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Showing posts with label medical. Show all posts
Showing posts with label medical. Show all posts

Wednesday, 26 September 2018

Bayesian networks for trauma prognosis


There is an excellent online resource produced by Barbaros Yet that summarises the results of collaboration between the Risk and Information Management research group at Queen Mary and the Trauma Sciences Unit, Barts and the London School of Medicine and Dentistry. This work focused on developing Bayesian network (BN) models to improve decision support for trauma patients.

The website not only describes two BN models in detail (one for predicting acute traumatic coagulopathy in early stage of trauma care and one for predicting the outcomes of traumatic lower extremities with vascular injuries) but allows you to run the models in real time showing summary risk calculations after you enter observations about a patient.

The models are powered by AgenaRisk.

Links:

  • http://traumamodels.com/
  •  Perkins ZB, Yet B, Glasgow S, Marsh DWR, Tai NRM, Rasmussen TE (2018). “Long-term, patient centered outcomes of Lower Extremity Vascular Trauma”, Journal of Trauma and Acute Surgery. DOI:10.1097/TA.0000000000001956 
  • Yet B, Perkins ZB, Tai NR, and Marsh DWR (2017). “Clinical Evidence Framework for Bayesian Networks” Knowledge and Information Systems, 50(1), pp.117-143.DOI:10.1007/s10115-016-0932-1 
  •  Perkins ZB, Yet B, Glasgow S, Cole E, Marsh W, Brohi K, Rasmussen TE, Tai NRM (2015). “Meta-analysis of prognostic factors for amputation following surgical repair of lower extremity vascular trauma” British Journal of Surgery, 12 (5), pp. 436-450. DOI:10.1002/bjs.9689
  • Yet B, Perkins ZB, Rasmussen TE et al.(2014). Combining data and meta-analysis to build Bayesian networks for clinical decision support. J Biomed Inform vol. 52, 373-385. http://dx.doi.org/10.1016/j.jbi.2014.07.018   http://qmro.qmul.ac.uk/xmlui/handle/123456789/23055
  • Perkins ZB, Yet B, Glasgow S, Cole E, Marsh W, Brohi K, Rasmussen TE, Tai NRM (2015). “Meta-analysis of prognostic factors for amputation following surgical repair of lower extremity vascular trauma” British Journal of Surgery, 12 (5), pp. 436-450. DOI:10.1002/bjs.9689
  • Yet B, Perkins ZB, Rasmussen TE, Tai NR, and Marsh DWR (2014). “Combining Data and Meta-analysis to Build Bayesian Networks for Clinical Decision Support” Journal of Biomedical Informatics , 52, pp.373-385. DOI:10.1016/j.jbi.2014.07.018
  • Yet B, Perkins Z, Fenton N et al.(2014). Not just data: a method for improving prediction with knowledge. J Biomed Inform vol. 48, 28-37. http://dx.doi.org/10.1016/j.jbi.2013.10.012
  • Yet B, Perkins Z, Tai N et al.(2014). Explicit evidence for prognostic Bayesian network models. Stud Health Technol Inform vol. 205, 53-57. http://dx.doi.org/10.3233/978-1-61499-432-9-53
  • Perkins Z, Yet B, Glasgow S et al. (2013). EARLY PREDICTION OF TRAUMATIC COAGULOPATHY USING ADMISSION CLINICAL VARIABLES. SHOCK. vol. 40, 25-25.

Saturday, 19 March 2016

Turning poorly structured data into intelligent Bayesian Network models for medical decision support



Medical data is very often badly structured, incomplete and inconsistent. This limits our ability to  generate useful models for prediction and decision support if we rely purely on machine learning techniques. That means we need to exploit expert knowledge at various model development stages. This problem - which is common in many application domains - is tackled in a paper** published in the latest issue of Artificial Intelligence in Medicine.

The paper describes a rigorous and repeatable method for building effective Bayesian Network (BN) models from complex data - much of which comes in unstructured and incomplete responses by patients from questionnaires and interviews. Such data inevitably contains repetitive, redundant and contradictory responses; without expert knowledge learning a BN model from the data alone is especially problematic where we are interested in simulating causal interventions for risk management. The novelty of this work is that it provides a rigorous consolidated and generalised framework that addresses the whole life-cycle of BN model development. The method is validated using data from forensic psychiatry. The resulting BN models demonstrate competitive to superior predictive performance against the data-driven state-of-the-art models. More importantly, the resulting BN models go beyond improving predictive accuracy and into usefulness for risk management through intervention, and enhanced decision support in terms of answering complex clinical questions that are based on unobserved evidence.

The method is applicable to any application domain involving large-scale decision analysis based on such complex and unstructured information. It challenges decision scientists to reason about building models based on what information is really required for inference, rather than based on what data is available. Hence, it forces decision scientists to use available data in a much smarter way.

