arXiv subjects

Hoifung Poon

Publications and source records attributed to Hoifung Poon.

At least 73 records · Page 4Linked to original sources

arXiv2023

Compositional Zero-Shot Domain Transfer with Text-to-Text Models

Label scarcity is a bottleneck for improving task performance in specialised domains. We propose a novel compositional transfer learning framework (DoT5 - domain compositional zero-shot T5) for zero-shot domain transfer. Without access to in-domain labels, DoT5 jointly learns domain knowledge (from MLM 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 NLG for in-domain label-to-data generation which enables data augmentation for self-finetuning and NLU for label prediction. We evaluate DoT5 on the biomedical domain and the resource-lean subdomain of radiology, focusing on NLI, text summarisation and embedding learning. DoT5 demonstrates the effectiveness of compositional transfer learning through multi-task learning. In particular, DoT5 outperforms the current SOTA 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.

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arXiv2023

Optimizing Bi-Encoder for Named Entity Recognition via Contrastive Learning

We present a bi-encoder framework for named entity recognition (NER), which applies contrastive learning to map candidate text spans and entity types into the same vector representation space. Prior work predominantly approaches NER as sequence labeling or span classification. We instead frame NER as a representation learning problem that maximizes the similarity between the vector representations of an entity mention and its type. This makes it easy to handle nested and flat NER alike, and can better leverage noisy self-supervision signals. A major challenge to this bi-encoder formulation for NER lies in separating non-entity spans from entity mentions. Instead of explicitly labeling all non-entity spans as the same class $\texttt{Outside}$ ($\texttt{O}$) as in most prior methods, we introduce a novel dynamic thresholding loss. Experiments show that our method performs well in both supervised and distantly supervised settings, for nested and flat NER alike, establishing new state of the art across standard datasets in the general domain (e.g., ACE2004, ACE2005) and high-value verticals such as biomedicine (e.g., GENIA, NCBI, BC5CDR, JNLPBA). We release the code at github.com/microsoft/binder.

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arXiv2023

BLIAM: Literature-based Data Synthesis for Synergistic Drug Combination Prediction

Language models pre-trained on scientific literature corpora have substantially advanced scientific discovery by offering high-quality feature representations for downstream applications. However, these features are often not interpretable, and thus can reveal limited insights to domain experts. Instead of obtaining features from language models, we propose BLIAM, a literature-based data synthesis approach to directly generate training data points that are interpretable and model-agnostic to downstream applications. The key idea of BLIAM is to create prompts using existing training data and then use these prompts to synthesize new data points. BLIAM performs these two steps iteratively as new data points will define more informative prompts and new prompts will in turn synthesize more accurate data points. Notably, literature-based data augmentation might introduce data leakage since labels of test data points in downstream applications might have already been mentioned in the language model corpus. To prevent such leakage, we introduce GDSC-combo, a large-scale drug combination discovery dataset that was published after the biomedical language model was trained. We found that BLIAM substantially outperforms a non-augmented approach and manual prompting in this rigorous data split setting. BLIAM can be further used to synthesize data points for novel drugs and cell lines that were not even measured in biomedical experiments. In addition to the promising prediction performance, the data points synthesized by BLIAM are interpretable and model-agnostic, enabling in silico augmentation for in vitro experiments.

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arXiv2022

Making the Most of Text Semantics to Improve Biomedical Vision--Language Processing

Multi-modal data abounds in biomedicine, such as radiology images and reports. Interpreting this data at scale is essential for improving clinical care and accelerating clinical research. Biomedical text with its complex semantics poses additional challenges in vision--language modelling compared to the general domain, and previous work has used insufficiently adapted models that lack domain-specific language understanding. In this paper, we show that principled textual semantic modelling can substantially improve contrastive learning in self-supervised vision--language processing. We release a language model that achieves state-of-the-art results in radiology natural language inference through its improved vocabulary and novel language pretraining objective leveraging semantics and discourse characteristics in radiology reports. Further, we propose a self-supervised joint vision--language approach with a focus on better text modelling. It establishes new state of the art results on a wide range of publicly available benchmarks, in part by leveraging our new domain-specific language model. We release a new dataset with locally-aligned phrase grounding annotations by radiologists to facilitate the study of complex semantic modelling in biomedical vision--language processing. A broad evaluation, including on this new dataset, shows that our contrastive learning approach, aided by textual-semantic modelling, outperforms prior methods in segmentation tasks, despite only using a global-alignment objective.

cs.CV↗

arXiv2022

Knowledge-Rich Self-Supervision for Biomedical Entity Linking

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 ($\tt KRISS$) 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 $\tt KRISSBERT$, 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.

