arXiv subjects

Xiang Yue

Publications and source records attributed to Xiang Yue.

80 records · Page 5Linked to original sources

arXiv2021

Differential Privacy for Text Analytics via Natural Text Sanitization

Texts convey sophisticated knowledge. However, texts also convey sensitive information. Despite the success of general-purpose language models and domain-specific mechanisms with differential privacy (DP), existing text sanitization mechanisms still provide low utility, as cursed by the high-dimensional text representation. The companion issue of utilizing sanitized texts for downstream analytics is also under-explored. This paper takes a direct approach to text sanitization. Our insight is to consider both sensitivity and similarity via our new local DP notion. The sanitized texts also contribute to our sanitization-aware pretraining and fine-tuning, enabling privacy-preserving natural language processing over the BERT language model with promising utility. Surprisingly, the high utility does not boost up the success rate of inference attacks.

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arXiv2020

PHICON: Improving Generalization of Clinical Text De-identification Models via Data Augmentation

De-identification is the task of identifying protected health information (PHI) in the clinical text. Existing neural de-identification models often fail to generalize to a new dataset. We propose a simple yet effective data augmentation method PHICON to alleviate the generalization issue. PHICON consists of PHI augmentation and Context augmentation, which creates augmented training corpora by replacing PHI entities with named-entities sampled from external sources, and by changing background context with synonym replacement or random word insertion, respectively. Experimental results on the i2b2 2006 and 2014 de-identification challenge datasets show that PHICON can help three selected de-identification models boost F1-score (by at most 8.6%) on cross-dataset test setting. We also discuss how much augmentation to use and how each augmentation method influences the performance.

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arXiv2020

Towards Making the Most of Context in Neural Machine Translation

Document-level machine translation manages to outperform sentence level models by a small margin, but have failed to be widely adopted. We argue that previous research did not make a clear use of the global context, and propose a new document-level NMT framework that deliberately models the local context of each sentence with the awareness of the global context of the document in both source and target languages. We specifically design the model to be able to deal with documents containing any number of sentences, including single sentences. This unified approach allows our model to be trained elegantly on standard datasets without needing to train on sentence and document level data separately. Experimental results demonstrate that our model outperforms Transformer baselines and previous document-level NMT models with substantial margins of up to 2.1 BLEU on state-of-the-art baselines. We also provide analyses which show the benefit of context far beyond the neighboring two or three sentences, which previous studies have typically incorporated.

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arXiv2020

Clinical Reading Comprehension: A Thorough Analysis of the emrQA Dataset

Machine reading comprehension has made great progress in recent years owing to large-scale annotated datasets. In the clinical domain, however, creating such datasets is quite difficult due to the domain expertise required for annotation. Recently, Pampari et al. (EMNLP'18) tackled this issue by using expert-annotated question templates and existing i2b2 annotations to create emrQA, the first large-scale dataset for question answering (QA) based on clinical notes. In this paper, we provide an in-depth analysis of this dataset and the clinical reading comprehension (CliniRC) task. From our qualitative analysis, we find that (i) emrQA answers are often incomplete, and (ii) emrQA questions are often answerable without using domain knowledge. From our quantitative experiments, surprising results include that (iii) using a small sampled subset (5%-20%), we can obtain roughly equal performance compared to the model trained on the entire dataset, (iv) this performance is close to human expert's performance, and (v) BERT models do not beat the best performing base model. Following our analysis of the emrQA, we further explore two desired aspects of CliniRC systems: the ability to utilize clinical domain knowledge and to generalize to unseen questions and contexts. We argue that both should be considered when creating future datasets.

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arXiv2020

Tensor Decomposition with Relational Constraints for Predicting Multiple Types of MicroRNA-disease Associations

MicroRNAs (miRNAs) play crucial roles in multifarious biological processes associated with human diseases. Identifying potential miRNA-disease associations contributes to understanding the molecular mechanisms of miRNA-related diseases. Most of the existing computational methods mainly focus on predicting whether a miRNA-disease association exists or not. However, the roles of miRNAs in diseases are prominently diverged, for instance, Genetic variants of microRNA (mir-15) may affect expression level of miRNAs leading to B cell chronic lymphocytic leukemia, while circulating miRNAs (including mir-1246, mir-1307-3p, etc.) have potentials to detecting breast cancer in the early stage. In this paper, we aim to predict multi-type miRNA-disease associations instead of taking them as binary. To this end, we innovatively represent miRNA-disease-type triplets as a tensor and introduce Tensor Decomposition methods to solve the prediction task. Experimental results on two widely-adopted miRNA-disease datasets: HMDD v2.0 and HMDD v3.2 show that tensor decomposition methods improve a recent baseline in a large scale (up to 38% in top-1 F1). We further propose a novel method, Tensor Decomposition with Relational Constraints (TDRC), which incorporates biological features as relational constraints to further the existing tensor decomposition methods. Compared with two existing tensor decomposition methods, TDRC can produce better performance while being more efficient.

