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@ -0,0 +1,39 @@
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|||
@inproceedings{pimentel:2019:msr:large,
|
||||
author = {Pimentel, Jo\~{a}o Felipe and Murta, Leonardo and Braganholo, Vanessa and Freire, Juliana},
|
||||
booktitle = {MSR},
|
||||
title = {A Large-scale Study About Quality and Reproducibility of Jupyter Notebooks},
|
||||
year = 2019
|
||||
}
|
||||
|
||||
@article{yang2015lenses,
|
||||
author = {Yang, Ying and Meneghetti, Niccolo and Fehling, Ronny and Liu, Zhen Hua and Kennedy, Oliver},
|
||||
dateadded = {2015-06-24 20:23:11 +0000},
|
||||
datemodified = {2015-06-24 20:25:09 +0000},
|
||||
journal = {Proc. VLDB Endow.},
|
||||
number = 12,
|
||||
title = {Lenses: An On-Demand Approach to ETL},
|
||||
volume = 8,
|
||||
year = 2015
|
||||
}
|
||||
|
||||
@misc{vizier,
|
||||
author = {The VizierDB Group},
|
||||
howpublished = {http://vizierdb.info},
|
||||
title = {Vizier: Built for Data Exploration}
|
||||
}
|
||||
|
||||
@inproceedings{DBLP:conf/sigmod/BrachmannBCFFGK19,
|
||||
author = {Mike Brachmann and Carlos Bautista and Sonia Castelo and Su Feng and Juliana Freire and Boris Glavic and Oliver Kennedy and Heiko Mueller and R{\'{e}}mi Rampin and William Spoth and Ying Yang},
|
||||
booktitle = {{SIGMOD} Conference},
|
||||
pages = {1877--1880},
|
||||
publisher = {{ACM}},
|
||||
title = {Data Debugging and Exploration with Vizier},
|
||||
year = 2019
|
||||
}
|
||||
|
||||
@inproceedings{freire:2016:hilda:exception,
|
||||
author = {Freire, Juliana and Glavic, Boris and Kennedy, Oliver and Mueller, Heiko},
|
||||
booktitle = {HILDA},
|
||||
title = {The Exception That Improves The Rule},
|
||||
year = 2016
|
||||
}
|
|
@ -0,0 +1,32 @@
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|||
\relax
|
||||
\citation{pimentel:2019:msr:large}
|
||||
\citation{jobevers:2018:jupyterOrderOfExec}
|
||||
\citation{vanderplass:2017:reproducibility}
|
||||
\citation{zelnicki:2017:nodebook}
|
||||
\citation{DBLP:conf/sigmod/BrachmannBCFFGK19}
|
||||
\citation{freire:2016:hilda:exception}
|
||||
\citation{yang2015lenses}
|
||||
\@writefile{toc}{\contentsline {section}{\numberline {1}Introduction}{\thepage }}
|
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\newlabel{sec:intro}{{1}{\thepage }}
|
||||
\@writefile{tdo}{\contentsline {todo}{\textbf {Oliver: } Another way to pitch this is to center it on provenance and error tracking. Honestly, I wasn't able to build a more compelling argument for that than what I got above with Juliana's Notebooks aren't reproducible paper.}{\thepage }}
|
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|
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|
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\bibcite{jobevers:2018:jupyterOrderOfExec}{2}
|
||||
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|
||||
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|
||||
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|
||||
\bibcite{yang2015lenses}{6}
|
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|
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\@writefile{toc}{\contentsline {section}{\numberline {4}Gluing Cells}{\thepage }}
|
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\newlabel{sec:provenance}{{4}{\thepage }}
|
||||
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||||
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\newlabel{sec:experiments}{{6}{\thepage }}
|
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\@writefile{toc}{\contentsline {section}{\numberline {7}References}{\thepage }}
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@ -0,0 +1,40 @@
|
|||
\begin{thebibliography}{1}
|
||||
|
||||
\bibitem{DBLP:conf/sigmod/BrachmannBCFFGK19}
|
||||
M.~Brachmann, C.~Bautista, S.~Castelo, S.~Feng, J.~Freire, B.~Glavic,
|
||||
O.~Kennedy, H.~Mueller, R.~Rampin, W.~Spoth, and Y.~Yang.
