Predictive Entropy Search for Bayesian optimization with unknown constraints

Unknown constraints arise in many types of expensive black-box optimization problems. Several methods have been proposed recently for performing Bayesian optimization with constraints, based on the expected improvement (EI) heuristic. However, EI can lead to pathologies when used with constraints. For example, in the case of decoupled constraints---i.e., when one can independently evaluate the objective or the constraints---EI can encounter a pathology that prevents exploration. Additionally, computing EI requires a current best solution, which may not exist if none of the data collected so far satisfy the constraints. By contrast, information-based approaches do not suffer from these failure modes. In this paper, we present a new information-based method called Predictive Entropy Search with Constraints (PESC). We analyze the performance of PESC and show that it compares favorably to EI-based approaches on synthetic and benchmark problems, as well as several real-world examples. We demonstrate that PESC is an effective algorithm that provides a promising direction towards a unified solution for constrained Bayesian optimization.José Miguel Hernández-Lobato acknowledges support from the Rafael del Pino Foundation. Zoubin Ghahramani acknowledges support from Google Focused Research Award and EPSRC grant EP/I036575/1. Matthew W. Hoffman acknowledges support from EPSRC grant EP/J012300/1.This is the final published version. It first appeared at http://jmlr.org/proceedings/papers/v37/hernandez-lobatob15.html

A General Framework for Constrained Bayesian Optimization using Information-based Search

We present an information-theoretic framework for solving global black-box optimization problems that also have black-box constraints. Of particular interest to us is to efficiently solve problems with $\textit{decoupled}$ constraints, in which subsets of the objective and constraint functions may be evaluated independently. For example, when the objective is evaluated on a CPU and the constraints are evaluated independently on a GPU. These problems require an acquisition function that can be separated into the contributions of the individual function evaluations. We develop one such acquisition function and call it Predictive Entropy Search with Constraints (PESC). PESC is an approximation to the expected information gain criterion and it compares favorably to alternative approaches based on improvement in several synthetic and real-world problems. In addition to this, we consider problems with a mix of functions that are fast and slow to evaluate. These problems require balancing the amount of time spent in the meta-computation of PESC and in the actual evaluation of the target objective. We take a bounded rationality approach and develop a partial update for PESC which trades off accuracy against speed. We then propose a method for adaptively switching between the partial and full updates for PESC. This allows us to interpolate between versions of PESC that are efficient in terms of function evaluations and those that are efficient in terms of wall-clock time. Overall, we demonstrate that PESC is an effective algorithm that provides a promising direction towards a unified solution for constrained Bayesian optimization.Rafael del Pino Foundation, Google Focused Research Award, Engineering and Physical Sciences Research Council (Grant IDs: EP/I036575/1, EP/J012300/1

Double-chambered right ventricle in an adult patient diagnosed by transthoracic echocardiography

BACKGROUND: Double-chambered right ventricle is a rare congenital disease frequently misdiagnosed in the adult patient. An anomalous muscle band divides the right ventricle in two cavities causing variable degree of obstruction. Although echocardiography is considered a useful method for the diagnosis of this pathology in children, it has been recognized the transthoracic scanning limitation in adults. CASE PRESENTATION: A 29 year-old patient with double-chambered right ventricle presenting mild exercise intolerance referred for follow up of a known ventricular septal defect in whom a complete diagnosis was obtained based only on transthoracic two dimensional echocardiography without the needing of cardiac catheterization. CONCLUSION: Based on non invasive echocardiographic diagnosis, patient was referred to surgical correction, which was completely successful

Data requirements for crop modelling-Applying the learning curve approach to the simulation of winter wheat flowering time under climate change

A prerequisite for application of crop models is a careful parameterization based on observational data. However, there are limited studies investigating the link between quality and quantity of observed data and its suitability for model parameterization. Here, we explore the interactions between number of measurements, noise and model predictive skills to simulate the impact of 2050′s climate change (RCP8.5) on winter wheat flowering time. The learning curve of two winter wheat phenology models is analysed under different assumptions about the size of the calibration dataset, the measurement error and the accuracy of the model structure. Our assessment confirms that prediction skills improve asymptotically with the size of the calibration dataset, as with statistical models. Results suggest that less precise but larger training datasets can improve the predictive abilities of models. However, the non-linear relationship between number of measurements, measurement error, and prediction skills limit the compensation between data quality and quantity. We find that the model performance does not improve significantly with a theoretical minimum size of 7–9 observations when the model structure is approximate. While simulation of crop phenology is critical to crop model simulation, more studies are needed to explore data needs for assessing entire crop models

