Recent works in relation extraction (RE) have achieved promising benchmark accuracy; however, our adversarial attack experiments show that these works excessively rely on entities, making their generalization capability questionable. To address this issue, we propose an adversarial training method specifically designed for RE. Our approach introduces both sequence- and token-level perturbations to the sample and uses a separate perturbation vocabulary to improve the search for entity and context perturbations.Furthermore, we introduce a probabilistic strategy for leaving clean tokens in the context during adversarial training. This strategy enables a larger attack budget for entities and coaxes the model to leverage relational patterns embedded in the context. Extensive experiments show that compared to various adversarial training methods, our method significantly improves both the accuracy and robustness of the model. Additionally, experiments on different data availability settings highlight the effectiveness of our method in low-resource scenarios.We also perform in-depth analyses of our proposed method and provide further hints.We will release our code at https://github.com/David-Li0406/READ.

The interplay between microbiota and diseases has emerged as a significant area of research facilitated by the proliferation of cost-effective and precise sequencing technologies. To keep track of the many findings, domain experts manually review publications to extract reported microbe-disease associations and compile them into knowledge bases. However, manual curation efforts struggle to keep up with the pace of publications. Relation extraction has demonstrated remarkable success in other domains, yet the availability of datasets supporting such methods within the domain of microbiome research remains limited. To bridge this gap, we introduce the Microbe-Disease Relation Extraction Dataset (MiDRED); a human-annotated dataset containing 3,116 annotations of fine-grained relationships between microbes and diseases. We hope this dataset will help address the scarcity of data in this crucial domain and facilitate the development of advanced text-mining solutions to automate the creation and maintenance of microbiome knowledge bases.

Open-world Relation Extraction (OpenRE) has recently garnered significant attention. However, existing approaches tend to oversimplify the problem by assuming that all instances of unlabeled data belong to novel classes, thereby limiting the practicality of these methods. We argue that the OpenRE setting should be more aligned with the characteristics of real-world data. Specifically, we propose two key improvements: (a) unlabeled data should encompass known and novel classes, including negative instances; and (b) the set of novel classes should represent long-tail relation types. Furthermore, we observe that popular relations can often be implicitly inferred through specific patterns, while long-tail relations tend to be explicitly expressed. Motivated by these insights, we present a method called KNoRD (Known and Novel Relation Discovery), which effectively classifies explicitly and implicitly expressed relations from known and novel classes within unlabeled data. Experimental evaluations on several Open-world RE benchmarks demonstrate that KNoRD consistently outperforms other existing methods, achieving significant performance gains.

Recent relation extraction (RE) works have shown encouraging improvements by conducting contrastive learning on silver labels generated by distant supervision before fine-tuning on gold labels. Existing methods typically assume all these silver labels are accurate and treat them equally; however, distant supervision is inevitably noisy–some silver labels are more reliable than others. In this paper, we propose fine-grained contrastive learning (FineCL) for RE, which leverages fine-grained information about which silver labels are and are not noisy to improve the quality of learned relationship representations for RE. We first assess the quality of silver labels via a simple and automatic approach we call “learning order denoising,” where we train a language model to learn these relations and record the order of learned training instances. We show that learning order largely corresponds to label accuracy–early-learned silver labels have, on average, more accurate labels than later-learned silver labels. Then, during pre-training, we increase the weights of accurate labels within a novel contrastive learning objective. Experiments on several RE benchmarks show that FineCL makes consistent and significant performance gains over state-of-the-art methods.

NLP has emerged as an essential tool to extract knowledge from the exponentially increasing volumes of biomedical texts. Many NLP tasks, such as named entity recognition and named entity normalization, are especially challenging in the biomedical domain partly because of the prolific use of acronyms. Long names for diseases, bacteria, and chemicals are often replaced by acronyms. We propose Biomedical Local Acronym Resolver (BLAR), a high-performing acronym resolver that leverages state-of-the-art (SOTA) pre-trained language models to accurately resolve local acronyms in biomedical texts. We test BLAR on the Ab3P corpus and achieve state-of-the-art results compared to the current best-performing local acronym resolution algorithms and models.