| 1. |
- Bennich-Björkman, Oscar, et al.
(author)
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The Next 700 Unit of Measurement Checkers
- 2018
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In: Proceedings of the 11th ACM SIGPLAN International Conference on Software Language Engineering (SLE '18). - New York, NY, USA : Association for Computing Machinery (ACM). - 9781450360296 ; , s. 121-132
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Conference paper (peer-reviewed)abstract
- In scientific applications, physical quantities and units of measurement are used regularly. If the inherent incompatibility between these units is not handled properly it can lead to major, sometimes catastrophic, problems. Although the risk of a miscalculation is high and the cost equally so, almost none of the major programming languages has support for physical quantities. Instead, scientific code developers often make their own tools or rely on external libraries to help them spot or prevent these mistakes. We employed a systematic approach to examine and analyse all available physical quantity open-source libraries. Approximately 3700 search results across seven repository hosting sites were condensed into a list of 82 of the most comprehensive and well-developed libraries currently available. In this group, 30 different programming languages are represented. Out of these 82 libraries, 38 have been updated within the last two years. These 38 are summarised in this paper as they are deemed the most relevant. The conclusion we draw from these results is that there is clearly too much diversity, duplicated efforts, and a lack of code sharing and harmonisation which discourages use and adoption.
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| 2. |
- Gallina, Barbara, et al.
(author)
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Towards Explainable, Compliant and Adaptive Human-Automation Interaction
- 2020
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In: Proceedings of the 3rd EXplainable AI in Law Workshop (XAILA 2020).
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Conference paper (peer-reviewed)abstract
- AI-based systems use trained machine learning models to make important decisions in critical contexts. The EU guidelines for trustworthy AI emphasise the respect for human autonomy, prevention of harm, fairness, and explicability. Many successful machine learning methods, however, deliver opaque models where the reasons for decisions remain unclear to the end user. Hence, accountability and trust are difficult to ascertain. In this position paper, we focus on AI systems that are expected to interact with humans and we propose our visionary architecture, called ECA-HAI (Explainable, Compliant and Adaptive Human-Automation Interaction)-RefArch. ECA-HAI-RefArch allows for building intelligent systems where humans and AIs form teams, able to learn from data but also to learn from each other by playing “serious games”, for a continuous improvement of the overall system. Finally, conclusions are drawn.
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| 3. |
- Johnson, David, et al.
(author)
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Dealing with Diversity in Computational Cancer Modeling
- 2013
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In: Cancer Informatics. - : Libertas Academica Ltd. - 1176-9351. ; 12, s. 115-124
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Journal article (peer-reviewed)abstract
- This paper discusses the need for interconnecting computational cancer models from different sources and scales within clinically relevant scenarios to increase the accuracy of the models and speed up their clinical adaptation, validation, and eventual translation. We briefly review current interoperability efforts drawing upon our experiences with the development of in silico models for predictive oncology within a number of European Commission Virtual Physiological Human initiative projects on cancer. A clinically relevant scenario, addressing brain tumor modeling that illustrates the need for coupling models from different sources and levels of complexity, is described. General approaches to enabling interoperability using XML-based markup languages for biological modeling are reviewed, concluding with a discussion on efforts towards developing cancer-specific XML markup to couple multiple component models for predictive in silico oncology.
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| 4. |
- Johnson, David, et al.
(author)
-
Modular markup for simulating vascular tumour growth
- 2012
-
Conference paper (peer-reviewed)abstract
- In this paper we present preliminary results of the first application of TumorML being developed outside of the context of the Transatlantic TUmor Model Repositories project (TUMOR). Based on a domain-specific software framework for developing models to simulate vascular tumour growth, we have developed a corresponding domain-specific language (DSL) for use with the framework. The DSL script is directly embedded into TumorML model descriptions serving as an example of how within a single model description document, we can fully describe cancer models as functional components. We introduce the framework that our DSL orchestrates; show fragments of DSL script we have developed to describe tumour-induced angiogenesis; and how these functional model descriptions can be integrated and executed with TumorML markup.
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| 5. |
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| 6. |
- Johnson, David, et al.