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arXiv2022

Towards Structuring Real-World Data at Scale: Deep Learning for Extracting Key Oncology Information from Clinical Text with Patient-Level Supervision

Objective: The majority of detailed patient information in real-world data (RWD) is only consistently available in free-text clinical documents. Manual curation is expensive and time-consuming. Developing natural language processing (NLP) methods for structuring RWD is thus essential for scaling real-world evidence generation. Materials and Methods: Traditional rule-based systems are vulnerable to the prevalent linguistic variations and ambiguities in clinical text, and prior applications of machine-learning methods typically require sentence-level or report-level labeled examples that are hard to produce at scale. We propose leveraging patient-level supervision from medical registries, which are often readily available and capture key patient information, for general RWD applications. To combat the lack of sentence-level or report-level annotations, we explore advanced deep-learning methods by combining domain-specific pretraining, recurrent neural networks, and hierarchical attention. Results: We conduct an extensive study on 135,107 patients from the cancer registry of a large integrated delivery network (IDN) comprising healthcare systems in five western US states. Our deep learning methods attain test AUROC of 94-99% for key tumor attributes and comparable performance on held-out data from separate health systems and states. Discussion and Conclusion: Ablation results demonstrate clear superiority of these advanced deep-learning methods over prior approaches. Error analysis shows that our NLP system sometimes even corrects errors in registrar labels. We also conduct a preliminary investigation in accelerating registry curation and general RWD structuring via assisted curation for over 1.2 million cancer patients in this healthcare network.

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arXiv2021

Fine-Tuning Large Neural Language Models for Biomedical Natural Language Processing

Motivation: A perennial challenge for biomedical researchers and clinical practitioners is to stay abreast with the rapid growth of publications and medical notes. Natural language processing (NLP) has emerged as a promising direction for taming information overload. In particular, large neural language models facilitate transfer learning by pretraining on unlabeled text, as exemplified by the successes of BERT models in various NLP applications. However, fine-tuning such models for an end task remains challenging, especially with small labeled datasets, which are common in biomedical NLP. Results: We conduct a systematic study on fine-tuning stability in biomedical NLP. We show that finetuning performance may be sensitive to pretraining settings, especially in low-resource domains. Large models have potential to attain better performance, but increasing model size also exacerbates finetuning instability. We thus conduct a comprehensive exploration of techniques for addressing fine-tuning instability. We show that these techniques can substantially improve fine-tuning performance for lowresource biomedical NLP applications. Specifically, freezing lower layers is helpful for standard BERT-BASE models, while layerwise decay is more effective for BERT-LARGE and ELECTRA models. For low-resource text similarity tasks such as BIOSSES, reinitializing the top layer is the optimal strategy. Overall, domainspecific vocabulary and pretraining facilitate more robust models for fine-tuning. Based on these findings, we establish new state of the art on a wide range of biomedical NLP applications. Availability and implementation: To facilitate progress in biomedical NLP, we release our state-of-the-art pretrained and fine-tuned models: https://aka.ms/BLURB.

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arXiv2021

Domain-Specific Pretraining for Vertical Search: Case Study on Biomedical Literature

Information overload is a prevalent challenge in many high-value domains. A prominent case in point is the explosion of the biomedical literature on COVID-19, which swelled to hundreds of thousands of papers in a matter of months. In general, biomedical literature expands by two papers every minute, totalling over a million new papers every year. Search in the biomedical realm, and many other vertical domains is challenging due to the scarcity of direct supervision from click logs. Self-supervised learning has emerged as a promising direction to overcome the annotation bottleneck. We propose a general approach for vertical search based on domain-specific pretraining and present a case study for the biomedical domain. Despite being substantially simpler and not using any relevance labels for training or development, our method performs comparably or better than the best systems in the official TREC-COVID evaluation, a COVID-related biomedical search competition. Using distributed computing in modern cloud infrastructure, our system can scale to tens of millions of articles on PubMed and has been deployed as Microsoft Biomedical Search, a new search experience for biomedical literature: https://aka.ms/biomedsearch.

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arXiv2021

Domain-Specific Language Model Pretraining for Biomedical Natural Language Processing

Pretraining large neural language models, such as BERT, has led to impressive gains on many natural language processing (NLP) tasks. However, most pretraining efforts focus on general domain corpora, such as newswire and Web. A prevailing assumption is that even domain-specific pretraining can benefit by starting from general-domain language models. In this paper, we challenge this assumption by showing that for domains with abundant unlabeled text, such as biomedicine, pretraining language models from scratch results in substantial gains over continual pretraining of general-domain language models. To facilitate this investigation, we compile a comprehensive biomedical NLP benchmark from publicly-available datasets. Our experiments show that domain-specific pretraining serves as a solid foundation for a wide range of biomedical NLP tasks, leading to new state-of-the-art results across the board. Further, in conducting a thorough evaluation of modeling choices, both for pretraining and task-specific fine-tuning, we discover that some common practices are unnecessary with BERT models, such as using complex tagging schemes in named entity recognition (NER). To help accelerate research in biomedical NLP, we have released our state-of-the-art pretrained and task-specific models for the community, and created a leaderboard featuring our BLURB benchmark (short for Biomedical Language Understanding & Reasoning Benchmark) at https://aka.ms/BLURB.

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arXiv2021

Modular Self-Supervision for Document-Level Relation Extraction

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.

