Lucy Lu Wang

David Wadden, Kyle Lo, Bailey Kuehl et al. · allen-ai, uw

While research on scientific claim verification has led to the development of powerful systems that appear to approach human performance, these approaches have yet to be tested in a realistic setting against large corpora of scientific literature. Moving to this open-domain evaluation setting, however, poses unique challenges; in particular, it is infeasible to exhaustively annotate all evidence documents. In this work, we present SciFact-Open, a new test collection designed to evaluate the performance of scientific claim verification systems on a corpus of 500K research abstracts. Drawing upon pooling techniques from information retrieval, we collect evidence for scientific claims by pooling and annotating the top predictions of four state-of-the-art scientific claim verification models. We find that systems developed on smaller corpora struggle to generalize to SciFact-Open, exhibiting performance drops of at least 15 F1. In addition, analysis of the evidence in SciFact-Open reveals interesting phenomena likely to appear when claim verification systems are deployed in practice, e.g., cases where the evidence supports only a special case of the claim. Our dataset is available at https://github.com/dwadden/scifact-open.

Rodney Kinney, Chloe Anastasiades, Russell Authur et al. · allen-ai, microsoft-research

The volume of scientific output is creating an urgent need for automated tools to help scientists keep up with developments in their field. Semantic Scholar (S2) is an open data platform and website aimed at accelerating science by helping scholars discover and understand scientific literature. We combine public and proprietary data sources using state-of-the-art techniques for scholarly PDF content extraction and automatic knowledge graph construction to build the Semantic Scholar Academic Graph, the largest open scientific literature graph to-date, with 200M+ papers, 80M+ authors, 550M+ paper-authorship edges, and 2.4B+ citation edges. The graph includes advanced semantic features such as structurally parsed text, natural language summaries, and vector embeddings. In this paper, we describe the components of the S2 data processing pipeline and the associated APIs offered by the platform. We will update this living document to reflect changes as we add new data offerings and improve existing services.

Kyle Lo, Joseph Chee Chang, Andrew Head et al. · allen-ai, cmu

Scholarly publications are key to the transfer of knowledge from scholars to others. However, research papers are information-dense, and as the volume of the scientific literature grows, the need for new technology to support the reading process grows. In contrast to the process of finding papers, which has been transformed by Internet technology, the experience of reading research papers has changed little in decades. The PDF format for sharing research papers is widely used due to its portability, but it has significant downsides including: static content, poor accessibility for low-vision readers, and difficulty reading on mobile devices. This paper explores the question "Can recent advances in AI and HCI power intelligent, interactive, and accessible reading interfaces -- even for legacy PDFs?" We describe the Semantic Reader Project, a collaborative effort across multiple institutions to explore automatic creation of dynamic reading interfaces for research papers. Through this project, we've developed ten research prototype interfaces and conducted usability studies with more than 300 participants and real-world users showing improved reading experiences for scholars. We've also released a production reading interface for research papers that will incorporate the best features as they mature. We structure this paper around challenges scholars and the public face when reading research papers -- Discovery, Efficiency, Comprehension, Synthesis, and Accessibility -- and present an overview of our progress and remaining open challenges.

Dustin Wright, David Wadden, Kyle Lo et al. · allen-ai, uw

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

Hancheng Cao, Jesse Dodge, Kyle Lo et al. · allen-ai, cmu

In recent years, funding agencies and journals increasingly advocate for open science practices (e.g. data and method sharing) to improve the transparency, access, and reproducibility of science. However, quantifying these practices at scale has proven difficult. In this work, we leverage a large-scale dataset of 1.1M papers from arXiv that are representative of the fields of physics, math, and computer science to analyze the adoption of data and method link-sharing practices over time and their impact on article reception. To identify links to data and methods, we train a neural text classification model to automatically classify URL types based on contextual mentions in papers. We find evidence that the practice of link-sharing to methods and data is spreading as more papers include such URLs over time. Reproducibility efforts may also be spreading because the same links are being increasingly reused across papers (especially in computer science); and these links are increasingly concentrated within fewer web domains (e.g. Github) over time. Lastly, articles that share data and method links receive increased recognition in terms of citation count, with a stronger effect when the shared links are active (rather than defunct). Together, these findings demonstrate the increased spread and perceived value of data and method sharing practices in open science.