(author)
-
TumorML : Concept and requirements of an in silico cancer modelling markup language
- 2011
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Conference paper (peer-reviewed)abstract
- This paper describes the initial groundwork car- ried out as part of the European Commission funded Transatlantic Tumor Model Repositories project, to develop a new markup language for computational cancer modelling, TumorML. In this paper we describe the motivations for such a language, arguing that current state-of-the-art biomodelling languages are not suited to the cancer modelling domain. We go on to describe the work that needs to be done to develop TumorML, the conceptual design, and a description of what existing markup languages will be used to compose the language specification.
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| 7. |
- McKeever, Steve, 1969-, et al.
(author)
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Abstraction in Physiological Modelling Languages
- 2013
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In: Symposium On Theory of Modeling and Simulation. - 9781627480321 ; , s. 76-83
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Conference paper (peer-reviewed)abstract
- In this paper we discuss two projects looking at applying advanced abstraction mechanisms from software engineering to the field of physiological modelling. We focus on two abstraction mechanisms commonly found in modern object-oriented programming languages: generics and inheritance. Generics allows classes to take other classes as parameters, allowing common behaviour to be described with particularities abstracted away. We demonstrate this technique on an example from heart modelling. Inheritance allows one to reuse code and to establish a subtype of an existing object. We focus on the benefits reaped from inheritance where this property enables run-time substitutability. This technique is demonstrated within the context of multi-scale tumour modelling. Finally, we look at how combining both techniques enables greater modularity and the construction of a model driven framework for the rapid creation and extension of families of biological models.
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| 8. |
- McKeever, Steve, 1969-
(author)
-
Acknowledging Implementation Trade-Offs When Developing with Units of Measurement
- 2023
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In: Model-Driven Engineering and Software Development. - Switzerland : Springer. - 9783031388200 - 9783031388217 ; , s. 25-47
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Book chapter (peer-reviewed)abstract
- Physical quantities expressed as units of measurement (UoM) are used regularly in scientific and engineering applications. The loss of the Mars climate orbiter, attributed to a confusion between the metric and imperial unit systems, popularised the disastrous consequences of incorrectly handling measurement values. We aim to classify the many solutions that have been proposed by looking at their capabilities and computational overheads. We assume an overall view, starting with a quantity aware Software Model, and then looking at the various approaches which allow these annotations to be transferred into code. Through a formal definition of both dimension checking and UoM conversion we are able to categorise the various options with regards to the stage at which they can be undertaken, their useability, and their coverage of potential errors.
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| 9. |
- McKeever, Steve, 1969-
(author)
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Discerning Quantities from Units of Measurement
- 2022
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In: Proceedings of the 10th International Conference on Model-Driven Engineering and Software Development. - Portugal : INSTICC Press. ; , s. 105-115
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Conference paper (peer-reviewed)abstract
- In scientific and engineering applications, physical quantities embodied as units of measurement (UoM) are frequently used. While managing units of measurement is a fairly mature topic in software engineering, more subtle metrological concepts such as named quantities have had little traction within the scientific programming community. The loss of the Mars climate orbiter, attributed to a confusion between the metric and imperial unit systems, popularised the disastrous consequences of incorrectly handling measurement values. This has led to the development of a large number of libraries, languages and tools to ensure developers can specify and validate UoM information in their designs and codes. However these systems do not differentiate between quantities and dimensions. For instance torque and work, which share the same UoM, can not be interchanged because they do not represent the same entity. We present a named quantity layer that sits on top of a dimension checker and unit con verter ensuring values of different quantities are correctly managed without undue restrictions. Our quantity algebra works alongside the unit dimensions to ensure we maintain named quantities when we perform arithmetic and function calls.
