Case board, traces, & chicanes: Diagrams for an archaeology of algorithmic prediction through critical design practice

This PhD thesis utilises diagrams as a language for research and design practice to critically investigate algorithmic prediction. As a tool for practice-based research, the language of diagrams is presented as a way to read algorithmic prediction as a set of intricate computational geometries, and to write it through critical practice immersed in the very materials in question: data and code. From a position rooted in graphic and interaction design, the research uses diagrams to gain purchase on algorithmic prediction, making it available for examination, experimentation, and critique. The project is framed by media archaeology, used here as a methodology through which both the technical and historical "depths" of algorithmic systems are excavated. My main research question asks: How can diagrams be used as a language to critically investigate algorithmic prediction through design practice? This thesis presents two secondary questions for critical examination, asking: Through which mechanisms does thinking/writing/designing in diagrammatic terms inform research and practice focused on algorithmic prediction? As algorithmic systems claim to produce objective knowledge, how can diagrams be used as instruments for speculative and/or conjectural knowledge production? I contextualise my research by establishing three registers of relations between diagrams and algorithmic prediction. These are identified as: Data Diagrams to describe the algorithmic forms and processes through which data are turned into predictions; Control Diagrams to afford critical perspectives on algorithmic prediction, framing the latter as an apparatus of prescription and control; and Speculative Diagrams to open up opportunities for reclaiming the generative potential of computation. These categories form the scaffolding for the three practice-oriented chapters where I evidence a range of meaningful ways to investigate algorithmic prediction through diagrams. This includes, the 'case board' where I unpack some of the historical genealogies of algorithmic prediction. A purpose-built graph application materialises broader reflections about how such genealogies might be conceptualised, and facilitates a visual and subjective mode of knowledge production. I then move to producing 'traces', namely probing the output of an algorithmic prediction system|in this case YouTube recommendations. Traces, and the purpose-built instruments used to visualise them, interrogate both the mechanisms of algorithmic capture and claims to make these mechanisms transparent through data visualisations. Finally, I produce algorithmic predictions and examine the diagrammatic "tricks," or 'chicanes', that this involves. I revisit a historical prototype for algorithmic prediction, the almanac publication, and use it to question the boundaries between data-science and divination. This is materialised through a new version of the almanac - an automated publication where algorithmic processes are used to produce divinatory predictions. My original contribution to knowledge is an approach to practice-based research which draws from media archaeology and focuses on diagrams to investigate algorithmic prediction through design practice. I demonstrate to researchers and practitioners with interests in algorithmic systems, prediction, and/or speculation, that diagrams can be used as a language to engage critically with these themes

Bringing LTL Model Checking to Biologists

The BioModelAnalyzer (BMA) is a web based tool for the development of discrete models of biological systems. Through a graphical user interface, it allows rapid development of complex models of gene and protein interaction networks and stability analysis without requiring users to be proficient computer programmers. Whilst stability is a useful specification for testing many systems, testing temporal specifications in BMA presently requires the user to perform simulations. Here we describe the LTL module, which includes a graphical and natural language interfaces to testing LTL queries. The graphical interface allows for graphical construction of the queries and presents results visually in keeping with the current style of BMA. The Natural language interface complements the graphical interface by allowing a gentler introduction to formal logic and exposing educational resources

Drug target optimization in chronic myeloid leukemia using innovative computational platform.

