Self-Correcting Bayesian Optimization through Bayesian Active Learning

Gaussian processes are cemented as the model of choice in Bayesian optimization and active learning. Yet, they are severely dependent on cleverly chosen hyperparameters to reach their full potential, and little effort is devoted to finding the right hyperparameters in the literature. We demonstrate the impact of selecting good hyperparameters for GPs and present two acquisition functions that explicitly prioritize this goal. Statistical distance-based Active Learning (SAL) considers the average disagreement among samples from the posterior, as measured by a statistical distance. It is shown to outperform the state-of-the-art in Bayesian active learning on a number of test functions. We then introduce Self-Correcting Bayesian Optimization (SCoreBO), which extends SAL to perform Bayesian optimization and active hyperparameter learning simultaneously. SCoreBO learns the model hyperparameters at improved rates compared to vanilla BO, while outperforming the latest Bayesian optimization methods on traditional benchmarks. Moreover, the importance of self-correction is demonstrated on an array of exotic Bayesian optimization task

BaCO: A Fast and Portable Bayesian Compiler Optimization Framework

We introduce the Bayesian Compiler Optimization framework (BaCO), a general purpose autotuner for modern compilers targeting CPUs, GPUs, and FPGAs. BaCO provides the flexibility needed to handle the requirements of modern autotuning tasks. Particularly, it deals with permutation, ordered, and continuous parameter types along with both known and unknown parameter constraints. To reason about these parameter types and efficiently deliver high-quality code, BaCO uses Bayesian optimiza tion algorithms specialized towards the autotuning domain. We demonstrate BaCO's effectiveness on three modern compiler systems: TACO, RISE & ELEVATE, and HPVM2FPGA for CPUs, GPUs, and FPGAs respectively. For these domains, BaCO outperforms current state-of-the-art autotuners by delivering on average 1.36x-1.56x faster code with a tiny search budget, and BaCO is able to reach expert-level performance 2.9x-3.9x faster

Evaluating modelled winds over an urban area using ground-based Doppler lidar observations

Wind information in urban areas is essential for many applications related to air pollution, urban climate and planning, safety of drone-related operations, and assessment of urban wind energy potential. These applications require accurate wind forecasts, and obtaining this information in an urban environment is challenging as the morphology of a city varies from street to street, altering the wind flow. Remote sensing techniques such as Doppler lidars (light detection and ranging) provide a unique opportunity for wind forecast verification as they can provide both the vertical profile of the horizontal wind and the spatial variation in the horizontal domain at high resolution. In this study, the performance of numerical weather prediction (NWP) models, analysis systems, and large-eddy simulation (LES) models have been analysed by comparing the modelled winds against Doppler lidar observations under various atmospheric conditions and from season to season, in the coastal environment of Helsinki, Finland. The long-term mean vertical profile of the modelled horizontal wind shows good agreement with observations; the NWP model and the analysis systems selected here exhibit different strengths and weaknesses depending on the atmospheric conditions but no significant diurnal variation in performance. However, both the model and analysis systems show differences in their spatially-averaged bias when investigating different wind directions. LES verification shows that these models can potentially provide winds down to street level, given pre-computed scenarios of atmospheric conditions. For Helsinki, the observed winds are stronger during winter than summer, and, on average, higher wind speeds were observed at the urban site than the sub-urban site.Peer reviewe

PL - 026 Mismatch between skeletal muscle glucose delivery, interstitial concentration and membrane permeability may limit insulin sensitivity after exercise

