Category Archives: Datathon 2019

ESICM Datathon: Day 3

Hemodynamics in septic shock Speaker: G. Baselli
Amazing how a ‘routine’ haemodynamic system can be viewed so differently from the point of view of an engineer/data scientist/medic

In conclusion

  1. Autonomic nervous system function and CV regulation is dynamic and hence the data needs to be dynamic and not a constant
  2. Need to pick out the meaningful physiological parameters to feed into the machine learning algorithm
  3. Important to have large open-access databases
  4. These databases need to integrate multi-scale information both in dimension and in time

Neurointensive care Speaker: A. Ercole

The concept of cerebral perfusion pressure = MAP – ICP is an example of a simple mathematical concept

We measure what we can, NOT what we should

Perhaps the autoregulation status of the TBI pt is more important – cerebrovascular pressure reactivity (PRx) Link

Data studies needs the same robustness as any other drug studies

Data Access quality and Curation for Observational Research Designs

Reinforcement learning in sepsis Speaker: M. Komorowski

The Artificial Intelligence Clinicians learns optimal treatment strategies for sepsis in intensive care

Can a computer help the clinician do the right thing?

Looked at 2 groups of treatment in septic patients – vasopressor use and fluid administration.

In general pts received more IV fluids and less vasopressors than recommended by the AI policy.

The machine considered much more variables compared to the human clinician


  • Reinforcement learning could provide clinically interpretable treatment suggestions
  • The models could improve outcomes in sepsis
  • Flexible framework transferable to other clinical questions

Gradient-boosted decision trees Speaker: C. Cosgriff

“Its not about doctors versus computers, its doctors with computers versus doctors without computers – @cosgriffc”

If you don’t know what gradient boost is (I don’t) but would like to find out more OR want to learn some basic coding in R/Python/SQL, have a look at

The power of XGBoost for the ICU is to shift towards ‘human intelligence’, supporting clinicians and intensivists (NOT REPLACING THEM)


  • Introduction to Statistical Learning
  • Elements of statistical learning
  • Deep Learning with Python
  • xgBoost: A scalable tree boosting system

Clinical research and AI Speaker: R. Furlan

This is highlighted by a local project looking at the ability to diagnose syncope using natural language algorithms of EHR compared to human clinicians

Moving models to the bedside Speaker: P. Thoral

Insight into the challenges on bringing machine learning and artificial intelligence models to the bed side.

Highlights the various legislative requirement with regards to introducing system (medical software is still considered a medical device)

Need to engage the stakeholders

The future: physicians, engineers, machines Speaker: R. Barbieri

Various scenarios of the future predicted by Prof Barbieri


  • Technology used in warfare
  • Technology cannot overcome environmental disasters

Best Scenario

  • Technology cures, predicts and prevents diseases
  • No need for ICUs


  • Technology blunts human knowledge
  • Humans lose ability to think
  • Technology takes over but are unable to make critical decisions

Oligarchy (aka BladeRunner)

  • Technology and knowledge controlled by a few
  • Progress without common wealth
  • Humans and machines start merging


  • Machines takes over
  • Humans and human nature are irrelevant


ESICM Datathon: Day 2

Session 3: Advanced data analysis Chairs: J. De Waele, A. Girbes

AI & machine learning for clinical predictive analytics Speaker: M. Ferrario

An Interpretable Machine Learning Model for Accurate Prediction of Sepsis in the ICU.

The combination of genomics, metabonomics coupled with Artificial Intelligence and Machine Learning is an incredible one. BUT its application is still an open challenge.

Given the complexity and heterogeneity of the data, there are no well-defined set of procedures to interrogate them.

BUT THERE ARE ISSUES WITH MACHINE LEARNING – Potential Biases in Machine Learning Algorithms Using Electronic Health Record Data

New meaning to observational studies Speaker: S. Finazzi

Data sources

  • Prospective data collection
  • Administrative databases
  • Registries
  • Electronic health records

Research question that can be tackled

  • Evaluation of quality of care
  • Study clinical and decision making processes
  • Analyse pathophysiological phenomena

Besides MIMIC/PhysioNet, there are other collaborative databases out there

These data have been used to improve care and processes in participating departments. Also can act as benchmarking exercise.

The big issue is the quality of the data!

Predictive models and clinical support Speaker: G. Meyfroidt

Examples of application:

Computerized prediction of intensive care unit discharge after cardiac surgery: development and validation of a Gaussian processes model

Predictive models may help us to predict patients discharge form the ICU, to predict intracranial pressure increase and acute kidney injury onset.

Predictive models may help us to predict patients discharge form the ICU, to predict intracranial pressure increase and acute kidney injury onset.

Medical data science 101 Speaker: M. Komorowski

Why should we conduct secondary analysis of EHR?

  • RCT results not always applicable to real life patients
  • RCTs are negative!
  • RCTs won’t allow precision medicine
  • Not using the data is unethical


  • Observational data: difficult to examine causality
  • Availability of the data?
  • Data quality

Matt then did a LIVE demo on how to build a machine learning model – follow my thoughts here

State of the art of EMRs in Europe Speaker: T. Kyprianou

Cognitive Informatics in Health and Biomedicine

Adverse effects in medicine: easy to count, complicated to understand and complex to prevent.

There needs to be a shift in focus from error intolerance to error recognition and recovery.

The data for EHR are driven by 4 sources:

  • Patient
  • Unit
  • Education
  • Research

Problems and promises of innovation: why healthcare needs to rethink its love/hate relationship with the new

Improving the Electronic Health Record—Are Clinicians Getting What They Wished For?

