SRG Seminar: “Simulating a pulmonary tuberculosis infection using a network-based metapopulation model” by Michael Pitcher and “A Fake City of People: Modeling the Co-evolution of City and Citizens” by Xue Guo

Event details
When: 28th September 2017 13:00 – 14:00
Where: Cole 1.33b
Series: Systems Seminars Series
Format: Seminar

Michael Pitcher’s abstract

Tuberculosis (TB) is one of the world’s most deadly infectious diseases, claiming over 1.4 million lives every year. TB infections typically affect the lungs and treatment regimens are long and arduous, requiring at least 6 months of daily chemotherapy. Previous investigations have shown TB to have unique localisations within the lung at varying stages of infection. The initial implant and the primary lesion which arises from it can occur anywhere in the lungs, with a greater probability of occurrence in the lower to middle regions of the lung. However, reactivation of a previously latent form of disease always involves cavitation of the tissue at the apical regions. This difference in spatial location of TB infections suggests two important factors: i) bacteria are able to disseminate across the lung in some manner, and ii) the environment at the top of the lung has some properties that make it preferential for TB replication.

In this project, we aim to build a whole-organ model of the lung and surrounding lymphatics which incorporates both bacterial dissemination possibilities and lung tissue spatial heterogeneity in order to understand their impact on TB. We develop ComMeN (Compartmentalised Metapopulation Network), a Python framework designed to allow the easy creation of complex network-based metapopulations with spatial heterogeneity upon which interaction dynamics can be applied, with discrete event modelling using the Gillespie Algorithm. We then extend this framework to create a TB-specific model, PTBComMeN, which models a TB infection occurring over lung tissue which is divided into patches, each of which contains spatial attributes appropriate to its position in the lung, such as ventilation, perfusion and oxygen tension. Events dictate the interactions between cells and bacteria and their interaction with the environment, with dissemination occurring between edges joining patches on the lung network. This model allows experimentation into studying the effects spatial heterogeneities and bacterial dissemination may have on the progression of disease and the model is designed to provide insight into the factors that result in long treatment times for TB.

Xue Guo’s abstract

By the year 2050, the global urban population will reach 2.5 billion. While the fast pace of urbanisation brings improved quality of life initially, the surging population will inevitably lead to unique urban issues. Emerging research fields, with the aim of creating smarter cities, plan to counteract these problems. To facilitate this research, we need solid models to generate ’fake cities’, which cannot be easily produced by existing random graph algorithms due to spatial constraints. Therefore, we propose a new model for the co-evolution of city and population, which can show how street network forms, how population spreads and how settlements emerge and diminish. The new model will be a random city generator, which could be used to backtrack the history and predict the future of a city, or act as test cases for the validation and evaluation of urban optimisation algorithms.

n-Queens Completion is NP-Complete

Peter Nightingale and Ian Gent at Falkland Palace, Wednesday, 17 August 2017.
©Stuart Nicol Photography, 2017

Ian Gent, Christopher Jefferson and Peter Nightingale have shown that a classic chess puzzle is NP-Complete. Their paper “Complexity of n-Queens Completion” was published in the Journal of Artificial Intelligence Research on August 30.

The n-Queens puzzle is a classic chess problem: given a chessboard of size n by n, can you place n queens so that no two queens attack each other?  That is, can you place the queens with no two queens are on the same row, column, or diagonal? The n-Queens puzzle has long been known to be simple to solve:  you can solve the problem for all n except 2 and 3, and solutions for all other n can be described in a few lines.  This very simplicity has led to repeated controversy in Artificial Intelligence (AI). The n-Queens puzzle is often used as a benchmark problem, but good results on the problem can always be challenged because the problem is so simple to solve without using AI methods.

The new work follows a challenge on Facebook on New Year’s Day, 2015, when a friend of Ian’s asked him how hard n-Queens is if some queens were already placed on the board.  It turns out, this version (dating from 1850) of the puzzle is only two years younger than the more famous n-Queens problem. The picture shows Peter (left) and Ian (right) with queens on the board at positions suggested by Nauck in 1850, the squares b4 and d5.  Can you put another 6 queens on the board so that the entire board is a solution of 8-Queens?  The general version with some number of queens preplaced on an n by n board is the n-Queens Completion puzzle.

 

With queens at b4 and d5, can you place 6 more queens to get a solution to the 8-queens puzzle? ©Stuart Nicol Photography, 2017

Ian, Christopher and Peter have shown that the n-Queens puzzle is in fact hard, not simple.  It belongs to the complexity classes NP-Complete and #P-Complete. Other NP-Complete problems include the “travelling salesperson problem”, finding cliques in graphs, and many other important problems, from scheduling to circuit layout. This puts n-Queens Completion at the centre of the most important theoretical problem in computer science — it has long been known that either all NP-complete problems are easy, or none of them are. Most computer scientists believe that this means there is no efficient algorithm possible for solving this problem, compared to the very simple techniques long known for n-Queens.
The importance of this work is that it provides researchers with a benchmark that can be used for evaluating AI techniques. Moreover, it helps to explain why so many AI techniques have been used on the n-Queens puzzle. Most techniques do most of their work with some queens partially placed, using some form of (hopefully intelligent) trial and error. In fact it turns out that many researchers – in order to solve a simple problem – have solved it by turning the simple problem of n-Queens into the hard problem of n-Queens Completion.
It does seem that AI researchers should not use n-Queens as a benchmark, but the very closely related n-Queens Completion puzzle is a valid benchmark. As well as the theoretical results, the paper shows how example instances can be generated which appear to be hard in practice. Some caution is still needed, though. It does seem to be quite hard to generate hard instances of n-Queens Completion.
The University has also issued an article on the same paper, under the title “Simple” chess puzzle holds key to $1m prize

Containers for HPC environments

Rethinking High performance computing Platforms: Challenges, Opportunities and Recommendations, co-authored by Adam Barker and a team (Ole Weidner, Malcolm Atkinson, Rosa Filgueira Vicente) in the School of Informatics, University of Edinburgh was recently featured in the Communications of the ACM and HPC Wire.

