Exploratory analysis using machine learning to predict for chest wall pain in patients with stage I non-small-cell lung cancer treated with stereotactic body radiation therapy.

Background and purposeChest wall toxicity is observed after stereotactic body radiation therapy (SBRT) for peripherally located lung tumors. We utilize machine learning algorithms to identify toxicity predictors to develop dose-volume constraints.Materials and methodsTwenty-five patient, tumor, and dosimetric features were recorded for 197 consecutive patients with Stage I NSCLC treated with SBRT, 11 of whom (5.6%) developed CTCAEv4 grade ≥2 chest wall pain. Decision tree modeling was used to determine chest wall syndrome (CWS) thresholds for individual features. Significant features were determined using independent multivariate methods. These methods incorporate out-of-bag estimation using Random forests (RF) and bootstrapping (100 iterations) using decision trees.ResultsUnivariate analysis identified rib dose to 1 cc < 4000 cGy (P = 0.01), chest wall dose to 30 cc < 1900 cGy (P = 0.035), rib Dmax < 5100 cGy (P = 0.05) and lung dose to 1000 cc < 70 cGy (P = 0.039) to be statistically significant thresholds for avoiding CWS. Subsequent multivariate analysis confirmed the importance of rib dose to 1 cc, chest wall dose to 30 cc, and rib Dmax. Using learning-curve experiments, the dataset proved to be self-consistent and provides a realistic model for CWS analysis.ConclusionsUsing machine learning algorithms in this first of its kind study, we identify robust features and cutoffs predictive for the rare clinical event of CWS. Additional data in planned subsequent multicenter studies will help increase the accuracy of multivariate analysis

Validation and clinical implementation of an accurate Monte Carlo code for pencil beam scanning proton therapy.

Monte Carlo (MC)-based dose calculations are generally superior to analytical dose calculations (ADC) in modeling the dose distribution for proton pencil beam scanning (PBS) treatments. The purpose of this paper is to present a methodology for commissioning and validating an accurate MC code for PBS utilizing a parameterized source model, including an implementation of a range shifter, that can independently check the ADC in commercial treatment planning system (TPS) and fast Monte Carlo dose calculation in opensource platform (MCsquare). The source model parameters (including beam size, angular divergence and energy spread) and protons per MU were extracted and tuned at the nozzle exit by comparing Tool for Particle Simulation (TOPAS) simulations with a series of commissioning measurements using scintillation screen/CCD camera detector and ionization chambers. The range shifter was simulated as an independent object with geometric and material information. The MC calculation platform was validated through comprehensive measurements of single spots, field size factors (FSF) and three-dimensional dose distributions of spread-out Bragg peaks (SOBPs), both without and with the range shifter. Differences in field size factors and absolute output at various depths of SOBPs between measurement and simulation were within 2.2%, with and without a range shifter, indicating an accurate source model. TOPAS was also validated against anthropomorphic lung phantom measurements. Comparison of dose distributions and DVHs for representative liver and lung cases between independent MC and analytical dose calculations from a commercial TPS further highlights the limitations of the ADC in situations of highly heterogeneous geometries. The fast MC platform has been implemented within our clinical practice to provide additional independent dose validation/QA of the commercial ADC for patient plans. Using the independent MC, we can more efficiently commission ADC by reducing the amount of measured data required for low dose "halo" modeling, especially when a range shifter is employed

Assessment of parameters describing representativeness of air quality in-situ measurement sites

The atmospheric layer closest to the ground is strongly influenced by variable surface fluxes (emissions, surface deposition) and can therefore be very heterogeneous. In order to perform air quality measurements that are representative of a larger domain or a certain degree of pollution, observatories are placed away from population centres or within areas of specific population density. Sites are often categorised based on subjective criteria that are not uniformly applied by the atmospheric community within different administrative domains yielding an inconsistent global air quality picture. A novel approach for the assessment of parameters reflecting site representativeness is presented here, taking emissions, deposition and transport towards 34 sites covering Western and Central Europe into account. These parameters are directly inter-comparable among the sites and can be used to select sites that are, on average, more or less suitable for data assimilation and comparison with satellite and model data. Advection towards these sites was simulated by backward Lagrangian Particle Dispersion Modelling (LPDM) to determine the sites' average catchment areas for the year 2005 and advection times of 12, 24 and 48 h. Only variations caused by emissions and transport during these periods were considered assuming that these dominate the short-term variability of most but especially short lived trace gases. The derived parameters describing representativeness were compared between sites and a novel, uniform and observation-independent categorisation of the sites based on a clustering approach was established. Six groups of European background sites were identified ranging from <i>generally remote</i> to more polluted <i>agglomeration</i> sites. These six categories explained 50 to 80% of the inter-site variability of median mixing ratios and their standard deviation for NO<sub>2</sub> and O<sub>3</sub>, while differences between group means of the longer-lived trace gas CO were insignificant. The derived annual catchment areas strongly depended on the applied LPDM and input wind fields, the catchment settings and the year of analysis. Nevertheless, the parameters describing representativeness showed considerably less variability than the catchment geometry, supporting the applicability of the derived station categorisation

Long-term straw management and N fertilizer rate effects on soil organic C and N, and some chemical properties in a Black Chernozem

Non-Peer Reviewe

Long-term straw management and N fertilizer rate effects on soil organic C and N, and some chemical properties in a Gray Luvisol

Non-Peer Reviewe

Building more accurate decision trees with the additive tree.

