arXiv subjects

Liang Yao

Publications and source records attributed to Liang Yao.

52 records · Page 3Linked to original sources

arXiv2022

MedGCN: Medication recommendation and lab test imputation via graph convolutional networks

Laboratory testing and medication prescription are two of the most important routines in daily clinical practice. Developing an artificial intelligence system that can automatically make lab test imputations and medication recommendations can save costs on potentially redundant lab tests and inform physicians of a more effective prescription. We present an intelligent medical system (named MedGCN) that can automatically recommend the patients' medications based on their incomplete lab tests, and can even accurately estimate the lab values that have not been taken. In our system, we integrate the complex relations between multiple types of medical entities with their inherent features in a heterogeneous graph. Then we model the graph to learn a distributed representation for each entity in the graph based on graph convolutional networks (GCN). By the propagation of graph convolutional networks, the entity representations can incorporate multiple types of medical information that can benefit multiple medical tasks. Moreover, we introduce a cross regularization strategy to reduce overfitting for multi-task training by the interaction between the multiple tasks. In this study, we construct a graph to associate 4 types of medical entities, i.e., patients, encounters, lab tests, and medications, and applied a graph neural network to learn node embeddings for medication recommendation and lab test imputation. we validate our MedGCN model on two real-world datasets: NMEDW and MIMIC-III. The experimental results on both datasets demonstrate that our model can outperform the state-of-the-art in both tasks. We believe that our innovative system can provide a promising and reliable way to assist physicians to make medication prescriptions and to save costs on potentially redundant lab tests.

cs.LG↗

arXiv2022

CFNet: Learning Correlation Functions for One-Stage Panoptic Segmentation

Recently, there is growing attention on one-stage panoptic segmentation methods which aim to segment instances and stuff jointly within a fully convolutional pipeline efficiently. However, most of the existing works directly feed the backbone features to various segmentation heads ignoring the demands for semantic and instance segmentation are different: The former needs semantic-level discriminative features, while the latter requires features to be distinguishable across instances. To alleviate this, we propose to first predict semantic-level and instance-level correlations among different locations that are utilized to enhance the backbone features, and then feed the improved discriminative features into the corresponding segmentation heads, respectively. Specifically, we organize the correlations between a given location and all locations as a continuous sequence and predict it as a whole. Considering that such a sequence can be extremely complicated, we adopt Discrete Fourier Transform (DFT), a tool that can approximate an arbitrary sequence parameterized by amplitudes and phrases. For different tasks, we generate these parameters from the backbone features in a fully convolutional way which is optimized implicitly by corresponding tasks. As a result, these accurate and consistent correlations contribute to producing plausible discriminative features which meet the requirements of the complicated panoptic segmentation task. To verify the effectiveness of our methods, we conduct experiments on several challenging panoptic segmentation datasets and achieve state-of-the-art performance on MS COCO with $45.1$\% PQ and ADE20k with $32.6$\% PQ.

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arXiv2021

Towards User-Driven Neural Machine Translation

A good translation should not only translate the original content semantically, but also incarnate personal traits of the original text. For a real-world neural machine translation (NMT) system, these user traits (e.g., topic preference, stylistic characteristics and expression habits) can be preserved in user behavior (e.g., historical inputs). However, current NMT systems marginally consider the user behavior due to: 1) the difficulty of modeling user portraits in zero-shot scenarios, and 2) the lack of user-behavior annotated parallel dataset. To fill this gap, we introduce a novel framework called user-driven NMT. Specifically, a cache-based module and a user-driven contrastive learning method are proposed to offer NMT the ability to capture potential user traits from their historical inputs under a zero-shot learning fashion. Furthermore, we contribute the first Chinese-English parallel corpus annotated with user behavior called UDT-Corpus. Experimental results confirm that the proposed user-driven NMT can generate user-specific translations.