The paper focuses on container technology and argues that a number of “second generation” high-performance computing applications with heterogeneous, dynamic and data-intensive properties have an extended set of requirements, which are not met by the current production HPC platform models and policies. These applications (and users) require a new approach to supporting infrastructure, which draws on container-like technology and services. The paper then goes on to describe cHPC: an early prototype of an implementation based on Linux Containers (LXC).

Ali Khajeh-Hosseini, Co-founder of AbarCloud and former co-founder of ShopForCloud (acquired by RightScale as PlanForCloud) said of this research, “Containers have helped speed-up the development and deployment of applications in heterogeneous environments found in larger enterprises. It’s interesting to investigate their applications in similar types of environments in newer HPC applications.

DHSI Seminar Series (Digital Health Science Initiative)

Event details

  • When: 14th June 2017 12:00 - 14:00
  • Where: N Haugh, St Andrews
  • Format: Seminar

“Addiction”

Seminar Room 1 School of Medicine

12:00: Alex Baldacchino- Introduction

12:15: Ognjen Arandjelović & Aniqa Aslam- Understanding Fatal and Non-Fatal Drug Overdose Risk Factors in Fife: Overdose Risk (OdRi) tool

12:45: Damien Williams & Fergus Neville- Transdermal alcohol monitoring

13:15: David Harris-Birtill & David Morrison- Narco Cat – waste water analysis in substance misuse – a novel epidemiological tool

13:15 – 14.00: All Questions & Opportunities

Seminar: Propagation and Reification: SAT and SMT in Prolog (continued)

Event details

  • When: 23rd June 2017 13:00 - 14:00
  • Where: Cole 1.33a
  • Series: AI Seminar Series
  • Format: Seminar

Jacob Howe, City University, London

Abstract: This talk will recap how a watched literal DPLL based SAT solver can be succinctly coded in 20 lines of Prolog. The focus of the talk will be the extension of this solver to an SMT solver which will be discussed with a particular focus on the case where the theory is that of rational-tree constraints, and its application in a reverse engineering problem.
[Note change of time from that previously advertised]

SRG Seminar: Evaluation Techniques for Detection Model Performance in Anomaly Network Intrusion Detection System by Amjad Al Tobi

Event details

  • When: 1st June 2017 13:00 - 14:00
  • Where: Cole 1.33b
  • Series: Systems Seminars Series
  • Format: Seminar

Everyday advancements in technology brings with it novel challenges and threats. Such advancement imposes greater risks than ever on systems and services, including individual privacy information. Relying on intrusion specialists to come up with new signatures to detect different types of new attacks, does not seem to scale with excessive traffic growth. Therefore, anomaly-based detection provides a promising solution for this problem area.

Anomaly-based IDS applies machine learning, data mining and/or artificial intelligence along with many other methods to solve this problem. Currently, these solutions seem not to be tractable for real production environments due to the high false alarms rate. This might be a result of such systems not being able to determine the point at which an update is required. It is not clear how detection models will behave over time, when traffic behaviour has changed since the last time the model was re-generated.
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SRG Seminar: New Network Functionality using ILNPv6 and DNS by Khawar Shehzad

Event details

  • When: 18th May 2017 13:00 - 14:00
  • Where: Cole 1.33b
  • Series: Systems Seminars Series
  • Format: Seminar

This research deals with the introduction of a new network functionality based on Identifier-Locator Network Protocol version 6 (ILNPv6), and Domain Name System (DNS). The chosen area of concern is security and specifically mitigation of Distributed Denial of Service (DDoS). The functionality proposed and tested deals with the issues of vulnerability testing, probing, and scanning which directly lead to a successful DDoS attack. The solutions presented can be used as a reactive measure to these security issues. The DDoS is chosen because in recent years DDoS have become the most common and hard to defend attacks. These attacks are on the availability of system/site. There are multiple solutions in the literature but no one solution is based on ILNPv6, and are complex in nature. Similarly, the solutions in literature either require modification in the providers’ networks or they are complex if they are only site-based solutions. Most of these solutions are based on IPv6 protocol and they do not use the concept of naming, as proposed by ILNPv6.

The prime objectives of this research are:

  • to defend against DDoS attacks with the use of naming and DNS
  • to increase the attacker’s effort, reduce vulnerability testing, and random probing by attackers
  • to practically demonstrate the effectiveness of the ILNPv6-based solution for security

SRG Seminar: Investigation of Virtual Network Isolation Security in Cloud Computing Using Penetration Testing by Haifa Al Nasseri

Event details

  • When: 4th May 2017 13:00 - 14:00
  • Where: Cole 1.33b
  • Series: Systems Seminars Series
  • Format: Talk

Software Defined Networking (SDN) or Virtual Networks (VNs) are required for cloud tenants to leverage demands. However, multi-tenancy can be compromised without proper isolation. Much research has been conducted into VN Isolation; many researchers are not tackling security aspects or checking if their isolation evaluation is complete. Therefore, data leakage is a major security concern in the cloud in general.

This research uses an OpenStack VN and OpenStack Tenant Network to test multi-tenancy features. We are evaluating the relationship between isolation methods used in cloud VN and the amount of data being leaked through using penetration tests. These tests will be used to identify the vulnerabilities causing cloud VN data leakage and to investigate how the vulnerabilities, and the leaked data, can compromise the tenant Virtual Networks.