Family coordination in families who have a child with autism spectrum disorder

Little is known about the interactions of families where there is a child with autism spectrum disorder (ASD). The present study applies the Lausanne Trilogue Play (LTP) to explore both its applicability to this population as well as to assess resources and areas of deficit in these families. The sample consisted of 68 families with a child with ASD, and 43 families with a typically developing (TD) child. With respect to the global score for family coordination there were several negative correlations: the more severe the symptoms (based on the child’s ADOS score), the more family coordination was dysfunctional. This correlation was particularly high when parents had to play together with the child. In the parts in which only one of the parents played actively with the child, while the other was simply present, some families did achieve scores in the functional range, despite the child’s symptom severity. The outcomes are discussed in terms of their clinical implications both for assessment and for interventio

Systematic inclusion of mandatory interprofessional education in health professions curricula at Gunma University: a report of student self-assessment in a nine-year implementation

<p>Abstract</p> <p>Background</p> <p>The mandatory interprofessional education programme at Gunma University was initiated in 1999. This paper is a statistical evaluation of the programme from 1999 to 2007.</p> <p>Methods</p> <p>A questionnaire of 10 items to assess the achievement levels of the programme, which was developed independently of other assessment systems published previously, was distributed, as well as two or three open-ended questions to be answered at the end of each annual module. A multivariate analysis of variance model was used, and the factor analysis of the responses was performed with varimax rotation.</p> <p>Results</p> <p>Over all, 1418 respondents of a possible 1629 students completed the survey, for a total response rate of 87.1%. Cronbach's alpha of 10 items was 0.793, revealing high internal consistency. Our original questionnaire was categorized into four subscales as follows: "Role and responsibilities", "Teamwork and collaboration", "Structure and function of training facilities", and "Professional identity". Students in the Department of Occupational Therapy reached a relatively lower level of achievement. In the replies to the open-ended questions, requests for the participation of the medical students were repeated throughout the evaluation period.</p> <p>Conclusion</p> <p>The present four subscales measure "understanding", and may take into account the development of interprofessional education programmes with clinical training in various facilities. The content and quality of clinical training subjects may be remarkably dependent on training facilities, suggesting the importance of full consultation mechanisms in the local network with the relevant educational institutes for medicine, health care and welfare.</p

Effect of anakinra on arthropathy in CINCA/NOMID syndrome

CINCA/NOMID is an autoinflammatory disorder characterized by the triad of neonatal onset of cutaneous symptoms, chronic meningitis, and recurrent fever and it presents with distinctive osteoarthropathy, synovitis mainly of the large joints and overgrowth of epimetaphyseal cartilage, particularly of the long bones. The cartilage overgrowth eventually causes osseous overgrowth and deformity that persists beyond skeletal maturity and leads to limb length discrepancy, joint contracture, and early degenerative arthropathy. Autoinflammation in CAPS/NOMID has been proven to derive from excessive release of interleukin-1 (IL-1). It has been well documented that the IL-1 receptor antagonist anakinra (Kineret(R)) helps mitigate systemic inflammation in the disorder. However, a general consensus has not been reached on its beneficial effect on osteoarthropathy. The case of a girl with CINCA/NOMID syndrome who showed dramatic improvement of osteoarthropathy after anakinra treatment is reported. A 4-year-old girl suffered at the age of 10 months from a generalized urticarial skin lesion with recurrent episodes of fever and growth disorder. Blood examination revealed persistent massive neutrophilia, anemia and intense acute phase response. She manifested knee joint swelling with limited ROM when she was 20 months old and was diagnosed as being CINCA/NOMID based on characteristic findings of radiograph despite negative CIAS1 mutation. Radiological examination demonstrated metaphyseal fraying and cupping and widening of the growth plate in the distal femur. MR imaging showed mottled gadolinium enhancement at the chondrosseous junction. Neither significant joint effusion nor synovitis was identified. At 2 years and 7 months of age, anakinra, 2 mg/kg/day given by regular daily subcutaneous injections, was started. A few days after the initiation of the treatment, her clinical symptoms and laboratory findings of active inflammation were promptly alleviated. She was not able to walk unaided prior to the treatment, but she walked independently 1 month after the treatment. Follow-up radiographs and MR imaging showed that growth plate widening and gadolinium enhancement at the chondrosseous junction were less conspicuous. Furthermore, longitudinal growth of the femur and tibia was identified during 20 months of observation

PomBase – the scientific resource for fission yeast

The fission yeast Schizosaccharomyces pombe has become well established as a model species for studying conserved cell-level biological processes, especially the mechanics and regulation of cell division. PomBase integrates the S. pombe genome sequence with traditional genetic, molecular and cell biological experimental data as well as the growing body of large datasets generated by emerging high-throughput methods. This chapter provides insight into the curation philosophy and data organization at PomBase, and provides a guide to using PomBase for infrequent visitors and anyone considering exploring S. pombe in their research