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Guodong Long

Guodong Long contributes to research discovery and scholarly infrastructure.

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Published work

25 published item(s)

preprint2026arXiv

Federated Weather Modeling on Sensor Data

Federated weather modeling on sensor data is a distributed system underpinned by federated learning, enabling multiple sensor data sources, including ground weather stations, satellites and IoT devices, to collaboratively train deep learning models without sharing raw data. This method safeguards data privacy and security while leverages diverse, geographically distributed datasets to improve the accuracy and robustness of global/regional weather modeling tasks such as forecasting and anomaly detection.

preprint2026arXiv

MIPO: Mutual Integration of Patient Journey and Medical Ontology for Healthcare Representation Learning

Representation learning on electronic health records (EHRs) plays a vital role in downstream medical prediction tasks. Although natural language processing techniques, such as recurrent neural networks, and self-attention, have been adapted for learning medical representations from hierarchical, time-stamped EHR data, they often struggle when either general or task-specific data are limited. Recent efforts have attempted to mitigate this challenge by incorporating medical ontologies (i.e., knowledge graphs) into self-supervised tasks like diagnosis prediction. However, two main issues remain: (1) small and uniform ontologies that lack diversity for robust learning, and (2) insufficient attention to the critical contexts or dependencies underlying patient journeys, which could further enhance ontology-based learning. To address these gaps, we propose MIPO (Mutual Integration of Patient Journey and Medical Ontology), a robust end-to-end framework that employs a Transformer-based architecture for representation learning. MIPO emphasizes task-specific representation learning through a sequential diagnosis prediction task, while also incorporating an ontology-based disease-typing task. A graph-embedding module is introduced to integrate information from patient visit records, thus alleviating data insufficiency. This setup creates a mutually reinforcing loop, where both patient-journey embedding and ontology embedding benefit from each other. We validate MIPO on two real-world benchmark datasets, showing that it consistently outperforms baseline methods under both sufficient and limited data conditions. Furthermore, the resulting diagnosis embeddings offer improved interpretability, underscoring the promise of MIPO for real-world healthcare applications.

preprint2022arXiv

Beyond Low-pass Filtering: Graph Convolutional Networks with Automatic Filtering

Graph convolutional networks are becoming indispensable for deep learning from graph-structured data. Most of the existing graph convolutional networks share two big shortcomings. First, they are essentially low-pass filters, thus the potentially useful middle and high frequency band of graph signals are ignored. Second, the bandwidth of existing graph convolutional filters is fixed. Parameters of a graph convolutional filter only transform the graph inputs without changing the curvature of a graph convolutional filter function. In reality, we are uncertain about whether we should retain or cut off the frequency at a certain point unless we have expert domain knowledge. In this paper, we propose Automatic Graph Convolutional Networks (AutoGCN) to capture the full spectrum of graph signals and automatically update the bandwidth of graph convolutional filters. While it is based on graph spectral theory, our AutoGCN is also localized in space and has a spatial form. Experimental results show that AutoGCN achieves significant improvement over baseline methods which only work as low-pass filters.

preprint2022arXiv

ClarET: Pre-training a Correlation-Aware Context-To-Event Transformer for Event-Centric Generation and Classification

Generating new events given context with correlated ones plays a crucial role in many event-centric reasoning tasks. Existing works either limit their scope to specific scenarios or overlook event-level correlations. In this paper, we propose to pre-train a general Correlation-aware context-to-Event Transformer (ClarET) for event-centric reasoning. To achieve this, we propose three novel event-centric objectives, i.e., whole event recovering, contrastive event-correlation encoding and prompt-based event locating, which highlight event-level correlations with effective training. The proposed ClarET is applicable to a wide range of event-centric reasoning scenarios, considering its versatility of (i) event-correlation types (e.g., causal, temporal, contrast), (ii) application formulations (i.e., generation and classification), and (iii) reasoning types (e.g., abductive, counterfactual and ending reasoning). Empirical fine-tuning results, as well as zero- and few-shot learning, on 9 benchmarks (5 generation and 4 classification tasks covering 4 reasoning types with diverse event correlations), verify its effectiveness and generalization ability.

preprint2022arXiv

FedNoiL: A Simple Two-Level Sampling Method for Federated Learning with Noisy Labels

