Graph-based concept weighting for medical information retrieval

This paper presents a graph-based method to weight medical concepts in documents for the purposes of information retrieval. Medical concepts are extracted from free-text documents using a state-of-the-art technique that maps n-grams to concepts from the SNOMED CT medical ontology. In our graph-based concept representation, concepts are vertices in a graph built from a document, edges represent associations between concepts. This representation naturally captures dependencies between concepts, an important requirement for interpreting medical text, and a feature lacking in bag-of-words representations. We apply existing graph-based term weighting methods to weight medical concepts. Using concepts rather than terms addresses vocabulary mismatch as well as encapsulates terms belonging to a single medical entity into a single concept. In addition, we further extend previous graph-based approaches by injecting domain knowledge that estimates the importance of a concept within the global medical domain. Retrieval experiments on the TREC Medical Records collection show our method outperforms both term and concept baselines. More generally, this work provides a means of integrating background knowledge contained in medical ontologies into data-driven information retrieval approaches.

Tubule detection in testis images using boundary weighting and circular shortest path

In studies of germ cell transplantation, measureing tubule diameters and counting cells from different populations using antibodies as markers are very important. Manual measurement of tubule sizes and cell counts is a tedious and sanity grinding work. In this paper, we propose a new boundary weighting based tubule detection method. We first enhance the linear features of the input image and detect the approximate centers of tubules. Next, a boundary weighting transform is applied to the polar transformed image of each tubule region and a circular shortest path is used for the boundary detection. Then, ellipse fitting is carried out for tubule selection and measurement. The algorithm has been tested on a dataset consisting of 20 images, each having about 20 tubules. Experiments show that the detection results of our algorithm are very close to the results obtained manually. © 2013 IEEE.

Edge-weighting of gene expression graphs

In recent years, considerable research efforts have been directed to micro-array technologies and their role in providing simultaneous information on expression profiles for thousands of genes. These data, when subjected to clustering and classification procedures, can assist in identifying patterns and providing insight on biological processes. To understand the properties of complex gene expression datasets, graphical representations can be used. Intuitively, the data can be represented in terms of a bipartite graph, with weighted edges corresponding to gene-sample node couples in the dataset. Biologically meaningful subgraphs can be sought, but performance can be influenced both by the search algorithm, and, by the graph-weighting scheme and both merit rigorous investigation. In this paper, we focus on edge-weighting schemes for bipartite graphical representation of gene expression. Two novel methods are presented: the first is based on empirical evidence; the second on a geometric distribution. The schemes are compared for several real datasets, assessing efficiency of performance based on four essential properties: robustness to noise and missing values, discrimination, parameter influence on scheme efficiency and reusability. Recommendations and limitations are briefly discussed. Keywords: Edge-weighting; weighted graphs; gene expression; bi-clustering

Delay-dependent robust H-infinity control for uncertain systems with time-varying delay

This paper proposes a new approach for delay-dependent robust H-infinity stability analysis and control synthesis of uncertain systems with time-varying delay. The key features of the approach include the introduction of a new Lyapunov–Krasovskii functional, the construction of an augmented matrix with uncorrelated terms, and the employment of a tighter bounding technique. As a result, significant performance improvement is achieved in system analysis and synthesis without using either free weighting matrices or model transformation. Examples are given to demonstrate the effectiveness of the proposed approach.

International review of environmental assessment tools and databases

Existing widely known environmental assessment models, primarily those for Life Cycle Assessment of manufactured products and buildings, were reviewed to grasp their characteristics, since the past several years have seen a significant increase in interest and research activity in the development of building environmental assessment methods. Each method or tool was assessed under the headings of description, data requirement, end-use, assessment criteria (scale of assessment and scoring/ weighting system)and present status

Nation & internation practices in decision support tools in road asset management

