Minibatch training of neural network ensembles via trajectory sampling

Most iterative neural network training methods use estimates of the loss function over small random subsets (or minibatches) of the data to update the parameters, which aid in decoupling the training time from the (often very large) size of the training datasets. Here, we show that a minibatch approach can also be used to train neural network ensembles (NNEs) via trajectory methods in a highly efficent manner. We illustrate this approach by training NNEs to classify images in the MNIST datasets. This method gives an improvement to the training times, allowing it to scale as the ratio of the size of the dataset to that of the average minibatch size which, in the case of MNIST, gives a computational improvement typically of two orders of magnitude. We highlight the advantage of using longer trajectories to represent NNEs, both for improved accuracy in inference and reduced update cost in terms of the samples needed in minibatch updates.Comment: 11 pages, 4 figures, 1 algorith

Boundary conditions dependence of the phase transition in the quantum Newman-Moore model

We study the triangular plaquette model (TPM, also known as the Newman-Moore model) in the presence of a transverse magnetic field on a lattice with periodic boundaries in both spatial dimensions. We consider specifically the approach to the ground state phase transition of this quantum TPM (QTPM, or quantum Newman-Moore model) as a function of the system size and type of boundary conditions. Using cellular automata methods, we obtain a full characterization of the minimum energy configurations of the TPM for arbitrary tori sizes. For the QTPM, we use these cycle patterns to obtain the symmetries of the model, which we argue determine its quantum phase transition: we find it to be a first-order phase transition, with the addition of spontaneous symmetry breaking for system sizes which have degenerate classical ground states. For sizes accessible to numerics, we also find that this classification is consistent with exact diagonalization, Matrix Product States and Quantum Monte Carlo simulations.Comment: fixed unclear point, given the correct credit to citatio

Rejection-free quantum Monte Carlo in continuous time from transition path sampling

Continuous-time quantum Monte Carlo refers to a class of algorithms designed to sample the thermal distribution of a quantum Hamiltonian through exact expansions of the Boltzmann exponential in terms of stochastic trajectories which are periodic in imaginary time. Here, we show that for (sign-problem-free) quantum many-body systems with discrete degrees of freedom—such as spins on a lattice—this sampling can be done in a rejection-free manner using transition path sampling (TPS). The key idea is to converge the trajectory ensemble through updates where one individual degree of freedom is modified across all time while the remaining unaltered ones provide a time-dependent background. The ensuing single-body dynamics provides a way to generate trajectory updates exactly, allowing one to obtain the target ensemble efficiently via rejection-free TPS. We demonstrate our method on the transverse field Ising model in one and two dimensions, and on the quantum triangular plaquette (or Newman-Moore) model. We show that despite large autocorrelation times, our method is able to efficiently recover the respective quantum phase transition of each model. We also discuss the connection to rare event sampling in continuous-time Markov dynamics

An evaluation of 1 year of advice calls to a tropical and infectious disease referral Centre

OBJECTIVES:Many secondary care departments receive external advice calls. However, systematic advice-call documentation is uncommon and evidence on call nature and burden infrequent. The Liverpool tropical and infectious disease unit (TIDU) provides specialist advice locally, regionally and nationally. We created and evaluated a recording system to document advice calls received by TIDU. METHODS:An electronic advice-call recording system was created for TIDU specialist trainees to document complex, predominantly external calls. Fourteen months of advice calls were summarised, analysed and recommendations for other departments wishing to replicate this system made. RESULTS:Five-hundred and ninety calls regarding 362 patients were documented. Median patient age was 44 years (interquartile range 29-56 years) and 56% were male. Sixty-nine per cent of patients discussed were referred from secondary healthcare, half from emergency or acute medicine departments; 43% of patients were returning travellers; 59% of returning travellers had undifferentiated fever, one-third of whom returned from sub-Saharan Africa; 32% of patients discussed were further reviewed at TIDU. Interim 6-month review showed good user acceptability of the system. CONCLUSIONS:Implementing an advice-call recording system was feasible within TIDU. Call and follow-up burden was high with advice regarding fever in returned travellers predominating. Similar systems could improve clinical governance, patient care and service delivery in other secondary care departments

