Yifan Peng


2022

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CMU’s IWSLT 2022 Dialect Speech Translation System
Brian Yan | Patrick Fernandes | Siddharth Dalmia | Jiatong Shi | Yifan Peng | Dan Berrebbi | Xinyi Wang | Graham Neubig | Shinji Watanabe
Proceedings of the 19th International Conference on Spoken Language Translation (IWSLT 2022)

This paper describes CMU’s submissions to the IWSLT 2022 dialect speech translation (ST) shared task for translating Tunisian-Arabic speech to English text. We use additional paired Modern Standard Arabic data (MSA) to directly improve the speech recognition (ASR) and machine translation (MT) components of our cascaded systems. We also augment the paired ASR data with pseudo translations via sequence-level knowledge distillation from an MT model and use these artificial triplet ST data to improve our end-to-end (E2E) systems. Our E2E models are based on the Multi-Decoder architecture with searchable hidden intermediates. We extend the Multi-Decoder by orienting the speech encoder towards the target language by applying ST supervision as hierarchical connectionist temporal classification (CTC) multi-task. During inference, we apply joint decoding of the ST CTC and ST autoregressive decoder branches of our modified Multi-Decoder. Finally, we apply ROVER voting, posterior combination, and minimum bayes-risk decoding with combined N-best lists to ensemble our various cascaded and E2E systems. Our best systems reached 20.8 and 19.5 BLEU on test2 (blind) and test1 respectively. Without any additional MSA data, we reached 20.4 and 19.2 on the same test sets.

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EchoGen: Generating Conclusions from Echocardiogram Notes
Liyan Tang | Shravan Kooragayalu | Yanshan Wang | Ying Ding | Greg Durrett | Justin F. Rousseau | Yifan Peng
Proceedings of the 21st Workshop on Biomedical Language Processing

Generating a summary from findings has been recently explored (Zhang et al., 2018, 2020) in note types such as radiology reports that typically have short length. In this work, we focus on echocardiogram notes that is longer and more complex compared to previous note types. We formally define the task of echocardiography conclusion generation (EchoGen) as generating a conclusion given the findings section, with emphasis on key cardiac findings. To promote the development of EchoGen methods, we present a new benchmark, which consists of two datasets collected from two hospitals. We further compare both standard and start-of-the-art methods on this new benchmark, with an emphasis on factual consistency. To accomplish this, we develop a tool to automatically extract concept-attribute tuples from the text. We then propose an evaluation metric, FactComp, to compare concept-attribute tuples between the human reference and generated conclusions. Both automatic and human evaluations show that there is still a significant gap between human-written and machine-generated conclusions on echo reports in terms of factuality and overall quality.

2021

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Leveraging Deep Representations of Radiology Reports in Survival Analysis for Predicting Heart Failure Patient Mortality
Hyun Gi Lee | Evan Sholle | Ashley Beecy | Subhi Al’Aref | Yifan Peng
Proceedings of the 2021 Conference of the North American Chapter of the Association for Computational Linguistics: Human Language Technologies

Utilizing clinical texts in survival analysis is difficult because they are largely unstructured. Current automatic extraction models fail to capture textual information comprehensively since their labels are limited in scope. Furthermore, they typically require a large amount of data and high-quality expert annotations for training. In this work, we present a novel method of using BERT-based hidden layer representations of clinical texts as covariates for proportional hazards models to predict patient survival outcomes. We show that hidden layers yield notably more accurate predictions than predefined features, outperforming the previous baseline model by 5.7% on average across C-index and time-dependent AUC. We make our work publicly available at https://github.com/bionlplab/heart_failure_mortality.

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Improving BERT Model Using Contrastive Learning for Biomedical Relation Extraction
Peng Su | Yifan Peng | K. Vijay-Shanker
Proceedings of the 20th Workshop on Biomedical Language Processing

Contrastive learning has been used to learn a high-quality representation of the image in computer vision. However, contrastive learning is not widely utilized in natural language processing due to the lack of a general method of data augmentation for text data. In this work, we explore the method of employing contrastive learning to improve the text representation from the BERT model for relation extraction. The key knob of our framework is a unique contrastive pre-training step tailored for the relation extraction tasks by seamlessly integrating linguistic knowledge into the data augmentation. Furthermore, we investigate how large-scale data constructed from the external knowledge bases can enhance the generality of contrastive pre-training of BERT. The experimental results on three relation extraction benchmark datasets demonstrate that our method can improve the BERT model representation and achieve state-of-the-art performance. In addition, we explore the interpretability of models by showing that BERT with contrastive pre-training relies more on rationales for prediction. Our code and data are publicly available at: https://github.com/AnonymousForNow.

