Korea, Republic of

Recently, Biomedical Question Answering has attracted growing attention due to its application value and technical challenges. Most existing works treat it as a semantic matching task that predicts answers by computing confidence among questions, options and evidence paragraphs, which is insufficient for scenarios that require complex reasoning based on a deep understanding of biomedical evidences. We propose a novel model termed Hierarchical Representation-based Dynamic Reasoning Network to tackle this problem. It first constructs the hierarchical representations for biomedical evidences to learn semantics within and among evidences. It then performs dynamic reasoning based on the hierarchical representations of evidences to solve complex biomedical problems.

COLING 2022

Hierarchical Representation-based Dynamic Reasoning Network for Biomedical Question Answering

biomedical question answering

representation learning

reasoning

poster

[![](https://assets.underline.io/uploads/markdown_image/1/image/81a3c0317d24f663b49b996875024d45.png)](https://aclanthology.org/volumes/2022.coling-1/)



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COLING, the International Conference on Computational Linguistics, is one of the premier conferences for the natural language processing and computational linguistics.

In a text, entities mentioned earlier can be referred to in later discourse by a more general description. For example, Celine Dion and Justin Bieber can be referred to by "Canadian singers" or "celebrities". In this presentation, we present this phenomenon in the context of summarization, where entities from a source text are generalized in the summary. We call such instances source-summary entity aggregations. We categorize these aggregations into two types and analyze them in the Cnn/Dailymail corpus, showing that they are reasonably frequent. We then examine how well three state-of-the-art summarization systems can generate such aggregations within summaries. We also develop techniques to encourage them to generate more aggregations. Our results show that there is significant room for improvement in producing semantically correct aggregations.

Source-summary Entity Aggregation in Abstractive Summarization

This paper aims to improve the performance of text-to-SQL parsing by exploring the intrinsic uncertainties in the neural network based approaches (called SUN). From the data uncertainty perspective, it is indisputable that a single SQL can be learned from multiple semantically-equivalent questions. Different from previous methods that are limited to one-to-one mapping, we propose a data uncertainty constraint to explore the under- lying complementary semantic information among multiple semantically-equivalent questions (many-to-one) and learn the robust feature representations with reduced spurious associations. In this way, we can reduce the sensitivity of the learned representations and improve the robustness of the parser. From the model uncertainty perspective, there is often structural information (dependence) among the weights of neural networks. To improve the generalizability and stability of neural text-to-SQL parsers, we propose a model uncertainty constraint to refine the query representations by enforcing the output representations of different perturbed encoding networks to be consistent with each other. Ex- tensive experiments on five benchmark datasets demonstrate that our method significantly outperforms strong competitors and achieves new state-of-the-art results.

SUN: Exploring Intrinsic Uncertainties in Text-to-SQL Parsers

Knowledge Graphs (KGs) stores world knowledge that benefits various reasoning-based applications. Due to their incompleteness, a fundamental task for KGs, which is known as Knowledge Graph Completion (KGC), is to perform link prediction and infer new facts based on the known facts. Recently, link prediction on the temporal KGs becomes an active research topic. Numerous Temporal Knowledge Graph Completion (TKGC) methods have been proposed by mapping the entities and relations in TKG to the high-dimensional representations. However, most existing TKGC methods are mainly based on deterministic vector embeddings, which are not flexible and expressive enough. In this paper, we propose a novel TKGC method, TKGC-AGP, by mapping the entities and relations in TKG to the approximations of multivariate Gaussian processes (MGPs). Equipped with the flexibility and capacity of MGP, the global trends as well as the local fluctuations in the TKGs can be simultaneously modeled. Moreover, the temporal uncertainties can be also captured with the kernel function and the covariance matrix of MGP. Moreover, a first-order Markov assumptionbased training algorithm is proposed to effective optimize the proposed method. Experimental results show the effectiveness of the proposed approach on two real-world benchmark datasets compared with some state-of-the-art TKGC methods.

Temporal Knowledge Graph Completion with Approximated Gaussian Process Embedding

Driven by recent advances in neural networks, various Deep Embedding Clustering (DEC) based short text clustering models are being developed. In these works, latent representation learning and text clustering are performed simultaneously. Although these methods are becoming increasingly popular, they use pure cluster-oriented objectives, which can produce meaningless representations. To alleviate this problem, several improvements have been developed to introduce additional learning objectives in the clustering process, such as models based on contrastive learning. However, existing efforts rely heavily on learning meaningful representations at the instance level. They have limited focus on learning global representations, which are necessary to capture the overall data structure at the cluster level. In this paper, we propose a novel DEC model, which we named the deep embedded clustering model with cluster-level representation learning (DECCRL) to jointly learn cluster and instance level representations. Here, we extend the embedded topic modelling approach to introduce reconstruction constraints to help learn cluster-level representations. Experimental results on real-world short text datasets demonstrate that our model produces meaningful clusters.