|
||||
\newblock Data debugging and exploration with vizier.
|
||||
\newblock In {\em {SIGMOD} Conference}, pages 1877--1880. {ACM}, 2019.
|
||||
|
||||
\bibitem{jobevers:2018:jupyterOrderOfExec}
|
||||
J.~Evers-Meltzer.
|
||||
\newblock Enforce a top-down order of execution.
|
||||
\newblock https://github.com/jupyter/notebook/issues/3229.
|
||||
|
||||
\bibitem{freire:2016:hilda:exception}
|
||||
J.~Freire, B.~Glavic, O.~Kennedy, and H.~Mueller.
|
||||
\newblock The exception that improves the rule.
|
||||
\newblock In {\em HILDA}, 2016.
|
||||
|
||||
\bibitem{pimentel:2019:msr:large}
|
||||
J.~a.~F. Pimentel, L.~Murta, V.~Braganholo, and J.~Freire.
|
||||
\newblock A large-scale study about quality and reproducibility of jupyter
|
||||
notebooks.
|
||||
\newblock In {\em MSR}, 2019.
|
||||
|
||||
\bibitem{vanderplass:2017:reproducibility}
|
||||
J.~VanderPlas.
|
||||
\newblock Idea: Jupyter notebooks could have a "reproducibility mode".
|
||||
\newblock https://twitter.com/jakevdp/status/935178916490223616.
|
||||
|
||||
\bibitem{yang2015lenses}
|
||||
Y.~Yang, N.~Meneghetti, R.~Fehling, Z.~H. Liu, and O.~Kennedy.
|
||||
\newblock Lenses: An on-demand approach to etl.
|
||||
\newblock {\em Proc. VLDB Endow.}, 8(12), 2015.
|
||||
|
||||
\bibitem{zelnicki:2017:nodebook}
|
||||
K.~Zielnicki.
|
||||
\newblock Nodebook.
|
||||
\newblock https://multithreaded.stitchfix.com/blog/2017/07/26/nodebook/.
|
||||
|
||||
\end{thebibliography}
|
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@ -0,0 +1,47 @@
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Capacity: max_strings=100000, hash_size=100000, hash_prime=85009
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Database file #1: oliver.bib
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|
||||
\doi{10.475/123_4}
|
||||
|
||||
% ISBN
|
||||
\isbn{123-4567-24-567/08/06}
|
||||
|
||||
%Conference
|
||||
\conferenceinfo{PLDI '13}{June 16--19, 2013, Seattle, WA, USA}
|
||||
|
||||
\acmPrice{\$15.00}
|
||||
|
||||
%
|
||||
% --- Author Metadata here ---
|
||||
\conferenceinfo{WOODSTOCK}{'97 El Paso, Texas USA}
|
||||
%\CopyrightYear{2007} % Allows default copyright year (20XX) to be over-ridden - IF NEED BE.
|
||||
%\crdata{0-12345-67-8/90/01} % Allows default copyright data (0-89791-88-6/97/05) to be over-ridden - IF NEED BE.
|
||||
% --- End of Author Metadata ---
|
||||
|
||||
\title{What needs to be REPLaced in notebooks}
|
||||
%
|
||||
% You need the command \numberofauthors to handle the 'placement
|
||||
% and alignment' of the authors beneath the title.
|
||||
%
|
||||
% For aesthetic reasons, we recommend 'three authors at a time'
|
||||
% i.e. three 'name/affiliation blocks' be placed beneath the title.
|
||||
%
|
||||
% NOTE: You are NOT restricted in how many 'rows' of
|
||||
% "name/affiliations" may appear. We just ask that you restrict
|
||||
% the number of 'columns' to three.
|
||||
%
|
||||
% Because of the available 'opening page real-estate'
|
||||
% we ask you to refrain from putting more than six authors
|
||||
% (two rows with three columns) beneath the article title.
|
||||
% More than six makes the first-page appear very cluttered indeed.
