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Despite the widespread success of self-supervised learning via masked language models (MLM), accurately capturing fine-grained semantic relationships in the biomedical domain remains a challenge. This is of paramount importance for entity-level tasks such as entity linking where the ability to model entity relations (especially synonymy) is pivotal. To address this challenge, we propose SapBERT, a pretraining scheme that self-aligns the representation space of biomedical entities. We design a scalable metric learning framework that can leverage UMLS, a massive collection of biomedical ontologies with 4M+ concepts. In contrast with previous pipeline-based hybrid systems, SapBERT offers an elegant one-model-for-all solution to the problem of medical entity linking (MEL), achieving a new state-of-the-art (SOTA) on six MEL benchmarking datasets. In the scientific domain, we achieve SOTA even without task-specific supervision. With substantial improvement over various domain-specific pretrained MLMs such as BioBERT, SciBERTand and PubMedBERT, our pretraining scheme proves to be both effective and robust.

NAACL 2021

Self-Alignment Pretraining for Biomedical Entity Representations

2021 Annual Conference of the North American Chapter of the Association for Computational Linguistics.

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technical paper

We introduce a grey-box adversarial attack and defence framework for sentiment classification. We address the issues of differentiability, label preservation and input reconstruction for adversarial attack and defence in one unified framework. Our results show that once trained, the attacking model is capable of generating high-quality adversarial examples substantially faster (one order of magnitude less in time) than state-of-the-art attacking methods. These examples also preserve the original sentiment according to human evaluation. Additionally, our framework produces an improved classifier that is robust in defending against multiple adversarial attacking methods. Code is available at: https://github.com/ibm-aur-nlp/adv-def-text-dist. 


Grey-box Adversarial Attack And Defence For Sentiment Classification

Natural language processing (NLP) research combines the study of universal principles, through basic science, with applied science targeting specific use cases and settings. However, the process of exchange between basic NLP and applications is often assumed to emerge naturally, resulting in many innovations going unapplied and many important questions left unstudied. We describe a new paradigm of Translational NLP, which aims to structure and facilitate the processes by which basic and applied NLP research inform one another. Translational NLP thus presents a third research paradigm, focused on understanding the challenges posed by application needs and how these challenges can drive innovation in basic science and technology design. We show that many significant advances in NLP research have emerged from the intersection of basic principles with application needs, and present a conceptual framework outlining the stakeholders and key questions in translational research. Our framework provides a roadmap for developing Translational NLP as a dedicated research area, and identifies general translational principles to facilitate exchange between basic and applied research.


Translational NLP: A New Paradigm and General Principles for Natural Language Processing Research

Previous work indicates that discourse information benefits summarization. In this paper, we explore whether this synergy between discourse and summarization is bidirectional, by inferring document-level discourse trees from pre-trained neural summarizers. In particular, we generate unlabeled RST-style discourse trees from the self-attention matrices of the transformer model. Experiments across models and datasets reveal that the summarizer learns both, dependency- and constituency-style discourse information, which is typically encoded in a single head, covering long- and short-distance discourse dependencies. Overall, the experimental results suggest that the learned discourse information is general and transferable inter-domain.


Predicting Discourse Trees from Transformer-based Neural Summarizers

Coherent discourse is distinguished from a mere collection of utterances by the satisfaction of a diverse set of constraints, for example choice of expression, logical relation between denoted events, and implicit compatibility with world-knowledge. Do neural language models encode such constraints? We design an extendable set of test suites addressing different aspects of discourse and dialogue coherence. Unlike most previous coherence evaluation studies, we address specific linguistic devices beyond sentence order perturbations, allowing for a more fine-grained analysis of what constitutes coherence and what neural models trained on a language modelling objective do encode. Extending the targeted evaluation paradigm for neural language models (Marvin and Linzen, 2018) to phenomena beyond syntax, we show that this paradigm is equally suited to evaluate linguistic qualities that contribute to the notion of coherence.


Is Incoherence Surprising? Targeted Evaluation of Coherence Prediction from Language Models

The state-of-the-art on basic, single-antecedent anaphora has greatly improved in recent years. Researchers have therefore started to pay more attention to more complex cases of anaphora such as split-antecedent anaphora, as in "Time-Warner is considering a legal challenge to Telecommunications Inc’s plan to buy half of Showtime Networks Inc–a move that could lead to all-out war between the two powerful companies". Split-antecedent anaphora is rarer and more complex to resolve than single-antecedent anaphora; as a result, it is not annotated in many datasets designed to test coreference, and previous work on resolving this type of anaphora was carried out in unrealistic conditions that assume gold mentions and/or gold split-antecedent anaphors are available. These systems also focus on split-antecedent anaphors only. In this work, we introduce a system that resolves both single and split-antecedent anaphors, and evaluate it in a more realistic setting that uses predicted mentions. We also start addressing the question of how to evaluate single and split-antecedent anaphors together using standard coreference evaluation metrics.


