Faculty and Staff Research

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A distributed model to expand the reach of drug checking
(Drugs Habits and Social Policy, 2022) Wallace, Bruce; Gozdzialski, Lea; Qbaich, Abdelhakim; Azam, Md. Shafiul; Burek, Piotr; Hutchison, Abby; Teal, Taylor; Louw, Rebecca; Kielty, Collin; Robinson, Derek; Moa, Belaid; Storey, Margaret-Anne; Gill, Chris; Hore, Dennis K.
Purpose – While there is increasing interest in implementing drug checking within overdose prevention, we must also consider how to scale-up these responses so that they have significant reach and impact for people navigating the unpredictable and increasingly complex drug supplies linked to overdose. The purpose of this paper is to present a distributed model of community drug checking that addresses multiple barriers to increasing the reach of drug checking as a response to the illicit drug overdose crisis. Design/methodology/approach – A detailed description of the key components of a distributed model of community drug checking is provided. This includes an integrated software platform that links a multi-instrument, multi-site service design with online service options, a foundational database that provides storage and reporting functions and a community of practice to facilitate engagement and capacity building. Findings – The distributed model diminishes the need for technicians at multiple sites while still providing point-of-care results with local harm reduction engagement and access to confirmatory testing online and in localized reporting. It also reduces the need for training in the technical components of drug checking (e.g. interpreting spectra) for harm reduction workers. Moreover, its real-time reporting capability keeps communities informed about the crisis. Sites are additionally supported by a community of practice. Originality/value – This paper presents innovations in drug checking technologies and service design that attempt to overcome current financial and technical barriers towards scaling-up services to a more equitable and impactful level and effectively linking multiple urban and rural communities to report concentration levels for substances most linked to overdose.
A methodological approach to extracting patterns of service utilization from a cross-continuum high dimensional healthcare dataset to support care delivery optimization for patients with complex problems
(BioMedInformatics, 2024) Bambi, Jonas; Santoso, Yudi; Sadri, Hanieh; Moselle, Ken; Rudnick, Abraham; Robertson, Stan; Chang, Ernie; Kuo, Alex; Howie, Joseph; Dong, Gracia Yunruo; Olobatuyi, Kehinde; Hajiabadi, Mahdi; Richardson, Ashlin
Background: Optimizing care for patients with complex problems entails the integration of clinically appropriate problem-specific clinical protocols, and the optimization of service-system-encompassing clinical pathways. However, alignment of service system operations with Clinical Practice Guidelines (CPGs) is far more challenging than the time-bounded alignment of procedures with protocols. This is due to the challenge of identifying longitudinal patterns of service utilization in the cross-continuum data to assess adherence to the CPGs. Method: This paper proposes a new methodology for identifying patients’ patterns of service utilization (PSUs) within sparse high-dimensional cross-continuum health datasets using graph community detection. Result: The result has shown that by using iterative graph community detections, and graph metrics combined with input from clinical and operational subject matter experts, it is possible to extract meaningful functionally integrated PSUs. Conclusions: This introduces the possibility of influencing the reorganization of some services to provide better care for patients with complex problems. Additionally, this introduces a novel analytical framework relying on patients’ service pathways as a foundation to generate the basic entities required to evaluate conformance of interventions to cohort-specific clinical practice guidelines, which will be further explored in our future research.
An aggregative approach for scalable detection of DoS attacks
(IEEE, 2008-12) Hamidi, Alireza; Ganti, Sudhakar; Wu, Kui
In Voice Over IP (VoIP) systems, intruders can launch DoS attacks by establishing a large number of open connections to prevent the system from serving legitimate users. Existing defenses against DoS attacks on VoIP systems maintain full state information and thus are not scalable to implement at core routers. To this end, we adopt a two-layer aggregation scheme, termed Advanced Partial Completion Filters (APCF), to defend against DoS attacks without tracking state information of each individual connection. APCF provides adjustable control parameters so that both false alarms and detection rate can be controlled.