Federated learning (FL) aims at training a global model on the server side while the training data are collected and located at the local devices. Hence, the labels in practice are usually annotated by clients of varying expertise or criteria and thus contain different amounts of noises. Local training on noisy labels can easily result in overfitting to noisy labels, which is devastating to the global model through aggregation. Although recent robust FL methods take malicious clients into account, they have not addressed local noisy labels on each device and the impact to the global model. In this paper, we develop a simple two-level sampling method "FedNoiL" that (1) selects clients for more robust global aggregation on the server; and (2) selects clean labels and correct pseudo-labels at the client end for more robust local training. The sampling probabilities are built upon clean label detection by the global model. Moreover, we investigate different schedules changing the local epochs between aggregations over the course of FL, which notably improves the communication and computation efficiency in noisy label setting. In experiments with homogeneous/heterogeneous data distributions and noise ratios, we observed that direct combinations of SOTA FL methods with SOTA noisy-label learning methods can easily fail but our method consistently achieves better and robust performance.

preprint2022arXiv

FedProto: Federated Prototype Learning across Heterogeneous Clients

Heterogeneity across clients in federated learning (FL) usually hinders the optimization convergence and generalization performance when the aggregation of clients' knowledge occurs in the gradient space. For example, clients may differ in terms of data distribution, network latency, input/output space, and/or model architecture, which can easily lead to the misalignment of their local gradients. To improve the tolerance to heterogeneity, we propose a novel federated prototype learning (FedProto) framework in which the clients and server communicate the abstract class prototypes instead of the gradients. FedProto aggregates the local prototypes collected from different clients, and then sends the global prototypes back to all clients to regularize the training of local models. The training on each client aims to minimize the classification error on the local data while keeping the resulting local prototypes sufficiently close to the corresponding global ones. Moreover, we provide a theoretical analysis to the convergence rate of FedProto under non-convex objectives. In experiments, we propose a benchmark setting tailored for heterogeneous FL, with FedProto outperforming several recent FL approaches on multiple datasets.

preprint2022arXiv

Omni-Scale CNNs: a simple and effective kernel size configuration for time series classification

The Receptive Field (RF) size has been one of the most important factors for One Dimensional Convolutional Neural Networks (1D-CNNs) on time series classification tasks. Large efforts have been taken to choose the appropriate size because it has a huge influence on the performance and differs significantly for each dataset. In this paper, we propose an Omni-Scale block (OS-block) for 1D-CNNs, where the kernel sizes are decided by a simple and universal rule. Particularly, it is a set of kernel sizes that can efficiently cover the best RF size across different datasets via consisting of multiple prime numbers according to the length of the time series. The experiment result shows that models with the OS-block can achieve a similar performance as models with the searched optimal RF size and due to the strong optimal RF size capture ability, simple 1D-CNN models with OS-block achieves the state-of-the-art performance on four time series benchmarks, including both univariate and multivariate data from multiple domains. Comprehensive analysis and discussions shed light on why the OS-block can capture optimal RF sizes across different datasets. Code available [https://github.com/Wensi-Tang/OS-CNN]

preprint2022arXiv

On the Convergence of Clustered Federated Learning

Knowledge sharing and model personalization are essential components to tackle the non-IID challenge in federated learning (FL). Most existing FL methods focus on two extremes: 1) to learn a shared model to serve all clients with non-IID data, and 2) to learn personalized models for each client, namely personalized FL. There is a trade-off solution, namely clustered FL or cluster-wise personalized FL, which aims to cluster similar clients into one cluster, and then learn a shared model for all clients within a cluster. This paper is to revisit the research of clustered FL by formulating them into a bi-level optimization framework that could unify existing methods. We propose a new theoretical analysis framework to prove the convergence by considering the clusterability among clients. In addition, we embody this framework in an algorithm, named Weighted Clustered Federated Learning (WeCFL). Empirical analysis verifies the theoretical results and demonstrates the effectiveness of the proposed WeCFL under the proposed cluster-wise non-IID settings.

preprint2022arXiv

Personalized Federated Learning With Graph

Knowledge sharing and model personalization are two key components in the conceptual framework of personalized federated learning (PFL). Existing PFL methods focus on proposing new model personalization mechanisms while simply implementing knowledge sharing by aggregating models from all clients, regardless of their relation graph. This paper aims to enhance the knowledge-sharing process in PFL by leveraging the graph-based structural information among clients. We propose a novel structured federated learning (SFL) framework to learn both the global and personalized models simultaneously using client-wise relation graphs and clients' private data. We cast SFL with graph into a novel optimization problem that can model the client-wise complex relations and graph-based structural topology by a unified framework. Moreover, in addition to using an existing relation graph, SFL could be expanded to learn the hidden relations among clients. Experiments on traffic and image benchmark datasets can demonstrate the effectiveness of the proposed method. All implementation codes are available on Github

