Hoifung Poon


2024

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DocLens: Multi-aspect Fine-grained Medical Text Evaluation
Yiqing Xie | Sheng Zhang | Hao Cheng | Pengfei Liu | Zelalem Gero | Cliff Wong | Tristan Naumann | Hoifung Poon | Carolyn Rose
Proceedings of the 62nd Annual Meeting of the Association for Computational Linguistics (Volume 1: Long Papers)

Medical text generation aims to assist with administrative work and highlight salient information to support decision-making.To reflect the specific requirements of medical text, in this paper, we propose a set of metrics to evaluate the completeness, conciseness, and attribution of the generated text at a fine-grained level. The metrics can be computed by various types of evaluators including instruction-following (both proprietary and open-source) and supervised entailment models. We demonstrate the effectiveness of the resulting framework, DocLens, with three evaluators on three tasks: clinical note generation, radiology report summarization, and patient question summarization. A comprehensive human study shows that DocLens exhibits substantially higher agreement with the judgments of medical experts than existing metrics. The results also highlight the need to improve open-source evaluators and suggest potential directions. We released the code at https://github.com/yiqingxyq/DocLens.

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Pareto Optimal Learning for Estimating Large Language Model Errors
Theodore Zhao | Mu Wei | J. Preston | Hoifung Poon
Proceedings of the 62nd Annual Meeting of the Association for Computational Linguistics (Volume 1: Long Papers)

Large Language Models (LLMs) have shown impressive abilities in many applications. When a concrete and precise answer is desired, it is important to have a quantitative estimation of the potential error rate. However, this can be challenging due to the text-in-text-out nature of the generative models. We present a method based on Pareto optimization that generates a risk score to estimate the probability of error in an LLM response by integrating multiple sources of information. We prove theoretically that the error estimator optimized in our framework aligns with the LLM and the information sources in an Pareto optimal manner. Experimental results show that the risk scores estimated by our method are well correlated with the true LLM error rate, thus facilitating error correction. By dynamically combining with prompting strategies such as self-verification and information retrieval, we demonstrate the proposed method can be utilized to increase the performance of an LLM, surpassing state-of-the-art task specific model.

2023

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Continual Contrastive Finetuning Improves Low-Resource Relation Extraction
Wenxuan Zhou | Sheng Zhang | Tristan Naumann | Muhao Chen | Hoifung Poon
Proceedings of the 61st Annual Meeting of the Association for Computational Linguistics (Volume 1: Long Papers)

Relation extraction (RE), which has relied on structurally annotated corpora for model training, has been particularly challenging in low-resource scenarios and domains. Recent literature has tackled low-resource RE by self-supervised learning, where the solution involves pretraining the entity pair embedding by RE-based objective and finetuning on labeled data by classification-based objective. However, a critical challenge to this approach is the gap in objectives, which prevents the RE model from fully utilizing the knowledge in pretrained representations. In this paper, we aim at bridging the gap and propose to pretrain and finetune the RE model using consistent objectives of contrastive learning. Since in this kind of representation learning paradigm, one relation may easily form multiple clusters in the representation space, we further propose a multi-center contrastive loss that allows one relation to form multiple clusters to better align with pretraining. Experiments on two document-level RE datasets, BioRED and Re-DocRED, demonstrate the effectiveness of our method. Particularly, when using 1% end-task training data, our method outperforms PLM-based RE classifier by 10.5% and 6.1% on the two datasets, respectively.

