| 1. |
- Aarrestad, Thea, et al.
(författare)
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Benchmark data and model independent event classification for the large hadron collider
- 2022
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Ingår i: SciPost Physics. - 2542-4653. ; 12:1
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Tidskriftsartikel (refereegranskat)abstract
- We describe the outcome of a data challenge conducted as part of the Dark Machines (https://www.darkmachines.org) initiative and the Les Houches 2019 workshop on Physics at TeV colliders. The challenged aims to detect signals of new physics at the Large Hadron Collider (LHC) using unsupervised machine learning algorithms. First, we propose how an anomaly score could be implemented to define model-independent signal regions in LHC searches. We define and describe a large benchmark dataset, consisting of > 1 billion simulated LHC events corresponding to 10 fb−1 of proton-proton collisions at a center-of-mass energy of 13 TeV. We then review a wide range of anomaly detection and density estimation algorithms, developed in the context of the data challenge, and we measure their performance in a set of realistic analysis environments. We draw a number of useful conclusions that will aid the development of unsupervised new physics searches during the third run of the LHC, and provide our benchmark dataset for future studies at https://www.phenoMLdata.org. Code to reproduce the analysis is provided at https://github.com/bostdiek/DarkMachines-UnsupervisedChallenge.
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| 2. |
- Aarrestad, Thea, et al.
(författare)
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Fast convolutional neural networks on FPGAs with hls4ml
- 2021
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Ingår i: Machine Learning: Science and Technology. - : IOP Publishing. - 2632-2153. ; 2:4
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Tidskriftsartikel (refereegranskat)abstract
- We introduce an automated tool for deploying ultra low-latency, low-power deep neural networks with convolutional layers on field-programmable gate arrays (FPGAs). By extending the hls4ml library, we demonstrate an inference latency of 5 mu s using convolutional architectures, targeting microsecond latency applications like those at the CERN Large Hadron Collider. Considering benchmark models trained on the Street View House Numbers Dataset, we demonstrate various methods for model compression in order to fit the computational constraints of a typical FPGA device used in trigger and data acquisition systems of particle detectors. In particular, we discuss pruning and quantization-aware training, and demonstrate how resource utilization can be significantly reduced with little to no loss in model accuracy. We show that the FPGA critical resource consumption can be reduced by 97% with zero loss in model accuracy, and by 99% when tolerating a 6% accuracy degradation.
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| 3. |
- Boras, Julia, et al.
(författare)
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Effect of viruses and protists on bacteria in eddies of the Canary Current region (subtropical Northeast Atlantic).
- 2010
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Ingår i: Limnology and Oceanography. - 0024-3590 .- 1939-5590. ; 55:2, s. 885-898
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Tidskriftsartikel (refereegranskat)abstract
- The effect of oceanic eddies on microbial processes, with emphasis on bacterial losses due to protists and phages, was examined in the Canary Current region (subtropical northeast Atlantic) through the water column (down to 1000 m) during August 2006. Sampling stations were located in cyclonic and anticyclonic eddies, as well as in regions situated outside the influence of the eddy field (far-field stations). In the euphotic zone, in cyclonic eddies losses of bacteria due to viruses and protists were from 25.6% to 69.8%, and from not detected to 46.8% of bacterial production (BP) d(-1), respectively. In anticyclonic eddies, these values ranged from 20.6% to 90.2% of BP d(-1) for viruses, and from 8.0% to 79.4% of BP d(-1) for protists. At far-field stations, losses of bacteria ranged from 48.7% to 66.9% for viruses, and from not detected to 44.8% for protists. In addition, covering all stations and depths (from the epipelagic to the bathypelagic layer), bacterial losses due to viruses were significantly higher than losses by protists, and did not differ significantly among depths except for the stations situated in anticyclonic eddies, where they were significantly higher in the epipelagic layer. Lysogenic infection was more frequent at anticyclonic stations, where the highest pressure of protists on bacteria was observed. Because of the importance of viral activity, we suggest that lysis products from bacteria may be a source of regenerated nutrients in the surface of the oligotrophic ocean, in addition to the input of nutrients upwelled by eddies.
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| 4. |
- Gasol, Josep M., et al.