Bingbing Wen, Jihan Yao, Shangbin Feng et al. · allen-ai, uw

Abstention, the refusal of large language models (LLMs) to provide an answer, is increasingly recognized for its potential to mitigate hallucinations and enhance safety in LLM systems. In this survey, we introduce a framework to examine abstention from three perspectives: the query, the model, and human values. We organize the literature on abstention methods, benchmarks, and evaluation metrics using this framework, and discuss merits and limitations of prior work. We further identify and motivate areas for future research, such as whether abstention can be achieved as a meta-capability that transcends specific tasks or domains, and opportunities to optimize abstention abilities in specific contexts. In doing so, we aim to broaden the scope and impact of abstention methodologies in AI systems.

John Giorgi, Luca Soldaini, Bo Wang et al. · allen-ai, utoronto

Multi-document summarization (MDS) assumes a set of topic-related documents are provided as input. In practice, this document set is not always available; it would need to be retrieved given an information need, i.e. a question or topic statement, a setting we dub "open-domain" MDS. We study this more challenging setting by formalizing the task and bootstrapping it using existing datasets, retrievers and summarizers. Via extensive automatic and human evaluation, we determine: (1) state-of-the-art summarizers suffer large reductions in performance when applied to open-domain MDS, (2) additional training in the open-domain setting can reduce this sensitivity to imperfect retrieval, and (3) summarizers are insensitive to the retrieval of duplicate documents and the order of retrieved documents, but highly sensitive to other errors, like the retrieval of irrelevant documents. Based on our results, we provide practical guidelines to enable future work on open-domain MDS, e.g. how to choose the number of retrieved documents to summarize. Our results suggest that new retrieval and summarization methods and annotated resources for training and evaluation are necessary for further progress in the open-domain setting.

Yue Guo, Joseph Chee Chang, Maria Antoniak et al. · allen-ai, uw

Scientific jargon can impede researchers when they read materials from other domains. Current methods of jargon identification mainly use corpus-level familiarity indicators (e.g., Simple Wikipedia represents plain language). However, researchers' familiarity of a term can vary greatly based on their own background. We collect a dataset of over 10K term familiarity annotations from 11 computer science researchers for terms drawn from 100 paper abstracts. Analysis of this data reveals that jargon familiarity and information needs vary widely across annotators, even within the same sub-domain (e.g., NLP). We investigate features representing individual, sub-domain, and domain knowledge to predict individual jargon familiarity. We compare supervised and prompt-based approaches, finding that prompt-based methods including personal publications yields the highest accuracy, though zero-shot prompting provides a strong baseline. This research offers insight into features and methods to integrate personal data into scientific jargon identification.

Donghoon Shin, Bingcan Guo, Jaewook Lee et al.

Although HCI research papers offer valuable design insights, designers often struggle to apply them in design workflows due to difficulties in finding relevant literature, understanding technical jargon, the lack of contextualization, and limited actionability. To address these challenges, we present ReFinE, a Figma plugin that supports real-time design iteration by surfacing contextualized insights from research papers. ReFinE identifies and synthesizes design implications from HCI literature relevant to the mockup's design context, and tailors this research evidence to a specific design mockup by providing actionable visual guidance on how to update the mockup. To assess the system's effectiveness, we conducted a technical evaluation and a user study. Results show that ReFinE effectively synthesizes and contextualizes design implications, reducing cognitive load and improving designers' ability to integrate research evidence into UI mockups. This work contributes to bridging the gap between research and design practice by presenting a tool for embedding scholarly insights into the UI design process.

Anthony Hevia, Sanjana Chintalapati, Veronica Ka Wai Lai et al.

We present ROBOTO2, an open-source, web-based platform for large language model (LLM)-assisted risk of bias (ROB) assessment of clinical trials. ROBOTO2 streamlines the traditionally labor-intensive ROB v2 (ROB2) annotation process via an interactive interface that combines PDF parsing, retrieval-augmented LLM prompting, and human-in-the-loop review. Users can upload clinical trial reports, receive preliminary answers and supporting evidence for ROB2 signaling questions, and provide real-time feedback or corrections to system suggestions. ROBOTO2 is publicly available at https://roboto2.vercel.app/, with code and data released to foster reproducibility and adoption. We construct and release a dataset of 521 pediatric clinical trial reports (8954 signaling questions with 1202 evidence passages), annotated using both manually and LLM-assisted methods, serving as a benchmark and enabling future research. Using this dataset, we benchmark ROB2 performance for 4 LLMs and provide an analysis into current model capabilities and ongoing challenges in automating this critical aspect of systematic review.