This document provides a review of international and national practices in investment decision support tools in road asset management. Efforts were concentrated on identifying analytic frameworks, evaluation methodologies and criteria adopted by current tools. Emphasis was also given to how current approaches support Triple Bottom Line decision-making. Benefit Cost Analysis and Multiple Criteria Analysis are principle methodologies in supporting decision-making in Road Asset Management. The complexity of the applications shows significant differences in international practices. There is continuing discussion amongst practitioners and researchers regarding to which one is more appropriate in supporting decision-making. It is suggested that the two approaches should be regarded as complementary instead of competitive means. Multiple Criteria Analysis may be particularly helpful in early stages of project development, say strategic planning. Benefit Cost Analysis is used most widely for project prioritisation and selecting the final project from amongst a set of alternatives. Benefit Cost Analysis approach is useful tool for investment decision-making from an economic perspective. An extension of the approach, which includes social and environmental externalities, is currently used in supporting Triple Bottom Line decision-making in the road sector. However, efforts should be given to several issues in the applications. First of all, there is a need to reach a degree of commonality on considering social and environmental externalities, which may be achieved by aggregating the best practices. At different decision-making level, the detail of consideration of the externalities should be different. It is intended to develop a generic framework to coordinate the range of existing practices. The standard framework will also be helpful in reducing double counting, which appears in some current practices. Cautions should also be given to the methods of determining the value of social and environmental externalities. A number of methods, such as market price, resource costs and Willingness to Pay, are found in the review. The use of unreasonable monetisation methods in some cases has discredited Benefit Cost Analysis in the eyes of decision makers and the public. Some social externalities, such as employment and regional economic impacts, are generally omitted in current practices. This is due to the lack of information and credible models. It may be appropriate to consider these externalities in qualitative forms in a Multiple Criteria Analysis. Consensus has been reached in considering noise and air pollution in international practices. However, Australia practices generally omitted these externalities. Equity is an important consideration in Road Asset Management. The considerations are either between regions, or social groups, such as income, age, gender, disable, etc. In current practice, there is not a well developed quantitative measure for equity issues. More research is needed to target this issue. Although Multiple Criteria Analysis has been used for decades, there is not a generally accepted framework in the choice of modelling methods and various externalities. The result is that different analysts are unlikely to reach consistent conclusions about a policy measure. In current practices, some favour using methods which are able to prioritise alternatives, such as Goal Programming, Goal Achievement Matrix, Analytic Hierarchy Process. The others just present various impacts to decision-makers to characterise the projects. Weighting and scoring system are critical in most Multiple Criteria Analysis. However, the processes of assessing weights and scores were criticised as highly arbitrary and subjective. It is essential that the process should be as transparent as possible. Obtaining weights and scores by consulting local communities is a common practice, but is likely to result in bias towards local interests. Interactive approach has the advantage in helping decision-makers elaborating their preferences. However, computation burden may result in lose of interests of decision-makers during the solution process of a large-scale problem, say a large state road network. Current practices tend to use cardinal or ordinal scales in measure in non-monetised externalities. Distorted valuations can occur where variables measured in physical units, are converted to scales. For example, decibels of noise converts to a scale of -4 to +4 with a linear transformation, the difference between 3 and 4 represents a far greater increase in discomfort to people than the increase from 0 to 1. It is suggested to assign different weights to individual score. Due to overlapped goals, the problem of double counting also appears in some of Multiple Criteria Analysis. The situation can be improved by carefully selecting and defining investment goals and criteria. Other issues, such as the treatment of time effect, incorporating risk and uncertainty, have been given scant attention in current practices. This report suggested establishing a common analytic framework to deal with these issues.

Illegal pedestrian crossing at signalised intersections : Incidence and relative risk

Illegal pedestrian behaviour is common and is reported as a factor in many pedestrian crashes. Since walking is being promoted for its health and environmental benefits, minimisation of its associated risks is of interest. The risk associated with illegal road crossing is unclear, and better information would assist in setting a rationale for enforcement and priorities for public education. An observation survey of pedestrian behaviour was conducted at signalised intersections in the Brisbane CBD (Queensland, Australia) on typical workdays, using behavioural categories that were identifiable in police crash reports. The survey confirmed high levels of crossing against the lights, or close enough to the lights that they should legally have been used. Measures of exposure for crossing legally, against the lights, and close to the lights were generated by weighting the observation data. Relative risk ratios were calculated for these categories using crash data from the observation sites and adjacent midblocks. Crossing against the lights and crossing close to the lights both exhibited a crash risk per crossing event approximately eight times that of legal crossing at signalised intersections. The implications of these results for enforcement and education are discussed, along with the limitations of the study.

