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IDEBench: A Benchmark for Interactive Data Exploration [article]

Philipp Eichmann, Carsten Binnig, Tim Kraska, Emanuel Zgraggen
2018 arXiv   pre-print
Existing benchmarks for analytical database systems such as TPC-DS and TPC-H are designed for static reporting scenarios. The main metric of these benchmarks is the performance of running individual SQL queries over a synthetic database. In this paper, we argue that such benchmarks are not suitable for evaluating database workloads originating from interactive data exploration (IDE) systems where most queries are ad-hoc, not based on predefined reports, and built incrementally. As a main
more » ... ution, we present a novel benchmark called IDEBench that can be used to evaluate the performance of database systems for IDE workloads. As opposed to traditional benchmarks for analytical database systems, our goal is to provide more meaningful workloads and datasets that can be used to benchmark IDE query engines, with a particular focus on metrics that capture the trade-off between query performance and quality of the result. As a second contribution, this paper evaluates and discusses the performance results of selected IDE query engines using our benchmark. The study includes two commercial systems, as well as two research prototypes (IDEA, approXimateDB/XDB), and one traditional analytical database system (MonetDB).
arXiv:1804.02593v1 fatcat:4bzoyltuazbu7ndtcuwtg2xx6e

α-Synuclein plasma membrane localization correlates with cellular phosphatidylinositol polyphosphate levels [article]

Cedric Eichmann, Reeba Susan Jacob, Alessandro Dema, Davide Mercadante, Philipp Selenko
2020 bioRxiv   pre-print
The Parkinson′s disease protein α-synuclein (αSyn) promotes membrane fusion and fission by interacting with various negatively charged phospholipids. Despite postulated roles in endocytosis and exocytosis, plasma membrane (PM) interactions of αSyn are poorly understood. Here, we show that phosphatidylinositol 4,5-bisphosphate (PIP2) and phosphatidylinositol 3,4,5-trisphosphate (PIP3), two highly acidic components of inner PM leaflets, mediate plasma membrane localization of endogenous pools of
more » ... Syn in A2780, HeLa, SH-SY5Y and SK-MEL-2 cells. We demonstrate that αSyn binds reconstituted PIP2-membranes in a helical conformation in vitro and that PIP2 kinases and phosphatases reversibly redistribute αSyn in cells. We further delineate that αSyn-PM targeting follows phosphoinositide-3 kinase (PI3K)-dependent changes of cellular PIP2 and PIP3 levels, which collectively suggests that phosphatidylinositol polyphosphates contribute to αSyn′s cellular function(s) at the plasma membrane.
doi:10.1101/2020.07.31.224600 fatcat:rdd2rucyefbvneb3es3zr6pu7m

Tableur

Emanuel Zgraggen, Robert Zeleznik, Philipp Eichmann
2016 Proceedings of the 2016 CHI Conference Extended Abstracts on Human Factors in Computing Systems - CHI EA '16  
The need for back-of-the-envelope calculations, such as rough projections or simple budget estimations, occurs frequently and oftentimes while being away from desktop computers. While major software vendors have optimized their spreadsheet applications for mobile environments their generality still makes them heavyweight for such tasks. We have built Tableur a spreadsheet-like pen-& touch-based system targeted towards these use cases. Our design revolves around handwriting recognition -all data
more » ... is represented as digital ink -and gestural commands. Through a rethought cell referencing system and by incorporating standard math notation recognition Tableur allows for simple formula creation and we experiment with techniques that support pattern-based prefilling of cells (Smart Fill) and exploration of what-if scenarios (Reverse Editing).
doi:10.1145/2851581.2892326 dblp:conf/chi/ZgraggenZE16 fatcat:f4gkk6ia2jaxtejwhaxdlhhsfu

Towards a Benchmark for Interactive Data Exploration

Philipp Eichmann, Emanuel Zgraggen, Zheguang Zhao, Carsten Binnig, Tim Kraska
2016 IEEE Data Engineering Bulletin  
Existing benchmarks for analytical database systems such as TPC-DS and TPC-H are designed for static reporting scenarios. The main metric of these benchmarks is the performance of running different SQL queries over a predefined database. In this paper, we argue that such benchmarks are not suitable for evaluating modern interactive data exploration (IDE) systems, which allow data scientists of varying skill levels to manipulate, analyze, and explore large data sets, as well as to build models
more » ... d apply machine learning at interactive speeds. While query performance is still important for data exploration, we believe that a much better metric would reflect the number and complexity of insights users gain in a given amount of time. This paper discusses challenges of creating such a metric and presents ideas towards a new benchmark that simulates typical user behavior and allows IDE systems to be compared in a reproducible way.
dblp:journals/debu/EichmannZZBK16 fatcat:2xpoac44endftamwxrsvxkariq

