Lucy Lu Wang


2022

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MultiVerS: Improving scientific claim verification with weak supervision and full-document context
David Wadden | Kyle Lo | Lucy Lu Wang | Arman Cohan | Iz Beltagy | Hannaneh Hajishirzi
Findings of the Association for Computational Linguistics: NAACL 2022

The scientific claim verification task requires an NLP system to label scientific documents which Support or Refute an input claim, and to select evidentiary sentences (or rationales) justifying each predicted label. In this work, we present MultiVerS, which predicts a fact-checking label and identifies rationales in a multitask fashion based on a shared encoding of the claim and full document context. This approach accomplishes two key modeling goals. First, it ensures that all relevant contextual information is incorporated into each labeling decision. Second, it enables the model to learn from instances annotated with a document-level fact-checking label, but lacking sentence-level rationales. This allows MultiVerS to perform weakly-supervised domain adaptation by training on scientific documents labeled using high-precision heuristics. Our approach outperforms two competitive baselines on three scientific claim verification datasets, with particularly strong performance in zero / few-shot domain adaptation experiments. Our code and data are available at https://github.com/dwadden/multivers.

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Literature-Augmented Clinical Outcome Prediction
Aakanksha Naik | Sravanthi Parasa | Sergey Feldman | Lucy Lu Wang | Tom Hope
Findings of the Association for Computational Linguistics: NAACL 2022

We present BEEP (Biomedical Evidence-Enhanced Predictions), a novel approach for clinical outcome prediction that retrieves patient-specific medical literature and incorporates it into predictive models. Based on each individual patient’s clinical notes, we train language models (LMs) to find relevant papers and fuse them with information from notes to predict outcomes such as in-hospital mortality. We develop methods to retrieve literature based on noisy, information-dense patient notes, and to augment existing outcome prediction models with retrieved papers in a manner that maximizes predictive accuracy. Our approach boosts predictive performance on three important clinical tasks in comparison to strong recent LM baselines, increasing F1 by up to 5 points and precision@Top-K by a large margin of over 25%.

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Proceedings of the Third Workshop on Scholarly Document Processing
Arman Cohan | Guy Feigenblat | Dayne Freitag | Tirthankar Ghosal | Drahomira Herrmannova | Petr Knoth | Kyle Lo | Philipp Mayr | Michal Shmueli-Scheuer | Anita de Waard | Lucy Lu Wang
Proceedings of the Third Workshop on Scholarly Document Processing

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Overview of the Third Workshop on Scholarly Document Processing
Arman Cohan | Guy Feigenblat | Dayne Freitag | Tirthankar Ghosal | Drahomira Herrmannova | Petr Knoth | Kyle Lo | Philipp Mayr | Michal Shmueli-Scheuer | Anita de Waard | Lucy Lu Wang
Proceedings of the Third Workshop on Scholarly Document Processing

With the ever-increasing pace of research and high volume of scholarly communication, scholars face a daunting task. Not only must they keep up with the growing literature in their own and related fields, scholars increasingly also need to rebut pseudo-science and disinformation. These needs have motivated an increasing focus on computational methods for enhancing search, summarization, and analysis of scholarly documents. However, the various strands of research on scholarly document processing remain fragmented. To reach out to the broader NLP and AI/ML community, pool distributed efforts in this area, and enable shared access to published research, we held the 3rd Workshop on Scholarly Document Processing (SDP) at COLING as a hybrid event (https://sdproc.org/2022/). The SDP workshop consisted of a research track, three invited talks and five Shared Tasks: 1) MSLR22: Multi-Document Summarization for Literature Reviews, 2) DAGPap22: Detecting automatically generated scientific papers, 3) SV-Ident 2022: Survey Variable Identification in Social Science Publications, 4) SKGG: Scholarly Knowledge Graph Generation, 5) MuP 2022: Multi Perspective Scientific Document Summarization. The program was geared towards NLP, information retrieval, and data mining for scholarly documents, with an emphasis on identifying and providing solutions to open challenges.

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Overview of MSLR2022: A Shared Task on Multi-document Summarization for Literature Reviews
Lucy Lu Wang | Jay DeYoung | Byron Wallace
Proceedings of the Third Workshop on Scholarly Document Processing

We provide an overview of the MSLR2022 shared task on multi-document summarization for literature reviews. The shared task was hosted at the Third Scholarly Document Processing (SDP) Workshop at COLING 2022. For this task, we provided data consisting of gold summaries extracted from review papers along with the groups of input abstracts that were synthesized into these summaries, split into two subtasks. In total, six teams participated, making 10 public submissions, 6 to the Cochrane subtask and 4 to the MSˆ2 subtask. The top scoring systems reported over 2 points ROUGE-L improvement on the Cochrane subtask, though performance improvements are not consistently reported across all automated evaluation metrics; qualitative examination of the results also suggests the inadequacy of current evaluation metrics for capturing factuality and consistency on this task. Significant work is needed to improve system performance, and more importantly, to develop better methods for automatically evaluating performance on this task.

