Madeleine van Zuylen


2021

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MSˆ2: Multi-Document Summarization of Medical Studies
Jay DeYoung | Iz Beltagy | Madeleine van Zuylen | Bailey Kuehl | Lucy Lu Wang
Proceedings of the 2021 Conference on Empirical Methods in Natural Language Processing

To assess the effectiveness of any medical intervention, researchers must conduct a time-intensive and manual literature review. NLP systems can help to automate or assist in parts of this expensive process. In support of this goal, we release MSˆ2 (Multi-Document Summarization of Medical Studies), a dataset of over 470k documents and 20K summaries derived from the scientific literature. This dataset facilitates the development of systems that can assess and aggregate contradictory evidence across multiple studies, and is the first large-scale, publicly available multi-document summarization dataset in the biomedical domain. We experiment with a summarization system based on BART, with promising early results, though significant work remains to achieve higher summarization quality. We formulate our summarization inputs and targets in both free text and structured forms and modify a recently proposed metric to assess the quality of our system’s generated summaries. Data and models are available at https://github.com/allenai/ms2.

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Extracting a Knowledge Base of Mechanisms from COVID-19 Papers
Tom Hope | Aida Amini | David Wadden | Madeleine van Zuylen | Sravanthi Parasa | Eric Horvitz | Daniel Weld | Roy Schwartz | Hannaneh Hajishirzi
Proceedings of the 2021 Conference of the North American Chapter of the Association for Computational Linguistics: Human Language Technologies

The COVID-19 pandemic has spawned a diverse body of scientific literature that is challenging to navigate, stimulating interest in automated tools to help find useful knowledge. We pursue the construction of a knowledge base (KB) of mechanisms—a fundamental concept across the sciences, which encompasses activities, functions and causal relations, ranging from cellular processes to economic impacts. We extract this information from the natural language of scientific papers by developing a broad, unified schema that strikes a balance between relevance and breadth. We annotate a dataset of mechanisms with our schema and train a model to extract mechanism relations from papers. Our experiments demonstrate the utility of our KB in supporting interdisciplinary scientific search over COVID-19 literature, outperforming the prominent PubMed search in a study with clinical experts. Our search engine, dataset and code are publicly available.

2020

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SciREX: A Challenge Dataset for Document-Level Information Extraction
Sarthak Jain | Madeleine van Zuylen | Hannaneh Hajishirzi | Iz Beltagy
Proceedings of the 58th Annual Meeting of the Association for Computational Linguistics

Extracting information from full documents is an important problem in many domains, but most previous work focus on identifying relationships within a sentence or a paragraph. It is challenging to create a large-scale information extraction (IE) dataset at the document level since it requires an understanding of the whole document to annotate entities and their document-level relationships that usually span beyond sentences or even sections. In this paper, we introduce SciREX, a document level IE dataset that encompasses multiple IE tasks, including salient entity identification and document level N-ary relation identification from scientific articles. We annotate our dataset by integrating automatic and human annotations, leveraging existing scientific knowledge resources. We develop a neural model as a strong baseline that extends previous state-of-the-art IE models to document-level IE. Analyzing the model performance shows a significant gap between human performance and current baselines, inviting the community to use our dataset as a challenge to develop document-level IE models. Our data and code are publicly available at https://github.com/allenai/SciREX .

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MedICaT: A Dataset of Medical Images, Captions, and Textual References
Sanjay Subramanian | Lucy Lu Wang | Ben Bogin | Sachin Mehta | Madeleine van Zuylen | Sravanthi Parasa | Sameer Singh | Matt Gardner | Hannaneh Hajishirzi
Findings of the Association for Computational Linguistics: EMNLP 2020

Understanding the relationship between figures and text is key to scientific document understanding. Medical figures in particular are quite complex, often consisting of several subfigures (75% of figures in our dataset), with detailed text describing their content. Previous work studying figures in scientific papers focused on classifying figure content rather than understanding how images relate to the text. To address challenges in figure retrieval and figure-to-text alignment, we introduce MedICaT, a dataset of medical images in context. MedICaT consists of 217K images from 131K open access biomedical papers, and includes captions, inline references for 74% of figures, and manually annotated subfigures and subcaptions for a subset of figures. Using MedICaT, we introduce the task of subfigure to subcaption alignment in compound figures and demonstrate the utility of inline references in image-text matching. Our data and code can be accessed at https://github.com/allenai/medicat.