α-Synuclein plasma membrane localization correlates with cellular phosphatidylinositol polyphosphate levels

Reeba Susan Jacob, Cedric Eichmann, Alessandro Dema, Davide Mercadante, Philipp Selenko
2021 eLife  
Jacob, Eichmann, et al. eLife 2021;10:e61951. DOI: https://doi.org/10.7554/eLife.61951  ... 
doi:10.7554/elife.61951 fatcat:tp3foouh6rgrljvmlxj5cimncu

α-Synuclein plasma membrane localization correlates with cellular phosphatidylinositol polyphosphate levels

Reeba Susan Jacob, Cedric Eichmann, Alessandro Dema, Davide Mercadante, Philipp Selenko
2021 eLife  
The Parkinson's disease protein α-synuclein (aSyn) promotes membrane fusion and fission by interacting with various negatively charged phospholipids. Despite postulated roles in endocytosis and exocytosis, plasma membrane (PM) interactions of αSyn are poorly understood. Here, we show that phosphatidylinositol 4,5-bisphosphate (PIP2) and phosphatidylinositol 3,4,5-trisphosphate (PIP3), two highly acidic components of inner PM leaflets, mediate plasma membrane localization of endogenous pools of
more » ... Syn in A2780, HeLa, SK-MEL-2 and differentiated and undifferentiated neuronal SH-SY5Y cells. We demonstrate that αSyn binds to reconstituted PIP2-membranes in a helical conformation in vitro and that PIP2 synthesizing kinases and hydrolyzing phosphatases reversibly redistribute αSyn in cells. We further delineate that αSyn-PM targeting follows phosphoinositide-3 kinase (PI3K)-dependent changes of cellular PIP2 and PIP3 levels, which collectively suggests that phosphatidylinositol polyphosphates contribute to αSyn's cellular function(s) at the plasma membrane.
doi:10.7554/elife.61951 pmid:33587036 pmcid:PMC7929559 fatcat:epnkil7hljefdelndh5gphz3ny

Structural Optimization of Locally Continuous Fiber-Reinforcements for Short Fiber-Reinforced Plastics

Konstantin Mehl, Sebastian Schmeer, Nicole Motsch-Eichmann, Philipp Bauer, Ingolf Müller, Joachim Hausmann
2021 Journal of Composites Science  
The integration of continuous fiber-reinforced structures into short or long fiber-reinforced plastics allows a significant increase in stiffness and strength. In order to make the best possible use of the high stiffness and strength of continuous fiber-reinforcements, they must be placed in the direction of load in the most stressed areas. A frequently used tool for identifying the most heavily loaded areas is topology optimization. Commercial topology optimization programs usually do not take
more » ... into account the material properties associated with continuous fiber-reinforced hybrid structures. The anisotropy of the reinforcing material and the stiffness of the base material surrounding the reinforcement are not considered during topology optimization, but only in subsequent steps. Therefore in this publication, existing optimization methods for hybrid and anisotropic materials are combined to a new approach, which takes into account both the anisotropy of the continuous fiber-reinforcement and the stiffness of the base material. The results of the example calculations not only show an increased stiffness at the same material input but also a simplification of the resulting reinforcement structures, which allows more economical manufacturing.
doi:10.3390/jcs5050118 doaj:9cfc92752c40476b813da1f3433b390b fatcat:wvctac5asfhkhoalrotdc46fe4

Mass Photometry of Membrane Proteins [article]