Algae adhesion onto silicone is sensitive to environment-induced surface restructuring
(Langmuir, 2021) Wan, Zhijing; Azam, Md. Shafiul; Wyatt, Shea; Ramsay, Kaitlyn; Korner, Jaime L.; Elvira, Katherine S.; Padmawar, Rajkumar; Varela, Diana; Hore, Dennis K.
Resistance to algae contamination is an important characteristic of insulators used in overhead power distribution in coastal environments. It is therefore important to understand the parameters governing algae adhesion onto polymer insulator materials such as silicone. Flow cell-based shear experiments were conducted in order to characterize the adhesion strength of algae onto polydimethylsiloxane surfaces, comparing fresh polymer substrates with those that have been soaked in water and saline solutions for 1 month. Both freshwater algae and seawater species could withstand considerably less drag force and were therefore more easily removed when the polymer was soaked in salt water. The polymer surface was found to be unaltered in terms of its roughness, contact angle, and lack of water uptake; no macroscopic surface characterization was therefore able to account for the differences in cell adhesion strength resulting from the soaking treatment. Surface-specific nonlinear vibrational spectroscopy, however, revealed subtle differences in the orientation of surface methyl groups that resulted from the water and saline exposure.
Approaches to extracting patterns of service utilization for patients with complex conditions: graph community detection vs. natural language processing clustering
(BioMedInformatics, 2024) Bambi, Jonas; Sadri, Hanieh; Moselle, Ken; Chang, Ernie; Santoso, Yudi; Howie, Joseph; Rudnick, Abraham; Elliott, Lloyd T.; Kuo, Alex
Background: As patients interact with a healthcare service system, patterns of service utilization (PSUs) emerge. These PSUs are embedded in the sparse high-dimensional space of longitudinal cross-continuum health service encounter data. Once extracted, PSUs can provide quality assurance/quality improvement (QA/QI) efforts with the information required to optimize service system structures and functions. This may improve outcomes for complex patients with chronic diseases. Method: Working with longitudinal cross-continuum encounter data from a regional health service system, various pattern detection analyses were conducted, employing (1) graph community detection algorithms, (2) natural language processing (NLP) clustering, and (3) a hybrid NLP–graph method. Result: These approaches produced similar PSUs, as determined from a clinical perspective by clinical subject matter experts and service system operations experts. Conclusions: The similarity in the results provides validation for the methodologies. Moreover, the results stress the need to engage with clinical or service system operations experts, both in providing the taxonomies and ontologies of the service system, the cohort definitions, and determining the level of granularity that produces the most clinically meaningful results. Finally, the uniqueness of each approach provides an opportunity to take advantage of the various analytical capabilities that each approach brings, which will be further explored in our future research.
Architecting complex, long-lived scientific software
(Journal of Systems and Software, 2023) Ernst, Neil A.; Klein, John; Bartolini, Marco; Coles, Jeremy; Rees, Nick
Software is a critical aspect of large-scale science, providing essential capabilities for making scientific discoveries. Large-scale scientific projects are vast in scope, with lifespans measured in decades and costs exceeding hundreds of millions of dollars. Successfully designing software that can exist for that span of time, at that scale, is challenging for even the most capable software companies. Yet scientific endeavors face challenges with funding, staffing, and operate in complex, poorly understood software settings. In this paper we discuss the practice of early-phase software architecture in the Square Kilometre Array Observatory’s Science Data Processor. The Science Data Processor is a critical software component in this next-generation radio astronomy instrument. We customized an existing set of processes for software architecture analysis and design to this project’s unique circumstances. We report on the series of comprehensive software architecture plans that were the result. The plans were used to obtain construction approval in a critical design review with outside stakeholders. We conclude with implications for other long-lived software architectures in the scientific domain, including potential risks and mitigations.
