A problem structuring method for ecosystem-based management : the DPSIR modelling process

The purpose of this paper is to learn from Complex Adaptive Systems (CAS) theory to inform the development of Problem Structuring Methods (PSMs) both in general and in the specific context of marine management. The focus on marine management is important because it is concerned with a CAS (formed through the interconnection between natural systems, designed systems and social systems) which exemplifies their particularly ‘wicked' nature. Recognition of this compels us to take seriously the need to develop tools for knowledge elicitation and structuring which meet the demands of CAS. In marine management, chief among those tools is the DPSIR (Drivers - Pressures - State Changes - Impacts - Responses) model and, although widely applied, the extent to which it is appropriate for dealing with the demands of a CAS is questionable. Such questioning is particularly pertinent in the context of the marine environment where there is a need to not only recognise a broad range of stakeholders (a question of boundary critique) but also to manage competing knowledge (economic, local and scientific) and value claims. Hence this paper emphasises how a CAS perspective might add impetus to the development of a critical perspective on DPSIR and PSM theory and practice to promote a more systemic view of decision-making and policy development

The non-codified use of problem structuring methods and the need for a generic constitutive definition

This is the author accepted manuscript. The final version is available from the publisher via the DOI in this record.When we use a PSM what is it we are actually doing? An answer to this question would enable the PSM community to considerably enlarge the available source of case studies by the inclusion of examples of non-codified PSM use. We start from Checkland's own proposal for a "constitutive definition" of SSM, which originated from trying to answer the question of knowing when a claim of SSM use was legitimate. By extending this idea to a generic constitutive definition for all PSMs leads us to propose a self-consistent labelling schema for observed phenomena arising from PSMs in action. This consists of a set of testable propositions, which, through observation of putative PSM use, can be used to assess validity of claims of PSM use. Such evidential support for the propositions as may be found in putative PSM use can then make it back into a broader axiomatic formulation of PSMs through the use of a set-Theoretic approach, which enables our method to scale to large data sets. The theoretical underpinning to our work is in causal realism and middle range theory. We illustrate our approach through the analysis of three case studies drawn from engineering organisations, a rich source of possible non-codified PSM use. The combination of a method for judging cases of non-codified PSM use, sound theoretical underpinning, and scalability to large data sets, we believe leads to a demystification of PSMs and should encourage their wider use. © 2014 Elsevier B.V. All rights reserved

MUMAL: multivariate analysis in shotgun proteomics using machine learning techniques.

BACKGROUND: The shotgun strategy (liquid chromatography coupled with tandem mass spectrometry) is widely applied for identification of proteins in complex mixtures. This method gives rise to thousands of spectra in a single run, which are interpreted by computational tools. Such tools normally use a protein database from which peptide sequences are extracted for matching with experimentally derived mass spectral data. After the database search, the correctness of obtained peptide-spectrum matches (PSMs) needs to be evaluated also by algorithms, as a manual curation of these huge datasets would be impractical. The target-decoy database strategy is largely used to perform spectrum evaluation. Nonetheless, this method has been applied without considering sensitivity, i.e., only error estimation is taken into account. A recently proposed method termed MUDE treats the target-decoy analysis as an optimization problem, where sensitivity is maximized. This method demonstrates a significant increase in the retrieved number of PSMs for a fixed error rate. However, the MUDE model is constructed in such a way that linear decision boundaries are established to separate correct from incorrect PSMs. Besides, the described heuristic for solving the optimization problem has to be executed many times to achieve a significant augmentation in sensitivity. RESULTS: Here, we propose a new method, termed MUMAL, for PSM assessment that is based on machine learning techniques. Our method can establish nonlinear decision boundaries, leading to a higher chance to retrieve more true positives. Furthermore, we need few iterations to achieve high sensitivities, strikingly shortening the running time of the whole process. Experiments show that our method achieves a considerably higher number of PSMs compared with standard tools such as MUDE, PeptideProphet, and typical target-decoy approaches. CONCLUSION: Our approach not only enhances the computational performance, and thus the turn around time of MS-based experiments in proteomics, but also improves the information content with benefits of a higher proteome coverage. This improvement, for instance, increases the chance to identify important drug targets or biomarkers for drug development or molecular diagnostics

Understanding participant actions in OR interventions using practice theories: a research agenda

This is the author accepted manuscript. The final version is available on open access from Elsevier via the DOI in this recordPractice theory is a collective concept embodying a group of social theories that take practice, in other words actions, as the central focus of their theorising. In this paper we examine the intellectual development of practice theory, highlighting the importance of the key ideas that have shaped thinking on organisational activities and show their relevance to OR. In particular, we examine the social theories that OR researchers have adopted, what data was captured, and how it was analysed in order to establish empirical grounding in case studies involving workshops and meetings published by OR researchers. The cases thus provide a useful empirical basis for comparison to outline the prospects for the use of practice theories by OR academic researchers. Finally, we propose an agenda to advance the understanding of practice theories and their contribution to the theory and practice of OR

Problem structuring methods for collaboration: A conceptual development, with an application to a construction partnership in the UK.

Problem structuring methods (PSMs) have been developed within operational research (OR) to assist a set of actors to agree on a problem structure and make commitments to consequential action. Their characteristic feature is the use of a model to represent alternative versions of the problem of common interest, combined with facilitation to help actors make constructive mutual adjustments. Whilst most PSMs have traditionally been applied with actors confronting problems within organizations, others have also been applied with actors working between and across organisations to address a problem of common interest. This research will explore the significance of PSMs in collaborative contexts of this kind. The aim of this research is to investigate the possible roles of PSMs in assisting actors of an inter-organisational domain who engage in collaboration to address a problematique of common interest in order to reach joint agreements with respect to it. The hypothesis investigated in this research is that the analytical assistance provided by PSMs can be expected to contribute to a collaboration process principally through improving actors' sense-making of their problematique, and through providing structure to the product of this sense- making activity. The interpretation of our hypothesis is that PSMs generate this effect through improving the quality of dialogue between actors. This effect should tend to impact positively on the ownership of the commitments resulting from the dialogue, and on mutual accommodations in the power balance among actors. In order to articulate this hypothesis, it has been necessary to conduct some conceptual clarification to achieve a clear meaning for the terms 'shared meaning', 'power', and 'dialogue'. Building upon this conceptual clarification, a model of collaboration as a process has been developed, which identifies the factors, pre-requisites and processes involved in actors' ability to achieve the intended products of collaboration. This model provides the basis for identifying the possible effects of PSMs, and for evaluating their effectiveness. To explore our hypothesis and the adequacy of the conceptual model, a case study drawn from an action research project in the UK construction industry was carried out. This action research project was industry-academic collaboration aimed at contributing to build a high value construction environment, and its principal output was the development of a PSM-based methodology for construction project reviews. The case study reported in this thesis involved the application of this methodology in a multi-organizational construction partnership in the hotel business. This involved engagement in and observation of ongoing partnership activity of three construction project teams. Reasonably clear and positive effects from the application of the methodology were found in the dialogue between participants, consistent with the hypothesis. Additional positive effects in terms of achieving inter-organisational learning within the selected partnership were also identified. Overall the results of the case study are encouraging; however, as they result from the application of a particular PSM-based methodology, extrapolation to more general conclusions about the potential of PSMs for multi-organisational collaboration should be made with caution. Nevertheless, the results of this research suggest valuable potential avenues for further research. The case experience also was generally supportive of the conceptual model of the collaboration process, in that the activities and processes observed could be interpreted without difficulties within the model's framework. The model offers a means for further theoretical and empirical work aimed at confirming and enriching its structure and validity