Improving Simulation Efficiency of MCMC for Inverse Modeling of Hydrologic Systems with a Kalman-Inspired Proposal Distribution

Bayesian analysis is widely used in science and engineering for real-time forecasting, decision making, and to help unravel the processes that explain the observed data. These data are some deterministic and/or stochastic transformations of the underlying parameters. A key task is then to summarize the posterior distribution of these parameters. When models become too difficult to analyze analytically, Monte Carlo methods can be used to approximate the target distribution. Of these, Markov chain Monte Carlo (MCMC) methods are particularly powerful. Such methods generate a random walk through the parameter space and, under strict conditions of reversibility and ergodicity, will successively visit solutions with frequency proportional to the underlying target density. This requires a proposal distribution that generates candidate solutions starting from an arbitrary initial state. The speed of the sampled chains converging to the target distribution deteriorates rapidly, however, with increasing parameter dimensionality. In this paper, we introduce a new proposal distribution that enhances significantly the efficiency of MCMC simulation for highly parameterized models. This proposal distribution exploits the cross-covariance of model parameters, measurements and model outputs, and generates candidate states much alike the analysis step in the Kalman filter. We embed the Kalman-inspired proposal distribution in the DREAM algorithm during burn-in, and present several numerical experiments with complex, high-dimensional or multi-modal target distributions. Results demonstrate that this new proposal distribution can greatly improve simulation efficiency of MCMC. Specifically, we observe a speed-up on the order of 10-30 times for groundwater models with more than one-hundred parameters

Vector Search with OpenAI Embeddings: Lucene Is All You Need

We provide a reproducible, end-to-end demonstration of vector search with OpenAI embeddings using Lucene on the popular MS MARCO passage ranking test collection. The main goal of our work is to challenge the prevailing narrative that a dedicated vector store is necessary to take advantage of recent advances in deep neural networks as applied to search. Quite the contrary, we show that hierarchical navigable small-world network (HNSW) indexes in Lucene are adequate to provide vector search capabilities in a standard bi-encoder architecture. This suggests that, from a simple cost-benefit analysis, there does not appear to be a compelling reason to introduce a dedicated vector store into a modern "AI stack" for search, since such applications have already received substantial investments in existing, widely deployed infrastructure

Revealing charge-tunneling processes between a quantum dot and a superconducting island through gate sensing

We report direct detection of charge-tunneling between a quantum dot and a superconducting island through radio-frequency gate sensing. We are able to resolve spin-dependent quasiparticle tunneling as well as two-particle tunneling involving Cooper pairs. The quantum dot can act as an RF-only sensor to characterize the superconductor addition spectrum, enabling us to access subgap states without transport. Our results provide guidance for future dispersive parity measurements of Majorana modes, which can be realized by detecting the parity-dependent tunneling between dots and islands.Comment: 6 pages, 4 figures, supplemental material included as ancillary fil

A Genetic Programming Approach to Designing Convolutional Neural Network Architectures

The convolutional neural network (CNN), which is one of the deep learning models, has seen much success in a variety of computer vision tasks. However, designing CNN architectures still requires expert knowledge and a lot of trial and error. In this paper, we attempt to automatically construct CNN architectures for an image classification task based on Cartesian genetic programming (CGP). In our method, we adopt highly functional modules, such as convolutional blocks and tensor concatenation, as the node functions in CGP. The CNN structure and connectivity represented by the CGP encoding method are optimized to maximize the validation accuracy. To evaluate the proposed method, we constructed a CNN architecture for the image classification task with the CIFAR-10 dataset. The experimental result shows that the proposed method can be used to automatically find the competitive CNN architecture compared with state-of-the-art models.Comment: This is the revised version of the GECCO 2017 paper. The code of our method is available at https://github.com/sg-nm/cgp-cn

Supporting patient screening to identify suitable clinical trials.

To support the efficient execution of post-genomic multi-centric clinical trials in breast cancer we propose a solution that streamlines the assessment of the eligibility of patients for available trials. The assessment of the eligibility of a patient for a trial requires evaluating whether each eligibility criterion is satisfied and is often a time consuming and manual task. The main focus in the literature has been on proposing different methods for modelling and formalizing the eligibility criteria. However the current adoption of these approaches in clinical care is limited. Less effort has been dedicated to the automatic matching of criteria to the patient data managed in clinical care. We address both aspects and propose a scalable, efficient and pragmatic patient screening solution enabling automatic evaluation of eligibility of patients for a relevant set of trials. This covers the flexible formalization of criteria and of other relevant trial metadata and the efficient management of these representations

