Data compression and regression based on local principal curves.

Frequently the predictor space of a multivariate regression problem of the type y = m(x_1, …, x_p ) + ε is intrinsically one-dimensional, or at least of far lower dimension than p. Usual modeling attempts such as the additive model y = m_1(x_1) + … + m_p (x_p ) + ε, which try to reduce the complexity of the regression problem by making additional structural assumptions, are then inefficient as they ignore the inherent structure of the predictor space and involve complicated model and variable selection stages. In a fundamentally different approach, one may consider first approximating the predictor space by a (usually nonlinear) curve passing through it, and then regressing the response only against the one-dimensional projections onto this curve. This entails the reduction from a p- to a one-dimensional regression problem. As a tool for the compression of the predictor space we apply local principal curves. Taking things on from the results presented in Einbeck et al. (Classification – The Ubiquitous Challenge. Springer, Heidelberg, 2005, pp. 256–263), we show how local principal curves can be parametrized and how the projections are obtained. The regression step can then be carried out using any nonparametric smoother. We illustrate the technique using data from the physical sciences

Prediction of persistent post-surgery pain by preoperative cold pain sensitivity : biomarker development with machine-learning-derived analysis

Background. To prevent persistent post-surgery pain, early identification of patients at high risk is a clinical need. Supervised machine-learning techniques were used to test how accurately the patients' performance in a preoperatively performed tonic cold pain test could predict persistent post-surgery pain. Methods. We analysed 763 patients from a cohort of 900 women who were treated for breast cancer, of whom 61 patients had developed signs of persistent pain during three yr of follow-up. Preoperatively, all patients underwent a cold pain test (immersion of the hand into a water bath at 2-4 degrees C). The patients rated the pain intensity using a numerical ratings scale (NRS) from 0 to 10. Supervised machine-learning techniques were used to construct a classifier that could predict patients at risk of persistent pain. Results. Whether or not a patient rated the pain intensity at NRS=10 within less than 45 s during the cold water immersion test provided a negative predictive value of 94.4% to assign a patient to the "persistent pain" group. If NRS=10 was never reached during the cold test, the predictive value for not developing persistent pain was almost 97%. However, a low negative predictive value of 10% implied a high false positive rate. Conclusion. Results provide a robust exclusion of persistent pain in women with an accuracy of 94.4%. Moreover, results provide further support for the hypothesis that the endogenous pain inhibitory system may play an important role in the process of pain becoming persistent.Peer reviewe

Data compression and regression based on local principal curves

Frequently the predictor space of a multivariate regression problem of the type y = m(x_1, …, x_p ) + ε is intrinsically one-dimensional, or at least of far lower dimension than p. Usual modeling attempts such as the additive model y = m_1(x_1) + … + m_p (x_p ) + ε, which try to reduce the complexity of the regression problem by making additional structural assumptions, are then inefficient as they ignore the inherent structure of the predictor space and involve complicated model and variable selection stages. In a fundamentally different approach, one may consider first approximating the predictor space by a (usually nonlinear) curve passing through it, and then regressing the response only against the one-dimensional projections onto this curve. This entails the reduction from a p- to a one-dimensional regression problem. As a tool for the compression of the predictor space we apply local principal curves. Taking things on from the results presented in Einbeck et al. (Classification – The Ubiquitous Challenge. Springer, Heidelberg, 2005, pp. 256–263), we show how local principal curves can be parametrized and how the projections are obtained. The regression step can then be carried out using any nonparametric smoother. We illustrate the technique using data from the physical sciences

The BioDICE Taverna plugin for clustering and visualization of biological data: a workflow for molecular compounds exploration

Background: In many experimental pipelines, clustering of multidimensional biological datasets is used to detect hidden structures in unlabelled input data. Taverna is a popular workflow management system that is used to design and execute scientific workflows and aid in silico experimentation. The availability of fast unsupervised methods for clustering and visualization in the Taverna platform is important to support a data-driven scientific discovery in complex and explorative bioinformatics applications. Results: This work presents a Taverna plugin, the Biological Data Interactive Clustering Explorer (BioDICE), that performs clustering of high-dimensional biological data and provides a nonlinear, topology preserving projection for the visualization of the input data and their similarities. The core algorithm in the BioDICE plugin is Fast Learning Self Organizing Map (FLSOM), which is an improved variant of the Self Organizing Map (SOM) algorithm. The plugin generates an interactive 2D map that allows the visual exploration of multidimensional data and the identification of groups of similar objects. The effectiveness of the plugin is demonstrated on a case study related to chemical compounds. Conclusions: The number and variety of available tools and its extensibility have made Taverna a popular choice for the development of scientific data workflows. This work presents a novel plugin, BioDICE, which adds a data-driven knowledge discovery component to Taverna. BioDICE provides an effective and powerful clustering tool, which can be adopted for the explorative analysis of biological datasets