Chronic Myeloid Leukemia (CML) represents a paradigm for the wider cancer field. Despite the fact that tyrosine kinase inhibitors have established targeted molecular therapy in CML, patients often face the risk of developing drug resistance, caused by mutations and/or activation of alternative cellular pathways. To optimize drug development, one needs to systematically test all possible combinations of drug targets within the genetic network that regulates the disease. The BioModelAnalyzer (BMA) is a user-friendly computational tool that allows us to do exactly that. We used BMA to build a CML network-model composed of 54 nodes linked by 104 interactions that encapsulates experimental data collected from 160 publications. While previous studies were limited by their focus on a single pathway or cellular process, our executable model allowed us to probe dynamic interactions between multiple pathways and cellular outcomes, suggest new combinatorial therapeutic targets, and highlight previously unexplored sensitivities to Interleukin-3.We would like to thank the members of the Fisher laboratory, in particular to Gavin Smyth and Caroline Dahl for their help with the BMA development, and Alex Hajnal for valuable comments on the manuscript and insightful discussions. Research in BG laboratory is supported by the Medical Research Council, Leukaemia and Lymphoma Research, The Leukemia and Lymphoma Society, Microsoft Research and core support grants by the Wellcome Trust to the Cambridge Institute for Medical Research and Wellcome Trust-MRC Cambridge Stem Cell Institute.This is the final published version. It was originally published in Scientific Reports 5: 8190. DOI: 10.1038/srep08190

Cancer screening in France: subjects’ and physicians’ attitudes

International audienceOBJECTIVE: Since screening for cancer has been advocated, funded, and promoted in France, it is important to evaluate the attitudes of subjects in the general population and general practitioners (GPs) toward cancer screening strategies. METHODS: EDIFICE is a nationwide opinion poll that was carried out by telephone among a representative sample of 1,504 subjects living in France and aged between 40 and 75 years and among a representative sample of 600 GPs. The questionnaire administered to subjects queried about previous screening for cancer. RESULTS: Ninety-three percent of women stated that they had undergone at least one mammography. Although rated "A" recommendation-strongly recommended-by the US Preventive Services Task Force, screening for colorectal cancer received less attention than prostate cancer screening which is rated "I"-insufficient evidence-(reported screening rates of 25% and 36%, respectively). Six percent of subjects stated that they had undergone lung cancer screening. GPs' attitudes toward cancer screening showed similar inconsistencies. CONCLUSIONS: It thus appears that understanding of cancer screening practices in the French general population does not match scientific evidence. To a lesser extent, this also holds for GPs

A semi-Lagrangian micro-macro method for viscoelastic flow calculations

We present in this paper a semi-Lagrangian algorithm to calculate the viscoelastic flow in which a dilute polymer solution is modeled by the FENE dumbbell kinetic model. In this algorithm the material derivative operator of the Navier–Stokes equations (the macroscopic flow equations) is discretized in time by a semi-Lagrangian formulation of the second order backward difference formula (BDF2). This discretization leads to solving each time step a linear generalized Stokes problem. For the stochastic differential equations of the microscopic scale model, we use the second order predictor-corrector scheme proposed in [22] applied along the forward trajectories of the center of mass of the dumbbells. Important features of the algorithm are (1) the new semi-Lagrangian projection scheme; (2) the scheme to move and locate both the mesh-points and the dumbbells; and (3) the calculation and space discretization of the polymer stress. The algorithm has been tested on the 2d 10:1 contraction benchmark problem and has proved to be accurate and stable, being able to deal with flows at high Weissenberg (Wi) numbers; specifically, by adjusting the size of the time step we obtain solutions at Wi=444

Bringing LTL Model Checking to Biologists

Abstract The BioModelAnalyzer (BMA) is a web based tool for the development of discrete models of biological systems. Through a graphical user interface, it allows rapid development of complex models of gene and protein interaction networks and stability analysis without requiring users to be proficient computer programmers. Whilst stability is a useful specification for testing many systems, testing temporal specifications in BMA presently requires the user to perform simulations. Here we describe the LTL module, which includes a graphical and natural language interfaces to testing LTL queries. The graphical interface allows for graphical construction of the queries and presents results visually in keeping with the current style of BMA. The Natural language interface complements the graphical interface by allowing a gentler introduction to formal logic and exposing educational resources