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| 10. |
- McKeever, Steve, 1969-
(author)
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From Quantities in Software Models to Implementation
- 2021
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In: Proceedings of the 9th international conference on model-driven engineering and software development (MODELSWARD). - : SciTePress. - 9789897584879 ; , s. 199-206
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Conference paper (peer-reviewed)abstract
- In scientific and engineering applications, physical quantities expressed as units of measurement (UoM) are used regularly. If the algebraic properties of a system's UoM information are incorrectly handled at run-time then catastrophic problems can arise. Much work has gone into creating libraries, languages and tools to ensure developers can leverage UoM information in their designs and codes. While there are technical solutions that allow units of measurement to be specified at both the model and code level, a broader assessment of their strengths and weaknesses has not been undertaken. Inspired by a survey of practitioners, we review four competing methods that support unit checking of code bases. The most straightforward solution is for the programming language to Natively support UoM as this allows for efficient unit conversion and static checking. Alas, none of the mainstream languages provide such support. Libraries might seem compelling, and all popular programming languages have a myriad of options, but they're cumbersome in practice and have specific performance costs. Libraries are best suited to applications in which UoM checking is desirable at run-time. Lightweight methods, such as Component based checking or Black Box testing, provide many benefits of UoM libraries with minimal overheads but sacrifice coverage and thus robustness. By separating and analysing the various options, we hope to enable scientific developers to select the most appropriate approach to transferring UoM information from their software models to their programs.
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| 11. |
- McKeever, Steve, 1969-
(author)
-
Managing Quantities and Units of Measurement in Code Bases
- 2023
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In: Updates on Software Usability. - : InTech. - 9781803566368 - 9781803566351 - 9781803566375 ; , s. 1-20
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Book chapter (peer-reviewed)abstract
- Quantities in engineering and the physical sciences are expressed as units of measurement (UoM). If a software system fails to maintain the algebraic attributes of a system’s UoM information correctly when evaluating expressions then disastrous problems can arise. However, it is perhaps the more mundane unit mismatches and lack of interoperability that over time incurs a greater cost. Global and existential challenges, from infectious diseases to environmental breakdown, require high-quality data. Ensuring software systems support quantities explicitly is becoming less of a luxury and more of a necessity. While there are technical solutions that allow units of measurement to be specified at both the model and code level, a detailed assessment of their strengths and weaknesses has only recently been undertaken. This chapter provides both a formal introduction to managing quantities and a practical comparison of existing techniques so that software users can judge the robustness of their systems with regards to units of measurement.
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| 12. |
- McKeever, Steve, 1969-, et al.
(author)
-
Quantity Checking through Unit of Measurement Libraries, Current Status and Future Directions
- 2019
-
In: MODELSWARD. - : Scitepress. ; , s. 441-447
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Conference paper (peer-reviewed)abstract
- Unit errors are known to have caused some costly software engineering disasters, most notably the Mars Climate Orbiter back in 1999. As unit annotations are not mandatory for execution only dramatic events become newsworthy. Anecdotally however, there is evidence to suggest that these kinds of errors are recurrent and under-reported. There are an abundance of tools and most notably libraries to aid scientific developers manage unit definitions. In this paper we look in detail at how a number of prominent libraries in the most popular programming languages support units. We argue that even when these libraries are based on a sound design pattern, their implementation becomes too broad. Each library is distinct with varying features, lacking a core API, compromising both interoperability and thereby usage. We claim that further library or tool development is not needed to further adoption, but that a greater understanding of developers requirements is.
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| 13. |
- McKeever, Steve, 1969-, et al.
(author)
-
Unit of measurement libraries, their popularity and suitability
- 2021
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In: Software, practice & experience. - : John Wiley & Sons. - 0038-0644 .- 1097-024X. ; 51:4, s. 711-734
-
Journal article (peer-reviewed)abstract
- In scientific applications, physical quantities, and units of measurement are used regularly. If the inherent incompatibility between these units is not handled properly it can lead to potentially catastrophic problems. Although the risk of a miscalculation is high and the cost equally so, almost none of the major programming languages has support for physical quantities. We employed a systematic approach to examine and analyse available units of measurement (UoM) libraries. The search results were condensed into 38 libraries. These were the most comprehensive and well-developed, open-source libraries, chosen from approximately 3700 search results across seven repository hosting sites. Most libraries are implemented in a similar manner, but with varying features and evaluation strategies. Three developers and a scientist were interviewed and 91 practitioners of varying experiences from on-line forums were surveyed to explain their impressions of UoM libraries and their suitability. Our findings show several reasons for nonadoption, including insufficient awareness of UoM libraries, cumbersome in practice, specific performance concerns, and usage of development processes that exclude unit information We conclude with recommendations to UoM library creators derived from these observations. We also argue that so long as units are not part of the language, or not supported through an IDE extension, their use will be limited. Native language support allows for efficient unit conversion and static checking. While lightweight methods provide many benefits of UoM libraries with minimal overheads. Libraries are perhaps best suited to applications in which unit of measurement checking is desirable at run-time.