Zongwan Cao, Bingbing Wen, Lucy Lu Wang

Real-world visual question answering (VQA) is often context-dependent: an image-question pair may be under-specified, such that the correct answer depends on external information that is not observable in the image. In such cases, directly answering can lead to confident but incorrect predictions. We propose CoA(Clarify-or-Answer), an ask-or-answer agent that separately models the decision to ask or answer, and what to ask if needed. CoA first determines whether clarification is necessary; if so, it asks a single focused question and then incorporates the response to produce the final answer. We introduce CONTEXTCLARIFY with a set of ambiguous VQA questions and the contrast set that is non-ambiguous. We further introduce GRPO-CR (Clarification Reasoning), a reinforcement learning approach that optimizes clarification question generation with multiple reward signals encouraging well-formed, focused, non-trivial questions that resolve ambiguity. Across three VLLMs and three datasets, CoA achieves consistent improvements at both the module and system levels, improving end-to-end VQA accuracy by an average of +15.3 points (83%) over prompting-based baselines

John Giorgi, Amanpreet Singh, Doug Downey et al. · allen-ai, uw

Topic pages aggregate useful information about an entity or concept into a single succinct and accessible article. Automated creation of topic pages would enable their rapid curation as information resources, providing an alternative to traditional web search. While most prior work has focused on generating topic pages about biographical entities, in this work, we develop a completely automated process to generate high-quality topic pages for scientific entities, with a focus on biomedical concepts. We release TOPICAL, a web app and associated open-source code, comprising a model pipeline combining retrieval, clustering, and prompting, that makes it easy for anyone to generate topic pages for a wide variety of biomedical entities on demand. In a human evaluation of 150 diverse topic pages generated using TOPICAL, we find that the vast majority were considered relevant, accurate, and coherent, with correct supporting citations. We make all code publicly available and host a free-to-use web app at: https://s2-topical.apps.allenai.org

Yue Guo, Tal August, Gondy Leroy et al.

While there has been significant development of models for Plain Language Summarization (PLS), evaluation remains a challenge. PLS lacks a dedicated assessment metric, and the suitability of text generation evaluation metrics is unclear due to the unique transformations involved (e.g., adding background explanations, removing jargon). To address these questions, our study introduces a granular meta-evaluation testbed, APPLS, designed to evaluate metrics for PLS. We identify four PLS criteria from previous work -- informativeness, simplification, coherence, and faithfulness -- and define a set of perturbations corresponding to these criteria that sensitive metrics should be able to detect. We apply these perturbations to extractive hypotheses for two PLS datasets to form our testbed. Using APPLS, we assess performance of 14 metrics, including automated scores, lexical features, and LLM prompt-based evaluations. Our analysis reveals that while some current metrics show sensitivity to specific criteria, no single method captures all four criteria simultaneously. We therefore recommend a suite of automated metrics be used to capture PLS quality along all relevant criteria. This work contributes the first meta-evaluation testbed for PLS and a comprehensive evaluation of existing metrics. APPLS and our evaluation code is available at https://github.com/LinguisticAnomalies/APPLS.

David Wadden, Kyle Lo, Lucy Lu Wang et al.

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.

Zejiang Shen, Kyle Lo, Lucy Lu Wang et al.

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, e.g., each token's 2D position on the page, into language model pretraining. We introduce new methods that explicitly model VIsual LAyout (VILA) groups, i.e., 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.

Jay DeYoung, Iz Beltagy, Madeleine van Zuylen et al.

To assess the effectiveness of any medical intervention, researchers must conduct a time-intensive and highly manual literature review. NLP systems can help to automate or assist in parts of this expensive process. In support of this goal, we release MS^2 (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. 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

Sanjay Subramanian, Lucy Lu Wang, Sachin Mehta et al.

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.

David Wadden, Shanchuan Lin, Kyle Lo et al.

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.