The expansion of machine learning to high-stakes application domains such as medicine, finance, and criminal justice, where making informed decisions requires clear understanding of the model, has increased the interest in interpretable machine learning. The widely used Classification and Regression Trees (CART) have played a major role in health sciences, due to their simple and intuitive explanation of predictions. Ensemble methods like gradient boosting can improve the accuracy of decision trees, but at the expense of the interpretability of the generated model. Additive models, such as those produced by gradient boosting, and full interaction models, such as CART, have been investigated largely in isolation. We show that these models exist along a spectrum, revealing previously unseen connections between these approaches. This paper introduces a rigorous formalization for the additive tree, an empirically validated learning technique for creating a single decision tree, and shows that this method can produce models equivalent to CART or gradient boosted stumps at the extremes by varying a single parameter. Although the additive tree is designed primarily to provide both the model interpretability and predictive performance needed for high-stakes applications like medicine, it also can produce decision trees represented by hybrid models between CART and boosted stumps that can outperform either of these approaches

Expert-Augmented Machine Learning

Machine Learning is proving invaluable across disciplines. However, its success is often limited by the quality and quantity of available data, while its adoption by the level of trust that models afford users. Human vs. machine performance is commonly compared empirically to decide whether a certain task should be performed by a computer or an expert. In reality, the optimal learning strategy may involve combining the complementary strengths of man and machine. Here we present Expert-Augmented Machine Learning (EAML), an automated method that guides the extraction of expert knowledge and its integration into machine-learned models. We use a large dataset of intensive care patient data to predict mortality and show that we can extract expert knowledge using an online platform, help reveal hidden confounders, improve generalizability on a different population and learn using less data. EAML presents a novel framework for high performance and dependable machine learning in critical applications

The spirit of sport: the case for criminalisation of doping in the UK

This article examines public perceptions of doping in sport, critically evaluates the effectiveness of current anti-doping sanctions and proposes the criminalisation of doping in sport in the UK as part of a growing global movement towards such criminalisation at national level. Criminalising doping is advanced on two main grounds: as a stigmatic deterrent and as a form of retributive punishment enforced through the criminal justice system. The ‘spirit of sport’ defined by the World Anti-Doping Agency (WADA) as being based on the values of ethics, health and fair-play is identified as being undermined by the ineffectiveness of existing anti-doping policy in the current climate of doping revelations, and is assessed as relevant to public perceptions and the future of sport as a whole. The harm-reductionist approach permitting the use of certain performance enhancing drugs (PEDs) is considered as an alternative to anti-doping, taking into account athlete psychology, the problems encountered in containing doping in sport through anti-doping measures and the effect of these difficulties on the ‘spirit of sport’. This approach is dismissed in favour of criminalising doping in sport based on the offence of fraud. It will be argued that the criminalisation of doping could act as a greater deterrent than existing sanctions imposed by International Federations, and, when used in conjunction with those sanctions, will raise the overall ‘price’ of doping. The revelations of corruption within the existing system of self-governance within sport have contributed to a disbelieving public and it will be argued that the criminalisation of doping in sport could assist in satisfying the public that justice is being done and in turn achieve greater belief in the truth of athletic performances

Expert-augmented machine learning.

Machine learning is proving invaluable across disciplines. However, its success is often limited by the quality and quantity of available data, while its adoption is limited by the level of trust afforded by given models. Human vs. machine performance is commonly compared empirically to decide whether a certain task should be performed by a computer or an expert. In reality, the optimal learning strategy may involve combining the complementary strengths of humans and machines. Here, we present expert-augmented machine learning (EAML), an automated method that guides the extraction of expert knowledge and its integration into machine-learned models. We used a large dataset of intensive-care patient data to derive 126 decision rules that predict hospital mortality. Using an online platform, we asked 15 clinicians to assess the relative risk of the subpopulation defined by each rule compared to the total sample. We compared the clinician-assessed risk to the empirical risk and found that, while clinicians agreed with the data in most cases, there were notable exceptions where they overestimated or underestimated the true risk. Studying the rules with greatest disagreement, we identified problems with the training data, including one miscoded variable and one hidden confounder. Filtering the rules based on the extent of disagreement between clinician-assessed risk and empirical risk, we improved performance on out-of-sample data and were able to train with less data. EAML provides a platform for automated creation of problem-specific priors, which help build robust and dependable machine-learning models in critical applications