**The full reference for the paper is:
Constantinou, A. C., Fenton, N., Marsh, W., & Radlinski, L. (2016). "From complex questionnaire and interviewing data to intelligent Bayesian Network models for medical decision support".Artificial Intelligence in Medicine, Vol 67 pages 75-93. DOI http://dx.doi.org/10.1016/j.artmed.2016.01.002

For those who do not have access to the journal a pre-publication draft can be downloaded: http://constantinou.info/downloads/papers/complexBN.pdf 

Tuesday, 15 September 2015

Yet another flawed statistical study attracts massive unquestioning attention


The Guardian, 29 Sept 2015
A very widely reported story in today’s news (see, for example, the report in the Guardian and this Press release) claims that companies in which there is at least one female executive on the Board (‘gender diverse’ companies) in the US, UK and India outperform companies with male-only executives by a staggering US$655 billion per year. The story is based on a study by Grant Thornton whose representative Francesca Lagerberg concludes:
“The research clearly shows what we have been talking about for a while: that diversity leads to better decision-making”.
As is typical when the results of a statistical study fit a popular narrative, the story attracted massive, unquestioning attention. Unfortunately, while I am sure that most people agree that greater gender diversity in the Boardroom is a worthy objective, based on the ‘full report’ – and in the absence of other data - Lagerberg's claim is simply not supported. In fact, the study exemplifies some of the classic misuses of statistics that we wrote about in the first chapter of our book and highlights yet again the need for proper causal/explanatory models to be used in statistical studies such as these*.

Moreover, using the data in Lagerberg's study it is possible to construct a simple causal model (a Bayesian network) that replicates the results but with provably opposite conclusions: diversity decreases performance.

The full report and BN model are provided here. The model can be run in the free version of AgenaRisk.

*Making such an approach both universally feasible and acceptable is the major objective of BAYES-KNOWLEDGE.

Monday, 31 August 2015

Doctoring Data: Review of a must read book



Book Review:

Review by Norman Fenton and Martin Neil (a pdf version of this article can be found here)

This is an extremely important (and also entertaining) book that should be mandatory reading not just for anybody interested in finding out about what data-driven medical studies really mean, but also for anybody engaged in any kind of empirical work. What Kendrick shows brilliantly is the extent to which the vast majority of medical recommendations and guidelines are based on data-driven studies that are fundamentally flawed and often corrupt. He highlights how the resulting recommendations and guidelines have led (world-wide) to millions of unnecessarily early deaths, millions of people suffering unnecessary pain, and widespread use of drugs and treatments that do more harm than good (example: statins), as well as wasting billions of taxpayer dollars every year.

As researchers who have been involved in empirical studies in a very wide range of disciplines over many years we believe that much of what he says is also relevant to all of these disciplines (which include most branches of the physical, natural and environmental sciences, computer science, the social sciences, and law). Apart from the cases of deliberate corruption and bias (of which Kendrick provides many medical examples) most of the flaws boil down to a basic misunderstanding of statistics, probability and the scientific method.

There are two notable quotes that Kendrick uses, which we believe sum up most of the problems he identifies:
  1. When a man finds a conclusion agreeable, he accepts it without argument, but when he finds it disagreeable, he will bring against it all the forces of logic and reason” Thucydides.
  2.  “I know that most men, including those at ease with problems of the greatest complexity, can seldom accept even the simplest and most obvious truth if it be such as would oblige them to admit the falsity of conclusions which they have delighted in explaining to colleagues, which they have proudly taught to others, and which they have woven, thread by thread, into the fabric of their lives.” Leo Tolstoy
The first sums up the extent to which results of empirical work are doctored to suit the pre-conceived biases and hopes of those undertaking it (a phenomenon also known as ‘confirmation bias’). The second sums up the extent to which there are ideas that represent the ‘accepted orthodoxy’ in most disciplines that are impossible to challenge even when they are wrong. Those brave enough to challenge the accepted orthodoxy risk ruining their careers in their discipline. Hence, most researchers and practitioners simply accept the orthodoxy without question and help perpetuate flawed or useless ideas in order to get funding and progress their careers. Kendrick describes how these problems lie at the heart of the fundamentally fraudulent peer review system in medicine – which applies to both submitting articles to journals and submitting research grant applications. Once again, we believe that all of the areas of research where we have worked (maths, computer science, forensics, law, and AI) suffer from the same flawed peer review system.

