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GrapAL: Connecting the Dots in Scientific Literature
Christine Betts, Joanna Power, Waleed AmmarACL • 2019 We introduce GrapAL (Graph database of Academic Literature), a versatile tool for exploring and investigating a knowledge base of scientific literature, that was semi-automatically constructed using NLP methods. GrapAL satisfies a variety of use cases and…ScispaCy: Fast and Robust Models for Biomedical Natural Language Processing
Mark Neumann, Daniel King, Iz Beltagy, Waleed AmmarACL • BioNLP Workshop • 2019 Despite recent advances in natural language processing, many statistical models for processing text perform extremely poorly under domain shift. Processing biomedical and clinical text is a critically important application area of natural language processing…CEDR: Contextualized Embeddings for Document Ranking
Sean MacAvaney, Andrew Yates, Arman Cohan, Nazli GoharianSIGIR • 2019 Although considerable attention has been given to neural ranking architectures recently, far less attention has been paid to the term representations that are used as input to these models. In this work, we investigate how two pretrained contextualized…Ontology-Aware Clinical Abstractive Summarization
Sean MacAvaney, Sajad Sotudeh, Arman Cohan, Nazli Goharian, Ish Talati, Ross W. FiliceSIGIR • 2019 Automatically generating accurate summaries from clinical reports could save a clinician's time, improve summary coverage, and reduce errors. We propose a sequence-to-sequence abstractive summarization model augmented with domain-specific ontological…Quantifying Sex Bias in Clinical Studies at Scale With Automated Data Extraction
Sergey Feldman, Waleed Ammar, Kyle Lo, Elly Trepman, Madeleine van Zuylen, Oren EtzioniJAMA • 2019 Importance: Analyses of female representation in clinical studies have been limited in scope and scale. Objective: To perform a large-scale analysis of global enrollment sex bias in clinical studies. Design, Setting, and Participants: In this cross…Combining Distant and Direct Supervision for Neural Relation Extraction
Iz Beltagy, Kyle Lo, Waleed AmmarNAACL • 2019 In relation extraction with distant supervision, noisy labels make it difficult to train quality models. Previous neural models addressed this problem using an attention mechanism that attends to sentences that are likely to express the relations. We improve…Structural Scaffolds for Citation Intent Classification in Scientific Publications
Arman Cohan, Waleed Ammar, Madeleine van Zuylen, Field CadyNAACL • 2019 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 a multitask…Citation Count Analysis for Papers with Preprints
Sergey Feldman, Kyle Lo, Waleed AmmarArXiv • 2018 We explore the degree to which papers prepublished on arXiv garner more citations, in an attempt to paint a sharper picture of fairness issues related to prepublishing. A paper’s citation count is estimated using a negative-binomial generalized linear model…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 E. Peters, et al.NAACL-HLT • 2018 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…A Dataset of Peer Reviews (PeerRead): Collection, Insights and NLP Applications
Dongyeop Kang, Waleed Ammar, Bhavana Dalvi Mishra, Madeleine van Zuylen, Sebastian Kohlmeier, Eduard Hovy, Roy SchwartzNAACL-HLT • 2018 Peer reviewing is a central component in the scientific publishing process. We present the first public dataset of scientific peer reviews available for research pur- poses (PeerRead v1), providing an opportunity to study this important artifact. The dataset…