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arXiv2020

Practical Annotation Strategies for Question Answering Datasets

Annotating datasets for question answering (QA) tasks is very costly, as it requires intensive manual labor and often domain-specific knowledge. Yet strategies for annotating QA datasets in a cost-effective manner are scarce. To provide a remedy for practitioners, our objective is to develop heuristic rules for annotating a subset of questions, so that the annotation cost is reduced while maintaining both in- and out-of-domain performance. For this, we conduct a large-scale analysis in order to derive practical recommendations. First, we demonstrate experimentally that more training samples contribute often only to a higher in-domain test-set performance, but do not help the model in generalizing to unseen datasets. Second, we develop a model-guided annotation strategy: it makes a recommendation with regard to which subset of samples should be annotated. Its effectiveness is demonstrated in a case study based on domain customization of QA to a clinical setting. Here, remarkably, annotating a stratified subset with only 1.2% of the original training set achieves 97.7% of the performance as if the complete dataset was annotated. Hence, the labeling effort can be reduced immensely. Altogether, our work fulfills a demand in practice when labeling budgets are limited and where thus recommendations are needed for annotating QA datasets more cost-effectively.

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arXiv2020

Graph Embedding on Biomedical Networks: Methods, Applications, and Evaluations

Graph embedding learning that aims to automatically learn low-dimensional node representations, has drawn increasing attention in recent years. To date, most recent graph embedding methods are evaluated on social and information networks and are not comprehensively studied on biomedical networks under systematic experiments and analyses. On the other hand, for a variety of biomedical network analysis tasks, traditional techniques such as matrix factorization (which can be seen as a type of graph embedding methods) have shown promising results, and hence there is a need to systematically evaluate the more recent graph embedding methods (e.g. random walk-based and neural network-based) in terms of their usability and potential to further the state-of-the-art. We select 11 representative graph embedding methods and conduct a systematic comparison on 3 important biomedical link prediction tasks: drug-disease association (DDA) prediction, drug-drug interaction (DDI) prediction, protein-protein interaction (PPI) prediction; and 2 node classification tasks: medical term semantic type classification, protein function prediction. Our experimental results demonstrate that the recent graph embedding methods achieve promising results and deserve more attention in the future biomedical graph analysis. Compared with three state-of-the-art methods for DDAs, DDIs and protein function predictions, the recent graph embedding methods achieve competitive performance without using any biological features and the learned embeddings can be treated as complementary representations for the biological features. By summarizing the experimental results, we provide general guidelines for properly selecting graph embedding methods and setting their hyper-parameters for different biomedical tasks.

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arXiv2019

SurfCon: Synonym Discovery on Privacy-Aware Clinical Data

Unstructured clinical texts contain rich health-related information. To better utilize the knowledge buried in clinical texts, discovering synonyms for a medical query term has become an important task. Recent automatic synonym discovery methods leveraging raw text information have been developed. However, to preserve patient privacy and security, it is usually quite difficult to get access to large-scale raw clinical texts. In this paper, we study a new setting named synonym discovery on privacy-aware clinical data (i.e., medical terms extracted from the clinical texts and their aggregated co-occurrence counts, without raw clinical texts). To solve the problem, we propose a new framework SurfCon that leverages two important types of information in the privacy-aware clinical data, i.e., the surface form information, and the global context information for synonym discovery. In particular, the surface form module enables us to detect synonyms that look similar while the global context module plays a complementary role to discover synonyms that are semantically similar but in different surface forms, and both allow us to deal with the OOV query issue (i.e., when the query is not found in the given data). We conduct extensive experiments and case studies on publicly available privacy-aware clinical data, and show that SurfCon can outperform strong baseline methods by large margins under various settings.

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