We introduce ChemDisGene, a new dataset for training and evaluating multi-class multi-label biomedical relation extraction models. Our dataset contains 80k biomedical research abstracts labeled with mentions of chemicals, diseases, and genes, portions of which human experts labeled with 18 types of biomedical relationships between these entities (intended for evaluation), and the remainder of which (intended for training) has been distantly labeled via the CTD database with approximately 78% accuracy. In comparison to similar preexisting datasets, ours is both substantially larger and cleaner; it also includes annotations linking mentions to their entities. We also provide three baseline deep neural network relation extraction models trained and evaluated on our new dataset.
In this work, we introduce a method for enhancing distant supervision with state-change information for relation extraction. We provide a training dataset created via this process, along with manually annotated development and test sets. We present an analysis of the curation process and data, and compare it to standard distant supervision. We demonstrate that the addition of state-change information reduces noise when used for static relation extraction, and can also be used to train a relation-extraction system that detects a change of state in relations.
To understand a story with multiple events, it is important to capture the proper relations across these events. However, existing event relation extraction (ERE) framework regards it as a multi-class classification task and do not guarantee any coherence between different relation types, such as anti-symmetry. If a phone line “died” after “storm”, then it is obvious that the “storm” happened before the “died”. Current framework of event relation extraction do not guarantee this coherence and thus enforces it via constraint loss function (Wang et al., 2020). In this work, we propose to modify the underlying ERE model to guarantee coherence by representing each event as a box representation (BERE) without applying explicit constraints. From our experiments, BERE also shows stronger conjunctive constraint satisfaction while performing on par or better in F1 compared to previous models with constraint injection.
Learning representations of entities and relations in structured knowledge bases is an active area of research, with much emphasis placed on choosing the appropriate geometry to capture the hierarchical structures exploited in, for example, isa or haspart relations. Box embeddings (Vilnis et al., 2018; Li et al., 2019; Dasgupta et al., 2020), which represent concepts as n-dimensional hyperrectangles, are capable of embedding hierarchies when training on a subset of the transitive closure. In Patel et al., (2020), the authors demonstrate that only the transitive reduction is required and further extend box embeddings to capture joint hierarchies by augmenting the graph with new nodes. While it is possible to represent joint hierarchies with this method, the parameters for each hierarchy are decoupled, making generalization between hierarchies infeasible. In this work, we introduce a learned box-to-box transformation that respects the structure of each hierarchy. We demonstrate that this not only improves the capability of modeling cross-hierarchy compositional edges but is also capable of generalizing from a subset of the transitive reduction.
In this paper, we consider advancing web-scale knowledge extraction and alignment by integrating OpenIE extractions in the form of (subject, predicate, object) triples with Knowledge Bases (KB). Traditional techniques from universal schema and from schema mapping fall in two extremes: either they perform instance-level inference relying on embedding for (subject, object) pairs, thus cannot handle pairs absent in any existing triples; or they perform predicate-level mapping and completely ignore background evidence from individual entities, thus cannot achieve satisfying quality. We propose OpenKI to handle sparsity of OpenIE extractions by performing instance-level inference: for each entity, we encode the rich information in its neighborhood in both KB and OpenIE extractions, and leverage this information in relation inference by exploring different methods of aggregation and attention. In order to handle unseen entities, our model is designed without creating entity-specific parameters. Extensive experiments show that this method not only significantly improves state-of-the-art for conventional OpenIE extractions like ReVerb, but also boosts the performance on OpenIE from semi-structured data, where new entity pairs are abundant and data are fairly sparse.
Annotation projection is a practical method to deal with the low resource problem in incident languages (IL) processing. Previous methods on annotation projection mainly relied on word alignment results without any training process, which led to noise propagation caused by word alignment errors. In this paper, we focus on the named entity recognition (NER) task and propose a weakly-supervised framework to project entity annotations from English to IL through bitexts. Instead of directly relying on word alignment results, this framework combines advantages of rule-based methods and deep learning methods by implementing two steps: First, generates a high-confidence entity annotation set on IL side with strict searching methods; Second, uses this high-confidence set to weakly supervise the model training. The model is finally used to accomplish the projecting process. Experimental results on two low-resource ILs show that the proposed method can generate better annotations projected from English-IL parallel corpora. The performance of IL name tagger can also be improved significantly by training on the newly projected IL annotation set.