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Context-faithful Prompting for Large Language Models
Wenxuan Zhou | Sheng Zhang | Hoifung Poon | Muhao Chen
Findings of the Association for Computational Linguistics: EMNLP 2023

Large language models (LLMs) encode parametric knowledge about world facts and have shown remarkable performance in knowledge-driven NLP tasks. However, their reliance on parametric knowledge may cause them to overlook contextual cues, leading to incorrect predictions in context-sensitive NLP tasks (e.g., knowledge acquisition tasks). In this paper, we seek to assess and enhance LLMs’ contextual faithfulness in two aspects: knowledge conflict and prediction with abstention. We demonstrate that LLMs’ faithfulness can be significantly improved using carefully designed prompting strategies. In particular, we identify opinion-based prompts and counterfactual demonstrations as the most effective methods. Opinion-based prompts reframe the context as a narrator’s statement and inquire about the narrator’s opinions, while counterfactual demonstrations use instances containing false facts to improve faithfulness in knowledge conflict situations. Neither technique requires additional training. We conduct experiments on three datasets of two standard NLP tasks, machine reading comprehension and relation extraction, and the results demonstrate significant improvement in faithfulness to contexts. Code and data are released at https://github.com/wzhouad/context-faithful-llm.

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Exploring the Boundaries of GPT-4 in Radiology
Qianchu Liu | Stephanie Hyland | Shruthi Bannur | Kenza Bouzid | Daniel Castro | Maria Wetscherek | Robert Tinn | Harshita Sharma | Fernando Pérez-García | Anton Schwaighofer | Pranav Rajpurkar | Sameer Khanna | Hoifung Poon | Naoto Usuyama | Anja Thieme | Aditya Nori | Matthew Lungren | Ozan Oktay | Javier Alvarez-Valle
Proceedings of the 2023 Conference on Empirical Methods in Natural Language Processing

The recent success of general-domain large language models (LLMs) has significantly changed the natural language processing paradigm towards a unified foundation model across domains and applications. In this paper, we focus on assessing the performance of GPT-4, the most capable LLM so far, on the text-based applications for radiology reports, comparing against state-of-the-art (SOTA) radiology-specific models. Exploring various prompting strategies, we evaluated GPT-4 on a diverse range of common radiology tasks and we found GPT-4 either outperforms or is on par with current SOTA radiology models. With zero-shot prompting, GPT-4 already obtains substantial gains ( 10% absolute improvement) over radiology models in temporal sentence similarity classification (accuracy) and natural language inference (F1). For tasks that require learning dataset-specific style or schema (e.g. findings summarisation), GPT-4 improves with example-based prompting and matches supervised SOTA. Our extensive error analysis with a board-certified radiologist shows GPT-4 has a sufficient level of radiology knowledge with only occasional errors in complex context that require nuanced domain knowledge. For findings summarisation, GPT-4 outputs are found to be overall comparable with existing manually-written impressions.

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Interactive Span Recommendation for Biomedical Text
Louis Blankemeier | Theodore Zhao | Robert Tinn | Sid Kiblawi | Yu Gu | Akshay Chaudhari | Hoifung Poon | Sheng Zhang | Mu Wei | J. Preston
Proceedings of the 5th Clinical Natural Language Processing Workshop

Motivated by the scarcity of high-quality labeled biomedical text, as well as the success of data programming, we introduce KRISS-Search. By leveraging the Unified Medical Language Systems (UMLS) ontology, KRISS-Search addresses an interactive few-shot span recommendation task that we propose. We first introduce unsupervised KRISS-Search and show that our method outperforms existing methods in identifying spans that are semantically similar to a given span of interest, with >50% AUPRC improvement relative to PubMedBERT. We then introduce supervised KRISS-Search, which leverages human interaction to improve the notion of similarity used by unsupervised KRISS-Search. Through simulated human feedback, we demonstrate an enhanced F1 score of 0.68 in classifying spans as semantically similar or different in the low-label setting, outperforming PubMedBERT by 2 F1 points. Finally, supervised KRISS-Search demonstrates competitive or superior performance compared to PubMedBERT in few-shot biomedical named entity recognition (NER) across five benchmark datasets, with an average improvement of 5.6 F1 points. We envision KRISS-Search increasing the efficiency of programmatic data labeling and also providing broader utility as an interactive biomedical search engine.