Anna Olerinyova, Adar Sonn Segev, Joseph Gault, Cedric Eichmann, Johannes Schimpf, Adrian H Kopf, Lucas S.P. Rudden, Dzmitry Ashkinadze, Radoslaw Bomba, Jason Greenwald, Matteo T Degiacomi, J Antoinette Killian (+4 others)
2020 biorxiv/medrxiv   pre-print
Integral membrane proteins (IMPs) are biologically highly significant but challenging to study because they require maintaining a cellular lipid - like environment. Here, we explore the application of mass photometry (MP) to IMPs and membrane mimetic systems at the single particle level. We apply MP to amphipathic vehicles, such as detergents and amphipols, as well as to lipid and native nanodiscs, characterising the particle size, sample purity and heterogeneity. Using methods established for
more » ... ryogenic electron microscopy, we eliminate detergent background, enabling high - resolution studies of membrane protein structure and interactions. We find evidence that, when extracted from native membranes using native styrene - maleic acid nanodiscs, the potassium channel KcsA is present as a dimer of tetramers - in contrast to results obtained using detergent purification. Finally, using lipid nanodiscs, we show that MP can help distinguish between functional and non - functional nanodisc assemblies, as well as determine the critical factors for lipid nanodisc formation.
doi:10.1101/2020.02.28.969287 fatcat:aqdxngu7n5elhkisdcjh3a4p5q

Evaluating Visual Data Analysis Systems

Leilani Battle, Marco Angelini, Carsten Binnig, Tiziana Catarci, Philipp Eichmann, Jean-Daniel Fekete, Giuseppe Santucci, Michael Sedlmair, Wesley Willett
2018 Proceedings of the Workshop on Human-In-the-Loop Data Analytics - HILDA'18  
Visual data analysis is a key tool for helping people to make sense of and interact with massive data sets. However, existing evaluation methods (e.g., database benchmarks, individual user studies) fail to capture the key points that make systems for visual data analysis (or visual data systems) challenging to design. In November 2017, members of both the Database and Visualization communities came together in a Dagstuhl seminar to discuss the grand challenges in the intersection of data
more » ... s and interactive visualization. In this paper, we report on the discussions of the working group on the evaluation of visual data systems, which addressed questions centered around developing better evaluation methods, such as "How do the different communities evaluate visual data systems?" and "What we could learn from each other to develop evaluation techniques that cut across areas?". In their discussions, the group brainstormed initial steps towards new joint evaluation methods and developed a first concrete initiative -a trace repository of various real-world workloads and visual data systems -that enables researchers to derive evaluation setups (e.g., performance benchmarks, user studies) under more realistic assumptions, and enables new evaluation perspectives (e.g., broader meta analysis across analysis contexts, reproducibility and comparability across systems).
doi:10.1145/3209900.3209901 dblp:conf/sigmod/BattleABCEFSSW18 fatcat:k57wsmv2pbh53b7ronweskm7ga

Evaluating Subjective Accuracy in Time Series Pattern-Matching Using Human-Annotated Rankings

Philipp Eichmann, Emanuel Zgraggen
2015 Proceedings of the 20th International Conference on Intelligent User Interfaces - IUI '15  
Finding patterns is a common task in time series analysis which has gained a lot of attention across many fields. A multitude of similarity measures have been introduced to perform pattern searches. The accuracy of such measures is often evaluated objectively using a one nearest neighbor classification (1NN) on labeled time series or through clustering. Prior work often disregards the subjective similarity of time series which can be pivotal in systems where a user specified pattern is used as
more » ... nput and a similarity-based ranking is expected as output (query-by-example). In this paper, we describe how a human-annotated ranking based on real-world queries and datasets can be created using simple crowdsourcing tasks and use this ranking as ground-truth to evaluate the perceived accuracy of existing time series similarity measures. Furthermore, we show how different sampling strategies and time series representations of pen-drawn queries effect the precision of these similarity measures and provide a publicly available dataset which can be used to optimize existing and future similarity search algorithms.
doi:10.1145/2678025.2701379 dblp:conf/iui/EichmannZ15 fatcat:ndojmbvcprh3dnvwxewrv22ame

Democratizing Data Science through Interactive Curation of ML Pipelines

Zeyuan Shang, Emanuel Zgraggen, Benedetto Buratti, Ferdinand Kossmann, Philipp Eichmann, Yeounoh Chung, Carsten Binnig, Eli Upfal, Tim Kraska
2019 Proceedings of the 2019 International Conference on Management of Data - SIGMOD '19  
I would like to thank all my awazing collaborators, Carsten Binnig, Benedetto Buratti, Yeounoh Chung, Philipp Eichmann, Ferdinand Kossmann, Tim Kraska, Eli Upfal, Emanuel Zgraggen.  ...  I would also like to thank my friends at MIT and outside of school: Benedetto, Emanuel, Lei, Matt, Philipp, Wenbo, Yi, Yuzhe and many others. It is always enjoyable to hang out with you.  ... 
doi:10.1145/3299869.3319863 dblp:conf/sigmod/ShangZBKECBUK19 fatcat:c7pkyoxqvrbvnb4ztl3vuvweim