Shifting the child protection juggernaut to earlier intervention

"For every complex problem there is a solution that is simple, neat and wrong (M.L. Mencken, US writer and social commentator). Nowhere is this quote more apt than when applied to finding over-simplified solutions to the complex problem of looking after the safety and well-being of vulnerable children. The easiest formula is, of course, to ‘rescue children from dysfunctional families’, a line taken recently in the monograph by the right wing think tank, Centre for Independent Studies (Sammut & O’Brien 2009). It is reasoning with fatal flaws. This commentary provides a timely reminder of the strong arguments which lie behind the national and international shift to supporting children and families through universal and specialist community-based services, rather than weighting all resources into statutory child protection interventions. A brief outline of the value of developing the resources to support children in their families, and the problems with 'rescuing' children through the child protection system are discussed.

TraSe algorithm : automatic evolutionary morphing of electronic dance music

The TraSe (Transform-Select) algorithm has been developed to investigate the morphing of electronic music through automatically applying a series of deterministic compositional transformations to the source, guided towards a target by similarity metrics. This is in contrast to other morphing techniques such as interpolation or parameters or probabilistic variation. TraSe allows control over stylistic elements of the music through user-defined weighting of numerous compositional transformations. The formal evaluation of TraSe was mostly qualitative and occurred through nine participants completing an online questionnaire. The music generated by TraSe was generally felt to be less coherent than a human composed benchmark but in some cases judged as more creative.

New Approach on Robust Delay-Dependent H∞ Control for Uncertain T-S Fuzzy Systems With Interval Time-Varying Delay

This paper investigates the robust H∞ control for Takagi-Sugeno (T-S) fuzzy systems with interval time-varying delay. By employing a new and tighter integral inequality and constructing an appropriate type of Lyapunov functional, delay-dependent stability criteria are derived for the control problem. Because neither any model transformation nor free weighting matrices are employed in our theoretical derivation, the developed stability criteria significantly improve and simplify the existing stability conditions. Also, the maximum allowable upper delay bound and controller feedback gains can be obtained simultaneously from the developed approach by solving a constrained convex optimization problem. Numerical examples are given to demonstrate the effectiveness of the proposed methods.

Adaptive dual control of topic-based information retrieval

Information Retrieval is an important albeit imperfect component of information technologies. A problem of insufficient diversity of retrieved documents is one of the primary issues studied in this research. This study shows that this problem leads to a decrease of precision and recall, traditional measures of information retrieval effectiveness. This thesis presents an adaptive IR system based on the theory of adaptive dual control. The aim of the approach is the optimization of retrieval precision after all feedback has been issued. This is done by increasing the diversity of retrieved documents. This study shows that the value of recall reflects this diversity. The Probability Ranking Principle is viewed in the literature as the “bedrock” of current probabilistic Information Retrieval theory. Neither the proposed approach nor other methods of diversification of retrieved documents from the literature conform to this principle. This study shows by counterexample that the Probability Ranking Principle does not in general lead to optimal precision in a search session with feedback (for which it may not have been designed but is actively used). Retrieval precision of the search session should be optimized with a multistage stochastic programming model to accomplish the aim. However, such models are computationally intractable. Therefore, approximate linear multistage stochastic programming models are derived in this study, where the multistage improvement of the probability distribution is modelled using the proposed feedback correctness method. The proposed optimization models are based on several assumptions, starting with the assumption that Information Retrieval is conducted in units of topics. The use of clusters is the primary reasons why a new method of probability estimation is proposed. The adaptive dual control of topic-based IR system was evaluated in a series of experiments conducted on the Reuters, Wikipedia and TREC collections of documents. The Wikipedia experiment revealed that the dual control feedback mechanism improves precision and S-recall when all the underlying assumptions are satisfied. In the TREC experiment, this feedback mechanism was compared to a state-of-the-art adaptive IR system based on BM-25 term weighting and the Rocchio relevance feedback algorithm. The baseline system exhibited better effectiveness than the cluster-based optimization model of ADTIR. The main reason for this was insufficient quality of the generated clusters in the TREC collection that violated the underlying assumption.

