Maciej Wiatrak


On Masked Language Models for Contextual Link Prediction
Angus Brayne | Maciej Wiatrak | Dane Corneil
Proceedings of Deep Learning Inside Out (DeeLIO 2022): The 3rd Workshop on Knowledge Extraction and Integration for Deep Learning Architectures

In the real world, many relational facts require context; for instance, a politician holds a given elected position only for a particular timespan. This context (the timespan) is typically ignored in knowledge graph link prediction tasks, or is leveraged by models designed specifically to make use of it (i.e. n-ary link prediction models). Here, we show that the task of n-ary link prediction is easily performed using language models, applied with a basic method for constructing cloze-style query sentences. We introduce a pre-training methodology based around an auxiliary entity-linked corpus that outperforms other popular pre-trained models like BERT, even with a smaller model. This methodology also enables n-ary link prediction without access to any n-ary training set, which can be invaluable in circumstances where expensive and time-consuming curation of n-ary knowledge graphs is not feasible. We achieve state-of-the-art performance on the primary n-ary link prediction dataset WD50K and on WikiPeople facts that include literals - typically ignored by knowledge graph embedding methods.

Proxy-based Zero-Shot Entity Linking by Effective Candidate Retrieval
Maciej Wiatrak | Eirini Arvaniti | Angus Brayne | Jonas Vetterle | Aaron Sim
Proceedings of the 13th International Workshop on Health Text Mining and Information Analysis (LOUHI)

A recent advancement in the domain of biomedical Entity Linking is the development of powerful two-stage algorithms – an initial candidate retrieval stage that generates a shortlist of entities for each mention, followed by a candidate ranking stage. However, the effectiveness of both stages are inextricably dependent on computationally expensive components. Specifically, in candidate retrieval via dense representation retrieval it is important to have hard negative samples, which require repeated forward passes and nearest neighbour searches across the entire entity label set throughout training. In this work, we show that pairing a proxy-based metric learning loss with an adversarial regularizer provides an efficient alternative to hard negative sampling in the candidate retrieval stage. In particular, we show competitive performance on the recall@1 metric, thereby providing the option to leave out the expensive candidate ranking step. Finally, we demonstrate how the model can be used in a zero-shot setting to discover out of knowledge base biomedical entities.


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Simple Hierarchical Multi-Task Neural End-To-End Entity Linking for Biomedical Text
Maciej Wiatrak | Juha Iso-Sipila
Proceedings of the 11th International Workshop on Health Text Mining and Information Analysis

Recognising and linking entities is a crucial first step to many tasks in biomedical text analysis, such as relation extraction and target identification. Traditionally, biomedical entity linking methods rely heavily on heuristic rules and predefined, often domain-specific features. The features try to capture the properties of entities and complex multi-step architectures to detect, and subsequently link entity mentions. We propose a significant simplification to the biomedical entity linking setup that does not rely on any heuristic methods. The system performs all the steps of the entity linking task jointly in either single or two stages. We explore the use of hierarchical multi-task learning, using mention recognition and entity typing tasks as auxiliary tasks. We show that hierarchical multi-task models consistently outperform single-task models when trained tasks are homogeneous. We evaluate the performance of our models on the biomedical entity linking benchmarks using MedMentions and BC5CDR datasets. We achieve state-of-theart results on the challenging MedMentions dataset, and comparable results on BC5CDR.