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Compositional Zero-Shot Domain Transfer with Text-to-Text Models
Fangyu Liu | Qianchu Liu | Shruthi Bannur | Fernando Pérez-García | Naoto Usuyama | Sheng Zhang | Tristan Naumann | Aditya Nori | Hoifung Poon | Javier Alvarez-Valle | Ozan Oktay | Stephanie L. Hyland
Transactions of the Association for Computational Linguistics, Volume 11

Label scarcity is a bottleneck for improving task performance in specialized domains. We propose a novel compositional transfer learning framework (DoT51) for zero-shot domain transfer. Without access to in-domain labels, DoT5 jointly learns domain knowledge (from masked language modelling of unlabelled in-domain free text) and task knowledge (from task training on more readily available general-domain data) in a multi-task manner. To improve the transferability of task training, we design a strategy named NLGU: We simultaneously train natural language generation (NLG) for in-domain label-to-data generation, which enables data augmentation for self-finetuning and natural language understanding (NLU) for label prediction. We evaluate DoT5 on the biomedical domain and the resource-lean subdomain of radiology, focusing on natural language inference, text summarization, and embedding learning. DoT5 demonstrates the effectiveness of compositional transfer learning through multi-task learning. In particular, DoT5 outperforms the current state-of-the-art in zero-shot transfer by over 7 absolute points in accuracy on RadNLI. We validate DoT5 with ablations and a case study demonstrating its ability to solve challenging NLI examples requiring in-domain expertise.

2022

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Knowledge-Rich Self-Supervision for Biomedical Entity Linking
Sheng Zhang | Hao Cheng | Shikhar Vashishth | Cliff Wong | Jinfeng Xiao | Xiaodong Liu | Tristan Naumann | Jianfeng Gao | Hoifung Poon
Findings of the Association for Computational Linguistics: EMNLP 2022

Entity linking faces significant challenges such as prolific variations and prevalent ambiguities, especially in high-value domains with myriad entities. Standard classification approaches suffer from the annotation bottleneck and cannot effectively handle unseen entities. Zero-shot entity linking has emerged as a promising direction for generalizing to new entities, but it still requires example gold entity mentions during training and canonical descriptions for all entities, both of which are rarely available outside of Wikipedia. In this paper, we explore Knowledge-RIch Self-Supervision (KRISS) for biomedical entity linking, by leveraging readily available domain knowledge. In training, it generates self-supervised mention examples on unlabeled text using a domain ontology and trains a contextual encoder using contrastive learning. For inference, it samples self-supervised mentions as prototypes for each entity and conducts linking by mapping the test mention to the most similar prototype. Our approach can easily incorporate entity descriptions and gold mention labels if available. We conducted extensive experiments on seven standard datasets spanning biomedical literature and clinical notes. Without using any labeled information, our method produces KRISSBERT, a universal entity linker for four million UMLS entities that attains new state of the art, outperforming prior self-supervised methods by as much as 20 absolute points in accuracy. We released KRISSBERT at https://aka.ms/krissbert.

2021

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Targeted Adversarial Training for Natural Language Understanding
Lis Pereira | Xiaodong Liu | Hao Cheng | Hoifung Poon | Jianfeng Gao | Ichiro Kobayashi
Proceedings of the 2021 Conference of the North American Chapter of the Association for Computational Linguistics: Human Language Technologies

We present a simple yet effective Targeted Adversarial Training (TAT) algorithm to improve adversarial training for natural language understanding. The key idea is to introspect current mistakes and prioritize adversarial training steps to where the model errs the most. Experiments show that TAT can significantly improve accuracy over standard adversarial training on GLUE and attain new state-of-the-art zero-shot results on XNLI. Our code will be released upon acceptance of the paper.