2020

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Automatic recognition of abdominal lymph nodes from clinical text
Yifan Peng | Sungwon Lee | Daniel C. Elton | Thomas Shen | Yu-xing Tang | Qingyu Chen | Shuai Wang | Yingying Zhu | Ronald Summers | Zhiyong Lu
Proceedings of the 3rd Clinical Natural Language Processing Workshop

Lymph node status plays a pivotal role in the treatment of cancer. The extraction of lymph nodes from radiology text reports enables large-scale training of lymph node detection on MRI. In this work, we first propose an ontology of 41 types of abdominal lymph nodes with a hierarchical relationship. We then introduce an end-to-end approach based on the combination of rules and transformer-based methods to detect these abdominal lymph node mentions and classify their types from the MRI radiology reports. We demonstrate the superior performance of a model fine-tuned on MRI reports using BlueBERT, called MriBERT. We find that MriBERT outperforms the rule-based labeler (0.957 vs 0.644 in micro weighted F1-score) as well as other BERT-based variations (0.913 - 0.928). We make the code and MriBERT publicly available at https://github.com/ncbi-nlp/bluebert, with the hope that this method can facilitate the development of medical report annotators to produce labels from scratch at scale.

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An Empirical Study of Multi-Task Learning on BERT for Biomedical Text Mining
Yifan Peng | Qingyu Chen | Zhiyong Lu
Proceedings of the 19th SIGBioMed Workshop on Biomedical Language Processing

Multi-task learning (MTL) has achieved remarkable success in natural language processing applications. In this work, we study a multi-task learning model with multiple decoders on varieties of biomedical and clinical natural language processing tasks such as text similarity, relation extraction, named entity recognition, and text inference. Our empirical results demonstrate that the MTL fine-tuned models outperform state-of-the-art transformer models (e.g., BERT and its variants) by 2.0% and 1.3% in biomedical and clinical domain adaptation, respectively. Pairwise MTL further demonstrates more details about which tasks can improve or decrease others. This is particularly helpful in the context that researchers are in the hassle of choosing a suitable model for new problems. The code and models are publicly available at https://github.com/ncbi-nlp/bluebert.

2019

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Transfer Learning in Biomedical Natural Language Processing: An Evaluation of BERT and ELMo on Ten Benchmarking Datasets
Yifan Peng | Shankai Yan | Zhiyong Lu
Proceedings of the 18th BioNLP Workshop and Shared Task

Inspired by the success of the General Language Understanding Evaluation benchmark, we introduce the Biomedical Language Understanding Evaluation (BLUE) benchmark to facilitate research in the development of pre-training language representations in the biomedicine domain. The benchmark consists of five tasks with ten datasets that cover both biomedical and clinical texts with different dataset sizes and difficulties. We also evaluate several baselines based on BERT and ELMo and find that the BERT model pre-trained on PubMed abstracts and MIMIC-III clinical notes achieves the best results. We make the datasets, pre-trained models, and codes publicly available at https://github.com/ ncbi-nlp/BLUE_Benchmark.

2017

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Deep learning for extracting protein-protein interactions from biomedical literature
Yifan Peng | Zhiyong Lu
BioNLP 2017

State-of-the-art methods for protein-protein interaction (PPI) extraction are primarily feature-based or kernel-based by leveraging lexical and syntactic information. But how to incorporate such knowledge in the recent deep learning methods remains an open question. In this paper, we propose a multichannel dependency-based convolutional neural network model (McDepCNN). It applies one channel to the embedding vector of each word in the sentence, and another channel to the embedding vector of the head of the corresponding word. Therefore, the model can use richer information obtained from different channels. Experiments on two public benchmarking datasets, AIMed and BioInfer, demonstrate that McDepCNN provides up to 6% F1-score improvement over rich feature-based methods and single-kernel methods. In addition, McDepCNN achieves 24.4% relative improvement in F1-score over the state-of-the-art methods on cross-corpus evaluation and 12% improvement in F1-score over kernel-based methods on “difficult” instances. These results suggest that McDepCNN generalizes more easily over different corpora, and is capable of capturing long distance features in the sentences.

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BioCreative VI Precision Medicine Track: creating a training corpus for mining protein-protein interactions affected by mutations
Rezarta Islamaj Doğan | Andrew Chatr-aryamontri | Sun Kim | Chih-Hsuan Wei | Yifan Peng | Donald Comeau | Zhiyong Lu
BioNLP 2017

The Precision Medicine Track in BioCre-ative VI aims to bring together the Bi-oNLP community for a novel challenge focused on mining the biomedical litera-ture in search of mutations and protein-protein interactions (PPI). In order to support this track with an effective train-ing dataset with limited curator time, the track organizers carefully reviewed Pub-Med articles from two different sources: curated public PPI databases, and the re-sults of state-of-the-art public text mining tools. We detail here the data collection, manual review and annotation process and describe this training corpus charac-teristics. We also describe a corpus per-formance baseline. This analysis will provide useful information to developers and researchers for comparing and devel-oping innovative text mining approaches for the BioCreative VI challenge and other Precision Medicine related applica-tions.

2015

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An extended dependency graph for relation extraction in biomedical texts
Yifan Peng | Samir Gupta | Cathy Wu | Vijay Shanker
Proceedings of BioNLP 15