Tuberculosis diagnosis cascade in Blantyre, Malawi : a prospective cohort study

Wellcome Trust. PM is funded by Wellcome (206575/Z/17/Z). ELC is funded by Wellcome (200901/Z/16/Z). ELW received salary funding from the UK Medical Research Council (grant number MR/K012126/1), this award is jointly funded by the UK Medical Research Council (MRC) and the UK Department for International Development (DFID) under the MRC/DFID Concordat agreement and is also part of the EDCTP2 programme supported by the European Union.Background Tuberculosis (TB) control relies on early diagnosis and treatment. International guidelines recommend systematic TB screening at health facilities, but implementation is challenging. We investigated completion of recommended TB screening steps in Blantyre, Malawi. Methods A prospective cohort recruited adult outpatients attending Bangwe primary clinic. Entry interviews were linked to exit interviews. The proportion of participants progressing through each step of the diagnostic pathway were estimated. Factors associated with request for sputum were investigated using multivariable logistic regression. Results Of 5442 clinic attendances 2397 (44%) had exit interviews. In clinically indicated participants (n = 445) 256 (57.5%) were asked about cough, 36 (8.1%) were asked for sputum, 21 (4.7%) gave sputum and 1 (0.2%) received same-day results. Significant associations with request for sputum were: any TB symptom (aOR:3.20, 95%CI:2.02–5.06), increasing age (aOR:1.02, 95%CI:1.01–1.04 per year) and for HIV-negative participants only, a history of previous TB (aOR:3.37, 95%CI:1.45–7.81). Numbers requiring sputum tests (26/day) outnumbered diagnostic capacity (8–12/day). Conclusions Patients were lost at every stage of the TB care cascade, with same day sputum submission following all steps of the diagnosis cascade achieved in only 4.7% if clinically indicated. Infection control strategies should be implemented, with reporting on early steps of the TB care cascade formalised. High-throughput screening interventions, such as digital CXR, that can achieve same-day TB diagnosis are urgently needed to meet WHO End TB goals.Peer reviewe

Glycaemic control trends in people with Type 1 diabetes in Scotland 2004-2016

Aims/hypothesis: The aim of this work was to examine whether glycaemic control has improved in those with type 1 diabetes in Scotland between 2004 and 2016, and whether any trends differed by sociodemographic factors. Methods: We analysed records from 30,717 people with type 1 diabetes, registered anytime between 2004 and 2016 in the national diabetes database, which contained repeated measures of HbA1c. An additive mixed regression model was used to estimate calendar time and other effects on HbA1c. Results: Overall, median (IQR) HbA1c decreased from 72 (21) mmol/mol [8.7 (4.1)%] in 2004 to 68 (21) mmol/mol (8.4 [4.1]%) in 2016. However, all of the improvement across the period occurred in the latter 4 years: the regression model showed that the only period of significant change in HbA1c was 2012–2016 where there was a fall of 3 (95% CI 1.82, 3.43) mmol/mol. The largest reductions in HbA1c in this period were seen in children, from 69 (16) mmol/mol (8.5 [3.6]%) to 63 (14) mmol/mol (7.9 [3.4]%), and adolescents, from 75 (25) mmol/mol (9.0 [4.4]%) to 70 (23) mmol/mol (8.6 [4.3]%). Socioeconomic status (according to Scottish Index of Multiple Deprivation) affected the HbA1c values: from the regression model, the 20% of people living in the most-deprived areas had HbA1c levels on average 8.0 (95% CI 7.4, 8.9) mmol/mol higher than those of the 20% of people living in the least-deprived areas. However this difference did not change significantly over time. From the regression model HbA1c was on average 1.7 (95% CI 1.6, 1.8) mmol/mol higher in women than in men. This sex difference did not narrow over time. Conclusions/interpretation: In this high-income country, we identified a modest but important improvement in HbA1c since 2012 that was most marked in children and adolescents. These changes coincided with national initiatives to reduce HbA1c including an expansion of pump therapy. However, in most people, overall glycaemic control remains far from target levels and further improvement is badly needed, particularly in those from more-deprived areas

Glacier velocities and dynamic ice discharge from the Queen Elizabeth Islands, Nunavut, Canada

