CSE 599D: The Future of Scholarly Communication
Autumn 2022 · TuTh 11:30am-12:50pm · CSE2 G01
Instructor: Jeffrey Heer
Course Description
Despite the ubiquity of online computational media, scholarly communication remains rooted in centuries-old models of publication. In this course, we will research and prototype novel forms of reading, writing, reviewing, reusing, and disseminating academic work. Topics include computational media, interactive articles, augmented reading and writing, collaboration, mining the literature, and applications of NLP, computer vision, and other methods for content generation and extraction. In addition to ideation and prototyping exercises, students will complete a project developing and/or assessing alternative forms of scholarly communication.
The class is open to all interested UW students with a computer science background roughly equivalent to upper-level undergraduate courses. Depending on individual student interests, familiarity with human-computer interaction, data visualization, web programming, natural language processing, and/or computer vision may be particularly relevant.
Schedule
Readings in bold face are required and you should be prepared to discuss them in class. The other readings are optional; you are strongly encouraged to read the abstracts, skim the articles, and come to class with questions!
Th 9/29 Introduction & History
- T. Hope et al. (2022) A Computational Inflection for Scientific Discovery. ArXiv
- S. Ritchie. (2022) Should we get rid of the scientific paper? The Guardian
- G. Wolf. (1995) The Curse of Xanadu. WIRED
Tu 10/4 Explorable Explanations (Guest: Matthew Conlen)
- B. Victor. (2011) Explorable Explanations.
- B. Victor. (2011) Scientific Communication As Sequential Art.
- F. Hohman, M. Conlen, J. Heer, D. H. Chau. (2020) Communicating with Interactive Articles. Distill
- M. Conlen, A. Kale, J. Heer. (2019) Capture & Analysis of Active Reading Behaviors for Interactive Articles on the Web. Comput. Graph. Forum
Th 10/6 Computational Notebooks
- D. Knuth. (1984) Literate Programming. Comput. J.
- A. Rule, A. Tabard, J. Hollan. (2018) Exploration and Explanation in Computational Notebooks. CHI
- M. B. Kery et al. (2020) mage: Fluid Moves Between Code and Graphical Work in Computational Notebooks. UIST
- T. Kluyver et al. (2016) Jupyter Notebooks - a publishing format for reproducible computational workflows. ELPUB
- J. Perkel. (2021) Reactive, reproducible, collaborative: computational notebooks evolve. Nature
Tu 10/11 Authoring Tools (Guests: Carlos Scheidegger, Will Crichton)
- M. Conlen, J. Heer. (2018) Idyll: A Markup Language for Authoring and Publishing Interactive Articles on the Web. UIST
- D. S. Himmelstein et al. (2019) Open collaborative writing with Manubot. PLoS Comput. Biol.
- W. Crichton. (2021) A New Medium for Communicating Research on Programming Languages.
- CurveNote. (2022)
- Jupyter Book. (2020)
- Quarto. (2022)
Th 10/13 Augmented Reading (Guest: Andrew Head)
- A. Head et al. (2020) Augmenting Scientific Papers with Just-in-Time, Position-Sensitive Definitions of Terms and Symbols. CHI
- A. Head, A. Xie, M. A. Hearst. (2022) Math Augmentation: How Authors Enhance the Readability of Formulas using Novel Visual Design Practices. CHI
- N. Rachatasumrit, J. Bragg, A. X. Zhang, D. S. Weld. (2022) CiteRead: Integrating Localized Citation Contexts into Scientific Paper Reading. IUI
Tu 10/18 Literature Review
- T. Hope et al. (2020) SciSight: Combining faceted navigation and research group detection for COVID-19 exploratory scientific search. bioRxiv
- D. Russell, M. Stefik, P. Pirolli, S. Card. (1993) The cost structure of sensemaking. INTERCHI