Tumor and Endothelial Cell Hybrids Participate in Glioblastoma Vasculature

Soufiane El Hallani, Carole Colin, Younas El Houfi, Ahmed Idbaih, Blandine Boisselier, Yannick Marie, Philippe Ravassard, Marianne Labussière, Karima Mokhtari, Jean-Léon Thomas, Jean-Yves Delattre, Anne Eichmann (+1 others)
2014 BioMed Research International  
Philippe Ravassard (Pierre and Marie Curie University) as previously described [20] .  ... 
doi:10.1155/2014/827327 pmid:24868550 pmcid:PMC4017715 fatcat:n3c46u7uyjcw7m2kaapb5nl4vm

Quantitative mass imaging of single biological macromolecules

Gavin Young, Nikolas Hundt, Daniel Cole, Adam Fineberg, Joanna Andrecka, Andrew Tyler, Anna Olerinyova, Ayla Ansari, Erik G. Marklund, Miranda P. Collier, Shane A. Chandler, Olga Tkachenko (+13 others)
2018 Science  
The cellular processes underpinning life are orchestrated by proteins and their interactions. Investigating the structural and dynamic heterogeneity of proteins, despite being key to their function, and their interaction with drugs, poses a fundamental challenge to existing analytical and structural methodologies. We use interferometric scattering microscopy to mass-image single biomolecules in solution with less than 2% mass error, up to 19-kDa resolution, and 1-kDa precision. We resolve
more » ... eric distributions at high dynamic range, detect small-molecule binding, and mass-image proteins with associated lipids and sugars. These capabilities enable us to characterize the molecular dynamics of processes as diverse as glycoprotein cross-linking, amyloidogenic protein aggregation, and actin polymerization. Interferometric scattering mass spectrometry provides spatially-resolved access to a broad range of biomolecular interactions, one molecule at a time.
doi:10.1126/science.aar5839 pmid:29700264 fatcat:23qaemwsobc2bgmybdtoov5dci

Sediment-filled karst depressions and riyad – key archaeological environments of south Qatar

Max Engel, Stefanie Rückmann, Philipp Drechsler, Dominik Brill, Stephan Opitz, Jörg W. Fassbinder, Anna Pint, Kim Peis, Dennis Wolf, Christoph Gerber, Kristina Pfeiffer, Ricardo Eichmann (+1 others)
2020 Eiszeitalter und Gegenwart  
Stone structures of temporary character reflecting the presence of Bedouins are abundant (Eichmann et al., 2014; .  ...  ., 2011; Eichmann et al., 2014; Gerber et al., 2014; Drechsler, 2014; Drechsler et al., 2013 Drechsler et al., , 2016 Izquierdo Zamora et al., 2015; McPhillips et al., 2015) .  ... 
doi:10.5194/egqsj-68-215-2020 fatcat:rukvqkfgjfeutnhapiqnpsztri

Mass Photometry of Membrane Proteins

Anna Olerinyova, Adar Sonn-Segev, Joseph Gault, Cédric Eichmann, Johannes Schimpf, Adrian H. Kopf, Lucas S.P. Rudden, Dzmitry Ashkinadze, Radoslaw Bomba, Lukas Frey, Jason Greenwald, Matteo T. Degiacomi (+6 others)
2020 Chem  
Integral membrane proteins (IMPs) are biologically highly significant but challenging to study because they require maintaining a cellular lipid-like environment. Here, we explore the application of mass photometry (MP) to IMPs and membrane-mimetic systems at the single-particle level. We apply MP to amphipathic vehicles, such as detergents and amphipols, as well as to lipid and native nanodiscs, characterizing the particle size, sample purity, and heterogeneity. Using methods established for
more » ... yogenic electron microscopy, we eliminate detergent background, enabling high-resolution studies of membrane-protein structure and interactions. We find evidence that, when extracted from native membranes using native styrene-maleic acid nanodiscs, the potassium channel KcsA is present as a dimer of tetramers-in contrast to results obtained using detergent purification. Finally, using lipid nanodiscs, we show that MP can help distinguish between functional and non-functional nanodisc assemblies, as well as determine the critical factors for lipid nanodisc formation.
doi:10.1016/j.chempr.2020.11.011 pmid:33511302 pmcid:PMC7815066 fatcat:ti5oqz4imrb5pogph4chnujwxm
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