ETH Zurich

About: ETH Zurich is a education organization based out in Zurich, Switzerland. It is known for research contribution in the topics: Population & Computer science. The organization has 48393 authors who have published 122408 publications receiving 5111383 citations. The organization is also known as: Swiss Federal Institute of Technology in Zurich & Eidgenössische Technische Hochschule Zürich.

Code completion with statistical language models

Abstract: We address the problem of synthesizing code completions for programs using APIs. Given a program with holes, we synthesize completions for holes with the most likely sequences of method calls. Our main idea is to reduce the problem of code completion to a natural-language processing problem of predicting probabilities of sentences. We design a simple and scalable static analysis that extracts sequences of method calls from a large codebase, and index these into a statistical language model. We then employ the language model to find the highest ranked sentences, and use them to synthesize a code completion. Our approach is able to synthesize sequences of calls across multiple objects together with their arguments. Experiments show that our approach is fast and effective. Virtually all computed completions typecheck, and the desired completion appears in the top 3 results in 90% of the cases.

Efficient network flooding and time synchronization with Glossy

Abstract: This paper presents Glossy, a novel flooding architecture for wireless sensor networks. Glossy exploits constructive interference of IEEE 802.15.4 symbols for fast network flooding and implicit time synchronization. We derive a timing requirement to make concurrent transmissions of the same packet interfere constructively, allowing a receiver to decode the packet even in the absence of capture effects. To satisfy this requirement, our design temporally decouples flooding from other network activities. We analyze Glossy using a mixture of statistical and worst-case models, and evaluate it through experiments under controlled settings and on three wireless sensor testbeds. Our results show that Glossy floods packets within a few milliseconds and achieves an average time synchronization error below one microsecond. In most cases, a node receives the flooding packet with a probability higher than 99.99 %, while having its radio turned on for only a few milliseconds during a flood. Moreover, unlike existing flooding schemes, Glossy's performance exhibits no noticeable dependency on node density, which facilitates its application in diverse real-world settings.

MetFrag relaunched: incorporating strategies beyond in silico fragmentation.

Abstract: The in silico fragmenter MetFrag, launched in 2010, was one of the first approaches combining compound database searching and fragmentation prediction for small molecule identification from tandem mass spectrometry data. Since then many new approaches have evolved, as has MetFrag itself. This article details the latest developments to MetFrag and its use in small molecule identification since the original publication. MetFrag has gone through algorithmic and scoring refinements. New features include the retrieval of reference, data source and patent information via ChemSpider and PubChem web services, as well as InChIKey filtering to reduce candidate redundancy due to stereoisomerism. Candidates can be filtered or scored differently based on criteria like occurence of certain elements and/or substructures prior to fragmentation, or presence in so-called “suspect lists”. Retention time information can now be calculated either within MetFrag with a sufficient amount of user-provided retention times, or incorporated separately as “user-defined scores” to be included in candidate ranking. The changes to MetFrag were evaluated on the original dataset as well as a dataset of 473 merged high resolution tandem mass spectra (HR-MS/MS) and compared with another open source in silico fragmenter, CFM-ID. Using HR-MS/MS information only, MetFrag2.2 and CFM-ID had 30 and 43 Top 1 ranks, respectively, using PubChem as a database. Including reference and retention information in MetFrag2.2 improved this to 420 and 336 Top 1 ranks with ChemSpider and PubChem (89 and 71 %), respectively, and even up to 343 Top 1 ranks (PubChem) when combining with CFM-ID. The optimal parameters and weights were verified using three additional datasets of 824 merged HR-MS/MS spectra in total. Further examples are given to demonstrate flexibility of the enhanced features. In many cases additional information is available from the experimental context to add to small molecule identification, which is especially useful where the mass spectrum alone is not sufficient for candidate selection from a large number of candidates. The results achieved with MetFrag2.2 clearly show the benefit of considering this additional information. The new functions greatly enhance the chance of identification success and have been incorporated into a command line interface in a flexible way designed to be integrated into high throughput workflows. Feedback on the command line version of MetFrag2.2 available at http://c-ruttkies.github.io/MetFrag/ is welcome.

Global-scale hydrological response to future glacier mass loss

Abstract: Worldwide glacier retreat and associated future runoff changes raise major concerns over the sustainability of global water resources1–4, but global-scale assessments of glacier decline and the resulting hydrological consequences are scarce5,6. Here we compute global glacier runoff changes for 56 large-scale glacierized drainage basins to 2100 and analyse the glacial impact on streamflow. In roughly half of the investigated basins, the modelled annual glacier runoff continues to rise until a maximum (‘peak water’) is reached, beyond which runoff steadily declines. In the remaining basins, this tipping point has already been passed. Peak water occurs later in basins with larger glaciers and higher ice-cover fractions. Typically, future glacier runoff increases in early summer but decreases in late summer. Although most of the 56 basins have less than 2% ice coverage, by 2100 one-third of them might experience runoff decreases greater than 10% due to glacier mass loss in at least one month of the melt season, with the largest reductions in central Asia and the Andes. We conclude that, even in large-scale basins with minimal ice-cover fraction, the downstream hydrological effects of continued glacier wastage can be substantial, but the magnitudes vary greatly among basins and throughout the melt season.

Hydrostatic pressure and the actomyosin cortex drive mitotic cell rounding

Abstract: During mitosis, adherent animal cells undergo a drastic shape change, from essentially flat to round. Mitotic cell rounding is thought to facilitate organization within the mitotic cell and be necessary for the geometric requirements of division. However, the forces that drive this shape change remain poorly understood in the presence of external impediments, such as a tissue environment. Here we use cantilevers to track cell rounding force and volume. We show that cells have an outward rounding force, which increases as cells enter mitosis. We find that this mitotic rounding force depends both on the actomyosin cytoskeleton and the cells' ability to regulate osmolarity. The rounding force itself is generated by an osmotic pressure. However, the actomyosin cortex is required to maintain this rounding force against external impediments. Instantaneous disruption of the actomyosin cortex leads to volume increase, and stimulation of actomyosin contraction leads to volume decrease. These results show that in cells, osmotic pressure is balanced by inwardly directed actomyosin cortex contraction. Thus, by locally modulating actomyosin-cortex-dependent surface tension and globally regulating osmotic pressure, cells can control their volume, shape and mechanical properties.