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arXiv2021

Combining Probabilistic Logic and Deep Learning for Self-Supervised Learning

Deep learning has proven effective for various application tasks, but its applicability is limited by the reliance on annotated examples. Self-supervised learning has emerged as a promising direction to alleviate the supervision bottleneck, but existing work focuses on leveraging co-occurrences in unlabeled data for task-agnostic representation learning, as exemplified by masked language model pretraining. In this chapter, we explore task-specific self-supervision, which leverages domain knowledge to automatically annotate noisy training examples for end applications, either by introducing labeling functions for annotating individual instances, or by imposing constraints over interdependent label decisions. We first present deep probabilistic logic(DPL), which offers a unifying framework for task-specific self-supervision by composing probabilistic logic with deep learning. DPL represents unknown labels as latent variables and incorporates diverse self-supervision using probabilistic logic to train a deep neural network end-to-end using variational EM. Next, we present self-supervised self-supervision(S4), which adds to DPL the capability to learn new self-supervision automatically. Starting from an initial seed self-supervision, S4 iteratively uses the deep neural network to propose new self supervision. These are either added directly (a form of structured self-training) or verified by a human expert (as in feature-based active learning). Experiments on real-world applications such as biomedical machine reading and various text classification tasks show that task-specific self-supervision can effectively leverage domain expertise and often match the accuracy of supervised methods with a tiny fraction of human effort.

cs.LG↗

arXiv2021

Targeted Adversarial Training for Natural Language Understanding

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 at: https://github.com/namisan/mt-dnn.

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arXiv2020

Self-supervised self-supervision by combining deep learning and probabilistic logic

Labeling training examples at scale is a perennial challenge in machine learning. Self-supervision methods compensate for the lack of direct supervision by leveraging prior knowledge to automatically generate noisy labeled examples. Deep probabilistic logic (DPL) is a unifying framework for self-supervised learning that represents unknown labels as latent variables and incorporates diverse self-supervision using probabilistic logic to train a deep neural network end-to-end using variational EM. While DPL is successful at combining pre-specified self-supervision, manually crafting self-supervision to attain high accuracy may still be tedious and challenging. In this paper, we propose Self-Supervised Self-Supervision (S4), which adds to DPL the capability to learn new self-supervision automatically. Starting from an initial "seed," S4 iteratively uses the deep neural network to propose new self supervision. These are either added directly (a form of structured self-training) or verified by a human expert (as in feature-based active learning). Experiments show that S4 is able to automatically propose accurate self-supervision and can often nearly match the accuracy of supervised methods with a tiny fraction of the human effort.

cs.LG↗

arXiv2020

CMT in TREC-COVID Round 2: Mitigating the Generalization Gaps from Web to Special Domain Search

Neural rankers based on deep pretrained language models (LMs) have been shown to improve many information retrieval benchmarks. However, these methods are affected by their the correlation between pretraining domain and target domain and rely on massive fine-tuning relevance labels. Directly applying pretraining methods to specific domains may result in suboptimal search quality because specific domains may have domain adaption problems, such as the COVID domain. This paper presents a search system to alleviate the special domain adaption problem. The system utilizes the domain-adaptive pretraining and few-shot learning technologies to help neural rankers mitigate the domain discrepancy and label scarcity problems. Besides, we also integrate dense retrieval to alleviate traditional sparse retrieval's vocabulary mismatch obstacle. Our system performs the best among the non-manual runs in Round 2 of the TREC-COVID task, which aims to retrieve useful information from scientific literature related to COVID-19. Our code is publicly available at https://github.com/thunlp/OpenMatch.

cs.IR↗

arXiv2020

The Microsoft Toolkit of Multi-Task Deep Neural Networks for Natural Language Understanding

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.

cs.CL↗

arXiv2020

Adversarial Training for Large Neural Language Models

Generalization and robustness are both key desiderata for designing machine learning methods. Adversarial training can enhance robustness, but past work often finds it hurts generalization. In natural language processing (NLP), pre-training large neural language models such as BERT have demonstrated impressive gain in generalization for a variety of tasks, with further improvement from adversarial fine-tuning. However, these models are still vulnerable to adversarial attacks. In this paper, we show that adversarial pre-training can improve both generalization and robustness. We propose a general algorithm ALUM (Adversarial training for large neural LangUage Models), which regularizes the training objective by applying perturbations in the embedding space that maximizes the adversarial loss. We present the first comprehensive study of adversarial training in all stages, including pre-training from scratch, continual pre-training on a well-trained model, and task-specific fine-tuning. ALUM obtains substantial gains over BERT on a wide range of NLP tasks, in both regular and adversarial scenarios. Even for models that have been well trained on extremely large text corpora, such as RoBERTa, ALUM can still produce significant gains from continual pre-training, whereas conventional non-adversarial methods can not. ALUM can be further combined with task-specific fine-tuning to attain additional gains. The ALUM code is publicly available at https://github.com/namisan/mt-dnn.

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arXiv2019

Document-Level $N$-ary Relation Extraction with Multiscale Representation Learning

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.

cs.CL↗

arXiv2019

DoubleTransfer at MEDIQA 2019: Multi-Source Transfer Learning for Natural Language Understanding in the Medical Domain

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.

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