Nature Inspired Computing and Engineering (NICE) research group

Projects

Research projects in the Nature Inspired Computing and Engineering group.

We also run research projects as part of the Department of Computer Science, go to our Research projects section for more information.

Current

Modelling and Predicting the Progression of Chronic Kidney Disease

Dates

Start date: 1 September 2015
End date: 31 August 2018

Funding

MRC (Medical Research Council) MR/M023281/1

Details

Chronic Kidney Disease (CKD) is a significant cause of morbidity and mortality across the developed world. Patients with CKD have increased risk of death from cardiovascular disease and End Stage Kidney Failure, leading to dialysis and kidney transplant. Indeed, according to an NHS Kidney Care report in 2012 (http://goo.gl/oLJD2), CKD was estimated to cost £1.45 billion in 2009-10; 1.8 million people were diagnosed with CKD in England; and, there were potentially 900,000 to 1.8 million people with undiagnosed CKD. Therefore, the importance and urgency of managing CKD cannot be over-emphasized.

An overarching objective of this MRC research is to revisit the problem of modelling the progression of Chronic Kidney Disease (CKD) using state-of-the-art machine learning techniques and methodologies. We introduce three innovations in this project.

First, we shall investigate statistical models that directly predict key clinical variables so that clinicians can make more informed decisions. This approach is more consistent with guidelines-based prescribing that is used by general practitioners.

Second, we will develop a way to identify patient groups by using data-driven methods. The approach used is similar to 'market segmentation' used in Business Intelligence. The hypothesis is that patients can be divided into groups not by their disease or stages (as currently practised) but by their patient records that essentially capture their health history. In essence, this method of grouping will naturally group patients with similar treatments including drugs and procedures and similar physiological and pathological characteristics.

Third, as part of the process in predicting the efficacy of kidney function, we will develop a risk model for predicting and detecting Acute Kidney Injury (AKI). This novel model will inform clinicians how likely it is that a patient will suffer from AKI. In short, we propose a unified framework to predict the efficacy of kidney function that also considers the possibility of AKI. This represents a potential advancement in modelling and understanding CKD because the risks of end-stage of CKD and AKI are so far often treated independently.

The potential advantages of the proposed method include: (1) better tailoring of the method to patient subgroups via data-driven stratification; (2) ability to exploit many more variables that are specific to each patient stratum; (3) ability to predict eGFR (or estimated Glomerular Filtration rate, which characterises the efficiency of kidney function) and ACR (or Albumin:creatinine ratio) that can be used in conjunction with guidelines-based prescribing; (4) ability to predict the risk of Acute Kidney Injury.

These outputs are significant in the following ways. First, although risk models for CKD exist, there is no predictor for eGFR and ACR to date. Directly predicting these variables have significant clinical implication because the approach is consistent with guidelines-based prescribing. Unlike risk models, by directly predicting the observable outputs, these predictors convey the notions of severity and uncertainty at the same time (whilst risk models often predict only the worst outcome). Second, there is no AKI risk model and its association with CKD remains unclear; our model considers AKI risk when predicting eGFR, thus, combining the two pieces of related information in a principled way via the Bayesian framework. Third, we propose data-driven patient stratification as an alternative to disease and state-specific stratification. This will lead to a better understanding of CKD pathways and patient profiling. Indeed, our proof-of-concept experiment suggests that patients who have eGFR may be categorised into some 60 clusters. This patient stratification strategy inherently considers co-morbidities and disease-staging at the same time.

Co-investigator

Past projects

SPIKEFRAME: A framework for learning rules in networks of spiking neural networks

Dates

Start date: 1 April 2014
End date: 31 March 2016

Summary

In the project we are working on constructing a framework for the formulation of goal-oriented learning rules for spiking neural networks.

Existing algorithms do not relate to each other, use different terminologies and notations without making connection to each other. We aim at  developing a mathematical and conceptual framework within which goal-oriented learning algorithms can be formulated clearly and concisely for ease of their application, understanding and generalisation. This is important for the understanding of how neuron-scale plasticity "conspires" to bring about goal-oriented human and animal learning behaviours at the cognitive and behavioural scale.

Funding

EU Horizon 2020 Human Brain Project (HBP)

Collaborations

This project is a part of Subproject 4 Theoretical Neuroscience of the Human Brain Project, a multi-billion EU Horizon 2020 Flagship project, and will involve collaboration with the European Institute of Theoretical Neuroscience (EITN)in Paris (the hub of the Subproject 4). A brochure of Subproject 4 Theoretical Neuroscience can be found here.

Investigator

Delivering water security for all during shale gas production

Dates

Start date: 1 April 2015
End date: 30 November 2015

Summary

This project will entail feasibility studies to deliver water security for all during shale gas production.

