Jimeng Sun


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Text Augmented Open Knowledge Graph Completion via Pre-Trained Language Models
Pengcheng Jiang | Shivam Agarwal | Bowen Jin | Xuan Wang | Jimeng Sun | Jiawei Han
Findings of the Association for Computational Linguistics: ACL 2023

The mission of open knowledge graph (KG) completion is to draw new findings from known facts. Existing works that augment KG completion require either (1) factual triples to enlarge the graph reasoning space or (2) manually designed prompts to extract knowledge from a pre-trained language model (PLM), exhibiting limited performance and requiring expensive efforts from experts. To this end, we propose TagReal that automatically generates quality query prompts and retrieves support information from large text corpora to probe knowledge from PLM for KG completion. The results show that TagReal achieves state-of-the-art performance on two benchmark datasets. We find that TagReal has superb performance even with limited training data, outperforming existing embedding-based, graph-based, and PLM-based methods.

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AutoTrial: Prompting Language Models for Clinical Trial Design
Zifeng Wang | Cao Xiao | Jimeng Sun
Proceedings of the 2023 Conference on Empirical Methods in Natural Language Processing

Clinical trials are critical for drug development. Constructing the appropriate eligibility criteria (i.e., the inclusion/exclusion criteria for patient recruitment) is essential for the trial’s success. Proper design of clinical trial protocols should consider similar precedent trials and their eligibility criteria to ensure sufficient patient coverage. In this paper, we present a method named AutoTrial to aid the design of clinical eligibility criteria using language models. It allows (1) controllable generation under instructions via a hybrid of discrete and neural prompting, (2) scalable knowledge incorporation via in-context learning, and (3) explicit reasoning chains to provide rationales for understanding the outputs. Experiments on over 70K clinical trials verify that AutoTrial generates high-quality criteria texts that are fluent and coherent and with high accuracy in capturing the relevant clinical concepts to the target trial. It is noteworthy that our method, with a much smaller parameter size, gains around 60% winning rate against the GPT-3.5 baselines via human evaluations.

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DRGCoder: Explainable Clinical Coding for the Early Prediction of Diagnostic-Related Groups
Daniel Hajialigol | Derek Kaknes | Tanner Barbour | Daphne Yao | Chris North | Jimeng Sun | David Liem | Xuan Wang
Proceedings of the 2023 Conference on Empirical Methods in Natural Language Processing: System Demonstrations

Medical claim coding is the process of transforming medical records, usually presented as free texts written by clinicians, or discharge summaries, into structured codes in a classification system such as ICD-10 (International Classification of Diseases, Tenth Revision) or DRG (Diagnosis-Related Group) codes. This process is essential for medical billing and transitional care; however, manual coding is time-consuming, error-prone, and expensive. To solve these issues, we propose DRGCoder, an explainability-enhanced clinical claim coding system for the early prediction of medical severity DRGs (MS-DRGs), a classification system that categorizes patients’ hospital stays into various DRG groups based on the severity of illness and mortality risk. The DRGCoder framework introduces a novel multi-task Transformer model for MS-DRG prediction, modeling both the DRG labels of the discharge summaries and the important, or salient words within he discharge summaries. We allow users to inspect DRGCoder’s reasoning by visualizing the weights for each word of the input. Additionally, DRGCoder allows users to identify diseases within discharge summaries and compare across multiple discharge summaries. Our demo is available at https://huggingface.co/spaces/danielhajialigol/DRGCoder. A video demonstrating the demo can be found at https://www.youtube.com/watch?v=pcdiG6VwqlA


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Trial2Vec: Zero-Shot Clinical Trial Document Similarity Search using Self-Supervision
Zifeng Wang | Jimeng Sun
Findings of the Association for Computational Linguistics: EMNLP 2022

Clinical trials are essential for drug development but are extremely expensive and time-consuming to conduct. It is beneficial to study similar historical trials when designing a clinical trial. However, lengthy trial documents and lack of labeled data make trial similarity search difficult. We propose a zero-shotclinical trial retrieval method, called Trial2Vec, which learns through self-supervision without the need for annotating similar clinical trials. Specifically, the meta-structure of trial documents (e.g., title, eligibility criteria, target disease) along with clinical knowledge (e.g., UMLS knowledge base) are leveraged to automatically generate contrastive samples. Besides, encodes trial documents considering meta-structure thus producing compact embeddings aggregating multi-aspect information from the whole document. We show that our method yields medically interpretable embeddings by visualization and it gets 15% average improvement over the best baselines on precision/recall for trial retrieval, which is evaluated on our labeled 1600 trial pairs. In addition, we prove the pretrained embeddings benefit the downstream trial outcome prediction task over 240k trials. Software is available at https://github.com/RyanWangZf/Trial2Vec.