Incidental walking activity is sufficient to induce time-dependent conditioning of the Achilles tendon

The Achilles tendon has been seen to exhibit time-dependent conditioning when isometric muscle actions were of a prolonged duration, compared to those involved in dynamic activities, such as walking. Since, the effect of short duration muscle activation associated with dynamic activities is yet to be established, the present study aimed to investigate the effect of incidental walking activity on Achilles tendon diametral strain. Eleven healthy male participants refrained from physical activity in excess of the walking required to carry out necessary daily tasks and wore an activity monitor during the 24 h study period. Achilles tendon diametral strain, 2 cm proximal to the calcaneal insertion, was determined from sagittal sonograms. Baseline sonographic examinations were conducted at ∼08:00 h followed by replicate examinations at 12 and 24 h. Walking activity was measured as either present (1) or absent (0) and a linear weighting function was applied to account for the proximity of walking activity to tendon examination time. Over the course of the day the median (min, max) Achilles tendon diametral strain was −11.4 (4.5, −25.4)%. A statistically significant relationship was evident between walking activity and diametral strain (P < 0.01) and this relationship improved when walking activity was temporally weighted (AIC 131 to 126). The results demonstrate that the short yet repetitive loads generated during activities of daily living, such as walking, are sufficient to induce appreciable time-dependant conditioning of the Achilles tendon. Implications arise for the in vivo measurement of Achilles tendon properties and the rehabilitation of tendinopathy.

A process for the management of physical infrastructure

Physical infrastructure assets are important components of our society and our economy. They are usually designed to last for many years, are expected to be heavily used during their lifetime, carry considerable load, and are exposed to the natural environment. They are also normally major structures, and therefore present a heavy investment, requiring constant management over their life cycle to ensure that they perform as required by their owners and users. Given a complex and varied infrastructure life cycle, constraints on available resources, and continuing requirements for effectiveness and efficiency, good management of infrastructure is important. While there is often no one best management approach, the choice of options is improved by better identification and analysis of the issues, by the ability to prioritise objectives, and by a scientific approach to the analysis process. The abilities to better understand the effect of inputs in the infrastructure life cycle on results, to minimise uncertainty, and to better evaluate the effect of decisions in a complex environment, are important in allocating scarce resources and making sound decisions. Through the development of an infrastructure management modelling and analysis methodology, this thesis provides a process that assists the infrastructure manager in the analysis, prioritisation and decision making process. This is achieved through the use of practical, relatively simple tools, integrated in a modular flexible framework that aims to provide an understanding of the interactions and issues in the infrastructure management process. The methodology uses a combination of flowcharting and analysis techniques. It first charts the infrastructure management process and its underlying infrastructure life cycle through the time interaction diagram, a graphical flowcharting methodology that is an extension of methodologies for modelling data flows in information systems. This process divides the infrastructure management process over time into self contained modules that are based on a particular set of activities, the information flows between which are defined by the interfaces and relationships between them. The modular approach also permits more detailed analysis, or aggregation, as the case may be. It also forms the basis of ext~nding the infrastructure modelling and analysis process to infrastructure networks, through using individual infrastructure assets and their related projects as the basis of the network analysis process. It is recognised that the infrastructure manager is required to meet, and balance, a number of different objectives, and therefore a number of high level outcome goals for the infrastructure management process have been developed, based on common purpose or measurement scales. These goals form the basis of classifYing the larger set of multiple objectives for analysis purposes. A two stage approach that rationalises then weights objectives, using a paired comparison process, ensures that the objectives required to be met are both kept to the minimum number required and are fairly weighted. Qualitative variables are incorporated into the weighting and scoring process, utility functions being proposed where there is risk, or a trade-off situation applies. Variability is considered important in the infrastructure life cycle, the approach used being based on analytical principles but incorporating randomness in variables where required. The modular design of the process permits alternative processes to be used within particular modules, if this is considered a more appropriate way of analysis, provided boundary conditions and requirements for linkages to other modules, are met. Development and use of the methodology has highlighted a number of infrastructure life cycle issues, including data and information aspects, and consequences of change over the life cycle, as well as variability and the other matters discussed above. It has also highlighted the requirement to use judgment where required, and for organisations that own and manage infrastructure to retain intellectual knowledge regarding that infrastructure. It is considered that the methodology discussed in this thesis, which to the author's knowledge has not been developed elsewhere, may be used for the analysis of alternatives, planning, prioritisation of a number of projects, and identification of the principal issues in the infrastructure life cycle.