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Modular Self-Supervision for Document-Level Relation Extraction
Sheng Zhang | Cliff Wong | Naoto Usuyama | Sarthak Jain | Tristan Naumann | Hoifung Poon
Proceedings of the 2021 Conference on Empirical Methods in Natural Language Processing

Extracting relations across large text spans has been relatively underexplored in NLP, but it is particularly important for high-value domains such as biomedicine, where obtaining high recall of the latest findings is crucial for practical applications. Compared to conventional information extraction confined to short text spans, document-level relation extraction faces additional challenges in both inference and learning. Given longer text spans, state-of-the-art neural architectures are less effective and task-specific self-supervision such as distant supervision becomes very noisy. In this paper, we propose decomposing document-level relation extraction into relation detection and argument resolution, taking inspiration from Davidsonian semantics. This enables us to incorporate explicit discourse modeling and leverage modular self-supervision for each sub-problem, which is less noise-prone and can be further refined end-to-end via variational EM. We conduct a thorough evaluation in biomedical machine reading for precision oncology, where cross-paragraph relation mentions are prevalent. Our method outperforms prior state of the art, such as multi-scale learning and graph neural networks, by over 20 absolute F1 points. The gain is particularly pronounced among the most challenging relation instances whose arguments never co-occur in a paragraph.

2020

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The Microsoft Toolkit of Multi-Task Deep Neural Networks for Natural Language Understanding
Xiaodong Liu | Yu Wang | Jianshu Ji | Hao Cheng | Xueyun Zhu | Emmanuel Awa | Pengcheng He | Weizhu Chen | Hoifung Poon | Guihong Cao | Jianfeng Gao
Proceedings of the 58th Annual Meeting of the Association for Computational Linguistics: System Demonstrations

We present MT-DNN, an open-source natural language understanding (NLU) toolkit that makes it easy for researchers and developers to train customized deep learning models. Built upon PyTorch and Transformers, MT-DNN is designed to facilitate rapid customization for a broad spectrum of NLU tasks, using a variety of objectives (classification, regression, structured prediction) and text encoders (e.g., RNNs, BERT, RoBERTa, UniLM). A unique feature of MT-DNN is its built-in support for robust and transferable learning using the adversarial multi-task learning paradigm. To enable efficient production deployment, MT-DNN supports multi-task knowledge distillation, which can substantially compress a deep neural model without significant performance drop. We demonstrate the effectiveness of MT-DNN on a wide range of NLU applications across general and biomedical domains. The software and pre-trained models will be publicly available at https://github.com/namisan/mt-dnn.

2019

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Document-Level N-ary Relation Extraction with Multiscale Representation Learning
Robin Jia | Cliff Wong | Hoifung Poon
Proceedings of the 2019 Conference of the North American Chapter of the Association for Computational Linguistics: Human Language Technologies, Volume 1 (Long and Short Papers)

Most information extraction methods focus on binary relations expressed within single sentences. In high-value domains, however, n-ary relations are of great demand (e.g., drug-gene-mutation interactions in precision oncology). Such relations often involve entity mentions that are far apart in the document, yet existing work on cross-sentence relation extraction is generally confined to small text spans (e.g., three consecutive sentences), which severely limits recall. In this paper, we propose a novel multiscale neural architecture for document-level n-ary relation extraction. Our system combines representations learned over various text spans throughout the document and across the subrelation hierarchy. Widening the system’s purview to the entire document maximizes potential recall. Moreover, by integrating weak signals across the document, multiscale modeling increases precision, even in the presence of noisy labels from distant supervision. Experiments on biomedical machine reading show that our approach substantially outperforms previous n-ary relation extraction methods.

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DoubleTransfer at MEDIQA 2019: Multi-Source Transfer Learning for Natural Language Understanding in the Medical Domain
Yichong Xu | Xiaodong Liu | Chunyuan Li | Hoifung Poon | Jianfeng Gao
Proceedings of the 18th BioNLP Workshop and Shared Task

This paper describes our competing system to enter the MEDIQA-2019 competition. We use a multi-source transfer learning approach to transfer the knowledge from MT-DNN and SciBERT to natural language understanding tasks in the medical domain. For transfer learning fine-tuning, we use multi-task learning on NLI, RQE and QA tasks on general and medical domains to improve performance. The proposed methods are proved effective for natural language understanding in the medical domain, and we rank the first place on the QA task.