Aspect-oriented system structure
(IEEE, 2001) Coady, Y; Kiczales, G; Feeley, M; Hutchinson, N; Ong, JS; Gudmundson, S
Operating system structure is important; it leads to understandable, maintainable, 'pluggable' code. But despite our best efforts, some system elements have been difficult to structure. We propose a new analysis of this problem, and a new technology that can structure these elements. Aspect-oriented programming (AOP) (G. Kiczales et al., 1997) uses linguistic mechanisms to support the separation of crosscutting elements, or aspects of the system, from primary functionality. We have developed a proof-of-concept AOP implementation of prefetching in FreeBSD (www.cs.ubc.ca/labs/spl/aspects/aspectc.html). In our implementation, we have been able to modularize prefetching.
Aspects of memory management
(IEEE, 2005) Gibbs, C; Coady, Y
With the constant demand for system change and upgrades comes the need to simplify and ensure accuracy in this process. As structural boundaries decay, non-local modifications compound the costs of system evolution and adaptation. Aspect-Oriented Programming (AOP) aims to improve structural boundaries for concerns that are inherently crosscutting - no single hierarchical decomposition can localize both the crosscutting concern and the concerns it crosscuts. This paper provides a case study of three crosscutting concerns within a rapidly evolving memory management subsystem of a JVM. The study shows how aspects can be structured as a natural locus of control, and how this new modularity provides leverage for system evolution and adaptation. Demonstrated benefits include enhanced extensibility for a dynamic analysis tool, centralized configurability for a subsystem-wide synchronization mechanism, and increased verifiability for a domain-specific design pattern.
Assessing the Molecular Specificity and Orientation Sensitivity of Infrared, Raman, and Vibrational Sum-Frequency Spectra
(Symmetry, 2021) Chen, Fei; Gozdzialski, Lea; Hung, Kuo-Kai; Stege, Ulrike; Hore, Dennis K.
Linear programming was used to assess the ability of polarized infrared absorption, Raman scattering, and visible–infrared sum-frequency generation to correctly identify the composition of a mixture of molecules adsorbed onto a surface in four scenarios. The first two scenarios consisted of a distribution of species where the polarity of the orientation distribution is known, both with and without consideration of an arbitrary scaling factor between candidate spectra and the observed spectra of the mixture. The final two scenarios have repeated the tests, but assuming that the polarity of the orientation is unknown, so the symmetry-breaking attributes of the second-order nonlinear technique are required. The results indicate that polarized Raman spectra are more sensitive to orientation and molecular identity than the other techniques. However, further analysis reveals that this sensitivity is not due to the high-order angle dependence of Raman, but is instead attributed to the number of unique projections that can be measured in a polarized Raman experiment.
Best Rational Approximation and Strict Quasi-Convexity
(1971) Barrodale, I
If a continuous function is strictly quasi-convex on a convex set $\Gamma $, then every local minimum of the function must be a global minimum. Furthermore, every local maximum of the function on the interior of $\Gamma $ must also be a global minimum. Here, we prove that any minimax rational approximation problem defines a strictly quasi-convex function with the property that a best approximation (if one exists) is a minimum of that function. The same result is not true in general for best rational approximation in other norms.
Beyond Remediation: The Role of Textual Studies in Implementing New Knowledge Environments*
(Scholarly and Research Communication, 2012-03-26) Galey, Alan; Cunningham, Richard; Nelson, Brent; Siemens, Ray; Werstine, Paul
This article considers the role of textual studies in a digital world and reviews the work of a particular group of digital textual scholars. Specifically, the article examines the work of the Textual Studies team at the Implementing New Knowledge Environments project (INKE.ca), a group of digital textual scholars working on user experience, interface design, and information management with the goal of better understanding how reading is changing in the context of digital media. INKE’s work rethinks what the book can become and aims to generate prototypes to be shared on an open-source basis with the public.
Bipartite characterization of sign nonsingularity
(2010-04-13T22:54:01Z) Drew, J. H.; Green, B. C. J.; Johnson, C. R.; Olesky, D. D.; Van den Driessche, P.