preprint2022arXiv

Towards Robust Ranker for Text Retrieval

A ranker plays an indispensable role in the de facto 'retrieval & rerank' pipeline, but its training still lags behind -- learning from moderate negatives or/and serving as an auxiliary module for a retriever. In this work, we first identify two major barriers to a robust ranker, i.e., inherent label noises caused by a well-trained retriever and non-ideal negatives sampled for a high-capable ranker. Thereby, we propose multiple retrievers as negative generators improve the ranker's robustness, where i) involving extensive out-of-distribution label noises renders the ranker against each noise distribution, and ii) diverse hard negatives from a joint distribution are relatively close to the ranker's negative distribution, leading to more challenging thus effective training. To evaluate our robust ranker (dubbed R$^2$anker), we conduct experiments in various settings on the popular passage retrieval benchmark, including BM25-reranking, full-ranking, retriever distillation, etc. The empirical results verify the new state-of-the-art effectiveness of our model.

preprint2022arXiv

TraverseNet: Unifying Space and Time in Message Passing for Traffic Forecasting

This paper aims to unify spatial dependency and temporal dependency in a non-Euclidean space while capturing the inner spatial-temporal dependencies for traffic data. For spatial-temporal attribute entities with topological structure, the space-time is consecutive and unified while each node's current status is influenced by its neighbors' past states over variant periods of each neighbor. Most spatial-temporal neural networks for traffic forecasting study spatial dependency and temporal correlation separately in processing, gravely impaired the spatial-temporal integrity, and ignore the fact that the neighbors' temporal dependency period for a node can be delayed and dynamic. To model this actual condition, we propose TraverseNet, a novel spatial-temporal graph neural network, viewing space and time as an inseparable whole, to mine spatial-temporal graphs while exploiting the evolving spatial-temporal dependencies for each node via message traverse mechanisms. Experiments with ablation and parameter studies have validated the effectiveness of the proposed TraverseNet, and the detailed implementation can be found from https://github.com/nnzhan/TraverseNet.

preprint2021arXiv

Episodic memory governs choices: An RNN-based reinforcement learning model for decision-making task

Typical methods to study cognitive function are to record the electrical activities of animal neurons during the training of animals performing behavioral tasks. A key problem is that they fail to record all the relevant neurons in the animal brain. To alleviate this problem, we develop an RNN-based Actor-Critic framework, which is trained through reinforcement learning (RL) to solve two tasks analogous to the monkeys' decision-making tasks. The trained model is capable of reproducing some features of neural activities recorded from animal brain, or some behavior properties exhibited in animal experiments, suggesting that it can serve as a computational platform to explore other cognitive functions. Furthermore, we conduct behavioral experiments on our framework, trying to explore an open question in neuroscience: which episodic memory in the hippocampus should be selected to ultimately govern future decisions. We find that the retrieval of salient events sampled from episodic memories can effectively shorten deliberation time than common events in the decision-making process. The results indicate that salient events stored in the hippocampus could be prioritized to propagate reward information, and thus allow decision-makers to learn a strategy faster.

preprint2021arXiv

Isometric Propagation Network for Generalized Zero-shot Learning

Zero-shot learning (ZSL) aims to classify images of an unseen class only based on a few attributes describing that class but no access to any training sample. A popular strategy is to learn a mapping between the semantic space of class attributes and the visual space of images based on the seen classes and their data. Thus, an unseen class image can be ideally mapped to its corresponding class attributes. The key challenge is how to align the representations in the two spaces. For most ZSL settings, the attributes for each seen/unseen class are only represented by a vector while the seen-class data provide much more information. Thus, the imbalanced supervision from the semantic and the visual space can make the learned mapping easily overfitting to the seen classes. To resolve this problem, we propose Isometric Propagation Network (IPN), which learns to strengthen the relation between classes within each space and align the class dependency in the two spaces. Specifically, IPN learns to propagate the class representations on an auto-generated graph within each space. In contrast to only aligning the resulted static representation, we regularize the two dynamic propagation procedures to be isometric in terms of the two graphs' edge weights per step by minimizing a consistency loss between them. IPN achieves state-of-the-art performance on three popular ZSL benchmarks. To evaluate the generalization capability of IPN, we further build two larger benchmarks with more diverse unseen classes and demonstrate the advantages of IPN on them.