2018

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Deep Probabilistic Logic: A Unifying Framework for Indirect Supervision
Hai Wang | Hoifung Poon
Proceedings of the 2018 Conference on Empirical Methods in Natural Language Processing

Deep learning has emerged as a versatile tool for a wide range of NLP tasks, due to its superior capacity in representation learning. But its applicability is limited by the reliance on annotated examples, which are difficult to produce at scale. Indirect supervision has emerged as a promising direction to address this bottleneck, either by introducing labeling functions to automatically generate noisy examples from unlabeled text, or by imposing constraints over interdependent label decisions. A plethora of methods have been proposed, each with respective strengths and limitations. Probabilistic logic offers a unifying language to represent indirect supervision, but end-to-end modeling with probabilistic logic is often infeasible due to intractable inference and learning. In this paper, we propose deep probabilistic logic (DPL) as a general framework for indirect supervision, by composing probabilistic logic with deep learning. DPL models label decisions as latent variables, represents prior knowledge on their relations using weighted first-order logical formulas, and alternates between learning a deep neural network for the end task and refining uncertain formula weights for indirect supervision, using variational EM. This framework subsumes prior indirect supervision methods as special cases, and enables novel combination via infusion of rich domain and linguistic knowledge. Experiments on biomedical machine reading demonstrate the promise of this approach.

2017

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Distant Supervision for Relation Extraction beyond the Sentence Boundary
Chris Quirk | Hoifung Poon
Proceedings of the 15th Conference of the European Chapter of the Association for Computational Linguistics: Volume 1, Long Papers

The growing demand for structured knowledge has led to great interest in relation extraction, especially in cases with limited supervision. However, existing distance supervision approaches only extract relations expressed in single sentences. In general, cross-sentence relation extraction is under-explored, even in the supervised-learning setting. In this paper, we propose the first approach for applying distant supervision to cross-sentence relation extraction. At the core of our approach is a graph representation that can incorporate both standard dependencies and discourse relations, thus providing a unifying way to model relations within and across sentences. We extract features from multiple paths in this graph, increasing accuracy and robustness when confronted with linguistic variation and analysis error. Experiments on an important extraction task for precision medicine show that our approach can learn an accurate cross-sentence extractor, using only a small existing knowledge base and unlabeled text from biomedical research articles. Compared to the existing distant supervision paradigm, our approach extracted twice as many relations at similar precision, thus demonstrating the prevalence of cross-sentence relations and the promise of our approach.

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Cross-Sentence N-ary Relation Extraction with Graph LSTMs
Nanyun Peng | Hoifung Poon | Chris Quirk | Kristina Toutanova | Wen-tau Yih
Transactions of the Association for Computational Linguistics, Volume 5

Past work in relation extraction has focused on binary relations in single sentences. Recent NLP inroads in high-value domains have sparked interest in the more general setting of extracting n-ary relations that span multiple sentences. In this paper, we explore a general relation extraction framework based on graph long short-term memory networks (graph LSTMs) that can be easily extended to cross-sentence n-ary relation extraction. The graph formulation provides a unified way of exploring different LSTM approaches and incorporating various intra-sentential and inter-sentential dependencies, such as sequential, syntactic, and discourse relations. A robust contextual representation is learned for the entities, which serves as input to the relation classifier. This simplifies handling of relations with arbitrary arity, and enables multi-task learning with related relations. We evaluate this framework in two important precision medicine settings, demonstrating its effectiveness with both conventional supervised learning and distant supervision. Cross-sentence extraction produced larger knowledge bases. and multi-task learning significantly improved extraction accuracy. A thorough analysis of various LSTM approaches yielded useful insight the impact of linguistic analysis on extraction accuracy.