Improving Deep Embedded Clustering via Learning Cluster-level Representations

Question generation is the task of automatically generating questions based on given context and answers, and there are problems that the types of questions and answers do not match. In minority languages such as Tibetan, since the grammar rules are complex and the training data is small, the related research on question generation is still in its infancy. To solve the above problems, this paper constructs a question type classifier and a question generator. We perform fine-grained division of question types and integrate grammatical knowledge into question type classifiers to improve the accuracy of question types. Then, the types predicted by the question type classifier are fed into the question generator.

Question Generation Based on Grammar Knowledge and Fine-grained Classification

Despite their progress in high-resource language settings, unsupervised bilingual lexicon induction (UBLI) models often fail on corpora with low-resource distant language pairs due to insufficient initialization. In this work, we propose a cross-lingual feature extraction (CFE) method to learn the cross-lingual features from monolingual corpora for low-resource UBLI, enabling representations of words with the same meaning leveraged by the initialization step. By integrating cross-lingual representations with pre-trained word embeddings in a fully unsupervised initialization on UBLI, the proposed method outperforms existing state-of-the-art methods on low-resource language pairs (EN-VI, EN-TH, EN-ZH, EN-JA). The ablation study also proves that the learned cross-lingual features can enhance the representational ability and robustness of the existing embedding model.

Cross-lingual Feature Extraction from Monolingual Corpora for Low-resource Unsupervised Bilingual Lexicon Induction

Question answering over knowledge bases (KBQA) for complex questions is a challenging task in natural language processing. Recently, generation-based methods that translate natural language questions to executable logical forms have achieved promising performance. These methods use auxiliary information to augment the logical form generation of questions with unseen KB items or novel combinations, but the noise introduced can also leads to more incorrect results. In this work, we propose GMT-KBQA, a Generation-based KBQA method via Multi-Task learning, to better retrieve and utilize auxiliary information. GMT-KBQA first obtains candidate entities and relations through dense retrieval, and then introduces a multi-task model which jointly learns entity disambiguation, relation classification, and logical form generation. Experimental results show that GMT-KBQA achieves state-of-the-art results on both ComplexWebQuestions and WebQuestionsSP datasets. Furthermore, the detailed evaluation demonstrates that GMT-KBQA benefits from the auxiliary tasks and has a strong generalization capability.

Logical Form Generation via Multi-task Learning for Complex Question Answering over Knowledge Bases

Most graph-to-text works are built on the encoder-decoder framework with cross-attention mechanism. Recent studies have shown that explicitly modeling the input graph structure can significantly improve the performance. However, the vanilla structural encoder cannot capture all specialized information in a single forward pass for all decoding steps, resulting in inaccurate semantic representations. 
Meanwhile, the input graph is flatted as an unordered sequence in the cross attention, ignoring the original graph structure. As a result, the obtained input graph context vector in the decoder may be flawed. To address these issues, we propose a Structure-Aware Cross-Attention (SACA) mechanism to re-encode the input graph representation conditioning on the newly generated context at each decoding step in a structure aware manner. We further adapt SACA and introduce its variant Dynamic Graph Pruning (DGP) mechanism to dynamically drop irrelevant nodes in the decoding process. We achieve new state-of-the-art results on two graph-to-text datasets, LDC2020T02 and ENT-DESC, with only minor increase on computational cost.

Graph-to-Text Generation with Dynamic Structure Pruning

Relation extraction in the biomedical domain is challenging due to the lack of labeled data and high annotation costs, needing domain experts. Distant supervision is commonly used to tackle the scarcity of annotated data by automatically pairing knowledge graph relationships with raw texts. Such a pipeline is prone to noise and has added challenges to scale for covering a large number of biomedical concepts. We investigated existing broad-coverage distantly supervised biomedical relation extraction benchmarks and found a significant overlap between training and test relationships ranging from 26% to 86%. Furthermore, we noticed several inconsistencies in the data construction process of these benchmarks, and where there is no train-test leakage, the focus is on interactions between narrower entity types. This work presents a more accurate benchmark MedDistant19 for broad-coverage distantly supervised biomedical relation extraction that addresses these shortcomings and is obtained by aligning the MEDLINE abstracts with the widely used SNOMED Clinical Terms knowledge base. Lacking thorough evaluation with domain-specific language models, we also conduct experiments validating general domain relation extraction findings to biomedical relation extraction.

MedDistant19: Towards an Accurate Benchmark for Broad-Coverage Biomedical Relation Extraction

Transformer-based pre-trained language models such as BERT have achieved remarkable results in Semantic Sentence Matching. However, existing models still suffer from insufficient ability to capture subtle differences. Minor noise like word addition, deletion, and modification of sentences may cause flipped predictions .
To alleviate this problem, we propose a novel Dual Attention Enhanced BERT (DABERT) to enhance the ability of BERT to capture fine-grained differences in sentence pairs.

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Hierarchical Representation-based Dynamic Reasoning Network for Biomedical Question Answering

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Source-summary Entity Aggregation in Abstractive Summarization