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arXiv2020

Constraint Translation Candidates: A Bridge between Neural Query Translation and Cross-lingual Information Retrieval

Query translation (QT) is a key component in cross-lingual information retrieval system (CLIR). With the help of deep learning, neural machine translation (NMT) has shown promising results on various tasks. However, NMT is generally trained with large-scale out-of-domain data rather than in-domain query translation pairs. Besides, the translation model lacks a mechanism at the inference time to guarantee the generated words to match the search index. The two shortages of QT result in readable texts for human but inadequate candidates for the downstream retrieval task. In this paper, we propose a novel approach to alleviate these problems by limiting the open target vocabulary search space of QT to a set of important words mined from search index database. The constraint translation candidates are employed at both of training and inference time, thus guiding the translation model to learn and generate well performing target queries. The proposed methods are exploited and examined in a real-word CLIR system--Aliexpress e-Commerce search engine. Experimental results demonstrate that our approach yields better performance on both translation quality and retrieval accuracy than the strong NMT baseline.

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arXiv2020

Exploiting Neural Query Translation into Cross Lingual Information Retrieval

As a crucial role in cross-language information retrieval (CLIR), query translation has three main challenges: 1) the adequacy of translation; 2) the lack of in-domain parallel training data; and 3) the requisite of low latency. To this end, existing CLIR systems mainly exploit statistical-based machine translation (SMT) rather than the advanced neural machine translation (NMT), limiting the further improvements on both translation and retrieval quality. In this paper, we investigate how to exploit neural query translation model into CLIR system. Specifically, we propose a novel data augmentation method that extracts query translation pairs according to user clickthrough data, thus to alleviate the problem of domain-adaptation in NMT. Then, we introduce an asynchronous strategy which is able to leverage the advantages of the real-time in SMT and the veracity in NMT. Experimental results reveal that the proposed approach yields better retrieval quality than strong baselines and can be well applied into a real-world CLIR system, i.e. Aliexpress e-Commerce search engine. Readers can examine and test their cases on our website: https://aliexpress.com .

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arXiv2020

Towards Expressive Graph Representation

Graph Neural Network (GNN) aggregates the neighborhood of each node into the node embedding and shows its powerful capability for graph representation learning. However, most existing GNN variants aggregate the neighborhood information in a fixed non-injective fashion, which may map different graphs or nodes to the same embedding, reducing the model expressiveness. We present a theoretical framework to design a continuous injective set function for neighborhood aggregation in GNN. Using the framework, we propose expressive GNN that aggregates the neighborhood of each node with a continuous injective set function, so that a GNN layer maps similar nodes with similar neighborhoods to similar embeddings, different nodes to different embeddings and the equivalent nodes or isomorphic graphs to the same embeddings. Moreover, the proposed expressive GNN can naturally learn expressive representations for graphs with continuous node attributes. We validate the proposed expressive GNN (ExpGNN) for graph classification on multiple benchmark datasets including simple graphs and attributed graphs. The experimental results demonstrate that our model achieves state-of-the-art performances on most of the benchmarks.

cs.LG↗

arXiv2019

KG-BERT: BERT for Knowledge Graph Completion

Knowledge graphs are important resources for many artificial intelligence tasks but often suffer from incompleteness. In this work, we propose to use pre-trained language models for knowledge graph completion. We treat triples in knowledge graphs as textual sequences and propose a novel framework named Knowledge Graph Bidirectional Encoder Representations from Transformer (KG-BERT) to model these triples. Our method takes entity and relation descriptions of a triple as input and computes scoring function of the triple with the KG-BERT language model. Experimental results on multiple benchmark knowledge graphs show that our method can achieve state-of-the-art performance in triple classification, link prediction and relation prediction tasks.

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arXiv2019

Evaluating the Portability of an NLP System for Processing Echocardiograms: A Retrospective, Multi-site Observational Study

While natural language processing (NLP) of unstructured clinical narratives holds the potential for patient care and clinical research, portability of NLP approaches across multiple sites remains a major challenge. This study investigated the portability of an NLP system developed initially at the Department of Veterans Affairs (VA) to extract 27 key cardiac concepts from free-text or semi-structured echocardiograms from three academic medical centers: Weill Cornell Medicine, Mayo Clinic and Northwestern Medicine. While the NLP system showed high precision and recall measurements for four target concepts (aortic valve regurgitation, left atrium size at end systole, mitral valve regurgitation, tricuspid valve regurgitation) across all sites, we found moderate or poor results for the remaining concepts and the NLP system performance varied between individual sites.

