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Researcher profile

Hong Yu

Hong Yu contributes to research discovery and scholarly infrastructure.

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Computation and LanguageComputer VisionArtificial Intelligenceeess.IVMachine LearningSoundeess.ASOther Quantitative Biologyphysics.opticsApplicationsGenomicsphysics.soc-phPopulations and EvolutionQuantitative MethodsSocial and Information Networks

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Published work

25 published item(s)

preprint2026arXiv

From Where Things Are to What They Are For: Benchmarking Spatial-Functional Intelligence in Multimodal LLMs

Human-level agentic intelligence extends beyond low-level geometric perception, evolving from recognizing where things are to understanding what they are for. While existing benchmarks effectively evaluate the geometric perception capabilities of multimodal large language models (MLLMs), they fall short of probing the higher-order cognitive abilities required for grounded intelligence. To address this gap, we introduce the Spatial-Functional Intelligence Benchmark (SFI-Bench), a video-based benchmark with over 1,500 expert-annotated questions derived from diverse egocentric indoor video scans. SFI-Bench systematically evaluates two complementary dimensions of advanced reasoning: (1) Structured Spatial Reasoning, which requires understanding complex layouts and forming coherent spatial representations, and (2) Functional Reasoning, which involves inferring object affordances and their context-dependent utility. The benchmark includes tasks such as conditional counting, multi-hop relational reasoning, functional pairing, and knowledge-grounded troubleshooting, directly challenging models to integrate perception, memory, and inference. Our experiments reveal that current MLLMs consistently struggle to combine spatial memory with functional reasoning and external knowledge, highlighting a critical bottleneck in achieving grounded intelligence. SFI-Bench therefore provides a diagnostic tool for measuring progress toward more cognitively capable and truly grounded multimodal agents.

0 citations0 reviewsNo code linkedOpen access
preprint2026arXiv

MedQA-CS: Objective Structured Clinical Examination (OSCE)-Style Benchmark for Evaluating LLM Clinical Skills

Artificial intelligence (AI) and large language models (LLMs) in healthcare require advanced clinical skills (CS), yet current benchmarks fail to evaluate these comprehensively. We introduce MedQA-CS, an AI-SCE framework inspired by medical education's Objective Structured Clinical Examinations (OSCEs), to address this gap. MedQA-CS evaluates LLMs through two instruction-following tasks, LLM-as-medical-student and LLM-as-CS-examiner, designed to reflect real clinical scenarios. Our contributions include developing MedQA-CS, a comprehensive evaluation framework with publicly available data and expert annotations, and providing the quantitative and qualitative assessment of LLMs as reliable judges in CS evaluation. Our experiments show that MedQA-CS is a more challenging benchmark for evaluating clinical skills than traditional multiple-choice QA benchmarks (e.g., MedQA). Combined with existing benchmarks, MedQA-CS enables a more comprehensive evaluation of LLMs' clinical capabilities for both open- and closed-source LLMs.

0 citations0 reviewsNo code linkedOpen access
preprint2023arXiv

EHR Interaction Between Patients and AI: NoteAid EHR Interaction

With the rapid advancement of Large Language Models (LLMs) and their outstanding performance in semantic and contextual comprehension, the potential of LLMs in specialized domains warrants exploration. This paper introduces the NoteAid EHR Interaction Pipeline, an innovative approach developed using generative LLMs to assist in patient education, a task stemming from the need to aid patients in understanding Electronic Health Records (EHRs). Building upon the NoteAid work, we designed two novel tasks from the patient's perspective: providing explanations for EHR content that patients may not understand and answering questions posed by patients after reading their EHRs. We extracted datasets containing 10,000 instances from MIMIC Discharge Summaries and 876 instances from the MADE medical notes collection, respectively, executing the two tasks through the NoteAid EHR Interaction Pipeline with these data. Performance data of LLMs on these tasks were collected and constructed as the corresponding NoteAid EHR Interaction Dataset. Through a comprehensive evaluation of the entire dataset using LLM assessment and a rigorous manual evaluation of 64 instances, we showcase the potential of LLMs in patient education. Besides, the results provide valuable data support for future exploration and applications in this domain while also supplying high-quality synthetic datasets for in-house system training.