|
||||
%
|
||||
% Use the \alignauthor commands to handle the names
|
||||
% and affiliations for an 'aesthetic maximum' of six authors.
|
||||
% Add names, affiliations, addresses for
|
||||
% the seventh etc. author(s) as the argument for the
|
||||
% \additionalauthors command.
|
||||
% These 'additional authors' will be output/set for you
|
||||
% without further effort on your part as the last section in
|
||||
% the body of your article BEFORE References or any Appendices.
|
||||
|
||||
\numberofauthors{4} % in this sample file, there are a *total*
|
||||
% of EIGHT authors. SIX appear on the 'first-page' (for formatting
|
||||
% reasons) and the remaining two appear in the \additionalauthors section.
|
||||
%
|
||||
\author{
|
||||
% You can go ahead and credit any number of authors here,
|
||||
% e.g. one 'row of three' or two rows (consisting of one row of three
|
||||
% and a second row of one, two or three).
|
||||
%
|
||||
% The command \alignauthor (no curly braces needed) should
|
||||
% precede each author name, affiliation/snail-mail address and
|
||||
% e-mail address. Additionally, tag each line of
|
||||
% affiliation/address with \affaddr, and tag the
|
||||
% e-mail address with \email.
|
||||
%
|
||||
\alignauthor
|
||||
Michael Brachmann\\
|
||||
\affaddr{University at Buffalo}\\
|
||||
\email{mrb24@buffalo.edu}
|
||||
\alignauthor
|
||||
Heiko Mueller\\
|
||||
\affaddr{New York University}\\
|
||||
\email{heiko.mueller@nyu.edu}
|
||||
\alignauthor
|
||||
Sonia Castelo Quispe\\
|
||||
\affaddr{New York University}\\
|
||||
\email{s.castelo@nyu.edu}
|
||||
\and
|
||||
\alignauthor
|
||||
Juliana Freire\\
|
||||
\affaddr{New York University}\\
|
||||
\email{juliana.freire@nyu.edu}
|
||||
\alignauthor
|
||||
Boris Glavic\\
|
||||
\affaddr{Illinois Institute of Technology}\\
|
||||
\email{bglavic@iit.edu}
|
||||
\alignauthor
|
||||
Oliver Kennedy\\
|
||||
\affaddr{University at Buffalo}\\
|
||||
\email{okennedy@buffalo.edu}
|
||||
}
|
||||
% There's nothing stopping you putting the seventh, eighth, etc.
|
||||
% author on the opening page (as the 'third row') but we ask,
|
||||
% for aesthetic reasons that you place these 'additional authors'
|
||||
% in the \additional authors block, viz.
|
||||
% \additionalauthors{Additional authors: John Smith (The Th{\o}rv{\"a}ld Group,
|
||||
% email: {\texttt{jsmith@affiliation.org}}) and Julius P.~Kumquat
|
||||
% (The Kumquat Consortium, email: {\texttt{jpkumquat@consortium.net}}).}
|
||||
% \date{30 July 1999}
|
||||
% Just remember to make sure that the TOTAL number of authors
|
||||
% is the number that will appear on the first page PLUS the
|
||||
% number that will appear in the \additionalauthors section.
|
||||
|
||||
\maketitle
|
||||
\begin{abstract}
|
||||
\input{sections/abstract.tex}
|
||||
\end{abstract}
|
||||
|
||||
|
||||
%
|
||||
% The code below should be generated by the tool at
|
||||
% http://dl.acm.org/ccs.cfm
|
||||
% Please copy and paste the code instead of the example below.