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| 14. |
- Okhravi, Christopher, 1987-
(author)
-
Composing Policy Interventions for Antibiotic Development
- 2020
-
Doctoral thesis (other academic/artistic)abstract
- Antibiotic resistance is eroding the efficacy of the drugs we have and, unless future science dictates otherwise, bacteria will eventually become resistant to whatever new antibiotics we discover. We must therefore plan for a continuous stream of innovation. Unfortunately, pharmaceutical firms have left the scene to pursue more profitable areas. While the free market may eventually give rise to a solution, the question is how much destruction we are willing to accept on the way, and whether it eventually will be too late. A plethora of policy interventions, aimed at stimulating antibiotic research and development, have been suggested, and simulation modelers have begun estimating their effects. Suggested interventions range from prizes, grants, and competitions to regulatory fast-tracking and non-profit development. No unified picture of what to do has emerged. From the perspective of policy-makers, the need does not seem to be for more but for better information. This thesis suggests that to truly compare policy interventions, aimed at stimulating antibiotic development, we should draw on simulation model alignment techniques. To support such an endeavor this thesis presents the seeds of a compositional language capable of formally expressing policy interventions as offers that can be actualized into contracts. The language is not merely theoretical but implementable and usable within actual simulation models. The language is not only derived from previous research on compositional contracts in functional languages and the resources-events-agents ontology, but also the author's unique position as a participant in DRIVE-AB, which comprised 16 public and 7 private partners from 12 countries, and finally six separately published simulation experiments that are all based on work by the author. A constructive proof is provided to establish the utility of the solution in terms of its capacity to capture important facets of important policy interventions.
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| 15. |
- Okhravi, Christopher, et al.
(author)
-
Simulating Market Entry Rewards for Antibiotics Development
- 2018
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In: Journal of Law, Medicine & Ethics. - : SAGE PUBLICATIONS INC. - 1073-1105 .- 1748-720X. ; 46, s. 32-42
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Journal article (peer-reviewed)abstract
- We design an agent based Monte Carlo model of antibiotics research and development (R&D) to explore the effects of the policy intervention known as Market Entry Reward (MER) on the likelihood that an antibiotic entering pre-clinical development reaches the market. By means of sensitivity analysis we explore the interaction between the MER and four key parameters: projected net revenues, R&D costs, venture capitalists discount rates, and large pharmaceutical organizations' financial thresholds. We show that improving revenues may be more efficient than reducing costs, and thus confirm that this pull-based policy intervention effectively stimulates antibiotics R&D.
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| 16. |
- Okhravi, Christopher, et al.
(author)
-
Simulating Market-Oriented Policy Interventions for Stimulating Antibiotics Development
- 2017
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In: ANSS '17 Proceedings of the 50th Annual Simulation Symposium. - : ACM Digital Library.
-
Conference paper (peer-reviewed)abstract
- The relative efficacy of intervention policies, aimed at stimulating development of antibiotics, can be estimated using Agent Based simulation. We propose that antibiotics development can be modeled as Markov Chains with time and cash loaded transitions, and that many intervention policies can be modeled as alterations to the stochastic distributions of said Markov Chains. Through the combination of these two models, Agent Based simulation can be used to estimate the relationship between interventions and the Expected Net Present Value of products. We apply this modeling to an intervention policy proposed by the EU-initiative DRIVE-AB, targeting the urgent need for antibiotics research and development due to increasing resistance. We focus on variants fully delinking profit from volume sales, and show that (1) implementation variations lead to differences in outcomes, and that (2) they exhibit diminishing returns.