Objective The relationship between skeletal muscle perfusion, interstitial glucose concentration and sarcolemmal permeability to glucose in exercise-induced increases in muscle insulin sensitivity is not well established. A single bout of exercise increases skeletal muscle insulin sensitivity through coordinated increases in insulin-stimulated microvascular perfusion and insulin signalling  Reducing leg and muscle microvascular blood flow with local nitric oxide synthase (NOS) inhibition during a hyperinsulinaemic euglycaemic clamp reduces leg glucose uptake in a previously exercised, but not in a contralateral non-exercised leg, without affecting insulin signalling in either leg  (Sjoberg et al. 2017). Therefore, it is possible that the reduction in muscle perfusion decreases muscle interstitial glucose concentration to a point that limits skeletal muscle insulin-stimulated glucose uptake following exercise. We examined this using microdialysis of vastus lateralis muscle. Methods Ten healthy males (Age: 27±1 yr., Weight: 77.7±2.3 kg, BMI 23.9±0.5, VO2 peak: 50.7±1.5 ml·kg-1·min-1) performed 60 min of 1-legged knee extensor exercise at 80% of 1-legged peak work load with three 5 min intervals at 100% 1-legged peak work load. Participants then rested for 4 hours and catheters were inserted into the femoral artery and vein of both legs for subsequent measurement of leg glucose uptake and for femoral artery infusion of the NOS inhibitor NG-monomethyl L-arginine acetate (L-NMMA) and the vasodilator ATP. Catheters were also placed in antecubital veins for infusion of insulin and glucose. Three microdialysis catheters, with a semi-permeable membrane the length of 30 mm and a molecular cut-off at 20,000 dalton, were inserted into the vastus lateral muscle of both legs. Glucose and D-[6-3H(N)]glucose were added to the perfusate. Four hours after discontinuing the exercise a 225 minute euglycaemic hyperinsulinaemic clamp was initiated (insulin infusion 1.4 mU-1kg-1min). Ninety min into the clamp L-NMMA was infused at a constant rate (0.4 mg·kg-1 leg mass·min-1) into both femoral arteries for 45 min. The insulin infusion was maintained for another 90 min and during the last 45 min ATP (0.3 μmol∙ml-1) was infused locally into both femoral arteries at a rate of 200-350 μl∙min-1 to obtain a leg blood flow that was double the blood flow during insulin only infusion. A second control protocol was undertaken that was identical in regards to exercise and recovery but no insulin, L-NMMA or ATP was infused. Results During the clamp leg glucose uptake and leg blood flow were higher (P<0.05) in the previously exercised than the control leg whereas the interstitial glucose concentration decreased to lower (P<0.05) values in the exercised (~3.1mM) than the control (~4.8mM) leg. Estimated sarcolemmal glucose permeability was twice as high (P<0.05) in the exercised compared with the rested leg. The NOS inhibitor L-NMMA decreased LBF in both legs and interstitial glucose concentration dropped to ~2.3 mM in the exercised but only to ~3.7 mM in non-exercised muscle. This abrogated the augmented effect of insulin on LGU in the exercised leg while apparent sarcolemmal permeability to glucose remained unchanged with L-NMMA in both legs. Doubling leg blood flow by local infusion of ATP increased leg glucose uptake in both legs without any major change in interstitial glucose concentration or sarcolemmal permeability to glucose. Conclusions These findings suggest that during flow restriction due to L-NMMA, the interstitial glucose concentration becomes limiting for leg glucose uptake in exercised but not in non-exercised muscle. Therefore, the vasodilatory effect of insulin is an important component of the increased insulin sensitivity to stimulate glucose uptake following exercise by limiting the drop in the interstitial glucose concentration that occurs due to the increased sarcolemmal permeability to glucose. Reference Sjoberg, K. A., C. Frosig, R. Kjobsted, L. Sylow, M. Kleinert, A. C. Betik, C. S. Shaw, B. Kiens, J. F. P. Wojtaszewski, S. Rattigan, E. A. Richter, and G. K. McConell. Exercise Increases Human Skeletal Muscle Insulin Sensitivity via Coordinated Increases in Microvascular Perfusion and Molecular Signaling.  Diabetes  66: 1501-10, 2017

Assessing the societal benefits of river restoration using the ecosystem services approach

This paper is a contribution from the EU seventh framework funded research project REFORM (Grant Agreement 282656).The success of river restoration was estimated using the ecosystem services approach. In eight pairs of restored–unrestored reaches and floodplains across Europe, we quantified provisioning (agricultural products, wood, reed for thatching, infiltrated drinking water), regulating (flooding and drainage, nutrient retention, carbon sequestration) and cultural (recreational hunting and fishing, kayaking, biodiversity conservation, appreciation of scenic landscapes) services for separate habitats within each reach, and summed these to annual economic value normalized per reach area. We used locally available data and literature, did surveys among inhabitants and visitors, and used a range of economic methods (market value, shadow price, replacement cost, avoided damage, willingness-to-pay survey, choice experiment) to provide final monetary service estimates. Total ecosystem service value was significantly increased in the restored reaches (difference 1400 ± 600 € ha−1 year−1; 2500 − 1100, p = 0.03, paired t test). Removal of one extreme case did not affect this outcome. We analysed the relation between services delivered and with floodplain and catchment characteristics after reducing these 23 variables to four principal components explaining 80% of the variance. Cultural and regulating services correlated positively with human population density, cattle density and agricultural N surplus in the catchment, but not with the fraction of arable land or forest, floodplain slope, mean river discharge or GDP. Our interpretation is that landscape appreciation and flood risk alleviation are a function of human population density, but not wealth, in areas where dairy farming is the prime form of agriculture.PostprintPeer reviewe