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arXiv2018

Distribution Networks for Open Set Learning

In open set learning, a model must be able to generalize to novel classes when it encounters a sample that does not belong to any of the classes it has seen before. Open set learning poses a realistic learning scenario that is receiving growing attention. Existing studies on open set learning mainly focused on detecting novel classes, but few studies tried to model them for differentiating novel classes. In this paper, we recognize that novel classes should be different from each other, and propose distribution networks for open set learning that can model different novel classes based on probability distributions. We hypothesize that, through a certain mapping, samples from different classes with the same classification criterion should follow different probability distributions from the same distribution family. A deep neural network is learned to map the samples in the original feature space to a latent space where the distributions of known classes can be jointly learned with the network. We additionally propose a distribution parameter transfer and updating strategy for novel class modeling when a novel class is detected in the latent space. By novel class modeling, the detected novel classes can serve as known classes to the subsequent classification. Our experimental results on image datasets MNIST and CIFAR10 show that the distribution networks can detect novel classes accurately, and model them well for the subsequent classification tasks.

cs.LG↗

arXiv2018

Graph Convolutional Networks for Text Classification

Text classification is an important and classical problem in natural language processing. There have been a number of studies that applied convolutional neural networks (convolution on regular grid, e.g., sequence) to classification. However, only a limited number of studies have explored the more flexible graph convolutional neural networks (convolution on non-grid, e.g., arbitrary graph) for the task. In this work, we propose to use graph convolutional networks for text classification. We build a single text graph for a corpus based on word co-occurrence and document word relations, then learn a Text Graph Convolutional Network (Text GCN) for the corpus. Our Text GCN is initialized with one-hot representation for word and document, it then jointly learns the embeddings for both words and documents, as supervised by the known class labels for documents. Our experimental results on multiple benchmark datasets demonstrate that a vanilla Text GCN without any external word embeddings or knowledge outperforms state-of-the-art methods for text classification. On the other hand, Text GCN also learns predictive word and document embeddings. In addition, experimental results show that the improvement of Text GCN over state-of-the-art comparison methods become more prominent as we lower the percentage of training data, suggesting the robustness of Text GCN to less training data in text classification.

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arXiv2018

Early Prediction of Acute Kidney Injury in Critical Care Setting Using Clinical Notes

Acute kidney injury (AKI) in critically ill patients is associated with significant morbidity and mortality. Development of novel methods to identify patients with AKI earlier will allow for testing of novel strategies to prevent or reduce the complications of AKI. We developed data-driven prediction models to estimate the risk of new AKI onset. We generated models from clinical notes within the first 24 hours following intensive care unit (ICU) admission extracted from Medical Information Mart for Intensive Care III (MIMIC-III). From the clinical notes, we generated clinically meaningful word and concept representations and embeddings, respectively. Five supervised learning classifiers and knowledge-guided deep learning architecture were used to construct prediction models. The best configuration yielded a competitive AUC of 0.779. Our work suggests that natural language processing of clinical notes can be applied to assist clinicians in identifying the risk of incident AKI onset in critically ill patients upon admission to the ICU.

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arXiv2018

Deep Generative Classifiers for Thoracic Disease Diagnosis with Chest X-ray Images

Thoracic diseases are very serious health problems that plague a large number of people. Chest X-ray is currently one of the most popular methods to diagnose thoracic diseases, playing an important role in the healthcare workflow. However, reading the chest X-ray images and giving an accurate diagnosis remain challenging tasks for expert radiologists. With the success of deep learning in computer vision, a growing number of deep neural network architectures were applied to chest X-ray image classification. However, most of the previous deep neural network classifiers were based on deterministic architectures which are usually very noise-sensitive and are likely to aggravate the overfitting issue. In this paper, to make a deep architecture more robust to noise and to reduce overfitting, we propose using deep generative classifiers to automatically diagnose thorax diseases from the chest X-ray images. Unlike the traditional deterministic classifier, a deep generative classifier has a distribution middle layer in the deep neural network. A sampling layer then draws a random sample from the distribution layer and input it to the following layer for classification. The classifier is generative because the class label is generated from samples of a related distribution. Through training the model with a certain amount of randomness, the deep generative classifiers are expected to be robust to noise and can reduce overfitting and then achieve good performances. We implemented our deep generative classifiers based on a number of well-known deterministic neural network architectures, and tested our models on the chest X-ray14 dataset. The results demonstrated the superiority of deep generative classifiers compared with the corresponding deep deterministic classifiers.