Kendrick is not afraid to challenge the leading figures in medicine, often exposing examples of hypocrisy and corruption. Of special interest to us, however, is that he also challenges the attitude of revered figures in our own discipline. For example, Kendrick highlights two quotes in a recent article by Nobel prize-winner Daniel Kahneman, whose work in the psychology of decision theory and risk is held in the highest esteem.:
  1.  “The way scientists try to convince people is hopeless because they present evidence, figures, tables, arguments, and so on. But that’s not how to convince people. People aren’t convinced by arguments, they don’t believe conclusions because they believe in the arguments that they read in favour of them. They’re convinced because they read or hear the conclusions from people they trust. You trust someone and you believe what they say. That’s how ideas are communicated. The arguments come later.”
  2.  “Why do I believe global warming is happening? The answer isn’t that I have gone through all the arguments and analysed the evidence – because I haven’t. I believe the experts from the Academy of Sciences. We all have to rely on experts.
Kendrick notes the problem here:
“In one breath he states that people aren’t convinced by arguments; they’re convinced because they read or hear conclusions from people they trust. Then he says that we all have to rely on experts. But he does not link these two thoughts together to ask the obvious question. Just how, exactly, did the experts come to their conclusions?”
Having presented the BBC documentary on Climate Change by Numbers we also got an insight into the extent to which problems exist there.

As good as the book is (and indeed because of how good it is), we feel the need to highlight some points where we believe Kendrick gets it wrong. There are some statistical/probability errors and over-simplifications, which mostly seem to stem from a lack of awareness of Bayesian probability. For example, he says:
“… although association cannot prove causation, a lack of association does disprove causation”.
This is not true as can be proven by the simple counter example we provide below using a Bayesian network*.

Next we believe Kendrick’s faith in randomised control trials (RCTs) as being the (only) reliable empirical basis for medical decision making is misplaced. Because of Simpson’s paradox and the impossibility of accounting for all confounding variables there is, in principle, no solid basis for believing that the result of any RCT is ‘correct’. As is shown in the article here it is possible, for example, that an RCT can find a drug to be effective compared to a placebo in every possible categorisation of trial participants, yet the addition of a single confounding variable can result in an exact reversal of the results.

So, if we are saying that even RCTs cannot be accepted as valid empirical evidence, does that mean that we are even more pessimistic than Kendrick about the possibility of any useful empirical research? No - and this brings us to our final major area of disagreement with Kendrick’s thesis. In contrast to what Kendrick proposes we believe there is an important role for expert judgment in critical decision-making. In fact, we believe expert judgement is inevitable even if every attempt is made to remove it from an empirical study (it is, for example, impossible to remove expert judgment from the very problem of framing the study and choosing the variables and data to collect). Given the inevitability of expert judgment, we feel it should be made obvious, transparent, and open to refutation by experiment. Any scientist should be as open and honest about their judgment as possible and be prepared to make predictions and be contradicted by data.

By combining expert judgment with data it is possible to get far more reliable empirical results with much less data and effort than required for an RCT. This is essentially what we proposed in our book and which is being further developed in the EU project BayesKnowledge.


*Refuting the assertion “If there is no association (correlation) then there cannot be causation”.

Consider the two hypotheses:
  • H1: “If there is no association (correlation) then there cannot be causation”.
  • H2: “If there is causation there must be association (correlation).
Kendrick’s assertion (H1) is, of course, equivalent to H2. We can disprove H2 with a simple counter-example using two Boolean variables a, and b, i.e. whose states are True or False. We do this by introducing a third, latent, unobserved Boolean variable c. Specifically we define the relationship between a,b, and c via the following Bayesian network :



By definition b is completely causally dependent on a. This is because, when c is True the state of b will be the same as the state of a, and when c is False the state of b will be the opposite of the state of a.

However, suppose - as in many real-world situations – that c is both hidden and unobserved (i.e. a typical confounding variable). Also, assume that the priors for the variables a and c are uniform (i.e. 50% of the time they are False and 50% of the time they are True).

Then when a is False there is a 50% chance b is False and a 50% chance b is True. Similarly, when a is True there is a 50% chance b is False and a 50% chance b is True. In other words, what we actually observe is zero association (correlation) despite the underling mechanism being completely (causally) deterministic.

The above BN model can be downloaded here and run using the free version of AgenaRisk

Wednesday, 2 April 2014

Bayesian network approach to Drug Economics Decision Making


Consider the following problem:
A relatively cheap drug (drug A) has been used for many years to treat patients with disease X. The drug is considered quite successful since data reveals that 85% of patients using it have a ‘good outcome’ which means they survive for at least 2 years. The drug is also quite cheap, costing on average $100 for a prolonged course. The overall “financial benefit” of the drug (which assumes a ‘good outcome’ is worth $5000 and is defined as this figure minus the cost) has a mean of $4985.

There is an alternative drug (drug B) that a number of specialists in disease X strongly recommend. However, the data reveals that only 65% of patients using drug B survive for at least 2 years (Fig. 1(b)). Moreover, the average cost of a prolonged course is $500. The overall “financial benefit” of the drug has a mean of just $2777.
On seeing the data the Health Authority recommends a ban against the use of drug B. Is this a rational decision?

The answer turns out to be no. The short paper here explains this using a simple Bayesian network model that you can run (by downloading the free copy of AgenaRisk)