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Fact or Fiction: Verifying Scientific Claims
David Wadden | Shanchuan Lin | Kyle Lo | Lucy Lu Wang | Madeleine van Zuylen | Arman Cohan | Hannaneh Hajishirzi
Proceedings of the 2020 Conference on Empirical Methods in Natural Language Processing (EMNLP)

We introduce scientific claim verification, a new task to select abstracts from the research literature containing evidence that SUPPORTS or REFUTES a given scientific claim, and to identify rationales justifying each decision. To study this task, we construct SciFact, a dataset of 1.4K expert-written scientific claims paired with evidence-containing abstracts annotated with labels and rationales. We develop baseline models for SciFact, and demonstrate that simple domain adaptation techniques substantially improve performance compared to models trained on Wikipedia or political news. We show that our system is able to verify claims related to COVID-19 by identifying evidence from the CORD-19 corpus. Our experiments indicate that SciFact will provide a challenging testbed for the development of new systems designed to retrieve and reason over corpora containing specialized domain knowledge. Data and code for this new task are publicly available at https://github.com/allenai/scifact. A leaderboard and COVID-19 fact-checking demo are available at https://scifact.apps.allenai.org.

2019

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Structural Scaffolds for Citation Intent Classification in Scientific Publications
Arman Cohan | Waleed Ammar | Madeleine van Zuylen | Field Cady
Proceedings of the 2019 Conference of the North American Chapter of the Association for Computational Linguistics: Human Language Technologies, Volume 1 (Long and Short Papers)

Identifying the intent of a citation in scientific papers (e.g., background information, use of methods, comparing results) is critical for machine reading of individual publications and automated analysis of the scientific literature. We propose structural scaffolds, a multitask model to incorporate structural information of scientific papers into citations for effective classification of citation intents. Our model achieves a new state-of-the-art on an existing ACL anthology dataset (ACL-ARC) with a 13.3% absolute increase in F1 score, without relying on external linguistic resources or hand-engineered features as done in existing methods. In addition, we introduce a new dataset of citation intents (SciCite) which is more than five times larger and covers multiple scientific domains compared with existing datasets. Our code and data are available at: https://github.com/allenai/scicite.

2018

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A Dataset of Peer Reviews (PeerRead): Collection, Insights and NLP Applications
Dongyeop Kang | Waleed Ammar | Bhavana Dalvi | Madeleine van Zuylen | Sebastian Kohlmeier | Eduard Hovy | Roy Schwartz
Proceedings of the 2018 Conference of the North American Chapter of the Association for Computational Linguistics: Human Language Technologies, Volume 1 (Long Papers)

Peer reviewing is a central component in the scientific publishing process. We present the first public dataset of scientific peer reviews available for research purposes (PeerRead v1),1 providing an opportunity to study this important artifact. The dataset consists of 14.7K paper drafts and the corresponding accept/reject decisions in top-tier venues including ACL, NIPS and ICLR. The dataset also includes 10.7K textual peer reviews written by experts for a subset of the papers. We describe the data collection process and report interesting observed phenomena in the peer reviews. We also propose two novel NLP tasks based on this dataset and provide simple baseline models. In the first task, we show that simple models can predict whether a paper is accepted with up to 21% error reduction compared to the majority baseline. In the second task, we predict the numerical scores of review aspects and show that simple models can outperform the mean baseline for aspects with high variance such as ‘originality’ and ‘impact’.

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Construction of the Literature Graph in Semantic Scholar
Waleed Ammar | Dirk Groeneveld | Chandra Bhagavatula | Iz Beltagy | Miles Crawford | Doug Downey | Jason Dunkelberger | Ahmed Elgohary | Sergey Feldman | Vu Ha | Rodney Kinney | Sebastian Kohlmeier | Kyle Lo | Tyler Murray | Hsu-Han Ooi | Matthew Peters | Joanna Power | Sam Skjonsberg | Lucy Lu Wang | Chris Wilhelm | Zheng Yuan | Madeleine van Zuylen | Oren Etzioni
Proceedings of the 2018 Conference of the North American Chapter of the Association for Computational Linguistics: Human Language Technologies, Volume 3 (Industry Papers)

We describe a deployed scalable system for organizing published scientific literature into a heterogeneous graph to facilitate algorithmic manipulation and discovery. The resulting literature graph consists of more than 280M nodes, representing papers, authors, entities and various interactions between them (e.g., authorships, citations, entity mentions). We reduce literature graph construction into familiar NLP tasks (e.g., entity extraction and linking), point out research challenges due to differences from standard formulations of these tasks, and report empirical results for each task. The methods described in this paper are used to enable semantic features in www.semanticscholar.org.