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NLP for Precision Medicine
Hoifung Poon | Chris Quirk | Kristina Toutanova | Wen-tau Yih
Proceedings of the 55th Annual Meeting of the Association for Computational Linguistics: Tutorial Abstracts

We will introduce precision medicine and showcase the vast opportunities for NLP in this burgeoning field with great societal impact. We will review pressing NLP problems, state-of-the art methods, and important applications, as well as datasets, medical resources, and practical issues. The tutorial will provide an accessible overview of biomedicine, and does not presume knowledge in biology or healthcare. The ultimate goal is to reduce the entry barrier for NLP researchers to contribute to this exciting domain.

2016

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Compositional Learning of Embeddings for Relation Paths in Knowledge Base and Text
Kristina Toutanova | Xi Victoria Lin | Wen-tau Yih | Hoifung Poon | Chris Quirk
Proceedings of the 54th Annual Meeting of the Association for Computational Linguistics (Volume 1: Long Papers)

2015

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Model Selection for Type-Supervised Learning with Application to POS Tagging
Kristina Toutanova | Waleed Ammar | Pallavi Choudhury | Hoifung Poon
Proceedings of the Nineteenth Conference on Computational Natural Language Learning

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Grounded Semantic Parsing for Complex Knowledge Extraction
Ankur P. Parikh | Hoifung Poon | Kristina Toutanova
Proceedings of the 2015 Conference of the North American Chapter of the Association for Computational Linguistics: Human Language Technologies

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Representing Text for Joint Embedding of Text and Knowledge Bases
Kristina Toutanova | Danqi Chen | Patrick Pantel | Hoifung Poon | Pallavi Choudhury | Michael Gamon
Proceedings of the 2015 Conference on Empirical Methods in Natural Language Processing

2013

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Grounded Unsupervised Semantic Parsing
Hoifung Poon
Proceedings of the 51st Annual Meeting of the Association for Computational Linguistics (Volume 1: Long Papers)

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Probabilistic Frame Induction
Jackie Chi Kit Cheung | Hoifung Poon | Lucy Vanderwende
Proceedings of the 2013 Conference of the North American Chapter of the Association for Computational Linguistics: Human Language Technologies

2010

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Unsupervised Ontology Induction from Text
Hoifung Poon | Pedro Domingos
Proceedings of the 48th Annual Meeting of the Association for Computational Linguistics

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Joint Inference for Knowledge Extraction from Biomedical Literature
Hoifung Poon | Lucy Vanderwende
Human Language Technologies: The 2010 Annual Conference of the North American Chapter of the Association for Computational Linguistics

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Markov Logic in Natural Language Processing: Theory, Algorithms, and Applications
Hoifung Poon
NAACL HLT 2010 Tutorial Abstracts

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Machine Reading at the University of Washington
Hoifung Poon | Janara Christensen | Pedro Domingos | Oren Etzioni | Raphael Hoffmann | Chloe Kiddon | Thomas Lin | Xiao Ling | Mausam | Alan Ritter | Stefan Schoenmackers | Stephen Soderland | Dan Weld | Fei Wu | Congle Zhang
Proceedings of the NAACL HLT 2010 First International Workshop on Formalisms and Methodology for Learning by Reading

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Statistical Relational Learning for Knowledge Extraction from the Web
Hoifung Poon
Proceedings of the Second Workshop on NLP Challenges in the Information Explosion Era (NLPIX 2010)

2009

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Unsupervised Morphological Segmentation with Log-Linear Models
Hoifung Poon | Colin Cherry | Kristina Toutanova
Proceedings of Human Language Technologies: The 2009 Annual Conference of the North American Chapter of the Association for Computational Linguistics

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Language ID in the Context of Harvesting Language Data off the Web
Fei Xia | William Lewis | Hoifung Poon
Proceedings of the 12th Conference of the European Chapter of the ACL (EACL 2009)

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Unsupervised Semantic Parsing
Hoifung Poon | Pedro Domingos
Proceedings of the 2009 Conference on Empirical Methods in Natural Language Processing

2008

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Joint Unsupervised Coreference Resolution with Markov Logic
Hoifung Poon | Pedro Domingos
Proceedings of the 2008 Conference on Empirical Methods in Natural Language Processing