|
||||
%
|
||||
|
||||
%
|
||||
% End generated code
|
||||
%
|
||||
|
||||
%
|
||||
% Use this command to print the description
|
||||
%
|
||||
% \printccsdesc
|
||||
|
||||
\keywords{TBD}
|
||||
|
||||
\section{Introduction}
|
||||
\label{sec:intro}
|
||||
\input{sections/intro.tex}
|
||||
|
||||
\section{System Overview}
|
||||
\label{sec:system}
|
||||
\input{sections/system.tex}
|
||||
|
||||
\section{The Vizier Spreadsheet}
|
||||
\label{sec:spreadsheet}
|
||||
\input{sections/spreadsheet.tex}
|
||||
|
||||
\section{Gluing Cells}
|
||||
\label{sec:provenance}
|
||||
\input{sections/provenance.tex}
|
||||
|
||||
\section{Data Annotations}
|
||||
\label{sec:errors}
|
||||
\input{sections/errors.tex}
|
||||
|
||||
\section{Experiments}
|
||||
\label{sec:experiments}
|
||||
\input{sections/experiments.tex}
|
||||
|
||||
|
||||
|
||||
%ACKNOWLEDGMENTS are optional
|
||||
% \section{Acknowledgments}
|
||||
|
||||
%
|
||||
% The following two commands are all you need in the
|
||||
% initial runs of your .tex file to
|
||||
% produce the bibliography for the citations in your paper.
|
||||
\bibliographystyle{abbrv}
|
||||
\bibliography{oliver,quotes} % sigproc.bib is the name of the Bibliography in this case
|
||||
|
||||
\end{document}
|
|
@ -0,0 +1,20 @@
|
|||
% Optional fields: author, title, howpublished, month, year, note
|
||||
@MISC{vanderplass:2017:reproducibility,
|
||||
howpublished = {https://twitter.com/jakevdp/status/935178916490223616},
|
||||
title = {Idea: Jupyter notebooks could have a "reproducibility mode"},
|
||||
author = {Jake VanderPlas}
|
||||
}
|
||||
|
||||
% Optional fields: author, title, howpublished, month, year, note
|
||||
@MISC{zelnicki:2017:nodebook,
|
||||
howpublished = {https://multithreaded.stitchfix.com/blog/2017/07/26/nodebook/},
|
||||
author = {Kevin Zielnicki},
|
||||
title = {Nodebook}
|
||||
}
|
||||
|
||||
% Optional fields: author, title, howpublished, month, year, note
|
||||
@MISC{jobevers:2018:jupyterOrderOfExec,
|
||||
howpublished = {https://github.com/jupyter/notebook/issues/3229},
|
||||
author = {Job Evers-Meltzer},
|
||||
title = {Enforce a top-down order of execution}
|
||||
}
|
|
@ -0,0 +1,4 @@
|
|||
|
||||
% -*- root: ../paper.tex -*-
|
||||
|
||||
This is a section
|
|
@ -0,0 +1,11 @@
|
|||
|
||||
% -*- root: ../paper.tex -*-
|
||||
|
||||
Things to cover here:
|
||||
\begin{itemize}
|
||||
\item Recap Mimir/UADBs
|
||||
\item Marking cells as uncertain through DataWarnings / define data warning.
|
||||
\item Static analysis to discover families of data warnings
|
||||
\item LIMIT query for examples from each family
|
||||
\item COUNT query to summarize
|
||||
\end{itemize}
|
|
@ -0,0 +1,4 @@
|
|||
|
||||
% -*- root: ../paper.tex -*-
|
||||
|
||||
This is a section
|
|
@ -0,0 +1,39 @@
|
|||
|
||||
% -*- root: ../paper.tex -*-
|
||||
|
||||
Over the past decade, notebook tools like Jupyter and Zeppelin have emerged as a convenient programming abstraction for data exploration, model-building, and rapid prototyping.
|
||||
Notebooks are attractive for data engineers, as they promise to make introspecting code behavior easier, and to facilitate code re-use and reproducibility.
|
||||
Unfortunately, reality is far from this ideal: A recent study by Pimentel et. al. sampled a large number of Jupyter notebooks from GitHub~\cite{pimentel:2019:msr:large} and found only 4\% to be reproducible, and only 24\% to be re-usable without error.
|
||||
|
||||
These abysmal numbers are caused in large part by Jupyter's organic growth as a thin facade over a read-evaluate-print-loop (REPL).
|
||||
The core metaphor of a notebook is that groups of code are grouped into units called cells.
|
||||
Like most other popular notebooks, a Jupyter notebook runs alongside a kernel, a scripting language interpreter running as a REPL.
|
||||
When the user decides to execute a cell, the cell's code is piped into the REPL.