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VILA: Improving Structured Content Extraction from Scientific PDFs Using Visual Layout Groups
Zejiang Shen | Kyle Lo | Lucy Lu Wang | Bailey Kuehl | Daniel S. Weld | Doug Downey
Transactions of the Association for Computational Linguistics, Volume 10

Accurately extracting structured content from PDFs is a critical first step for NLP over scientific papers. Recent work has improved extraction accuracy by incorporating elementary layout information, for example, each token’s 2D position on the page, into language model pretraining. We introduce new methods that explicitly model VIsual LAyout (VILA) groups, that is, text lines or text blocks, to further improve performance. In our I-VILA approach, we show that simply inserting special tokens denoting layout group boundaries into model inputs can lead to a 1.9% Macro F1 improvement in token classification. In the H-VILA approach, we show that hierarchical encoding of layout-groups can result in up to 47% inference time reduction with less than 0.8% Macro F1 loss. Unlike prior layout-aware approaches, our methods do not require expensive additional pretraining, only fine-tuning, which we show can reduce training cost by up to 95%. Experiments are conducted on a newly curated evaluation suite, S2-VLUE, that unifies existing automatically labeled datasets and includes a new dataset of manual annotations covering diverse papers from 19 scientific disciplines. Pre-trained weights, benchmark datasets, and source code are available at https://github.com/allenai/VILA.

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Generating Scientific Claims for Zero-Shot Scientific Fact Checking
Dustin Wright | David Wadden | Kyle Lo | Bailey Kuehl | Arman Cohan | Isabelle Augenstein | Lucy Lu Wang
Proceedings of the 60th Annual Meeting of the Association for Computational Linguistics (Volume 1: Long Papers)

Automated scientific fact checking is difficult due to the complexity of scientific language and a lack of significant amounts of training data, as annotation requires domain expertise. To address this challenge, we propose scientific claim generation, the task of generating one or more atomic and verifiable claims from scientific sentences, and demonstrate its usefulness in zero-shot fact checking for biomedical claims. We propose CLAIMGEN-BART, a new supervised method for generating claims supported by the literature, as well as KBIN, a novel method for generating claim negations. Additionally, we adapt an existing unsupervised entity-centric method of claim generation to biomedical claims, which we call CLAIMGEN-ENTITY. Experiments on zero-shot fact checking demonstrate that both CLAIMGEN-ENTITY and CLAIMGEN-BART, coupled with KBIN, achieve up to 90% performance of fully supervised models trained on manually annotated claims and evidence. A rigorous evaluation study demonstrates significant improvement in generated claim and negation quality over existing baselines

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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Proceedings of the Second Workshop on Scholarly Document Processing
Iz Beltagy | Arman Cohan | Guy Feigenblat | Dayne Freitag | Tirthankar Ghosal | Keith Hall | Drahomira Herrmannova | Petr Knoth | Kyle Lo | Philipp Mayr | Robert M. Patton | Michal Shmueli-Scheuer | Anita de Waard | Kuansan Wang | Lucy Lu Wang
Proceedings of the Second Workshop on Scholarly Document Processing

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Overview of the Second Workshop on Scholarly Document Processing
Iz Beltagy | Arman Cohan | Guy Feigenblat | Dayne Freitag | Tirthankar Ghosal | Keith Hall | Drahomira Herrmannova | Petr Knoth | Kyle Lo | Philipp Mayr | Robert Patton | Michal Shmueli-Scheuer | Anita de Waard | Kuansan Wang | Lucy Lu Wang
Proceedings of the Second Workshop on Scholarly Document Processing

With the ever-increasing pace of research and high volume of scholarly communication, scholars face a daunting task. Not only must they keep up with the growing literature in their own and related fields, scholars increasingly also need to rebut pseudo-science and disinformation. These needs have motivated an increasing focus on computational methods for enhancing search, summarization, and analysis of scholarly documents. However, the various strands of research on scholarly document processing remain fragmented. To reach out to the broader NLP and AI/ML community, pool distributed efforts in this area, and enable shared access to published research, we held the 2nd Workshop on Scholarly Document Processing (SDP) at NAACL 2021 as a virtual event (https://sdproc.org/2021/). The SDP workshop consisted of a research track, three invited talks, and three Shared Tasks (LongSumm 2021, SCIVER, and 3C). The program was geared towards the application of NLP, information retrieval, and data mining for scholarly documents, with an emphasis on identifying and providing solutions to open challenges.