preprint2021arXiv

Structure-Augmented Text Representation Learning for Efficient Knowledge Graph Completion

Human-curated knowledge graphs provide critical supportive information to various natural language processing tasks, but these graphs are usually incomplete, urging auto-completion of them. Prevalent graph embedding approaches, e.g., TransE, learn structured knowledge via representing graph elements into dense embeddings and capturing their triple-level relationship with spatial distance. However, they are hardly generalizable to the elements never visited in training and are intrinsically vulnerable to graph incompleteness. In contrast, textual encoding approaches, e.g., KG-BERT, resort to graph triple's text and triple-level contextualized representations. They are generalizable enough and robust to the incompleteness, especially when coupled with pre-trained encoders. But two major drawbacks limit the performance: (1) high overheads due to the costly scoring of all possible triples in inference, and (2) a lack of structured knowledge in the textual encoder. In this paper, we follow the textual encoding paradigm and aim to alleviate its drawbacks by augmenting it with graph embedding techniques -- a complementary hybrid of both paradigms. Specifically, we partition each triple into two asymmetric parts as in translation-based graph embedding approach, and encode both parts into contextualized representations by a Siamese-style textual encoder. Built upon the representations, our model employs both deterministic classifier and spatial measurement for representation and structure learning respectively. Moreover, we develop a self-adaptive ensemble scheme to further improve the performance by incorporating triple scores from an existing graph embedding model. In experiments, we achieve state-of-the-art performance on three benchmarks and a zero-shot dataset for link prediction, with highlights of inference costs reduced by 1-2 orders of magnitude compared to a textual encoding method.

preprint2021arXiv

Task Aligned Generative Meta-learning for Zero-shot Learning

Zero-shot learning (ZSL) refers to the problem of learning to classify instances from the novel classes (unseen) that are absent in the training set (seen). Most ZSL methods infer the correlation between visual features and attributes to train the classifier for unseen classes. However, such models may have a strong bias towards seen classes during training. Meta-learning has been introduced to mitigate the basis, but meta-ZSL methods are inapplicable when tasks used for training are sampled from diverse distributions. In this regard, we propose a novel Task-aligned Generative Meta-learning model for Zero-shot learning (TGMZ). TGMZ mitigates the potentially biased training and enables meta-ZSL to accommodate real-world datasets containing diverse distributions. TGMZ incorporates an attribute-conditioned task-wise distribution alignment network that projects tasks into a unified distribution to deliver an unbiased model. Our comparisons with state-of-the-art algorithms show the improvements of 2.1%, 3.0%, 2.5%, and 7.6% achieved by TGMZ on AWA1, AWA2, CUB, and aPY datasets, respectively. TGMZ also outperforms competitors by 3.6% in generalized zero-shot learning (GZSL) setting and 7.9% in our proposed fusion-ZSL setting.

preprint2020arXiv

A Universal Representation Transformer Layer for Few-Shot Image Classification

Few-shot classification aims to recognize unseen classes when presented with only a small number of samples. We consider the problem of multi-domain few-shot image classification, where unseen classes and examples come from diverse data sources. This problem has seen growing interest and has inspired the development of benchmarks such as Meta-Dataset. A key challenge in this multi-domain setting is to effectively integrate the feature representations from the diverse set of training domains. Here, we propose a Universal Representation Transformer (URT) layer, that meta-learns to leverage universal features for few-shot classification by dynamically re-weighting and composing the most appropriate domain-specific representations. In experiments, we show that URT sets a new state-of-the-art result on Meta-Dataset. Specifically, it achieves top-performance on the highest number of data sources compared to competing methods. We analyze variants of URT and present a visualization of the attention score heatmaps that sheds light on how the model performs cross-domain generalization. Our code is available at https://github.com/liulu112601/URT.

preprint2020arXiv

Connecting the Dots: Multivariate Time Series Forecasting with Graph Neural Networks

Modeling multivariate time series has long been a subject that has attracted researchers from a diverse range of fields including economics, finance, and traffic. A basic assumption behind multivariate time series forecasting is that its variables depend on one another but, upon looking closely, it is fair to say that existing methods fail to fully exploit latent spatial dependencies between pairs of variables. In recent years, meanwhile, graph neural networks (GNNs) have shown high capability in handling relational dependencies. GNNs require well-defined graph structures for information propagation which means they cannot be applied directly for multivariate time series where the dependencies are not known in advance. In this paper, we propose a general graph neural network framework designed specifically for multivariate time series data. Our approach automatically extracts the uni-directed relations among variables through a graph learning module, into which external knowledge like variable attributes can be easily integrated. A novel mix-hop propagation layer and a dilated inception layer are further proposed to capture the spatial and temporal dependencies within the time series. The graph learning, graph convolution, and temporal convolution modules are jointly learned in an end-to-end framework. Experimental results show that our proposed model outperforms the state-of-the-art baseline methods on 3 of 4 benchmark datasets and achieves on-par performance with other approaches on two traffic datasets which provide extra structural information.