|
||||
The kernel executes the code, and the notebook formats it nicely for presentation alongside the cell.
|
||||
Critically, the kernel continues to run, preserving its state and allowing subsequently executed cells to re-use outputs from previous cells.
|
||||
|
||||
In this \emph{kernel-centric} notebook model, the state of the notebook ``program'' is simply the state of the kernel.
|
||||
All interactions with this state must be mediated through the kernel, and by extension through the language the kernel implements.
|
||||
Thus, inspecting state requires writing code, while use of domain-specific languages like SQL for specialized tasks is hindered by having to tunnel intent through the kernel's language.
|
||||
Far worse, however, is the fact that the kernel's state is universally treated as an opaque blob.
|
||||
This is one of the root causes of a common problem~\cite{jobevers:2018:jupyterOrderOfExec,vanderplass:2017:reproducibility,zelnicki:2017:nodebook} with notebooks: Although cells appear in a linear order in the notebook, they can be executed in a different order\footnote{
|
||||
In Pimentel's study, 36\% of sampled notebooks showed definitive evidence of out-of-order execution, with a total of 66\% that showed traces of possible out-of-order execution.
|
||||
}.
|
||||
Out-of-order execution is a natural consequence of relying on notebook state.
|
||||
To enforce in-order execution, we would need to revert the notebook's state to before the cell was executed.
|
||||
Checkpointing kernel state is frequently slow or memory intensive, making it difficult to revert without re-running \emph{all} preceding cells.
|
||||
Out-of-order execution avoids such re-execution for every altered cell.
|
||||
|
||||
In this paper, we introduce a new \emph{data-centric} notebook called Vizier\cite{DBLP:conf/sigmod/BrachmannBCFFGK19}.
|
||||
State in a data-centric notebook is structured in a standardized representation --- in Vizier's case as a set of named spark dataframes.
|
||||
This standard, language-agnostic state representation makes it possible to mix cells for different scripting languages, and even different interaction modalities.
|
||||
In Vizier for example, users interact with state through Python, Scala, or SQL script cells, through a spreadsheet-style interface~\cite{freire:2016:hilda:exception}, or by deploying canned data cleaning operators called lenses\cite{yang2015lenses}.
|
||||
Decoupling notebook state from an opaque kernel also makes dependency analysis and state checkpoints feasible, in turn making enforced in-order execution practical.
|
||||
|
||||
As a further benefit, allowing dependency analysis also brings into scope a wide range of provenance techniques.
|
||||
In this paper, we explore one such set of techniques for Vizier that track errors.
|
||||
|
||||
|
||||
|
||||
|
||||
\Oliver{Another way to pitch this is to center it on provenance and error tracking. Honestly, I wasn't able to build a more compelling argument for that than what I got above with Juliana's Notebooks aren't reproducible paper.}
|
|
@ -0,0 +1,9 @@
|
|||
|
||||
% -*- root: ../paper.tex -*-
|
||||
|
||||
Things to cover here:
|
||||
\begin{itemize}
|
||||
\item Using workflows to assemble views with tables + coarse-grained provenance as a fallback.
|
||||
\item The benefits of this approach for many small update steps.
|
||||
\end{itemize}
|
||||
This is a section
|
|
@ -0,0 +1,9 @@
|
|||
|
||||
% -*- root: ../paper.tex -*-
|
||||
|
||||
Things to include here:
|
||||
\begin{itemize}
|
||||
\item Transient updates
|
||||
\item Re-enactment
|
||||
\item Creates lots of small workflow steps.
|
||||
\end{itemize}
|
|
@ -0,0 +1,9 @@
|
|||
|
||||
% -*- root: ../paper.tex -*-
|
||||
|
||||
Things to cover here:
|
||||
\begin{itemize}
|
||||
\item Overview: Dataset/Dataframes as inter-cell operators
|
||||
\item The notebook workflow + gluing views together + how updates are registered --- what is the Cell API.
|
||||
\item Interface modalities: Notebook, Spreadsheet, Error List
|
||||
\end{itemize}
|
File diff suppressed because it is too large
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Reference in New Issue