Fan Bai

Fan Bai, Alan Ritter, Peter Madrid et al.

In this paper we present SynKB, an open-source, automatically extracted knowledge base of chemical synthesis protocols. Similar to proprietary chemistry databases such as Reaxsys, SynKB allows chemists to retrieve structured knowledge about synthetic procedures. By taking advantage of recent advances in natural language processing for procedural texts, SynKB supports more flexible queries about reaction conditions, and thus has the potential to help chemists search the literature for conditions used in relevant reactions as they design new synthetic routes. Using customized Transformer models to automatically extract information from 6 million synthesis procedures described in U.S. and EU patents, we show that for many queries, SynKB has higher recall than Reaxsys, while maintaining high precision. We plan to make SynKB available as an open-source tool; in contrast, proprietary chemistry databases require costly subscriptions.

Nghia T. Le, Fan Bai, Alan Ritter

Anaphora resolution is an important task for information extraction across a range of languages, text genres, and domains, motivating the need for methods that do not require large annotated datasets. In-context learning has emerged as a promising approach, yet there are a number of challenges in applying in-context learning to resolve anaphora. For example, encoding a single in-context demonstration that consists of: an anaphor, a paragraph-length context, and a list of corresponding antecedents, requires conditioning a language model on a long sequence of tokens, limiting the number of demonstrations per prompt. In this paper, we present MICE (Mixtures of In-Context Experts), which we demonstrate is effective for few-shot anaphora resolution in scientific protocols (Tamari et al., 2021). Given only a handful of training examples, MICE combines the predictions of hundreds of in-context experts, yielding a 30% increase in F1 score over a competitive prompt retrieval baseline. Furthermore, we show MICE can be used to train compact student models without sacrificing performance. As far as we are aware, this is the first work to present experimental results demonstrating the effectiveness of in-context learning on the task of few-shot anaphora resolution in scientific protocols.

Fan Bai, Junmo Kang, Gabriel Stanovsky et al.

In this paper, we explore the question of whether large language models can support cost-efficient information extraction from tables. We introduce schema-driven information extraction, a new task that transforms tabular data into structured records following a human-authored schema. To assess various LLM's capabilities on this task, we present a benchmark comprised of tables from four diverse domains: machine learning papers, chemistry literature, material science journals, and webpages. We use this collection of annotated tables to evaluate the ability of open-source and API-based language models to extract information from tables covering diverse domains and data formats. Our experiments demonstrate that surprisingly competitive performance can be achieved without requiring task-specific pipelines or labels, achieving F1 scores ranging from 74.2 to 96.1, while maintaining cost efficiency. Moreover, through detailed ablation studies and analyses, we investigate the factors contributing to model success and validate the practicality of distilling compact models to reduce API reliance.

Fan Bai, Keith Harrigian, Joel Stremmel et al.

Clinical Question Answering (QA) systems enable doctors to quickly access patient information from electronic health records (EHRs). However, training these systems requires significant annotated data, which is limited due to the expertise needed and the privacy concerns associated with clinical data. This paper explores generating Clinical QA data using large language models (LLMs) in a zero-shot setting. We find that naive prompting often results in easy questions that do not reflect the complexity of clinical scenarios. To address this, we propose two prompting strategies: 1) instructing the model to generate questions that do not overlap with the input context, and 2) summarizing the input record using a predefined schema to scaffold question generation. Experiments on two Clinical QA datasets demonstrate that our method generates more challenging questions, significantly improving fine-tuning performance over baselines. We compare synthetic and gold data and find a gap between their training efficacy resulting from the quality of synthetically generated answers.