Bruhat decomposition and numerical stability
(2010-02-19T22:38:19Z) Odeh, O.H.; Olesky, D.D.; van den Driessche, P.
Building a biomedical tokenizer using the token lattice design pattern and the adapted Viterbi algorithm
(BioMed Central, 2011-06-09) Barrett, Neil; Weber-Jahnke, Jens
Background: Tokenization is an important component of language processing yet there is no widely accepted tokenization method for English texts, including biomedical texts. Other than rule based techniques, tokenization in the biomedical domain has been regarded as a classification task. Biomedical classifier-based tokenizers either split or join textual objects through classification to form tokens. The idiosyncratic nature of each biomedical tokenizer’s output complicates adoption and reuse. Furthermore, biomedical tokenizers generally lack guidance on how to apply an existing tokenizer to a new domain (subdomain). We identify and complete a novel tokenizer design pattern and suggest a systematic approach to tokenizer creation. We implement a tokenizer based on our design pattern that combines regular expressions and machine learning. Our machine learning approach differs from the previous split-join classification approaches. We evaluate our approach against three other tokenizers on the task of tokenizing biomedical text. Results: Medpost and our adapted Viterbi tokenizer performed best with a 92.9% and 92.4% accuracy respectively. Conclusions: Our evaluation of our design pattern and guidelines supports our claim that the design pattern and guidelines are a viable approach to tokenizer construction (producing tokenizers matching leading custom-built tokenizers in a particular domain). Our evaluation also demonstrates that ambiguous tokenizations can be disambiguated through POS tagging. In doing so, POS tag sequences and training data have a significant impact on proper text tokenization.
Building A Social Edition of the Devonshire Manuscript
(Renaissance and Reformation / Renaissance et Réforme, 2014) Crompton, Constance; Powell, Daniel; Arbuckle, Alyssa; Siemens, Ray; Shirley, Maggie; Devonshire Manuscript Editorial Group
This article describes the context and development of A Social Edition of the Devonshire Manuscript, a collaboratively created Wikibook edition of the sixteenth-century verse miscellany known as the Devonshire Manuscript (BL MS Add. 17,492). This project began in 2001 when Dr. Ray Siemens led a group of researchers in an exploration of how to create a digital edition of the Devonshire Manuscript. Since then, the project has transitioned through many forms and formats, and A Social Edition of the Devonshire Manuscript is the most recent output of these academic experiments. Of note, a print version of A Social Edition of the Devonshire Manuscript is forthcoming from Iter and Medieval and Renaissance Texts and Studies (MRTS). Cet article retrace le contexte et le développement du projet A Social Edition of the Devonshire Manuscript, consistant en l’édition électronique (Wikibook) en collaboration d’un manuscrit du XVIe siècle de mélanges poétiques connu sous le nom de Devonshire Manuscript (BL MS Add. 17 492). Ce projet a été initié en 2001, lorsque le Dr Ray Siemens a dirigé un groupe de recherche explorant les possibilités de publier une édition numérique du Devonshire Manuscript. Depuis, le projet a pris plusieurs formes, et celui intitulé A Social Edition of the Devonshire Manuscript en est sa forme la plus récente issues des diverses expériences du groupe. Il doit être souligné que A Social Edition of the Devonshire Manuscript, sera bientôt publié en version imprimée par Iter et les Medieval and Renaissance Texts and Studies (MRTS).