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| 17. |
- Paçacı, Görkem, 1986-, et al.
(author)
-
Compositional Relational Programming with Name Projection and Compositional Synthesis
- 2018
-
In: Perspectives of System Informatics. - Cham : Springer. - 9783319743127 - 9783319743134 ; , s. 306-321
-
Conference paper (peer-reviewed)abstract
- CombInduce is a methodology for inductive synthesis of logic programs, which employs a reversible meta-interpreter for synthesis, and uses a compositional relational target language for ecient synthesis of recursive predicates.The target language, Combilog, has reduced usability due to the lack of variables, a feature enforced by the principle of compositionality, which is at the core of the synthesis process. We present a revision of Combilog, namely, Combilog with Name Projection (CNP), which brings improved usability by using argument names, whilst still staying devoid of variables, preserving the compositionality.
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| 18. |
- Paçacı, Görkem, 1986-, et al.
(author)
-
"Why did you do that?" : Explaining black box models with Inductive Synthesis
- 2019
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In: International Conference on Computational Science (ICCS). - Cham : Springer Nature.
-
Conference paper (peer-reviewed)abstract
- By their nature, the composition of black box models is opaque. This makes the ability to generate explanations for the response to stimuli challenging. The importance of explaining black box models has become increasingly important given the prevalence of AI and ML systems and the need to build legal and regulatory frameworks around them. Such explanations can also increase trust in these uncertain systems. In our paper we present RICE, a method for generating explanations of the behaviour of black box models by (1) probing a model to extract model output examples using sensitivity analysis; (2) applying CNPInduce, a method for inductive logic program synthesis, to generate logic programs based on critical input-output pairs; and (3) interpreting the target program as a human-readable explanation. We demonstrate the application of our method by generating explanations of an artificial neural network trained to follow simple traffic rules in a hypothetical self-driving car simulation. We conclude with a discussion on the scalability and usability of our approach and its potential applications to explanation-critical scenarios.
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| 19. |
- Rizk, Raya, et al.
(author)
-
Diftong : a tool for validating big data workflows
- 2019
-
In: Journal of Big Data. - : Springer Science and Business Media LLC. - 2196-1115. ; 6:1
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Journal article (peer-reviewed)abstract
- Data validation is about verifying the correctness of data. When organisations update and refine their data transformations to meet evolving requirements, it is imperative to ensure that the new version of a workflow still produces the correct output. We motivate the need for workflows and describe the implementation of a validation tool called Diftong. This tool compares two tabular databases resulting from different versions of a workflow to detect and prevent potential unwanted alterations. Row-based and column-based statistics are used to quantify the results of the database comparison. Diftong was shown to provide accurate results in test scenarios, bringing benefits to companies that need to validate the outputs of their workflows. By automating this process, the risk of human error is also eliminated. Compared to the more labour-intensive manual alternative, it has the added benefit of improved turnaround time for the validation process. Together this allows for a more agile way of updating data transformation workflows.
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| 20. |
- Salah, Omar-Alfred, et al.
(author)
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Lack of Adoption of Units of Measurement Libraries : Survey and Anecdotes
- 2020
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In: 2020 IEEE/ACM 42nd International Conference On Software Engineering. - New York : Association for Computing Machinery ACM. ; , s. 81-89
-
Conference paper (peer-reviewed)abstract
- Units of measurement (UoM) libraries are mostly used to appropriately encode unit variables and convert between them in a type-safe manner. Approximately 3700 functioning unit measurement libraries exist on the web, indicating that the wheel is being reinvented time and time again. Previous research has postulated that too much diversity, lack of code sharing and duplicated efforts are discouraging adoption, yet more remains to be known. Three developers and a scientist were interviewed and 91 practitioners of varying experiences from online forums were surveyed to explain their dissatisfaction with UoM libraries and possible reasons behind the lack of adoption. Our findings range from insufficient awareness of these UoM's, to development processes that exclude unit information through to specific performance concerns. We conclude with recommendations to UoM library creators stemming from these points that could help alleviate the problem and lead to an increased adoption rate of methodologies that support unit annotation and checking.
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