Towards exascale real-time RFI mitigation

We describe the design and implementation of an extremely scalable real-time RFI mitigation method, based on the offline AOFlagger. All algorithms scale linearly in the number of samples. We describe how we implemented the flagger in the LOFAR real-time pipeline, on both CPUs and GPUs. Additionally, we introduce a novel simple history-based flagger that helps reduce the impact of our small window on the data. By examining an observation of a known pulsar, we demonstrate that our flagger can achieve much higher quality than a simple thresholder, even when running in real time, on a distributed system. The flagger works on visibility data, but also on raw voltages, and beam formed data. The algorithms are scale-invariant, and work on microsecond to second time scales. We are currently implementing a prototype for the time domain pipeline of the SKA central signal processor.Comment: 2016 Radio Frequency Interference (RFI2016) Coexisting with Radio Frequency Interference, Socorro, New Mexico, USA, October 201

Real-Time Dedispersion for Fast Radio Transient Surveys, using Auto Tuning on Many-Core Accelerators

Dedispersion, the removal of deleterious smearing of impulsive signals by the interstellar matter, is one of the most intensive processing steps in any radio survey for pulsars and fast transients. We here present a study of the parallelization of this algorithm on many-core accelerators, including GPUs from AMD and NVIDIA, and the Intel Xeon Phi. We find that dedispersion is inherently memory-bound. Even in a perfect scenario, hardware limitations keep the arithmetic intensity low, thus limiting performance. We next exploit auto-tuning to adapt dedispersion to different accelerators, observations, and even telescopes. We demonstrate that the optimal settings differ between observational setups, and that auto-tuning significantly improves performance. This impacts time-domain surveys from Apertif to SKA.Comment: 8 pages, accepted for publication in Astronomy and Computin

Biochemical and molecular studies of atypical nevi

The results obtained in this thesis suggest that the most explicit differences between normal and atypical melanocytes are subtle changes in pigment biosynthesis and the functioning of the antioxidant system. Impairment of the antioxidant system and increased levels of pheomelanin result in increased levels of oxidative stress. It is anticipated that these increased levels of oxidative stress contribute to early melanoma development by inducing DNA mutations, but additional studies are required to prove this hypothesis.UBL - phd migration 201

De architectuur van Gustav Cornelis Bremer

From approximately 1910 to 1947 the architect ir. G.C. Bremer made an important contribution to Dutch architecture. For the greater part of that period, from 1924 to 1946, he was Government Architect. Bremer's oeuvre is quite divergent in character; it does not represent any clearly defined style or specific trend. The buildings executed by him comprise traditionalist elements as well as elements of 'New Realism', depending on what views the commission in question required of him. Indeed, Bremer did not play a part in the architecture debate between the representatives of 'New Building' and the traditionalists. This may well be one of the reasons why his work no longer attracts much attention from architectural historians. From 1910 onwards Bremer had an architects' firm in Arnhem, together with the architect A.R. Freem. From 1914 to 1915 he was temporarily appointed town architect of Arnhem. In 1916 he took up office with ‘Landsgebouwen’, the predecessor of the ‘Rijksgebouwendienst’ (i.e. a service of the Ministry of Housing and Construction). On January 1st 1924 Bremer was appointed Government Architect with the Rijksgebouwendienst, which had then just been established, where he was responsible for all new construction. Until his retirement on January 1st 1946 he remained in office there. Bremer had a preference for medieval architecture, both its form language and the underlying starting-points appealed to him. His view was that in medieval architecture there had still been room for the craftsman, and that the latter could be put on a par with the architect. Clear references, notably to Romanesque architecture, can also be traced in his buildings, although these often concern idiosyncratic interpretations, such as the frequent use of arches (in windows and portals), the use of natural stone as a building material and the intensive cooperation with artists, who made decorations for the buildings in the form of statues, murals and stained-glass windows. Some of Bremer's buildings show that his admiration for certain architects resulted in imitation. This is particularly evident with reference to Berlage (not only in his initial period, but continuing up to his last works) and also with reference to Oud and Friedhoff. As the person having final responsibility, Bremer has left his mark on the buildings executed by the Rijksgebouwendienst in the period until 1947. This is visible in several buildings, not built in his name, but nevertheless showing a close affinity with his work, such as the building for the National Giro Bank and the building for the Patent Office plus Post Office on the Willem Witsenplein in The Hague. With the Landsgebouwen/Rijksgebouwendienst Bremer mainly executed buildings for the Post Office Board - including post offices, telephone exchanges and amplifier stations - but also tax-collection offices, government buildings and a court-house. He also provided designs for laboratories and for the Wilhelmina bridge in Maastricht. It is not easy to define any sort of line in Bremer's oeuvre, to discover a constant or to recognize any order in his multiform designs. It is also difficult to place the various designs in a logical, chronological development. Neither does one design naturally evolve from another. Even within one and the same design he applied different styles. What appears to be characteristic of Bremer's work is the fact that it is homogeneous and heterogeneous at the same time. His conception is homogeneous, his style heterogeneous; the designs of his buildings are to a great extent determined by their purpose and environment. A list of fifty works by ir. G.C. Bremer is included in this article