2020

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S2ORC: The Semantic Scholar Open Research Corpus
Kyle Lo | Lucy Lu Wang | Mark Neumann | Rodney Kinney | Daniel Weld
Proceedings of the 58th Annual Meeting of the Association for Computational Linguistics

We introduce S2ORC, a large corpus of 81.1M English-language academic papers spanning many academic disciplines. The corpus consists of rich metadata, paper abstracts, resolved bibliographic references, as well as structured full text for 8.1M open access papers. Full text is annotated with automatically-detected inline mentions of citations, figures, and tables, each linked to their corresponding paper objects. In S2ORC, we aggregate papers from hundreds of academic publishers and digital archives into a unified source, and create the largest publicly-available collection of machine-readable academic text to date. We hope this resource will facilitate research and development of tools and tasks for text mining over academic text.

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SUPP.AI: finding evidence for supplement-drug interactions
Lucy Lu Wang | Oyvind Tafjord | Arman Cohan | Sarthak Jain | Sam Skjonsberg | Carissa Schoenick | Nick Botner | Waleed Ammar
Proceedings of the 58th Annual Meeting of the Association for Computational Linguistics: System Demonstrations

Dietary supplements are used by a large portion of the population, but information on their pharmacologic interactions is incomplete. To address this challenge, we present SUPP.AI, an application for browsing evidence of supplement-drug interactions (SDIs) extracted from the biomedical literature. We train a model to automatically extract supplement information and identify such interactions from the scientific literature. To address the lack of labeled data for SDI identification, we use labels of the closely related task of identifying drug-drug interactions (DDIs) for supervision. We fine-tune the contextualized word representations of the RoBERTa language model using labeled DDI data, and apply the fine-tuned model to identify supplement interactions. We extract 195k evidence sentences from 22M articles (P=0.82, R=0.58, F1=0.68) for 60k interactions. We create the SUPP.AI application for users to search evidence sentences extracted by our model. SUPP.AI is an attempt to close the information gap on dietary supplements by making up-to-date evidence on SDIs more discoverable for researchers, clinicians, and consumers. An informational video on how to use SUPP.AI is available at: https://youtu.be/dR0ucKdORwc

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CORD-19: The COVID-19 Open Research Dataset
Lucy Lu Wang | Kyle Lo | Yoganand Chandrasekhar | Russell Reas | Jiangjiang Yang | Doug Burdick | Darrin Eide | Kathryn Funk | Yannis Katsis | Rodney Michael Kinney | Yunyao Li | Ziyang Liu | William Merrill | Paul Mooney | Dewey A. Murdick | Devvret Rishi | Jerry Sheehan | Zhihong Shen | Brandon Stilson | Alex D. Wade | Kuansan Wang | Nancy Xin Ru Wang | Christopher Wilhelm | Boya Xie | Douglas M. Raymond | Daniel S. Weld | Oren Etzioni | Sebastian Kohlmeier
Proceedings of the 1st Workshop on NLP for COVID-19 at ACL 2020

The COVID-19 Open Research Dataset (CORD-19) is a growing resource of scientific papers on COVID-19 and related historical coronavirus research. CORD-19 is designed to facilitate the development of text mining and information retrieval systems over its rich collection of metadata and structured full text papers. Since its release, CORD-19 has been downloaded over 200K times and has served as the basis of many COVID-19 text mining and discovery systems. In this article, we describe the mechanics of dataset construction, highlighting challenges and key design decisions, provide an overview of how CORD-19 has been used, and describe several shared tasks built around the dataset. We hope this resource will continue to bring together the computing community, biomedical experts, and policy makers in the search for effective treatments and management policies for COVID-19.

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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.

2018

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Ontology alignment in the biomedical domain using entity definitions and context
Lucy Lu Wang | Chandra Bhagavatula | Mark Neumann | Kyle Lo | Chris Wilhelm | Waleed Ammar
Proceedings of the BioNLP 2018 workshop

Ontology alignment is the task of identifying semantically equivalent entities from two given ontologies. Different ontologies have different representations of the same entity, resulting in a need to de-duplicate entities when merging ontologies. We propose a method for enriching entities in an ontology with external definition and context information, and use this additional information for ontology alignment. We develop a neural architecture capable of encoding the additional information when available, and show that the addition of external data results in an F1-score of 0.69 on the Ontology Alignment Evaluation Initiative (OAEI) largebio SNOMED-NCI subtask, comparable with the entity-level matchers in a SOTA system.

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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.