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ClinQueryAgent: A Conversational Agent for Population Health Management
Authors:
Joseph S. Boyle,
Anthony Dranfield,
Mike O'Neil,
Maria Liakata,
Alison Q. Smithard
Abstract:
In this paper we introduce ClinQueryAgent, a system for translating natural language population health questions into executable database queries using agents with access to both local and external knowledge bases. Our novel architecture enables the use of powerful cloud-based language models whilst ensuring that no patient data leaves the secure environment. To combat inaccuracies over the course…
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In this paper we introduce ClinQueryAgent, a system for translating natural language population health questions into executable database queries using agents with access to both local and external knowledge bases. Our novel architecture enables the use of powerful cloud-based language models whilst ensuring that no patient data leaves the secure environment. To combat inaccuracies over the course of longer dialogues due to context rot, information retrieval is delegated to a sub-agent. We deploy the system via a chat window embedded within an existing population health management platform where it has been used by 128 staff from 15 healthcare practices covering a total of 148,319 patients in the UK's National Health Service (NHS). We evaluate the system's capacity to autonomously handle a range of health informatics tasks on a constructed dataset and via a beta-testing phase. Our results show that both analysts and clinicians are able to easily generate actionable information from patient health records using natural language requests requiring no programming expertise to verify. We make a public demo of the system available at: https://demo-899965260288.europe-west1.run.app/
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Submitted 13 April, 2026;
originally announced May 2026.
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University Rents Enabling Corporate Innovation: Mapping Academic Researcher Coding and Discursive Labour in the R Language Ecosystem
Authors:
Xiaolan Cai,
Mathieu O'Neil,
Stefano Zacchiroli
Abstract:
This article explores the role of unrecognised labour in corporate innovation systems via an analysis of researcher coding and discursive contributions to R, one of the largest statistical software ecosystems. Studies of online platforms typically focus on how platform affordances constrain participants' actions, and profit from their labour. We innovate by connecting the labour performed inside d…
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This article explores the role of unrecognised labour in corporate innovation systems via an analysis of researcher coding and discursive contributions to R, one of the largest statistical software ecosystems. Studies of online platforms typically focus on how platform affordances constrain participants' actions, and profit from their labour. We innovate by connecting the labour performed inside digital platforms to the professional employment of participants. Our case study analyses 8,924 R package repositories on GitHub, examining commits and communications. Our quantitative findings show that researchers, alongside non-affiliated contributors, are the most frequent owners of R package repositories and their most active contributors. Researchers are more likely to hold official roles compared to the average, and to engage in collaborative problem-solving and support work during package development. This means there is, underneath the 'recognised' category of star researchers who transition between academia and industry and secure generous funding, an 'unrecognised' category of researchers who not only create and maintain key statistical infrastructure, but also provide support to industry employees, for no remuneration. Our qualitative findings show how this unrecognised labour affects practitioners. Finally, our analysis of the ideology and practice of free, libre and open source software (FLOSS) shows how this ideology and practice legitimate the use of 'university rents' by Big Tech.
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Submitted 22 December, 2025;
originally announced December 2025.
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A fast boundary integral method for high-order multiscale mesh generation
Authors:
Felipe Vico,
Leslie Greengard,
Michael O'Neil,
Manas Rachh
Abstract:
In this work we present an algorithm to construct an infinitely differentiable smooth surface from an input consisting of a (rectilinear) triangulation of a surface of arbitrary shape. The original surface can have non-trivial genus and multiscale features, and our algorithm has computational complexity which is linear in the number of input triangles. We use a smoothing kernel to define a functio…
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In this work we present an algorithm to construct an infinitely differentiable smooth surface from an input consisting of a (rectilinear) triangulation of a surface of arbitrary shape. The original surface can have non-trivial genus and multiscale features, and our algorithm has computational complexity which is linear in the number of input triangles. We use a smoothing kernel to define a function $Φ$ whose level set defines the surface of interest. Charts are subsequently generated as maps from the original user-specified triangles to $\mathbb R^3$. The degree of smoothness is controlled locally by the kernel to be commensurate with the fineness of the input triangulation. The expression for~$Φ$ can be transformed into a boundary integral, whose evaluation can be accelerated using a fast multipole method. We demonstrate the effectiveness and cost of the algorithm with polyhedral and quadratic skeleton surfaces obtained from CAD and meshing software.
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Submitted 29 September, 2019;
originally announced September 2019.
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"We're on the Same Page": A Usability Study of Secure Email Using Pairs of Novice Users
Authors:
Scott Ruoti,
Jeff Andersen,
Scott Heidbrink,
Mark O'Neil,
Elham Vaziripour,
Justin Wu,
Daniel Zappala,
Kent Seamons
Abstract:
Secure email is increasingly being touted as usable by novice users, with a push for adoption based on recent concerns about government surveillance. To determine whether secure email is for grassroots adoption, we employ a laboratory user study that recruits pairs of novice to install and use several of the latest systems to exchange secure messages. We present quantitative and qualitative result…
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Secure email is increasingly being touted as usable by novice users, with a push for adoption based on recent concerns about government surveillance. To determine whether secure email is for grassroots adoption, we employ a laboratory user study that recruits pairs of novice to install and use several of the latest systems to exchange secure messages. We present quantitative and qualitative results from 25 pairs of novice users as they use Pwm, Tutanota, and Virtru. Participants report being more at ease with this type of study and better able to cope with mistakes since both participants are "on the same page". We find that users prefer integrated solutions over depot-based solutions, and that tutorials are important in helping first-time users. Hiding the details of how a secure email system provides security can lead to a lack of trust in the system. Participants expressed a desire to use secure email, but few wanted to use it regularly and most were unsure of when they might use it.
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Submitted 11 January, 2016; v1 submitted 28 October, 2015;
originally announced October 2015.
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User Attitudes Toward the Inspection of Encrypted Traffic
Authors:
Scott Ruoti,
Mark O'Neil,
Daniel Zappala,
Kent Seamons
Abstract:
This paper reports the results of a survey of 1,976 individuals regarding their opinions on TLS inspection, a controversial technique that can be used for both benevolent and malicious purposes. Responses indicate that participants hold nuanced opinions on security and privacy trade-offs, with most recognizing legitimate uses for the practice, but also concerned about threats from hackers or gover…
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This paper reports the results of a survey of 1,976 individuals regarding their opinions on TLS inspection, a controversial technique that can be used for both benevolent and malicious purposes. Responses indicate that participants hold nuanced opinions on security and privacy trade-offs, with most recognizing legitimate uses for the practice, but also concerned about threats from hackers or government surveillance. There is strong support for notification and consent when a system is intercepting their encrypted traffic, although this support varies depending on the situation. A significant concern about malicious uses of TLS inspection is identity theft, and many would react negatively and some would change their behavior if they discovered inspection occurring without their knowledge. We also find that there are a small but significant number of participants who are jaded by the current state of affairs and have no expectation of privacy.
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Submitted 10 June, 2016; v1 submitted 16 October, 2015;
originally announced October 2015.