Biomass burning in eastern Europe during spring 2006 caused high deposition of ammonium in northern Fennoscandia

High air concentrations of ammonium were detected at low and high altitude sites in Sweden, Finland and Norway during the spring 2006, coinciding with polluted air from biomass burning in eastern Europe passing over central and northern Fennoscandia. Unusually high values for throughfall deposition of ammonium were detected at one low altitude site and several high altitude sites in north Sweden. The occurrence of the high ammonium in throughfall differed between the summer months 2006, most likely related to the timing of precipitation events. The ammonia dry deposition may have contributed to unusual visible injuries on the tree vegetation in northern Fennoscandia that occurred during 2006, in combination with high ozone concentrations. It is concluded that long-range transport of ammonium from large-scale biomass burning may contribute substantially to the nitrogen load at northern latitudes. (C) 2013 Elsevier Ltd. All rights reserved

Coexisting Cyclic Parthenogens Comprise a Holocene Species Flock in Eubosmina

Background: Mixed breeding systems with extended clonal phases and weak sexual recruitment are widespread in nature but often thought to impede the formation of discrete evolutionary clusters. Thus, cyclic parthenogens, such as cladocerans and rotifers, could be predisposed to ‘‘species problems’ ’ and a lack of discrete species. However, species flocks have been proposed for one cladoceran group, Eubosmina, where putative species are sympatric, and there is a detailed paleolimnological record indicating a Holocene age. These factors make the Eubosmina system suitable for testing the hypotheses that extended clonal phases and weak sexual recruitment inhibit speciation. Although common garden experiments have revealed a genetic component to the morphotypic variation, the evolutionary significance of the morphotypes remains controversial. Methodology/Principal Findings: In the present study, we tested the hypothesis of a single polymorphic species (i.e., mixing occurs but selection maintains genes for morphology) in four northern European lakes where the morphotypes coexist. Our evidence is based on nuclear DNA sequence, mitochondrial DNA sequence, and morphometric analysis of coexisting morphotypes. We found significant genetic differentiation, genealogical exclusivity, and morphometric differentiation for coexisting morphotypes. Conclusions: We conclude that the studied morphotypes represent a group of young species undergoing speciation wit

EMG-Normalised Kinase Activation during Exercise Is Higher in Human Gastrocnemius Compared to Soleus Muscle

In mice, certain proteins show a highly confined expression in specific muscle groups. Also, resting and exercise/contraction-induced phosphorylation responses are higher in rat skeletal muscle with low mitochondrial content compared to muscles with high mitochondrial content, possibly related to differential reactive oxygen species (ROS)-scavenging ability or resting glycogen content. To evaluate these parameters in humans, biopsies from soleus, gastrocnemius and vastus lateralis muscles were taken before and after a 45 min inclined (15%) walking exercise bout at 69% VO2max aimed at simultaneously activating soleus and gastrocnemius in a comparable dynamic work-pattern. Hexokinase II and GLUT4 were 46–59% and 26–38% higher (p<0.05) in soleus compared to the two other muscles. The type I muscle fiber percentage was highest in soleus and lowest in vastus lateralis. No differences were found in protein expression of signalling proteins (AMPK subunits, eEF2, ERK1/2, TBC1D1 and 4), mitochondrial markers (F1 ATPase and COX1) or ROS-handling enzymes (SOD2 and catalase). Gastrocnemius was less active than soleus measured as EMG signal and glycogen use yet gastrocnemius displayed larger increases than soleus in phosphorylation of AMPK Thr172, eEF2 Thr56 and ERK 1/2 Thr202/Tyr204 when normalised to the mean relative EMG-signal. In conclusion, proteins with muscle-group restricted expression in mice do not show this pattern in human lower extremity muscle groups. Nonetheless the phosphorylation-response is greater for a number of kinase signalling pathways in human gastrocnemius than soleus at a given activation-intensity. This may be due to the combined subtle effects of a higher type I muscle fiber content and higher training status in soleus compared to gastrocnemius muscle