BioBridge: Bridging Biomedical Foundation Models via Knowledge Graph

Foundation models (FMs) are able to leverage large volumes of unlabeled data to demonstrate superior performance across a wide range of tasks. However, FMs developed for biomedical domains have largely remained unimodal, i.e., independently trained and used for tasks on protein sequences alone, small molecule structures alone, or clinical data alone. To overcome this limitation of biomedical FMs, we present BioBridge, a novel parameter-efficient learning framework, to bridge independently trained unimodal FMs to establish multimodal behavior. BioBridge achieves it by utilizing Knowledge Graphs (KG) to learn transformations between one unimodal FM and another without fine-tuning any underlying unimodal FMs. Our empirical results demonstrate that BioBridge can beat the best baseline KG embedding methods (on average by around 76.3%) in cross-modal retrieval tasks. We also identify BioBridge demonstrates out-of-domain generalization ability by extrapolating to unseen modalities or relations. Additionally, we also show that BioBridge presents itself as a general purpose retriever that can aid biomedical multimodal question answering as well as enhance the guided generation of novel drugs.

Instruction Tuning for Few-Shot Aspect-Based Sentiment Analysis

Aspect-based Sentiment Analysis (ABSA) is a fine-grained sentiment analysis task which involves four elements from user-generated texts: aspect term, aspect category, opinion term, and sentiment polarity. Most computational approaches focus on some of the ABSA sub-tasks such as tuple (aspect term, sentiment polarity) or triplet (aspect term, opinion term, sentiment polarity) extraction using either pipeline or joint modeling approaches. Recently, generative approaches have been proposed to extract all four elements as (one or more) quadruplets from text as a single task. In this work, we take a step further and propose a unified framework for solving ABSA, and the associated sub-tasks to improve the performance in few-shot scenarios. To this end, we fine-tune a T5 model with instructional prompts in a multi-task learning fashion covering all the sub-tasks, as well as the entire quadruple prediction task. In experiments with multiple benchmark data sets, we show that the proposed multi-task prompting approach brings performance boost (by absolute $6.75$ F1) in the few-shot learning setting.

Label Semantics for Few Shot Named Entity Recognition

We study the problem of few shot learning for named entity recognition. Specifically, we leverage the semantic information in the names of the labels as a way of giving the model additional signal and enriched priors. We propose a neural architecture that consists of two BERT encoders, one to encode the document and its tokens and another one to encode each of the labels in natural language format. Our model learns to match the representations of named entities computed by the first encoder with label representations computed by the second encoder. The label semantics signal is shown to support improved state-of-the-art results in multiple few shot NER benchmarks and on-par performance in standard benchmarks. Our model is especially effective in low resource settings.

Multi-Task Learning and Adapted Knowledge Models for Emotion-Cause Extraction

Detecting what emotions are expressed in text is a well-studied problem in natural language processing. However, research on finer grained emotion analysis such as what causes an emotion is still in its infancy. We present solutions that tackle both emotion recognition and emotion cause detection in a joint fashion. Considering that common-sense knowledge plays an important role in understanding implicitly expressed emotions and the reasons for those emotions, we propose novel methods that combine common-sense knowledge via adapted knowledge models with multi-task learning to perform joint emotion classification and emotion cause tagging. We show performance improvement on both tasks when including common-sense reasoning and a multitask framework. We provide a thorough analysis to gain insights into model performance.

Structured Prediction as Translation between Augmented Natural Languages

We propose a new framework, Translation between Augmented Natural Languages (TANL), to solve many structured prediction language tasks including joint entity and relation extraction, nested named entity recognition, relation classification, semantic role labeling, event extraction, coreference resolution, and dialogue state tracking. Instead of tackling the problem by training task-specific discriminative classifiers, we frame it as a translation task between augmented natural languages, from which the task-relevant information can be easily extracted. Our approach can match or outperform task-specific models on all tasks, and in particular, achieves new state-of-the-art results on joint entity and relation extraction (CoNLL04, ADE, NYT, and ACE2005 datasets), relation classification (FewRel and TACRED), and semantic role labeling (CoNLL-2005 and CoNLL-2012). We accomplish this while using the same architecture and hyperparameters for all tasks and even when training a single model to solve all tasks at the same time (multi-task learning). Finally, we show that our framework can also significantly improve the performance in a low-resource regime, thanks to better use of label semantics.

To BERT or Not to BERT: Comparing Task-specific and Task-agnostic Semi-Supervised Approaches for Sequence Tagging

Leveraging large amounts of unlabeled data using Transformer-like architectures, like BERT, has gained popularity in recent times owing to their effectiveness in learning general representations that can then be further fine-tuned for downstream tasks to much success. However, training these models can be costly both from an economic and environmental standpoint. In this work, we investigate how to effectively use unlabeled data: by exploring the task-specific semi-supervised approach, Cross-View Training (CVT) and comparing it with task-agnostic BERT in multiple settings that include domain and task relevant English data. CVT uses a much lighter model architecture and we show that it achieves similar performance to BERT on a set of sequence tagging tasks, with lesser financial and environmental impact.

Resource-Enhanced Neural Model for Event Argument Extraction

Event argument extraction (EAE) aims to identify the arguments of an event and classify the roles that those arguments play. Despite great efforts made in prior work, there remain many challenges: (1) Data scarcity. (2) Capturing the long-range dependency, specifically, the connection between an event trigger and a distant event argument. (3) Integrating event trigger information into candidate argument representation. For (1), we explore using unlabeled data in different ways. For (2), we propose to use a syntax-attending Transformer that can utilize dependency parses to guide the attention mechanism. For (3), we propose a trigger-aware sequence encoder with several types of trigger-dependent sequence representations. We also support argument extraction either from text annotated with gold entities or from plain text. Experiments on the English ACE2005 benchmark show that our approach achieves a new state-of-the-art.

Severing the Edge Between Before and After: Neural Architectures for Temporal Ordering of Events

In this paper, we propose a neural architecture and a set of training methods for ordering events by predicting temporal relations. Our proposed models receive a pair of events within a span of text as input and they identify temporal relations (Before, After, Equal, Vague) between them. Given that a key challenge with this task is the scarcity of annotated data, our models rely on either pretrained representations (i.e. RoBERTa, BERT or ELMo), transfer and multi-task learning (by leveraging complementary datasets), and self-training techniques. Experiments on the MATRES dataset of English documents establish a new state-of-the-art on this task.