelled images, organize the datasets, perform image transformations when required, train the predictive models and load them in the software platform. The DeepHealth toolkit will allow the IT staff to train models and run the training algorithms over Hybrid HPC + Big Data architectures without a profound knowledge of Deep Learning, HPC or Big Data, and increase their productivity reducing the required time to do it. This process is transparent to doctors, they just provide images to the system and get predictions such as indicators, biomarkers or the segmentation of an image for identifying tissues, bones, nerves, blood vessels, etc.