Stay Together: A System for Single and Split-antecedent Anaphora Resolution

We probe pre-trained transformer language models for bridging inference. We first investigate individual attention heads in BERT and observe that attention heads at higher layers prominently focus on bridging relations in-comparison with the lower and middle layers, also, few specific attention heads concentrate consistently on bridging. More importantly, we consider language models as a whole in our second approach where bridging anaphora resolution is formulated as a masked token prediction task (Of-Cloze test). Our formulation produces optimistic results without any fine-tuning, which indicates that pre-trained language models substantially capture bridging inference. Our further investigation shows that the distance between anaphor-antecedent and the context provided to language models play an important role in the inference.


Probing for Bridging Inference in Transformer Language Models

Models for question answering, dialogue agents, and summarization often interpret the meaning of a sentence in a rich context and use that meaning in a new context.

Decontextualization: Making Sentences Stand-Alone

Hierarchical multi-label text classification (HMTC) aims to tag each document with a set of classes from a class hierarchy. Most existing HMTC methods train classifiers using massive human-labeled documents, which are often too costly to obtain in real-world applications. In this paper, we explore to conduct HMTC based on only class surface names as supervision signals. We observe that to perform HMTC, human experts typically first pinpoint a few most essential classes for the document as its “core classes”, and then check core classes’ ancestor classes to ensure the coverage. To mimic human experts, we propose a novel HMTC framework, named TaxoClass. Specifically, TaxoClass (1) calculates document-class similarities using a textual entailment model, (2) identifies a document’s core classes and utilizes confident core classes to train a taxonomy-enhanced classifier, and (3) generalizes the classifier via multi-label self-training. Our experiments on two challenging datasets show TaxoClass can achieve around 0.71 Example- F1 using only class names, outperforming the best previous method by 25%.

TaxoClass: Hierarchical Multi-Label Text Classification Using Only Class Names

Though word embeddings and topics are complementary representations, several past works have only used pretrained word embeddings in (neural) topic modeling to address data sparsity in short-text or small collection of documents. This work presents a novel neural topic modeling framework using multi-view embedding spaces: (1) pretrained topic-embeddings, and (2) pretrained word-embeddings (context insensitive from Glove and context-sensitive from BERT models) jointly from one or many sources to improve topic quality and better deal with polysemy. In doing so, we first build respective pools of pretrained topic (i.e., TopicPool) and word embeddings (i.e., WordPool). We then identify one or more relevant source domain(s) and transfer knowledge to guide meaningful learning in the sparse target domain. Within neural topic modeling, we quantify the quality of topics and document representations via generalization (perplexity), interpretability (topic coherence) and information retrieval (IR) using short-text, long-text, small and large document collections from news and medical domains. Introducing the multi-source multi-view embedding spaces, we have shown state-of-the-art neural topic modeling using 6 source (high-resource) and 5 target (low-resource) corpora.

Multi-source Neural Topic Modeling in Multi-view Embedding Spaces

Graph convolutional networks (GCNs) have been applied recently to text classification and produced an excellent performance. However, existing GCN-based methods do not assume an explicit latent semantic structure of documents, making learned representations less effective and difficult to interpret. They are also transductive in nature, thus cannot handle out-of-graph documents. To address these issues, we propose a novel model named inductive Topic Variational Graph Auto-Encoder (T-VGAE), which incorporates a topic model into variational graph-auto-encoder (VGAE) to capture the hidden semantic information be- tween documents and words. T-VGAE inherits the interpretability of the topic model and the efficient information propagation mechanism of VGAE. It learns probabilistic representations of words and documents by jointly encoding and reconstructing the global word-level graph and bipartite graphs of documents, where each document is considered individually and decoupled from the global correlation graph so as to enable inductive learning. Our experiments on several benchmark datasets show that our method outperforms the existing competitive models on supervised and semi-supervised text classification, as well as unsupervised text representation learning. In addition, it has higher interpretability and is able to deal with unseen documents.

Self-Alignment Pretraining for Biomedical Entity Representations

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