Maria Antoniak, Aakanksha Naik, Carla S. Alvarado et al. · allen-ai, uw

Ethical frameworks for the use of natural language processing (NLP) are urgently needed to shape how large language models (LLMs) and similar tools are used for healthcare applications. Healthcare faces existing challenges including the balance of power in clinician-patient relationships, systemic health disparities, historical injustices, and economic constraints. Drawing directly from the voices of those most affected, and focusing on a case study of a specific healthcare setting, we propose a set of guiding principles for the use of NLP in maternal healthcare. We led an interactive session centered on an LLM-based chatbot demonstration during a full-day workshop with 39 participants, and additionally surveyed 30 healthcare workers and 30 birthing people about their values, needs, and perceptions of NLP tools in the context of maternal health. We conducted quantitative and qualitative analyses of the survey results and interactive discussions to consolidate our findings into a set of guiding principles. We propose nine principles for ethical use of NLP for maternal healthcare, grouped into three themes: (i) recognizing contextual significance (ii) holistic measurements, and (iii) who/what is valued. For each principle, we describe its underlying rationale and provide practical advice. This set of principles can provide a methodological pattern for other researchers and serve as a resource to practitioners working on maternal health and other healthcare fields to emphasize the importance of technical nuance, historical context, and inclusive design when developing NLP technologies for clinical use.

Donghoon Shin, Lucy Lu Wang, Gary Hsieh · allen-ai, uw

Communicating design implications is common within the HCI community when publishing academic papers, yet these papers are rarely read and used by designers. One solution is to use design cards as a form of translational resource that communicates valuable insights from papers in a more digestible and accessible format to assist in design processes. However, creating design cards can be time-consuming, and authors may lack the resources/know-how to produce cards. Through an iterative design process, we built a system that helps create design cards from academic papers using an LLM and text-to-image model. Our evaluation with designers (N=21) and authors of selected papers (N=12) revealed that designers perceived the design implications from our design cards as more inspiring and generative, compared to reading original paper texts, and the authors viewed our system as an effective way of communicating their design implications. We also propose future enhancements for AI-generated design cards.

Bingbing Wen, Bill Howe, Lucy Lu Wang · allen-ai, uw

The correct model response in the face of uncertainty is to abstain from answering a question so as not to mislead the user. In this work, we study the ability of LLMs to abstain from answering context-dependent science questions when provided insufficient or incorrect context. We probe model sensitivity in several settings: removing gold context, replacing gold context with irrelevant context, and providing additional context beyond what is given. In experiments on four QA datasets with six LLMs, we show that performance varies greatly across models, across the type of context provided, and also by question type; in particular, many LLMs seem unable to abstain from answering boolean questions using standard QA prompts. Our analysis also highlights the unexpected impact of abstention performance on QA task accuracy. Counter-intuitively, in some settings, replacing gold context with irrelevant context or adding irrelevant context to gold context can improve abstention performance in a way that results in improvements in task performance. Our results imply that changes are needed in QA dataset design and evaluation to more effectively assess the correctness and downstream impacts of model abstention.

Jihan Yao, Wenxuan Ding, Shangbin Feng et al. · allen-ai, uw

In the absence of abundant reliable annotations for challenging tasks and contexts, how can we expand the frontier of LLM capabilities with potentially wrong answers? We focus on two research questions: (1) Can LLMs generate reliable preferences among wrong options? And if so, (2) Would alignment with such wrong-over-wrong preferences be helpful? We employ methods based on self-consistency, token probabilities, and LLM-as-a-judge to elicit wrong-over-wrong preferences, and fine-tune language models with preference optimization approaches using these synthesized preferences. Extensive experiments with seven LLMs and eight datasets demonstrate that (1) LLMs do have preliminary capability in distinguishing various shades of wrong, achieving up to 20.9% higher performance than random guess; (2) Alignment with wrong-over-wrong preferences helps LLMs to produce less wrong and sometimes even outright correct answers, while overall improving model calibration.

Jun Hou, Lucy Lu Wang · allen-ai, uw

Explainable AI (XAI) techniques are necessary to help clinicians make sense of AI predictions and integrate predictions into their decision-making workflow. In this work, we conduct a survey study to understand clinician preference among different XAI techniques when they are used to interpret model predictions over text-based EHR data. We implement four XAI techniques (LIME, Attention-based span highlights, exemplar patient retrieval, and free-text rationales generated by LLMs) on an outcome prediction model that uses ICU admission notes to predict a patient's likelihood of experiencing in-hospital mortality. Using these XAI implementations, we design and conduct a survey study of 32 practicing clinicians, collecting their feedback and preferences on the four techniques. We synthesize our findings into a set of recommendations describing when each of the XAI techniques may be more appropriate, their potential limitations, as well as recommendations for improvement.