The tragedy of the electronic health record

Opportunities for ICU CIS/PDMS

  • Direct link/real time updates of patient’s medical records
  • Healthcare professionals access to all information and services they need in one place
  • Patients/family-centric decision-making based on best clinical evidence
  • Improve data quality and analysis
  • Development of better and more effective security protocols
  • Faster test turnaround times to provide quicker diagnosis for patients.

GDPR and pseudonymization Speaker: D. Fulco, A. Di Stasio

This was an absolutely fascinating insight into the GDPR from a legal prospective.

I really think that GDPR is a good thing.

General Data Protection Regulation (GDPR)

Privacy in the age of medical big data

Blackout: when IT fails Speaker: C. Hinske

*Great title slide*

3 types of failure

  • Failure to use (e.g. IT blackout)
  • Failure to support (e.g. incorrect information)
  • Failure to enable (e.g. too much information)

Top 3 tips

    Risk assessment

    • Contingency plan where you tolerate workflow disruption (with strict time limit) followed by a fallback plan

    Failure strategy

    • Failure prevention –> Failure management strategy

    Train your team

    • Simulated systems fail

Prediction and deep learning Speaker: A. Ercole

If you were blown away by Matt’s SQL and Python prowess, wait till you see Ari’s demo. I was mesmorised when he did his party trick at LIVES2016 in Milan.

This time around, he constructed mortality prediction models in real time using R (here)

Critical Care Health Informatics Collaborative (CCHIC): Data, tools and methods for reproducible research: A multi-centre UK intensive care database

Another mesmorising site he introduced us to was the Neural Network Playground


The issue of data quality Speaker: S. Vieira

A Data Quality Assessment Guideline for Electronic Health Record Data Reuse

The types of missing data

  • Missing at completely random e.g. loss of label in lab test
  • Missing at random e.g. arterial pH, PaCO2 measurements in blood
  • Missing Not at Random e.g. blood counts which doctor decides not to do

Harmonization of data sources Speaker: B. Illigence
This is a fascinating insight into the process in Germany introducing a national EHR (it’s not completed yet)

Making sense of a big data mess Speaker: H. Hovenkamp

From the founder of PACMED ( based in Amsterdam

Once upon a time: the story of MIMIC Speaker: R. Mark

This is probably my highlight of day 2. The story of how the MIMIC database came into being from Prof R Mark. Amazing and inspirational. A call for further collaboration. Furthermore, if you use the MIMIC data and publish your research, you must submit your code to an open repository.

ESICM Datathon: Day 1

This is my first datathon and this blog just summarises some of the themes/discussions at the conference. As a declaration of interest, I believe in the collaborative use of healthcare data to improve patient care BUT I am NOT a data scientist and barely write a Python/R script.

Physicians: the need for machine learning (G. Meyfroidt @GMeyfroid)

Predicting the Future — Big Data, Machine Learning, and Clinical Medicine

Do you know the difference??


There is just too much data in the ICU – you need to understand it.

Data by themselves are uselss. To be useful, data must be analysed, interpreted and acted upon. Thus, it is the algorithms – not data set – that will prove transformative.

The transformation will be in the form of:

– Decision support, prognostication and diagnostics

– Personalised medicine

– Continuous learning

– Knowledge discovery

By freeing physicians from the tasks that interfere with human connection, AI will create space for the real healing that takes place between a doctor who can listen and a patient who needs to be heard.

High-performance medicine: the convergence of human and artificial intelligence

Geert has a team of data scientist working with the clinical team. One should not try to be the other.




Data issues

  • Quality
    • Lack of standards
    • Missing or incomplete data
      • Can be unbiased or random
      • Most often biased (eg. lactate measurements in sickest pts)
    • Will influence the performance of Machine Learning models
  • Access to data, privacy and regulatory issues
    • Who owns shared data?
    • Who oversees the correct use
    • GDPR

Article | Published: 22 October 2018 The Artificial Intelligence Clinician learns optimal treatment strategies for sepsis in intensive care by @matkomorowski


Data analysts: why invest in ICM? (M. Flechet @FlechetMarine)

*I love her slideset

Data Scientist: The Sexiest Job of the 21st Century


The Vs of Big Data

– Velocity

– Volume

– Variety

– Value

– Veracity

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Healthcare Big Data and the Promise of Value-Based Care
The data scientist as part of the medical team and the doctor as an information coach (L. Celi @MITcriticaldata)

Healthcare is a failed business model

  • Under-reported and under-appreciated degree of medical errors
  • Inequalities in care delivery
  • Enormous waste of resources: over-testing, over-diagnosis, oer-treatment
  • Large information gaps from imperfect medical knowledge system
  • Inefficiencies in workflow
  • High level of workforce burnout

Why doctors hate their computers – Atul Gawande


Opportunities in AI in healthcare

  • Classification: image recognition, risk stratification
  • Prediction: disease trajectory and prognosis, clinical events for triaging, treatment response
  • Optimisation aka precision medicine: diagnostic and screening strategies, defining therapeutic targets

Challenges for AI in healthcare

  • Labelling, a requirement for classification and prediction, is not straightforward
  • Model validity is limited by time and space
  • Machine bias
  • Optimal outcomes may vary across different stakeholders
  • Short term gais may not translate to long term benefits
  • Over-diagnosis (and over-treatment) will surge

Using machine learning, the degree of uncertainty may actually increase

Tolerating Uncertainty — The Next Medical Revolution?

Artificial intelligence systems for complex decision-making in acute care medicine: a review

In the AI Age, “Being Smart” Will Mean Something Completely Different

The new smart will be determind not by what or how we know, but by the quality of our thinking, listening, relating, collaborating and learning.

* I would highly recommend the following links as a good starting point if you are interested in database research

MIT Critical Care Data

eICU Collaborative Research Database

MIMIC Critical Care Database

MIMICIII is arguably the most well known freely accessible critical care database.


Secondary analysis of electronic health records (FREE ebook)