A calculus for information-driven networks
(IEEE, 2009-07) Wu, Kui; Jiang, Yuming; Hu, Guoqiang
Information-driven networks include a large category of networking systems, where network nodes are aware of information delivered and thus can not only forward data packets but may also perform information processing. In many situations, the quality of service (QoS) in information-driven networks is provisioned with the redundancy in information. Traditional performance models generally adopt evaluation measures suitable for packet-oriented service guarantee, such as packet delay, throughput, and packet loss rate. These performance measures, however, do not align well with the actual need of information-driven networks. New performance measures and models for information-driven networks, despite their importance, have been mainly blank, largely because information processing is clearly application dependent and cannot be easily captured within a generic framework. To fill the vacancy, we develop a new performance evaluation framework particularly tailored for information-driven networks, based on the recent development of stochastic network calculus. Particularly, our model captures the information processing and the QoS guarantee with respect to stochastic information delivery rates, which have never been formally modeled before. This analytical model is very useful in deriving theoretical performance bounds for a large body of systems where QoS is stochastically guaranteed with a certain level of information delivery.
Classes of sign nonsingular matrices with a specified number of zero entries
(2009-09-04T18:22:14Z) Green, Bryan C.J.; Olesky, D.D.; van den Driessche, P.
CODE: Crowd-optimized design of environments
(Computer Animation & Virtual Worlds, 2017-03-22) Haworth, Brandon; Usman, Muhammad; Berseth, Glen; Kayatkhoei, Mahyar; Kapadia, Mubbasir; Faloutsos, Petros
We present crowd-optimized design of environments (CODE): a “crowd-aware” computational tool for designing environments (e.g., building floor plans). Our system analyses the impact of newly added environment elements (e.g., pillars or doorways) on the resulting crowd flow, using current-generation crowd simulators. The results of the simulation are used to provide feedback to the designer in terms of aggregate statistics and heat maps. Additionally, our system is able to “automatically” optimize the placement of environment elements to maximize crowd flow in egress scenarios, while satisfying constraints that are imposed by the designer. Using CODE, architects and environment designers can iteratively refine upon their original design to quickly accommodate the dynamic properties of crowd simulations in an interactive fashion. CODE is modular and flexible so that designers may build environments, select from different crowd simulators, and specify varying crowd configurations.
Codex Ultor: Toward a Conceptual and Theoretical Foundation for New Research on Books and Knowledge Environments
(Digital Studies/Le champ numérique, 2009) Siemens, Ray; Warwick, Claire; Cunningham, Richard; Dobson, Teresa; Galey, Alan; Ruecker, Stan; Schreibman, Susan; INKE Research Group
In this paper, we present the conceptual and theoretical foundations for work undertaken by the Implementing New Knowledge Environments (INKE) research group, a large international, interdisciplinary research team studying reading and texts, both digital and printed. The INKE team is comprised of researchers and stakeholders at the forefronts of fields relating to textual studies, user experience, interface design, and information management. We aim to contribute to the development of new digital information and knowledge environments that build on past textual practices. In this piece, we discuss our research questions, methods, aims and research objectives, the rationale behind our work and its expected significance.
Codex Ultor: Vers des fondations conceptuelles et théoriques pour de nouvelles recherches sur les livres et les environnements documentaires
(Mémoires du livre/Studies in Book Culture, 2009) Siemens, Ray; Warwick, Claire; Cunningham, Richard; Dobson, Teresa; Galey, Alan; Ruecker, Stan; Schreibman, Susan; INKE Research Group
Dans cet article, nous présentons les fondations conceptuelles et théoriques des travaux entrepris par le groupe de recherche Implementing New Knowledge Environments (INKE : Mise en oeuvre de nouveaux environnements documentaires), une importante équipe de recherche internationale et interdisciplinaire qui étudie la lecture et les textes, numériques et imprimés. L’équipe INKE est composée de chercheurs et de partenaires directement impliqués dans les domaines liés aux études textuelles, à l’expérience de l’utilisateur, à la conception d’interfaces et la gestion de l’information. Notre but est de contribuer à la mise au point de nouveaux environnements d’informations et de connaissances numériques qui tirent parti des pratiques textuelles antérieures. Dans cet article, nous abordons nos problématiques de recherches, nos méthodes, nos objectifs de recherche, le raisonnement qui sous-tend nos travaux et l’écho que nous espérons qu’ils auront.

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