preprint2020arXiv

Exploiting Structured Knowledge in Text via Graph-Guided Representation Learning

In this work, we aim at equipping pre-trained language models with structured knowledge. We present two self-supervised tasks learning over raw text with the guidance from knowledge graphs. Building upon entity-level masked language models, our first contribution is an entity masking scheme that exploits relational knowledge underlying the text. This is fulfilled by using a linked knowledge graph to select informative entities and then masking their mentions. In addition we use knowledge graphs to obtain distractors for the masked entities, and propose a novel distractor-suppressed ranking objective which is optimized jointly with masked language model. In contrast to existing paradigms, our approach uses knowledge graphs implicitly, only during pre-training, to inject language models with structured knowledge via learning from raw text. It is more efficient than retrieval-based methods that perform entity linking and integration during finetuning and inference, and generalizes more effectively than the methods that directly learn from concatenated graph triples. Experiments show that our proposed model achieves improved performance on five benchmark datasets, including question answering and knowledge base completion tasks.

preprint2020arXiv

Interpretable Time-series Classification on Few-shot Samples

Recent few-shot learning works focus on training a model with prior meta-knowledge to fast adapt to new tasks with unseen classes and samples. However, conventional time-series classification algorithms fail to tackle the few-shot scenario. Existing few-shot learning methods are proposed to tackle image or text data, and most of them are neural-based models that lack interpretability. This paper proposes an interpretable neural-based framework, namely \textit{Dual Prototypical Shapelet Networks (DPSN)} for few-shot time-series classification, which not only trains a neural network-based model but also interprets the model from dual granularity: 1) global overview using representative time series samples, and 2) local highlights using discriminative shapelets. In particular, the generated dual prototypical shapelets consist of representative samples that can mostly demonstrate the overall shapes of all samples in the class and discriminative partial-length shapelets that can be used to distinguish different classes. We have derived 18 few-shot TSC datasets from public benchmark datasets and evaluated the proposed method by comparing with baselines. The DPSN framework outperforms state-of-the-art time-series classification methods, especially when training with limited amounts of data. Several case studies have been given to demonstrate the interpret ability of our model.

preprint2020arXiv

Self-Attention Enhanced Patient Journey Understanding in Healthcare System

Understanding patients' journeys in healthcare system is a fundamental prepositive task for a broad range of AI-based healthcare applications. This task aims to learn an informative representation that can comprehensively encode hidden dependencies among medical events and its inner entities, and then the use of encoding outputs can greatly benefit the downstream application-driven tasks. A patient journey is a sequence of electronic health records (EHRs) over time that is organized at multiple levels: patient, visits and medical codes. The key challenge of patient journey understanding is to design an effective encoding mechanism which can properly tackle the aforementioned multi-level structured patient journey data with temporal sequential visits and a set of medical codes. This paper proposes a novel self-attention mechanism that can simultaneously capture the contextual and temporal relationships hidden in patient journeys. A multi-level self-attention network (MusaNet) is specifically designed to learn the representations of patient journeys that is used to be a long sequence of activities. The MusaNet is trained in end-to-end manner using the training data derived from EHRs. We evaluated the efficacy of our method on two medical application tasks with real-world benchmark datasets. The results have demonstrated the proposed MusaNet produces higher-quality representations than state-of-the-art baseline methods. The source code is available in https://github.com/xueping/MusaNet.

preprint2020arXiv

Suicidal Ideation Detection: A Review of Machine Learning Methods and Applications

Suicide is a critical issue in modern society. Early detection and prevention of suicide attempts should be addressed to save people's life. Current suicidal ideation detection methods include clinical methods based on the interaction between social workers or experts and the targeted individuals and machine learning techniques with feature engineering or deep learning for automatic detection based on online social contents. This paper is the first survey that comprehensively introduces and discusses the methods from these categories. Domain-specific applications of suicidal ideation detection are reviewed according to their data sources, i.e., questionnaires, electronic health records, suicide notes, and online user content. Several specific tasks and datasets are introduced and summarized to facilitate further research. Finally, we summarize the limitations of current work and provide an outlook of further research directions.