Bringing LTL Model Checking to Biologists

Abstract The BioModelAnalyzer (BMA) is a web based tool for the development of discrete models of biological systems. Through a graphical user interface, it allows rapid development of complex models of gene and protein interaction networks and stability analysis without requiring users to be proficient computer programmers. Whilst stability is a useful specification for testing many systems, testing temporal specifications in BMA presently requires the user to perform simulations. Here we describe the LTL module, which includes a graphical and natural language interfaces to testing LTL queries. The graphical interface allows for graphical construction of the queries and presents results visually in keeping with the current style of BMA. The Natural language interface complements the graphical interface by allowing a gentler introduction to formal logic and exposing educational resources

Impact of organised programs on colorectal cancer screening

<p>Abstract</p> <p>Purpose</p> <p>Colorectal cancer (CRC) screening has been shown to decrease CRC mortality. Organised mass screening programs are being implemented in France. Its perception in the general population and by general practitioners is not well known.</p> <p>Methods</p> <p>Two nationwide observational telephone surveys were conducted in early 2005. First among a representative sample of subjects living in France and aged between 50 and 74 years that covered both geographical departments with and without implemented screening services. Second among General Practionners (Gps). Descriptive and multiple logistic regression was carried out.</p> <p>Results</p> <p>Twenty-five percent of the persons(N = 1509) reported having undergone at least one CRC screening, 18% of the 600 interviewed GPs reported recommending a screening test for CRC systematically to their patients aged 50–74 years. The odds ratio (OR) of having undergone a screening test using FOBT was 3.91 (95% CI: 2.49–6.16) for those living in organised departments (referent group living in departments without organised screening), almost twice as high as impact educational level (OR = 2.03; 95% CI: 1.19–3.47).</p> <p>Conclusion</p> <p>CRC screening is improved in geographical departments where it is organised by health authorities. In France, an organised screening programs decrease inequalities for CRC screening.</p

Les médecins généralistes recherchent-ils l'hypovitaminose D chez l'adulte et le sujet âgé, la préviennent-ils, la corrigent-ils ? Enquête un jour donné

Background: Few studies have been made in general practice on vitamin D. Methods: An observational survey examines patients over 18 years, seen on a given day by general practitioners. Results: 34 primary care physicians have participated, 479 patients were included. 16% of patients have had a test (20, 9ng/mL on average, 78% < 30ng/mL, 27% < 10ng/mL) and 23% have had a supplementation. But some populations with risk factors are neglected. The prescription of vitamin D was determined by female sex, age and low sun exposure in the patients (p < 0,05). There is no significant variability among physicians. Conclusion: Diagnosis and treatment of vitamin D deficiency exist but are insufficient in primary care. Recommendations are welcome in France.Introduction : L’hypovitaminose D est un enjeu de santé publique, la littérature est abondante mais peu d’études ont été faites en médecine générale. Méthode : Enquête auprès de médecins généralistes concernant les patients de plus de 18 ans vus un jour donné.Résultats : 34 médecins ont participé permettant d’inclure 479 patients. 16% des patients ont déjà eu un dosage (20,9ng/mL en moyenne, 78% < 30ng/mL et 27% < 10ng/mL) et 23% ont une supplémentation. La prévalence de l’hypovitaminose D est importante mais la supplémentation est hétérogène et les dosages ou la supplémentation loin d’être systématiques dans les situations où ils sont recommandés, certaines populations à risque sont négligées. Les déterminants de la prescription liés aux patients sont le sexe féminin, l’âge, une faible exposition solaire (p<0,05). Aucune variabilité significative entre les médecins n’a été mise en évidence, mais leurs connaissances sur la vitamine D et l’existence d’une peur de l’intoxication semblent inversement liées à la quantité de dosages prescrits. 92% des médecins ayant participé souhaitent des recommandations. Conclusion : la recherche d’une hypovitaminose D et la prescription de vitamine D existent et ne sont pas négligeables en médecine générale, mais restent insuffisantes. Les posologies prescrites sont hétérogènes. La rédaction de recommandations serait nécessaire