cs.CV↗

arXiv2018

Clinical Text Classification with Rule-based Features and Knowledge-guided Convolutional Neural Networks

Clinical text classification is an important problem in medical natural language processing. Existing studies have conventionally focused on rules or knowledge sources-based feature engineering, but only a few have exploited effective feature learning capability of deep learning methods. In this study, we propose a novel approach which combines rule-based features and knowledge-guided deep learning techniques for effective disease classification. Critical Steps of our method include identifying trigger phrases, predicting classes with very few examples using trigger phrases and training a convolutional neural network with word embeddings and Unified Medical Language System (UMLS) entity embeddings. We evaluated our method on the 2008 Integrating Informatics with Biology and the Bedside (i2b2) obesity challenge. The results show that our method outperforms the state of the art methods.

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arXiv2018

Developing a Portable Natural Language Processing Based Phenotyping System

This paper presents a portable phenotyping system that is capable of integrating both rule-based and statistical machine learning based approaches. Our system utilizes UMLS to extract clinically relevant features from the unstructured text and then facilitates portability across different institutions and data systems by incorporating OHDSI's OMOP Common Data Model (CDM) to standardize necessary data elements. Our system can also store the key components of rule-based systems (e.g., regular expression matches) in the format of OMOP CDM, thus enabling the reuse, adaptation and extension of many existing rule-based clinical NLP systems. We experimented with our system on the corpus from i2b2's Obesity Challenge as a pilot study. Our system facilitates portable phenotyping of obesity and its 15 comorbidities based on the unstructured patient discharge summaries, while achieving a performance that often ranked among the top 10 of the challenge participants. This standardization enables a consistent application of numerous rule-based and machine learning based classification techniques downstream.

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arXiv2013

Context-based Diversification for Keyword Queries over XML Data

While keyword query empowers ordinary users to search vast amount of data, the ambiguity of keyword query makes it difficult to effectively answer keyword queries, especially for short and vague keyword queries. To address this challenging problem, in this paper we propose an approach that automatically diversifies XML keyword search based on its different contexts in the XML data. Given a short and vague keyword query and XML data to be searched, we firstly derive keyword search candidates of the query by a classifical feature selection model. And then, we design an effective XML keyword search diversification model to measure the quality of each candidate. After that, three efficient algorithms are proposed to evaluate the possible generated query candidates representing the diversified search intentions, from which we can find and return top-$k$ qualified query candidates that are most relevant to the given keyword query while they can cover maximal number of distinct results.At last, a comprehensive evaluation on real and synthetic datasets demonstrates the effectiveness of our proposed diversification model and the efficiency of our algorithms.

cs.DB↗

arXiv2013

Query-driven Frequent Co-occurring Term Extraction over Relational Data using MapReduce

In this paper we study how to efficiently compute \textit{frequent co-occurring terms} (FCT) in the results of a keyword query in parallel using the popular MapReduce framework. Taking as input a keyword query q and an integer k, an FCT query reports the k terms that are not in q, but appear most frequently in the results of the keyword query q over multiple joined relations. The returned terms of FCT search can be used to do query expansion and query refinement for traditional keyword search. Different from the method of FCT search in a single platform, our proposed approach can efficiently answer a FCT query using the MapReduce Paradigm without pre-computing the results of the original keyword query, which is run in parallel platform. In this work, we can output the final FCT search results by two MapReduce jobs: the first is to extract the statistical information of the data; and the second is to calculate the total frequency of each term based on the output of the first job. At the two MapReduce jobs, we would guarantee the load balance of mappers and the computational balance of reducers as much as possible. Analytical and experimental evaluations demonstrate the efficiency and scalability of our proposed approach using TPC-H benchmark datasets with different sizes.

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