preprint2019arXiv

A Comprehensive Survey on Graph Neural Networks

Deep learning has revolutionized many machine learning tasks in recent years, ranging from image classification and video processing to speech recognition and natural language understanding. The data in these tasks are typically represented in the Euclidean space. However, there is an increasing number of applications where data are generated from non-Euclidean domains and are represented as graphs with complex relationships and interdependency between objects. The complexity of graph data has imposed significant challenges on existing machine learning algorithms. Recently, many studies on extending deep learning approaches for graph data have emerged. In this survey, we provide a comprehensive overview of graph neural networks (GNNs) in data mining and machine learning fields. We propose a new taxonomy to divide the state-of-the-art graph neural networks into four categories, namely recurrent graph neural networks, convolutional graph neural networks, graph autoencoders, and spatial-temporal graph neural networks. We further discuss the applications of graph neural networks across various domains and summarize the open source codes, benchmark data sets, and model evaluation of graph neural networks. Finally, we propose potential research directions in this rapidly growing field.

preprint2019arXiv

Learning Graph Embedding with Adversarial Training Methods

Graph embedding aims to transfer a graph into vectors to facilitate subsequent graph analytics tasks like link prediction and graph clustering. Most approaches on graph embedding focus on preserving the graph structure or minimizing the reconstruction errors for graph data. They have mostly overlooked the embedding distribution of the latent codes, which unfortunately may lead to inferior representation in many cases. In this paper, we present a novel adversarially regularized framework for graph embedding. By employing the graph convolutional network as an encoder, our framework embeds the topological information and node content into a vector representation, from which a graph decoder is further built to reconstruct the input graph. The adversarial training principle is applied to enforce our latent codes to match a prior Gaussian or Uniform distribution. Based on this framework, we derive two variants of adversarial models, the adversarially regularized graph autoencoder (ARGA) and its variational version, adversarially regularized variational graph autoencoder (ARVGA), to learn the graph embedding effectively. We also exploit other potential variations of ARGA and ARVGA to get a deeper understanding on our designs. Experimental results compared among twelve algorithms for link prediction and twenty algorithms for graph clustering validate our solutions.

preprint2019arXiv

Learning Private Neural Language Modeling with Attentive Aggregation

Mobile keyboard suggestion is typically regarded as a word-level language modeling problem. Centralized machine learning technique requires massive user data collected to train on, which may impose privacy concerns for sensitive personal typing data of users. Federated learning (FL) provides a promising approach to learning private language modeling for intelligent personalized keyboard suggestion by training models in distributed clients rather than training in a central server. To obtain a global model for prediction, existing FL algorithms simply average the client models and ignore the importance of each client during model aggregation. Furthermore, there is no optimization for learning a well-generalized global model on the central server. To solve these problems, we propose a novel model aggregation with the attention mechanism considering the contribution of clients models to the global model, together with an optimization technique during server aggregation. Our proposed attentive aggregation method minimizes the weighted distance between the server model and client models through iterative parameters updating while attends the distance between the server model and client models. Through experiments on two popular language modeling datasets and a social media dataset, our proposed method outperforms its counterparts in terms of perplexity and communication cost in most settings of comparison.

preprint2019arXiv

Temporal Self-Attention Network for Medical Concept Embedding

In longitudinal electronic health records (EHRs), the event records of a patient are distributed over a long period of time and the temporal relations between the events reflect sufficient domain knowledge to benefit prediction tasks such as the rate of inpatient mortality. Medical concept embedding as a feature extraction method that transforms a set of medical concepts with a specific time stamp into a vector, which will be fed into a supervised learning algorithm. The quality of the embedding significantly determines the learning performance over the medical data. In this paper, we propose a medical concept embedding method based on applying a self-attention mechanism to represent each medical concept. We propose a novel attention mechanism which captures the contextual information and temporal relationships between medical concepts. A light-weight neural net, "Temporal Self-Attention Network (TeSAN)", is then proposed to learn medical concept embedding based solely on the proposed attention mechanism. To test the effectiveness of our proposed methods, we have conducted clustering and prediction tasks on two public EHRs datasets comparing TeSAN against five state-of-the-art embedding methods. The experimental results demonstrate that the proposed TeSAN model is superior to all the compared methods. To the best of our knowledge, this work is the first to exploit temporal self-attentive relations between medical events.