Funding

Innovate UK (TSB)

Collaborations

WSP UK Ltd (project lead)
Concepture Ltd
Imperial College London
Cardiff University

Investigator

Delivering water security for all during shale gas production

Dates

Start date: 1 April 2015
End date: 30 November 2015

Summary

This project will entail feasibility studies to deliver water security for all during shale gas production.

Funding

Innovate UK (TSB)

Collaborations

WSP UK Ltd (project lead)
Concepture Ltd
Imperial College London
Cardiff University

Investigator

Minimal access surgical training, enhancement and reporting software (MASTERS)

Dates

Start date: 1 June 2014
End date: 28 August 2015

Funding

EPSRC IAA and Moorfields Eye Hospital, NHS

Investigator

Automatic Reading of Digital Fundus Images for Large scale Eye Epidemiology Studies

Dates

Start date: 1 September 2012
End date: 31 March 2013

Funding

EPSRC Pathway to Impact

Investigator

Predictive Modelling of the Social Networks Influencing Obesity

Dates

Start date: 3 January 2012
End date: 21 December 2012

Summary

The incidence of obesity in the UK has risen significantly with treatment costs rising to over £5 billion by 2025.  The many social and biological causes of obesity have been explored in the Foresight obesity system map.  Although useful for illustration, the qualitative nature and complexity of this map have prevented consensus on targets for public health intervention.  In this project we will apply, for the first time, dynamic neural simulations to quantitatively model the social parameters influencing the increase in obesity rates to help identify variables best targeted by public health interventions.

Objectives

The aim of this project is to develop a spiking neural network model to quantify the social parameters influencing the increase in overweight and obesity in the UK over the last 30 years.

Specific objectives are to:

  1. Identify key social parameters from the Foresight qualitative map (e.g. watching television, walking to school, media) and obtain the relevant epidemiological data from the Economic and Social Data Service and map to network.
  2. Develop network models using these parameters to enable measurement of the spatial dynamics of the interactions between individuals observed.
  3. Quantify outcomes, specifically: the emergence of polychronous groups, the average firing rates and the connectivity pattern.
  4. Future expansion could include other parameters within Foresight and would focus on likely parameters for public health intervention.

This project clearly meets the MILES assessment criteria in initiating a multidisciplinary collaboration between biologists, computer scientists and mathematicians.  The research planned is an entirely novel exploitation of the dynamics of spiking neural networks in the context of how social parameters influence the development of obesity.  The modelling of connectivity, influence and information flow within this system will be predictive and therefore offer the potential of identifying critical nodes for public health intervention.  As such this project offers tremendous potential to lead to a successful bid securing external funding to continue this work.

Funding

EPSRC MILES (EP/I000992/1)

Details

In 2007 24% of adults and 17% of children in the UK were obese; the estimated costs of treating the consequences of obesity were £1 billion in 2002 and projected to be £5.3 billion by 2025 (NHS Information Centre, Lifestyle Statistics, 2009).  Numerous social and biological factors have been implicated in the aetiology of obesity, and in 2007 the Foresight Programme of the UK Government Office for Science published a conceptual obesity system map that illustrates the multifactorial nature of this disease.  With 108 variables this qualitative atlas highlights the tremendous complexity underlying obesity and the need to move away from single intervention approaches.  However, this very complexity and the qualitative nature of the map have also prevented the development of a consensus on where public health interventions are most likely to make a difference.

At first glance, an unlikely correlate of this multifactorial, highly interconnected and complex network of influences is the human brain.  The complexities of the brain have been studied at many levels, from chemical reactions in individual neurons through to high-level cognitive architectures. These studies have demonstrated that small-scale behaviour, such as when and how neurons fire, can have a large-scale influence on a population.  However, it is only recently that advances in modelling the dynamics of neural interactions have led to an increase in the scale of models that can be developed (Izhikevich & Edelman, 2008).  In these models, neurons are represented by biologically plausible dynamic equations, with each neuron highly connected with others.  By stimulating a handful of neurons over time, behaviour emerges from the model in the form of polychronous groups: repeating patterns of neurons that learn to activate together.  These patterns result from the stimulation but demonstrate the wide influence that single inputs can establish.

These emergent patterns of behaviour may, by analogy, represent the dissemination of social influences and consequent changes in behaviour.  For example, we can treat neurons as people within a population who are highly connected to others.  An increase by one person in, say, watching television, modelled as a pattern of neural activity, will influence those to whom the person is connected.  Over time, this influence causes the emergence of polychronous groups tuned to this pattern of activity, and hence a wider number of individuals have been influenced.  The challenges are identifying social parameters that we can model and developing a plausible architecture for the influences of the parameters to be observed.  With the computational efficiency of these spiking neural networks, many such parameters and architectures can be evaluated and compared with the known increase in obesity of the last 30 years in the UK to establish a benchmark.  We can then test different parameter values to find target interventions.

Bringing together a team of biologists, computer scientists and mathematicians, this project aims to develop a spiking neural network model to quantify key social parameters from the Foresight qualitative map influencing the increase in overweight and obesity in the UK over the last 30 years.