Recent studies indicate an increase in glacier mass loss from the Canadian Arctic Archipelago as a result of warmer summer air temperatures. However, no complete assessment of dynamic ice discharge from this region exists. We present the first complete surface velocity mapping of all ice masses in the Queen Elizabeth Islands and show that these ice masses discharged ~2.6 ± 0.8 Gt a−1 of ice to the oceans in winter 2012. Approximately 50% of the dynamic discharge was channeled through non surge-type Trinity and Wykeham Glaciers alone. Dynamic discharge of the surge-type Mittie Glacier varied from 0.90 ± 0.09 Gt a−1 during its 2003 surge to 0.02 ± 0.02 Gt a−1 during quiescence in 2012, highlighting the importance of surge-type glaciers for interannual variability in regional mass loss. Queen Elizabeth Islands glaciers currently account for ~7.5% of reported dynamic discharge from Arctic ice masses outside Greenland.We thank NSERC, Canada Foundation for Innovation, Ontario Research Fund, ArcticNet, Ontario Graduate Scholarship, University of Ottawa and the NSERC Canada Graduate Scholarship for funding. RADARSAT-2 data were provided by MacDonald, Dettwiler and Associates under the RADARSAT-2 Government Data Allocation administrated by the Canadian Space Agency. Support to DB is provided through the Climate Change Geosciences Program, Earth Sciences Sector, Natural Resources Canada (ESS Contribution #20130293). We also acknowledge support from U.K NERC for grants R3/12469 and NE/K004999 to JAD.This is the accepted version of an article published in Geophysical Research Letters. An edited version of this paper was published by AGU. Copyright (2014) American Geophysical Union. The final version is available at http://onlinelibrary.wiley.com/doi/10.1002/2013GL058558/abstract;jsessionid=6A3AD907C4383DA5D4E20C4924D6EC18.f02t02

Provider-initiated HIV testing and TB screening in the era of universal coverage: Are the right people being reached? A cohort study in Blantyre, Malawi.

Patients with tuberculosis (TB) symptoms have high prevalence of HIV, and should be prioritised for HIV testing. In a prospective cohort study in Bangwe primary care clinic, Blantyre, Malawi, all adults (18 years or older) presenting with an acute illness were screened for TB symptoms (cough, fever, night sweats, weight loss). Demographic characteristics were linked to exit interview by fingerprint bioidentification. Multivariable logistic regression models were constructed to estimate the proportion completing same-visit HIV testing, comparing between those with and without TB symptoms. There were 5427 adult attendees between 21/5/2018 and 6/9/2018. Exit interviews were performed for 2402 (44%). 276 patients were excluded from the analysis, being already on antiretroviral therapy (ART). Presentation with any TB symptom was common for men (54.6%) and women (57.4%). Overall 27.6% (585/ 2121) attenders reported being offered testing and 21.5% (455/2121) completed provider-initiated HIV testing and counselling (PITC) and received results. The proportions offered testing were similar among participants with and without TB symptoms (any TB symptom: 29.0% vs. 25.7%). This was consistent for each individual symptom; cough, weight loss, fever and night sweats. Multivariable regression models indicated men, younger adults and participants who had previously tested were more likely to complete PITC than women, older adults and those who had never previously tested. Same-visit completion of HIV testing was suboptimal, especially among groups known to have high prevalence of undiagnosed HIV. As countries approach universal coverage of ART, identifying and prioritising currently underserved groups for HIV testing will be essential

Tuberculosis diagnosis cascade in Blantyre, Malawi: a prospective cohort study.

BACKGROUND: Tuberculosis (TB) control relies on early diagnosis and treatment. International guidelines recommend systematic TB screening at health facilities, but implementation is challenging. We investigated completion of recommended TB screening steps in Blantyre, Malawi. METHODS: A prospective cohort recruited adult outpatients attending Bangwe primary clinic. Entry interviews were linked to exit interviews. The proportion of participants progressing through each step of the diagnostic pathway were estimated. Factors associated with request for sputum were investigated using multivariable logistic regression. RESULTS: Of 5442 clinic attendances 2397 (44%) had exit interviews. In clinically indicated participants (n = 445) 256 (57.5%) were asked about cough, 36 (8.1%) were asked for sputum, 21 (4.7%) gave sputum and 1 (0.2%) received same-day results. Significant associations with request for sputum were: any TB symptom (aOR:3.20, 95%CI:2.02-5.06), increasing age (aOR:1.02, 95%CI:1.01-1.04 per year) and for HIV-negative participants only, a history of previous TB (aOR:3.37, 95%CI:1.45-7.81). Numbers requiring sputum tests (26/day) outnumbered diagnostic capacity (8-12/day). CONCLUSIONS: Patients were lost at every stage of the TB care cascade, with same day sputum submission following all steps of the diagnosis cascade achieved in only 4.7% if clinically indicated. Infection control strategies should be implemented, with reporting on early steps of the TB care cascade formalised. High-throughput screening interventions, such as digital CXR, that can achieve same-day TB diagnosis are urgently needed to meet WHO End TB goals