Zaiqiao Meng


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Rewire-then-Probe: A Contrastive Recipe for Probing Biomedical Knowledge of Pre-trained Language Models
Zaiqiao Meng | Fangyu Liu | Ehsan Shareghi | Yixuan Su | Charlotte Collins | Nigel Collier
Proceedings of the 60th Annual Meeting of the Association for Computational Linguistics (Volume 1: Long Papers)

Knowledge probing is crucial for understanding the knowledge transfer mechanism behind the pre-trained language models (PLMs). Despite the growing progress of probing knowledge for PLMs in the general domain, specialised areas such as the biomedical domain are vastly under-explored. To facilitate this, we release a well-curated biomedical knowledge probing benchmark, MedLAMA, constructed based on the Unified Medical Language System (UMLS) Metathesaurus. We test a wide spectrum of state-of-the-art PLMs and probing approaches on our benchmark, reaching at most 3% of acc@10. While highlighting various sources of domain-specific challenges that amount to this underwhelming performance, we illustrate that the underlying PLMs have a higher potential for probing tasks. To achieve this, we propose Contrastive-Probe, a novel self-supervised contrastive probing approach, that adjusts the underlying PLMs without using any probing data. While Contrastive-Probe pushes the acc@10 to 28%, the performance gap still remains notable. Our human expert evaluation suggests that the probing performance of our Contrastive-Probe is still under-estimated as UMLS still does not include the full spectrum of factual knowledge. We hope MedLAMA and Contrastive-Probe facilitate further developments of more suited probing techniques for this domain. Our code and dataset are publicly available at


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Integrating Transformers and Knowledge Graphs for Twitter Stance Detection
Thomas Clark | Costanza Conforti | Fangyu Liu | Zaiqiao Meng | Ehsan Shareghi | Nigel Collier
Proceedings of the Seventh Workshop on Noisy User-generated Text (W-NUT 2021)

Stance detection (SD) entails classifying the sentiment of a text towards a given target, and is a relevant sub-task for opinion mining and social media analysis. Recent works have explored knowledge infusion supplementing the linguistic competence and latent knowledge of large pre-trained language models with structured knowledge graphs (KGs), yet few works have applied such methods to the SD task. In this work, we first perform stance-relevant knowledge probing on Transformers-based pre-trained models in a zero-shot setting, showing these models’ latent real-world knowledge about SD targets and their sensitivity to context. We then train and evaluate new knowledge-enriched stance detection models on two Twitter stance datasets, achieving state-of-the-art performance on both.

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Mixture-of-Partitions: Infusing Large Biomedical Knowledge Graphs into BERT
Zaiqiao Meng | Fangyu Liu | Thomas Clark | Ehsan Shareghi | Nigel Collier
Proceedings of the 2021 Conference on Empirical Methods in Natural Language Processing

Infusing factual knowledge into pre-trained models is fundamental for many knowledge-intensive tasks. In this paper, we proposed Mixture-of-Partitions (MoP), an infusion approach that can handle a very large knowledge graph (KG) by partitioning it into smaller sub-graphs and infusing their specific knowledge into various BERT models using lightweight adapters. To leverage the overall factual knowledge for a target task, these sub-graph adapters are further fine-tuned along with the underlying BERT through a mixture layer. We evaluate our MoP with three biomedical BERTs (SciBERT, BioBERT, PubmedBERT) on six downstream tasks (inc. NLI, QA, Classification), and the results show that our MoP consistently enhances the underlying BERTs in task performance, and achieves new SOTA performances on five evaluated datasets.

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Few-Shot Table-to-Text Generation with Prototype Memory
Yixuan Su | Zaiqiao Meng | Simon Baker | Nigel Collier
Findings of the Association for Computational Linguistics: EMNLP 2021

Neural table-to-text generation models have achieved remarkable progress on an array of tasks. However, due to the data-hungry nature of neural models, their performances strongly rely on large-scale training examples, limiting their applicability in real-world applications. To address this, we propose a new framework: Prototype-to-Generate (P2G), for table-to-text generation under the few-shot scenario. The proposed framework utilizes the retrieved prototypes, which are jointly selected by an IR system and a novel prototype selector to help the model bridging the structural gap between tables and texts. Experimental results on three benchmark datasets with three state-of-the-art models demonstrate that the proposed framework significantly improves the model performance across various evaluation metrics.

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Self-Alignment Pretraining for Biomedical Entity Representations
Fangyu Liu | Ehsan Shareghi | Zaiqiao Meng | Marco Basaldella | Nigel Collier
Proceedings of the 2021 Conference of the North American Chapter of the Association for Computational Linguistics: Human Language Technologies

Despite the widespread success of self-supervised learning via masked language models (MLM), accurately capturing fine-grained semantic relationships in the biomedical domain remains a challenge. This is of paramount importance for entity-level tasks such as entity linking where the ability to model entity relations (especially synonymy) is pivotal. To address this challenge, we propose SapBERT, a pretraining scheme that self-aligns the representation space of biomedical entities. We design a scalable metric learning framework that can leverage UMLS, a massive collection of biomedical ontologies with 4M+ concepts. In contrast with previous pipeline-based hybrid systems, SapBERT offers an elegant one-model-for-all solution to the problem of medical entity linking (MEL), achieving a new state-of-the-art (SOTA) on six MEL benchmarking datasets. In the scientific domain, we achieve SOTA even without task-specific supervision. With substantial improvement over various domain-specific pretrained MLMs such as BioBERT, SciBERTand and PubMedBERT, our pretraining scheme proves to be both effective and robust.