Characterization of clastic sedimentary enviroments by clustering algorithm and several statistical approaches — case study, Sava Depression in Northern Croatia

Abstract This study demonstrates a method to identify and characterize some facies of turbiditic depositional environments. The study area is a hydrocarbon field in the Sava Depression (Northern Croatia). Its Upper Miocene reservoirs have been proved to represent a lacustrine turbidite system. In the workflow, first an unsupervised neural network was applied as clustering method for two sandstone reservoirs. The elements of the input vectors were the basic petrophysical parameters. In the second step autocorrelation surfaces were used to reveal the hidden anisotropy of the grid. This anisotropy is supposed to identify the main continuity directions in the geometrical analyses of sandstone bodies. Finally, in the description of clusters several parametric and nonparametric statistics were used to characterize the identified facies. Obtained results correspond to the previously published interpretation of those reservoir facies

The physiology of hibernation among painted turtles: the midland painted turtle (Chrysemys picta marginata

Abstract Midland painted turtles from Michigan were submerged at 3°C in normoxic and anoxic water. In predive, and in turtles submerged for up to 150 days, plasma PO 2 , PCO 2 , pH, [ , total Mg, total Ca, lactate, glucose, and osmolality were measured; hematocrit and mass were determined, and plasma [HCO 3 − ] was calculated. Anoxic turtles developed a severe metabolic acidosis, accumulating lactate from a predive value of 4.4 mmol/L to a 150-day value of 185 mmol/L, associated with a fall in pH from 7.983 to 7.189. To buffer lactate increase, total calcium and magnesium rose from 3.7 and 2.6 to 58.9 and 11.8 mmol/L, respectively. Plasma [HCO 3 − ] was titrated from 39.2 to 4.8 mmol/L in anoxic turtles. Turtles in normoxic water had only minor disturbances of their acid -base and ionic statuses, associated with a much smaller increase of lactate to 23 mmol/L; there was a marked increase in hematocrit from 29.1% to 42.1%. We suggest that it is ecologic, rather than phylogenetic, relationships that determine the responses of painted turtles to prolonged submergence associated with hibernation

Scale-up of Digital Innovations in Health Care: Expert Commentary on Enablers and Barriers

Health care delivery is undergoing a rapid change from traditional processes toward the use of digital health interventions and personalized medicine. This movement has been accelerated by the COVID-19 crisis as a response to the need to guarantee access to health care services while reducing the risk of contagion. Digital health scale-up is now also vital to achieve population-wide impact: it will only accomplish sustainable effects if and when deployed into regular health care delivery services. The question of how sustainable digital health scale-up can be successfully achieved has, however, not yet been sufficiently resolved. This paper identifies and discusses enablers and barriers for scaling up digital health innovations. The results discussed in this paper were gathered by scientists and representatives of public bodies as well as patient organizations at an international workshop on scaling up digital health innovations. Results are explored in the context of prior research and implications for future work in achieving large-scale implementations that will benefit the population as a whole

Expert Commentary on Enablers and Barriers

©Hannes Schlieter, Lisa A Marsch, Diane Whitehouse, Lena Otto, Ana Rita Londral, Gisbert Wilhelm Teepe, Martin Benedict, Joseph Ollier, Tom Ulmer, Nathalie Gasser, Sabine Ultsch, Bastian Wollschlaeger, Tobias Kowatsch. Originally published in the Journal of Medical Internet Research (https://www.jmir.org), 11.03.2022.Health care delivery is undergoing a rapid change from traditional processes toward the use of digital health interventions and personalized medicine. This movement has been accelerated by the COVID-19 crisis as a response to the need to guarantee access to health care services while reducing the risk of contagion. Digital health scale-up is now also vital to achieve population-wide impact: it will only accomplish sustainable effects if and when deployed into regular health care delivery services. The question of how sustainable digital health scale-up can be successfully achieved has, however, not yet been sufficiently resolved. This paper identifies and discusses enablers and barriers for scaling up digital health innovations. The results discussed in this paper were gathered by scientists and representatives of public bodies as well as patient organizations at an international workshop on scaling up digital health innovations. Results are explored in the context of prior research and implications for future work in achieving large-scale implementations that will benefit the population as a whole.publishersversionpublishe