Varich Boonsanong, Vidhisha Balachandran, Xiaochuang Han et al. · allen-ai, cmu

With the widespread consumption of AI-generated content, there has been an increased focus on developing automated tools to verify the factual accuracy of such content. However, prior research and tools developed for fact verification treat it as a binary classification or a linear regression problem. Although this is a useful mechanism as part of automatic guardrails in systems, we argue that such tools lack transparency in the prediction reasoning and diversity in source evidence to provide a trustworthy user experience. We develop Facts&Evidence - an interactive and transparent tool for user-driven verification of complex text. The tool facilitates the intricate decision-making involved in fact-verification, presenting its users a breakdown of complex input texts to visualize the credibility of individual claims along with an explanation of model decisions and attribution to multiple, diverse evidence sources. Facts&Evidence aims to empower consumers of machine-generated text and give them agency to understand, verify, selectively trust and use such text.

Yi-Li Hsu, Katelyn X. Mei, Lucy Lu Wang

Medical multi-document summarization (MDS) is a complex task that requires effectively managing cross-document relationships. This paper investigates whether incorporating hierarchical structures in the inputs of MDS can improve a model's ability to organize and contextualize information across documents compared to traditional flat summarization methods. We investigate two ways of incorporating hierarchical organization across three large language models (LLMs), and conduct comprehensive evaluations of the resulting summaries using automated metrics, model-based metrics, and domain expert evaluation of preference, understandability, clarity, complexity, relevance, coverage, factuality, and coherence. Our results show that human experts prefer model-generated summaries over human-written summaries. Hierarchical approaches generally preserve factuality, coverage, and coherence of information, while also increasing human preference for summaries. Additionally, we examine whether simulated judgments from GPT-4 align with human judgments, finding higher agreement along more objective evaluation facets. Our findings demonstrate that hierarchical structures can improve the clarity of medical summaries generated by models while maintaining content coverage, providing a practical way to improve human preference for generated summaries.

Lucy Lu Wang, Yulia Otmakhova, Jay DeYoung et al.

Evaluating multi-document summarization (MDS) quality is difficult. This is especially true in the case of MDS for biomedical literature reviews, where models must synthesize contradicting evidence reported across different documents. Prior work has shown that rather than performing the task, models may exploit shortcuts that are difficult to detect using standard n-gram similarity metrics such as ROUGE. Better automated evaluation metrics are needed, but few resources exist to assess metrics when they are proposed. Therefore, we introduce a dataset of human-assessed summary quality facets and pairwise preferences to encourage and support the development of better automated evaluation methods for literature review MDS. We take advantage of community submissions to the Multi-document Summarization for Literature Review (MSLR) shared task to compile a diverse and representative sample of generated summaries. We analyze how automated summarization evaluation metrics correlate with lexical features of generated summaries, to other automated metrics including several we propose in this work, and to aspects of human-assessed summary quality. We find that not only do automated metrics fail to capture aspects of quality as assessed by humans, in many cases the system rankings produced by these metrics are anti-correlated with rankings according to human annotators.

Tal August, Lucy Lu Wang, Jonathan Bragg et al.

When seeking information not covered in patient-friendly documents, like medical pamphlets, healthcare consumers may turn to the research literature. Reading medical papers, however, can be a challenging experience. To improve access to medical papers, we introduce a novel interactive interface-Paper Plain-with four features powered by natural language processing: definitions of unfamiliar terms, in-situ plain language section summaries, a collection of key questions that guide readers to answering passages, and plain language summaries of the answering passages. We evaluate Paper Plain, finding that participants who use Paper Plain have an easier time reading and understanding research papers without a loss in paper comprehension compared to those who use a typical PDF reader. Altogether, the study results suggest that guiding readers to relevant passages and providing plain language summaries, or "gists," alongside the original paper content can make reading medical papers easier and give readers more confidence to approach these papers.

Aakanksha Naik, Sravanthi Parasa, Sergey Feldman et al.

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%.

Lucy Lu Wang, Isabel Cachola, Jonathan Bragg et al.