E.M. Izhikevich & G.M. Edelman (2008) Large-scale model of mammalian thalamocortical systems, PNAS, 105(9):3593-3598

Collaborations

Dr. Theresa A Hague, FHMS, PGMS

Fusion of EEG and fMRI; A novel approach based on NMF

Dates

Start date: 1 July 2009
End date: 31 July 2012

Summary

A constraint spatial non-negative matrix factorization (CSNMF) technique is proposed for separation of event-related, movement-related and activated regions of the brain from the rest of the fMRI sequence. NMF is a powerful decomposition approach and an emerging technique for analysis of multivariate. The goal of NMF is to decompose a data matrix X into two other matrices, which results in the extraction of some latent features whilst reducing some redundancies in the original data. Inherently, this is an ill-posed problem. Here, a solution to this optimisation problem will be given by incorporating EEG signals into a CSNMF system.

Funding

The Leverhulme Trust

Workshop on Biologically Inspired Information Fusion

Dates

Start date: 7 August 2006
End date: 6 October 2006

Summary

Our understanding of both natural and artificial cognitive systems is an exciting area of research that is developing into a multi-disciplinary subject with the potential for significant impact on science, engineering and society in general. There is considerable interest in how our understanding of natural systems may help us to apply biological strategies to artificial systems. Of particular interest is our understanding of how to build adaptive information fusion systems by combining knowledge from different domains. In natural systems, the integration of sensory information is learnt at an early stage of development. Therefore, through a better understanding of the structures and processes involved in this natural adaptive integration, we may be able to construct a truly artificial multi-sensory processing system. Conversely, knowledge from theoretical work on information fusion may give a better understanding of the biology and behaviour of natural sensory systems. Here then, psychological and physiological knowledge of multi-sensory processing, and particularly the low level influence that different modalities have on one another, can be used to build upon existing theoretical work on computational mechanisms, such as self organisation and the combination of multiple neural networks, to help build systems that can fuse together different information sources. However, success in this area depends upon a cross-discipline understanding of these subjects.

Objectives

The workshop on biologically inspired information fusion was held to address this issue, attempting to bring together both life and physical scientists to discuss research from the perspective of the different disciplines, focused on the common theme of information fusion. The aim was to promote collaboration between the disciplines to develop an understanding of how to build adaptive information fusion systems. This initial workshop was targeted at bringing the disciplines together and helping improve our understanding of both the natural and artificial domains. This was achieved through a two-day programme of tutorials, discussion sessions, student presentations and brainstorming.

Impacts

This project has successfully met its objectives with a workshop programme designed to promote training and discussion. Participation exceeded target with 47 international participants, drawn from the disciplines of biology, psychology, computer science and robotics, including international research leaders in each field. Papers and discussion session abstracts were submitted to the workshop from each of the disciplines, resulting in four tutorials, four discussion sessions and three student presentations, each of which provoked lively debate and demonstrated the necessity of cross-discipline collaboration. Workshop activities also included three brainstorming sessions to help form cross-discipline research priorities. As a result of these activities, cross-discipline collaboration has been achieved, with at least two follow-up projects already being planned to develop adaptive models of multi-sensory integration. Evaluation of the objectives was carried out at the end of the workshop through anonymous questionnaire returned by over half the participants, with the majority of respondents reporting that the aim of the workshop had been met. The programmeproceedings and the final report for the workshop are available. All materials resulting from the workshop have been widely distributed, with further dissemination of the work via a special issue of the Information Fusion journal.

Funding

EPSRC (EP/E012795/1), IAS

Details

This project was done in collaboration with Dr Hujun Yin of the School of Electrical and Electronic Engineering, University of Manchester.

The workshop consisted of invited tutorials from discipline leaders to help summarise current knowledge of their field for a multi-disciplinary audience. Rising to this challenge were Professor Barry Stein (Department of Neurobiology and Anatomy, Wake Forest University School of Medicine), Dr Gemma Calvert (Multisensory Research Group in the Department of Psychology, University of Bath), Dr Charles Spence (Department of Psychology, Oxford University), Professor John Foxe (School of Psychology, City College of New York), Dr Belur Dasarathy (Editor-in-Chief of the Elsevier Information Fusion Journal and technologies consultant) and Dr Gerard McKee (School of Systems Engineering, University of Reading). In addition to tutorials, discussion sessions were invited to provoke cross-discipline debate of ideas and questions. Accepted discussions were led by Professor Alex Thomson (Department of Pharmacology, University of London), Professor Hans Colonius (Department of Psychology, University of Oldenburg), Professor Robert Damper (School of Electronics and Computer Science, University of Southampton) and Professor Leslie Smith (Department of Computing Science and Mathematics, University of Stirling). Student papers were also invited for peer review, with three papers presented at the workshop.

Investigators