Biomedical entity linking is the task of linking entity mentions in a biomedical document to referent entities in a knowledge base. Recently, many BERT-based models have been introduced for the task. While these models achieve competitive results on many datasets, they are computationally expensive and contain about 110M parameters. Little is known about the factors contributing to their impressive performance and whether the over-parameterization is needed. In this work, we shed some light on the inner workings of these large BERT-based models. Through a set of probing experiments, we have found that the entity linking performance only changes slightly when the input word order is shuffled or when the attention scope is limited to a fixed window size. From these observations, we propose an efficient convolutional neural network with residual connections for biomedical entity linking. Because of the sparse connectivity and weight sharing properties, our model has a small number of parameters and is highly efficient. On five public datasets, our model achieves comparable or even better linking accuracy than the state-of-the-art BERT-based models while having about 60 times fewer parameters.

Compared to the general news domain, information extraction (IE) from biomedical text requires much broader domain knowledge. However, many previous IE methods do not utilize any external knowledge during inference. Due to the exponential growth of biomedical publications, models that do not go beyond their fixed set of parameters will likely fall behind. Inspired by how humans look up relevant information to comprehend a scientific text, we present a novel framework that utilizes external knowledge for joint entity and relation extraction named KECI (Knowledge-Enhanced Collective Inference). Given an input text, KECI first constructs an initial span graph representing its initial understanding of the text. It then uses an entity linker to form a knowledge graph containing relevant background knowledge for the the entity mentions in the text. To make the final predictions, KECI fuses the initial span graph and the knowledge graph into a more refined graph using an attention mechanism. KECI takes a collective approach to link mention spans to entities by integrating global relational information into local representations using graph convolutional networks. Our experimental results show that the framework is highly effective, achieving new state-of-the-art results in two different benchmark datasets: BioRelEx (binding interaction detection) and ADE (adverse drug event extraction). For example, KECI achieves absolute improvements of 4.59% and 4.91% in F1 scores over the state-of-the-art on the BioRelEx entity and relation extraction tasks

We propose a new task, Text2Mol, to retrieve molecules using natural language descriptions as queries. Natural language and molecules encode information in very different ways, which leads to the exciting but challenging problem of integrating these two very different modalities. Although some work has been done on text-based retrieval and structure-based retrieval, this new task requires integrating molecules and natural language more directly. Moreover, this can be viewed as an especially challenging cross-lingual retrieval problem by considering the molecules as a language with a very unique grammar. We construct a paired dataset of molecules and their corresponding text descriptions, which we use to learn an aligned common semantic embedding space for retrieval. We extend this to create a cross-modal attention-based model for explainability and reranking by interpreting the attentions as association rules. We also employ an ensemble approach to integrate our different architectures, which significantly improves results from 0.372 to 0.499 MRR. This new multimodal approach opens a new perspective on solving problems in chemistry literature understanding and molecular machine learning.

While monolingual data has been shown to be useful in improving bilingual neural machine translation (NMT), effectively and efficiently leveraging monolingual data for Multilingual NMT (MNMT) systems is a less explored area. In this work, we propose a multi-task learning (MTL) framework that jointly trains the model with the translation task on bitext data and two denoising tasks on the monolingual data. We conduct extensive empirical studies on MNMT systems with 10 language pairs from WMT datasets. We show that the proposed approach can effectively improve the translation quality for both high-resource and low-resource languages with large margin, achieving significantly better results than the individual bilingual models. We also demonstrate the efficacy of the proposed approach in the zero-shot setup for language pairs without bitext training data. Furthermore, we show the effectiveness of MTL over pre-training approaches for both NMT and cross-lingual transfer learning NLU tasks; the proposed approach outperforms massive scale models trained on single task.

Content of text data are often influenced by contextual factors which often evolve over time (e.g., content of social media are often influenced by topics covered in the major news streams). Existing language models do not consider the influence of such related evolving topics, and thus are not optimal. In this paper, we propose to incorporate such topical-influence into a language model to both improve its accuracy and enable cross-stream analysis of topical influences. Specifically, we propose a novel language model called Topical Influence Language Model (TILM), which is a novel extension of a neural language model to capture the influences on the contents in one text stream by the evolving topics in another related (or possibly same) text stream. Experimental results on six different text stream data comprised of conference paper titles show that the incorporation of evolving topical influence into a language model is beneficial and TILM outperforms multiple baselines in a challenging task of text forecasting. In addition to serving as a language model, TILM further enables interesting analysis of topical influence among multiple text streams.

We study the problem of automatically identifying humorous text from a new kind of text data, i.e., online reviews. We propose a generative language model, based on the theory of incongruity, to model humorous text, which allows us to leverage background text sources, such as Wikipedia entry descriptions, and enables construction of multiple features for identifying humorous reviews. Evaluation of these features using supervised learning for classifying reviews into humorous and non-humorous reviews shows that the features constructed based on the proposed generative model are much more effective than the major features proposed in the existing literature, allowing us to achieve almost 86% accuracy. These humorous review predictions can also supply good indicators for identifying helpful reviews.