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PromptEHR: Conditional Electronic Healthcare Records Generation with Prompt Learning
Zifeng Wang | Jimeng Sun
Proceedings of the 2022 Conference on Empirical Methods in Natural Language Processing

Accessing longitudinal multimodal Electronic Healthcare Records (EHRs) is challenging due to privacy concerns, which hinders the use of ML for healthcare applications. Synthetic EHRs generation bypasses the need to share sensitive real patient records. However, existing methods generate single-modal EHRs by unconditional generation or by longitudinal inference, which falls short of low flexibility and makes unrealistic EHRs. In this work, we propose to formulate EHRs generation as a text-to-text translation task by language models (LMs), which suffices to highly flexible event imputation during generation. We also design prompt learning to control the generation conditioned by numerical and categorical demographic features. We evaluate synthetic EHRs quality by two perplexity measures accounting for their longitudinal pattern (longitudinal imputation perplexity, lpl) and the connections cross modalities (cross-modality imputation perplexity, mpl). Moreover, we utilize two adversaries: membership and attribute inference attacks for privacy-preserving evaluation. Experiments on MIMIC-III data demonstrate the superiority of our methods on realistic EHRs generation (53.1% decrease of lpl and 45.3% decrease of mpl on average compared to the best baselines) with low privacy risks. Software is available at https://github.com/RyanWangZf/PromptEHR.

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MedCLIP: Contrastive Learning from Unpaired Medical Images and Text
Zifeng Wang | Zhenbang Wu | Dinesh Agarwal | Jimeng Sun
Proceedings of the 2022 Conference on Empirical Methods in Natural Language Processing

Existing vision-text contrastive learning like CLIP aims to match the paired image and caption embeddings while pushing others apart, which improves representation transferability and supports zero-shot prediction. However, medical image-text datasets are orders of magnitude below the general images and captions from the internet. Moreover, previous methods encounter many false negatives, i.e., images and reports from separate patients probably carry the same semantics but are wrongly treated as negatives. In this paper, we decouple images and texts for multimodal contrastive learning, thus scaling the usable training data in a combinatorial magnitude with low cost. We also propose to replace the InfoNCE loss with semantic matching loss based on medical knowledge to eliminate false negatives in contrastive learning. We prove that MedCLIP is a simple yet effective framework: it outperforms state-of-the-art methods on zero-shot prediction, supervised classification, and image-text retrieval. Surprisingly, we observe that with only 20K pre-training data, MedCLIP wins over the state-of-the-art method (using 200K data). The code is available at https://github.com/RyanWangZf/MedCLIP.


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Fusion: Towards Automated ICD Coding via Feature Compression
Junyu Luo | Cao Xiao | Lucas Glass | Jimeng Sun | Fenglong Ma
Findings of the Association for Computational Linguistics: ACL-IJCNLP 2021


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Clinical Concept Extraction for Document-Level Coding
Sarah Wiegreffe | Edward Choi | Sherry Yan | Jimeng Sun | Jacob Eisenstein
Proceedings of the 18th BioNLP Workshop and Shared Task

The text of clinical notes can be a valuable source of patient information and clinical assessments. Historically, the primary approach for exploiting clinical notes has been information extraction: linking spans of text to concepts in a detailed domain ontology. However, recent work has demonstrated the potential of supervised machine learning to extract document-level codes directly from the raw text of clinical notes. We propose to bridge the gap between the two approaches with two novel syntheses: (1) treating extracted concepts as features, which are used to supplement or replace the text of the note; (2) treating extracted concepts as labels, which are used to learn a better representation of the text. Unfortunately, the resulting concepts do not yield performance gains on the document-level clinical coding task. We explore possible explanations and future research directions.


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Explainable Prediction of Medical Codes from Clinical Text
James Mullenbach | Sarah Wiegreffe | Jon Duke | Jimeng Sun | Jacob Eisenstein
Proceedings of the 2018 Conference of the North American Chapter of the Association for Computational Linguistics: Human Language Technologies, Volume 1 (Long Papers)

Clinical notes are text documents that are created by clinicians for each patient encounter. They are typically accompanied by medical codes, which describe the diagnosis and treatment. Annotating these codes is labor intensive and error prone; furthermore, the connection between the codes and the text is not annotated, obscuring the reasons and details behind specific diagnoses and treatments. We present an attentional convolutional network that predicts medical codes from clinical text. Our method aggregates information across the document using a convolutional neural network, and uses an attention mechanism to select the most relevant segments for each of the thousands of possible codes. The method is accurate, achieving precision@8 of 0.71 and a Micro-F1 of 0.54, which are both better than the prior state of the art. Furthermore, through an interpretability evaluation by a physician, we show that the attention mechanism identifies meaningful explanations for each code assignment.