Improving novelty detection using the reconstructions of nearest neighbours

We show that using nearest neighbours in the latent space of autoencoders (AE) significantly improves performance of semi-supervised novelty detection in both single and multi-class contexts. Autoencoding methods detect novelty by learning to differentiate between the non-novel training class(es) and all other unseen classes. Our method harnesses a combination of the reconstructions of the nearest neighbours and the latent-neighbour distances of a given input's latent representation. We demonstrate that our nearest-latent-neighbours (NLN) algorithm is memory and time efficient, does not require significant data augmentation, nor is reliant on pre-trained networks. Furthermore, we show that the NLN-algorithm is easily applicable to multiple datasets without modification. Additionally, the proposed algorithm is agnostic to autoencoder architecture and reconstruction error method. We validate our method across several standard datasets for a variety of different autoencoding architectures such as vanilla, adversarial and variational autoencoders using either reconstruction, residual or feature consistent losses. The results show that the NLN algorithm grants up to a 17% increase in Area Under the Receiver Operating Characteristics (AUROC) curve performance for the multi-class case and 8% for single-class novelty detection

Learning to detect radio frequency interference in radio astronomy without seeing it

Radio Frequency Interference (RFI) corrupts astronomical measurements, thus affecting the performance of radio telescopes. To address this problem, supervised segmentation models have been proposed as candidate solutions to RFI detection. However, the unavailability of large labelled datasets, due to the prohibitive cost of annotating, makes these solutions unusable. To solve these shortcomings, we focus on the inverse problem; training models on only uncontaminated emissions thereby learning to discriminate RFI from all known astronomical signals and system noise. We use Nearest-Latent-Neighbours (NLN) - an algorithm that utilises both the reconstructions and latent distances to the nearest-neighbours in the latent space of generative autoencoding models for novelty detection. The uncontaminated regions are selected using weak-labels in the form of RFI flags (generated by classical RFI flagging methods) available from most radio astronomical data archives at no additional cost. We evaluate performance on two independent datasets, one simulated from the HERA telescope and another consisting of real observations from LOFAR telescope. Additionally, we provide a small expert-labelled LOFAR dataset (i.e., strong labels) for evaluation of our and other methods. Performance is measured using AUROC, AUPRC and the maximum F1-score for a fixed threshold. For the simulated data we outperform the current state-of-the-art by approximately 1% in AUROC and 3% in AUPRC for the HERA dataset. Furthermore, our algorithm offers both a 4% increase in AUROC and AUPRC at a cost of a degradation in F1-score performance for the LOFAR dataset, without any manual labelling