(författare)
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Mesopelagic prokaryotic bulk and single-cell heterotrophic activity and community composition in the NW Africa-Canary Islands coastal-transition zone
- 2009
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Ingår i: Progress in Oceanography. - : Elsevier BV. - 0079-6611 .- 1873-4472. ; 83, s. 189-196
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Tidskriftsartikel (refereegranskat)abstract
- Mesopelagic prokaryotic communities have often been assumed to be relatively inactive in comparison to those from epipelagic waters, and therefore unresponsive to the presence of nearby upwelled waters. We have studied the zonal (shelf-ocean), latitudinal, and depth (epipelagic-mesopelagic) variability of microbial assemblages in the NW Africa-Canary Islands coastal-transition zone (CTZ). Vertical profiles of bacterial bulk and single-cell activity through the epi- and mesopelagic waters were combined with point measurements of bacterial respiration, leucine-to-carbon conversion factors and leucine-to-thymidine incorporation ratios. The overall picture that emerges from our study is that prokaryotes in the mesopelagic zone of this area are less abundant than in the epipelagic but have comparable levels of activity. The relationship between prokaryotes and heterotrophic nanoflagellates, their main predators, remains constant throughout the water column, further contradicting the assumption that deep ocean bacterial communities are mostly inactive. Both bulk and single-cell activity showed clear differences between stations, with higher mesopelagic activities closer to the shelf or affected by upwelling features. We also tested whether differences in microbial function between stations could be related to differences in bacterial community structure, and conclude that bacterial communities are very similar at similar depths in the deep ocean, even if the stations present order-of-magnitude differences in bacterial function.
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| 5. |
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| 6. |
- Potapov, Anton M., et al.
(författare)
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Global fine-resolution data on springtail abundance and community structure
- 2024
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Ingår i: Scientific Data. - : Nature Publishing Group. - 2052-4463. ; 11:1
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Tidskriftsartikel (refereegranskat)abstract
- Springtails (Collembola) inhabit soils from the Arctic to the Antarctic and comprise an estimated ~32% of all terrestrial arthropods on Earth. Here, we present a global, spatially-explicit database on springtail communities that includes 249,912 occurrences from 44,999 samples and 2,990 sites. These data are mainly raw sample-level records at the species level collected predominantly from private archives of the authors that were quality-controlled and taxonomically-standardised. Despite covering all continents, most of the sample-level data come from the European continent (82.5% of all samples) and represent four habitats: woodlands (57.4%), grasslands (14.0%), agrosystems (13.7%) and scrublands (9.0%). We included sampling by soil layers, and across seasons and years, representing temporal and spatial within-site variation in springtail communities. We also provided data use and sharing guidelines and R code to facilitate the use of the database by other researchers. This data paper describes a static version of the database at the publication date, but the database will be further expanded to include underrepresented regions and linked with trait data.
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| 7. |
- Romero-Otero, Javier, et al.
(författare)
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Active surveillance for prostate cancer.
- 2016
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Ingår i: International journal of urology : official journal of the Japanese Urological Association. - : Wiley. - 1442-2042. ; 23:3, s. 211-8
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Tidskriftsartikel (refereegranskat)abstract
- It is worth distinguishing between the two strategies of expectant management for prostate cancer. Watchful waiting entails administering non-curative androgen deprivation therapy to patients on development of symptomatic progression, whereas active surveillance entails delivering curative treatment on signs of disease progression. The objectives of the two management strategies and the patients enrolled in either are different: (i) to review the role of active surveillance as a management strategy for patients with low-risk prostate cancer; and (ii) review the benefits and pitfalls of active surveillance. We carried out a systematic review of active surveillance for prostate cancer in the literature using the National Center for Biotechnology Information's electronic database, PubMed. We carried out a search in English using the terms: active surveillance, prostate cancer, watchful waiting and conservative management. Selected studies were required to have a comprehensive description of the demographic and disease characteristics of the patients at the time of diagnosis, inclusion criteria for surveillance, and a protocol for the patients' follow up. Review articles were included, but not multiple papers from the same datasets. Active surveillance appears to reduce overtreatment in patients with low-risk prostate cancer without compromising cancer-specific survival at 10years. Therefore, active surveillance is an option for select patients who want to avoid the side-effects inherent to the different types of immediate treatment. However, inclusion criteria for active surveillance and the most appropriate method of monitoring patients on active surveillance have not yet been standardized.
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