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Oliver Kennedy 2019-08-01 19:57:44 -04:00
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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
}

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\@writefile{toc}{\contentsline {section}{\numberline {1}Introduction}{\thepage }}
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\@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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\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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% This is "sig-alternate.tex" V2.1 April 2013
% This file should be compiled with V2.5 of "sig-alternate.cls" May 2012
%
% This example file demonstrates the use of the 'sig-alternate.cls'
% V2.5 LaTeX2e document class file. It is for those submitting
% articles to ACM Conference Proceedings WHO DO NOT WISH TO
% STRICTLY ADHERE TO THE SIGS (PUBS-BOARD-ENDORSED) STYLE.
% The 'sig-alternate.cls' file will produce a similar-looking,
% albeit, 'tighter' paper resulting in, invariably, fewer pages.
%
% ----------------------------------------------------------------------------------------------------------------
% This .tex file (and associated .cls V2.5) produces:
% 1) The Permission Statement
% 2) The Conference (location) Info information
% 3) The Copyright Line with ACM data
% 4) NO page numbers
%
% as against the acm_proc_article-sp.cls file which
% DOES NOT produce 1) thru' 3) above.
%
% Using 'sig-alternate.cls' you have control, however, from within
% the source .tex file, over both the CopyrightYear
% (defaulted to 200X) and the ACM Copyright Data
% (defaulted to X-XXXXX-XX-X/XX/XX).
% e.g.
% \CopyrightYear{2007} will cause 2007 to appear in the copyright line.
% \crdata{0-12345-67-8/90/12} will cause 0-12345-67-8/90/12 to appear in the copyright line.
%
% ---------------------------------------------------------------------------------------------------------------
% This .tex source is an example which *does* use
% the .bib file (from which the .bbl file % is produced).
% REMEMBER HOWEVER: After having produced the .bbl file,
% and prior to final submission, you *NEED* to 'insert'
% your .bbl file into your source .tex file so as to provide
% ONE 'self-contained' source file.
%
% ================= IF YOU HAVE QUESTIONS =======================
% Questions regarding the SIGS styles, SIGS policies and
% procedures, Conferences etc. should be sent to
% Adrienne Griscti (griscti@acm.org)
%
% Technical questions _only_ to
% Gerald Murray (murray@hq.acm.org)
% ===============================================================
%
% For tracking purposes - this is V2.0 - May 2012
\documentclass{sig-alternate}
\usepackage{todonotes}
\newcommand{\Oliver}[1]{\todo[inline,color=red]{\textbf{Oliver: } #1}}
\begin{document}
% Copyright
% \setcopyright{acmcopyright}
\setcopyright{acmlicensed}
%\setcopyright{rightsretained}
%\setcopyright{usgov}
%\setcopyright{usgovmixed}
%\setcopyright{cagov}
%\setcopyright{cagovmixed}
% DOI
\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}

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% 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}
}

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This is a section

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% -*- 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}

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% -*- root: ../paper.tex -*-
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% -*- 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.}

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% -*- 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

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% -*- root: ../paper.tex -*-
Things to include here:
\begin{itemize}
\item Transient updates
\item Re-enactment
\item Creates lots of small workflow steps.
\end{itemize}

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% -*- 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}

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