The majority of scientific papers are distributed in PDF, which pose challenges for accessibility, especially for blind and low vision (BLV) readers. We characterize the scope of this problem by assessing the accessibility of 11,397 PDFs published 2010--2019 sampled across various fields of study, finding that only 2.4% of these PDFs satisfy all of our defined accessibility criteria. We introduce the SciA11y system to offset some of the issues around inaccessibility. SciA11y incorporates several machine learning models to extract the content of scientific PDFs and render this content as accessible HTML, with added novel navigational features to support screen reader users. An intrinsic evaluation of extraction quality indicates that the majority of HTML renders (87%) produced by our system have no or only some readability issues. We perform a qualitative user study to understand the needs of BLV researchers when reading papers, and to assess whether the SciA11y system could address these needs. We summarize our user study findings into a set of five design recommendations for accessible scientific reader systems. User response to SciA11y was positive, with all users saying they would be likely to use the system in the future, and some stating that the system, if available, would become their primary workflow. We successfully produce HTML renders for over 12M papers, of which an open access subset of 1.5M are available for browsing at https://scia11y.org/

Kirk Roberts, Tasmeer Alam, Steven Bedrick et al.

We present an overview of the TREC-COVID Challenge, an information retrieval (IR) shared task to evaluate search on scientific literature related to COVID-19. The goals of TREC-COVID include the construction of a pandemic search test collection and the evaluation of IR methods for COVID-19. The challenge was conducted over five rounds from April to July, 2020, with participation from 92 unique teams and 556 individual submissions. A total of 50 topics (sets of related queries) were used in the evaluation, starting at 30 topics for Round 1 and adding 5 new topics per round to target emerging topics at that state of the still-emerging pandemic. This paper provides a comprehensive overview of the structure and results of TREC-COVID. Specifically, the paper provides details on the background, task structure, topic structure, corpus, participation, pooling, assessment, judgments, results, top-performing systems, lessons learned, and benchmark datasets.

Kelly Mack, Emma McDonnell, Dhruv Jain et al.

Accessibility research has grown substantially in the past few decades, yet there has been no literature review of the field. To understand current and historical trends, we created and analyzed a dataset of accessibility papers appearing at CHI and ASSETS since ASSETS' founding in 1994. We qualitatively coded areas of focus and methodological decisions for the past 10 years (2010-2019, N=506 papers), and analyzed paper counts and keywords over the full 26 years (N=836 papers). Our findings highlight areas that have received disproportionate attention and those that are underserved--for example, over 43% of papers in the past 10 years are on accessibility for blind and low vision people. We also capture common study characteristics, such as the roles of disabled and nondisabled participants as well as sample sizes (e.g., a median of 13 for participant groups with disabilities and older adults). We close by critically reflecting on gaps in the literature and offering guidance for future work in the field.

Ellen Voorhees, Tasmeer Alam, Steven Bedrick et al.

TREC-COVID is a community evaluation designed to build a test collection that captures the information needs of biomedical researchers using the scientific literature during a pandemic. One of the key characteristics of pandemic search is the accelerated rate of change: the topics of interest evolve as the pandemic progresses and the scientific literature in the area explodes. The COVID-19 pandemic provides an opportunity to capture this progression as it happens. TREC-COVID, in creating a test collection around COVID-19 literature, is building infrastructure to support new research and technologies in pandemic search.

Lucy Lu Wang, Kyle Lo, Yoganand Chandrasekhar et al.

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.

Kyle Lo, Lucy Lu Wang, Mark Neumann et al.

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.

Lucy Lu Wang, Oyvind Tafjord, Arman Cohan et al.

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.

Thomas Dean, Maurice Chiang, Marcus Gomez et al.

This document provides an overview of the material covered in a course taught at Stanford in the spring quarter of 2018. The course draws upon insight from cognitive and systems neuroscience to implement hybrid connectionist and symbolic reasoning systems that leverage and extend the state of the art in machine learning by integrating human and machine intelligence. As a concrete example we focus on digital assistants that learn from continuous dialog with an expert software engineer while providing initial value as powerful analytical, computational and mathematical savants. Over time these savants learn cognitive strategies (domain-relevant problem solving skills) and develop intuitions (heuristics and the experience necessary for applying them) by learning from their expert associates. By doing so these savants elevate their innate analytical skills allowing them to partner on an equal footing as versatile collaborators - effectively serving as cognitive extensions and digital prostheses, thereby amplifying and emulating their human partner's conceptually-flexible thinking patterns and enabling improved access to and control over powerful computing resources.

Lucy Lu Wang, Chandra Bhagavatula, Mark Neumann et al.

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.

Waleed Ammar, Dirk Groeneveld, Chandra Bhagavatula et al.

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