- D. H. Chau, A. Kittur, J. I. Hong, C. Faloutsos. (2011) Apolo: making sense of large network data by combining rich user interaction and machine learning. CHI
- Zotero. (2022)
Th 10/20 Collaboration & Annotation (Guest: Amy Zhang)
- W. Hill, J. Hollan, D. Wroblewski, T. P. McCandless. (1992) Edit wear and read wear. CHI
- S. Zyto, D. R. Karger, M. Ackerman, S. Mahajan. (2012) Successful classroom deployment of a social document annotation system. CHI
- T. Phelps, R. Wilensky. (2000) Robust intra-document locations. Comput. Networks
- J. Heer, F. Viégas, M. Wattenberg. (2009) Voyagers and voyeurs: Supporting asynchronous collaborative visualization. CACM
- G. Litt, S. Lim, M. Kleppmann, P. van Hardenberg. (2022) Peritext: A CRDT for Collaborative Rich Text Editing. ACM CSCW
- J. Day-Richter. (2010) What’s different about the new Google Docs: Working together, even apart. Google Drive Blog
- M. Neumann, Z. Shen, S. Skjonsberg. (2021) PAWLS: PDF Annotation With Labels and Structure. ACL
Tu 10/25 Citation
- M. Moravcsik, P. Murugesan. (1975) Some Results on the Function and Quality of Citations. Social Studies of Science
- M. Valenzuela, V. A. Ha, O. Etzioni. (2015) Identifying Meaningful Citations. AAAI Workshop: Scholarly Big Data
- S.-U. Hassan, A. Akram, P. Haddawy. (2017) Identifying Important Citations Using Contextual Information from Full Text. 2017 ACM/IEEE Joint Conference on Digital Libraries (JCDL)
- X.-D. Zhu, P. D. Turney, D. Lemire, A. Vellino. (2015) Measuring academic influence: Not all citations are equal. J. Assoc. Inf. Sci. Technol.
Th 10/27 Scientometrics (Guest: Jevin West)
- S. Fortunato et al. (2018) The Science of Science. Science
- J. Bollen et al. (2009) Clickstream Data Yields High-Resolution Maps of Science. PloS One
- C. T. Bergstrom. (2007) Eigenfactor Measuring the value and prestige of scholarly journals. College & Research Libraries News
- J. Bollen, H. V. D. Sompel, A. Hagberg, R. Chute. (2009) A Principal Component Analysis of 39 Scientific Impact Measures. PloS One
Tu 11/1 Automating Discovery (Guest: Tom Hope)
- A. Amini et al. (2020) Extracting a Knowledge Base of Mechanisms from COVID-19 Papers. NAACL
- V. Tshitoyan et al. (2019) Unsupervised word embeddings capture latent knowledge from materials science literature. Nature
- S. Henry, B. T. McInnes. (2017) Literature Based Discovery: Models, methods, and trends. J. Biomed. Informatics
- S. Zhao, C. Su, Z. Lu, F. Wang. (2020) Recent advances in biomedical literature mining. Briefings Bioinform.
Th 11/3 Final Project Proposals
- No readings
Tu 11/8 Information Extraction (Guest: Dan Weld)
- W. Ammar et al. (2018) Construction of the Literature Graph in Semantic Scholar. NAACL
- I. Cachola, K. Lo, A. Cohan, D. S. Weld. (2020) TLDR: Extreme Summarization of Scientific Documents. FINDINGS
- P. Lopez. (2009) GROBID: Combining Automatic Bibliographic Data Recognition and Term Extraction for Scholarship Publications. ECDL
- S. Peters, C. Zhang, M. Livny, C. Ré. (2014) A Machine Reading System for Assembling Synthetic Paleontological Databases. PloS One
- C. De Sa et al. (2015) Incremental Knowledge Base Construction Using DeepDive. The VLDB Journal
Th 11/10 Visual Extraction
- M. Savva et al. (2011) ReVision: automated classification, analysis and redesign of chart images. UIST
- Z. Shen et al. (2021) VILA: Improving Structured Content Extraction from Scientific PDFs Using Visual Layout Groups. TACL
- J. Poco, J. Heer. (2017) Reverse‐Engineering Visualizations: Recovering Visual Encodings from Chart Images. Comput. Graph. Forum
- P.-S. Lee, J. D. West, B. Howe. (2016) Viziometrics: Analyzing Visual Information in the Scientific Literature. IEEE Transactions on Big Data