Slot-mode-coupled optomechanical crystals

We present a design methodology and analysis of a cavity optomechanical system in which a localized GHz frequency mechanical mode of a nanobeam resonator is evanescently coupled to a high quality factor (Q>10^6) optical mode of a separate nanobeam optical cavity. Using separate nanobeams provides flexibility, enabling the independent design and optimization of the optics and mechanics of the system. In addition, the small gap (approx. 25 nm) between the two resonators gives rise to a slot mode effect that enables a large zero-point optomechanical coupling strength to be achieved, with g/2pi > 300 kHz in a Si3N4 system at 980 nm and g/2pi approx. 900 kHz in a Si system at 1550 nm. The fact that large coupling strengths to GHz mechanical oscillators can be achieved in SiN is important, as this material has a broad optical transparency window, which allows operation throughout the visible and near-infrared. As an application of this platform, we consider wide-band optical frequency conversion between 1300 nm and 980 nm, using two optical nanobeam cavities coupled on either side to the breathing mode of a mechanical nanobeam resonator

Holding chambers (spacers) versus nebulisers for beta-agonist treatment of acute asthma

In acute asthma inhaled beta 2-agonists are often administered to relieve bronchospasm by wet nebulisation, but some have argued that metered-dose inhalers with a holding chamber (spacer) can be equally effective. Nebulisers require a power source and need regular maintenance, and are more expensive in the community setting.ObjectivesTo assess the effects of holding chambers (spacers) compared to nebulisers for the delivery of beta 2-agonists for acute asthma.Search strategyWe last searched the Cochrane Airways Group trials register in January 2006 and the Cochrane Central Register of Controlled Trials (The Cochrane Library, Issue 4, 2005).Selection criteriaRandomised trials in adults and children (from two years of age) with asthma, where spacer beta 2-agonist delivery was compared with wet nebulisation.Data collection and analysisTwo reviewers independently applied study inclusion criteria (one reviewer for the first version of the review), extracted the data and assessed trial quality. Missing data were obtained from the authors or estimated. Results are reported with 95% confidence intervals (CI).Main resultsThis review has been updated in January 2006 and four new trials have been added. 2066 children and 614 adults are now included in 25 trials from emergency room and community settings. In addition, six trials on in-patients with acute asthma (213 children and 28 adults) have been reviewed. Method of delivery of beta 2-agonist did not appear to affect hospital admission rates. In adults, the relative risk of admission for spacer versus nebuliser was 0.97 (95% CI 0.63 to 1.49). The relative risk for children was 0.65 (95% CI: 0.4 to 1.06). In children, length of stay in the emergency department was significantly shorter when the spacer was used, with a mean difference of -0.47 hours (95% CI: -0.58 to -0.37). Length of stay in the emergency department for adults was similar for the two delivery methods. Peak flow and forced expiratory volume were also similar for the two delivery methods. Pulse rate was lower for spacer in children, mean difference -7.6% baseline (95% CI: -9.9 to -5.3% baseline).Authors' conclusionsMetered-dose inhalers with spacer produced outcomes that were at least equivalent to nebuliser delivery. Spacers may have some advantages compared to nebulisers for children with acute asthma

Holding chambers (spacers) versus nebulisers for beta-agonist treatment of acute asthma

Background In acute asthma inhaled beta₂-agonists are often administered by nebuliser to relieve bronchospasm, but some have argued that metered-dose inhalers with a holding chamber (spacer) can be equally effective. Nebulisers require a power source and need regular maintenance, and are more expensive in the community setting. Objectives To assess the effects of holding chambers (spacers) compared to nebulisers for the delivery of beta₂-agonists for acute asthma. Search methods We searched the Cochrane Airways Group Trial Register and reference lists of articles. We contacted the authors of studies to identify additional trials. Date of last search: February 2013. Selection criteria Randomised trials in adults and children (from two years of age) with asthma, where spacer beta₂-agonist delivery was compared with wet nebulisation. Data collection and analysis Two review authors independently applied study inclusion criteria (one review author for the first version of the review), extracted the data and assessed risks of bias. Missing data were obtained from the authors or estimated. Results are reported with 95% confidence intervals (CIs). Main results This review includes a total of 1897 children and 729 adults in 39 trials. Thirty-three trials were conducted in the emergency room and equivalent community settings, and six trials were on inpatients with acute asthma (207 children and 28 adults). The method of delivery of beta₂-agonist did not show a significant difference in hospital admission rates. In adults, the risk ratio (RR) of admission for spacer versus nebuliser was 0.94 (95% CI 0.61 to 1.43). The risk ratio for children was 0.71 (95% CI 0.47 to 1.08, moderate quality evidence). In children, length of stay in the emergency department was significantly shorter when the spacer was used. The mean duration in the emergency department for children given nebulised treatment was 103 minutes, and for children given treatment via spacers 33 minutes less (95% CI -43 to -24 minutes, moderate quality evidence). Length of stay in the emergency department for adults was similar for the two delivery methods. Peak flow and forced expiratory volume were also similar for the two delivery methods. Pulse rate was lower for spacer in children, mean difference -5% baseline (95% CI -8% to -2%, moderate quality evidence), as was the risk of developing tremor (RR 0.64; 95% CI 0.44 to 0.95, moderate quality evidence). Authors' conclusions Nebuliser delivery produced outcomes that were not significantly better than metered-dose inhalers delivered by spacer in adults or children, in trials where treatments were repeated and titrated to the response of the participant. Spacers may have some advantages compared to nebulisers for children with acute asthma