Tu 11/15 Accessibility (Guest: Frank Elavsky)
- L. L. Wang et al. (2021) Improving the Accessibility of Scientific Documents: Current State, User Needs, and a System Solution to Enhance Scientific PDF Accessibility for Blind and Low Vision Users
- J. P. Bigham et al. (2016) An Uninteresting Tour Through Why Our Research Papers Aren’t Accessible. CHI Extended Abstracts
- A. Lundgard, A. Satyanarayan. (2021) Accessible Visualization via Natural Language Descriptions: A Four-Level Model of Semantic Content. IEEE Transactions on Visualization and Computer Graphics
Th 11/17 Figures & Tables (Guest: Shannon Shen)
- J. Zong et al. (2022) Rich Screen Reader Experiences for Accessible Data Visualization. Computer Graphics Forum
- D. H. Kim, E. Hoque, J. Kim, M. Agrawala. (2018) Facilitating Document Reading by Linking Text and Tables. UIST
- J. Poco, A. Mayhua, J. Heer. (2018) Extracting and Retargeting Color Mappings from Bitmap Images of Visualizations. IEEE Transactions on Visualization and Computer Graphics
- N. Kong, M. Agrawala. (2012) Graphical Overlays: Using Layered Elements to Aid Chart Reading. IEEE Transactions on Visualization and Computer Graphics
- D. H. Kim, V. Setlur, M. Agrawala. (2021) Towards Understanding How Readers Integrate Charts and Captions: A Case Study with Line Charts. CHI
Tu 11/22 Layout & Formats (No Class Meeting)
- C. Jacobs et al. (2004) Adaptive document layout. CACM
- M. Conlen, J. Heer. (2022) Fidyll: A Compiler for Cross-Format Data Stories & Explorable Explanations. ArXiv
- A. Ibrahim, K. Lillemoe, M. Klingensmith, J. Dimick. (2017) Visual Abstracts to Disseminate Research on Social Media: A Prospective, Case-control Crossover Study. Annals of Surgery
- N. Hurst, W. Li, K. Marriott. (2009) Review of automatic document formatting. DocEng ‘09
- N. Hurst, K. Marriott, P. Moulder. (2005) Toward tighter tables. DocEng ‘05
Th 11/24 Thanksgiving (No Class)
- No readings
Tu 11/29 Final Project Check-In Review
- No readings
Th 12/1 Open Access & Open Science
- J. Willinsky. (2005) The unacknowledged convergence of open source, open access, and open science. First Monday
- B. A. Nosek et al. (2019) Preregistration Is Hard, And Worthwhile. Trends in Cognitive Sciences
- A. Szollosi et al. (2019) Is Preregistration Worthwhile?. Trends in Cognitive Sciences
- B. Fecher, S. Friesike. (2013) Open Science: One Term, Five Schools of Thought.
Tu 12/6 Libraries & Course Review (Guest: Shan Carter)
- D. Levy, C. Marshall. (1995) Going digital: a look at assumptions underlying digital libraries. CACM
- P. Ginsparg. (2011) ArXiv at 20. Nature
- Editorial Team. (2021) Distill Hiatus. Distill
Th 12/8 Final Project Showcase
- No readings
Assignments
- Course Participation 20%
- Exercise 1: Augmented Articles 20%
- Exercise 2: Literature Review 20%
- Final Project 40%
Policies
Plagiarism Policy: Assignments should consist primarily of original work. Building off of others’ work—including 3rd party libraries, public source code examples, and design ideas—is acceptable and in most cases encouraged. However, failure to cite such sources will result in score deductions proportional to the severity of the oversight.
Religious Accommodation: Washington state law requires that UW develop a policy for accommodation of student absences or significant hardship due to reasons of faith or conscience, or for organized religious activities. The UW’s policy, including more information about how to request an accommodation, is available here: Religious Accommodations Policy. Accommodations must be requested within the first two weeks of this course using the Religious Accommodations Request form.