0 citations0 reviewsNo code linkedOpen access
preprint2022arXiv

A Simple Meta-learning Paradigm for Zero-shot Intent Classification with Mixture Attention Mechanism

Zero-shot intent classification is a vital and challenging task in dialogue systems, which aims to deal with numerous fast-emerging unacquainted intents without annotated training data. To obtain more satisfactory performance, the crucial points lie in two aspects: extracting better utterance features and strengthening the model generalization ability. In this paper, we propose a simple yet effective meta-learning paradigm for zero-shot intent classification. To learn better semantic representations for utterances, we introduce a new mixture attention mechanism, which encodes the pertinent word occurrence patterns by leveraging the distributional signature attention and multi-layer perceptron attention simultaneously. To strengthen the transfer ability of the model from seen classes to unseen classes, we reformulate zero-shot intent classification with a meta-learning strategy, which trains the model by simulating multiple zero-shot classification tasks on seen categories, and promotes the model generalization ability with a meta-adapting procedure on mimic unseen categories. Extensive experiments on two real-world dialogue datasets in different languages show that our model outperforms other strong baselines on both standard and generalized zero-shot intent classification tasks.

0 citations0 reviewsNo code linkedOpen access
preprint2022arXiv

Advanced Conditional Variational Autoencoders (A-CVAE): Towards interpreting open-domain conversation generation via disentangling latent feature representation

Currently end-to-end deep learning based open-domain dialogue systems remain black box models, making it easy to generate irrelevant contents with data-driven models. Specifically, latent variables are highly entangled with different semantics in the latent space due to the lack of priori knowledge to guide the training. To address this problem, this paper proposes to harness the generative model with a priori knowledge through a cognitive approach involving mesoscopic scale feature disentanglement. Particularly, the model integrates the macro-level guided-category knowledge and micro-level open-domain dialogue data for the training, leveraging the priori knowledge into the latent space, which enables the model to disentangle the latent variables within the mesoscopic scale. Besides, we propose a new metric for open-domain dialogues, which can objectively evaluate the interpretability of the latent space distribution. Finally, we validate our model on different datasets and experimentally demonstrate that our model is able to generate higher quality and more interpretable dialogues than other models.

0 citations0 reviewsNo code linkedOpen access
preprint2022arXiv

Attention guided global enhancement and local refinement network for semantic segmentation

The encoder-decoder architecture is widely used as a lightweight semantic segmentation network. However, it struggles with a limited performance compared to a well-designed Dilated-FCN model for two major problems. First, commonly used upsampling methods in the decoder such as interpolation and deconvolution suffer from a local receptive field, unable to encode global contexts. Second, low-level features may bring noises to the network decoder through skip connections for the inadequacy of semantic concepts in early encoder layers. To tackle these challenges, a Global Enhancement Method is proposed to aggregate global information from high-level feature maps and adaptively distribute them to different decoder layers, alleviating the shortage of global contexts in the upsampling process. Besides, a Local Refinement Module is developed by utilizing the decoder features as the semantic guidance to refine the noisy encoder features before the fusion of these two (the decoder features and the encoder features). Then, the two methods are integrated into a Context Fusion Block, and based on that, a novel Attention guided Global enhancement and Local refinement Network (AGLN) is elaborately designed. Extensive experiments on PASCAL Context, ADE20K, and PASCAL VOC 2012 datasets have demonstrated the effectiveness of the proposed approach. In particular, with a vanilla ResNet-101 backbone, AGLN achieves the state-of-the-art result (56.23% mean IoU) on the PASCAL Context dataset. The code is available at https://github.com/zhasen1996/AGLN.

0 citations0 reviewsNo code linkedOpen access
preprint2022arXiv

Caption Feature Space Regularization for Audio Captioning

Audio captioning aims at describing the content of audio clips with human language. Due to the ambiguity of audio, different people may perceive the same audio differently, resulting in caption disparities (i.e., one audio may correlate to several captions with diverse semantics). For that, general audio captioning models achieve the one-to-many training by randomly selecting a correlated caption as the ground truth for each audio. However, it leads to a significant variation in the optimization directions and weakens the model stability. To eliminate this negative effect, in this paper, we propose a two-stage framework for audio captioning: (i) in the first stage, via the contrastive learning, we construct a proxy feature space to reduce the distances between captions correlated to the same audio, and (ii) in the second stage, the proxy feature space is utilized as additional supervision to encourage the model to be optimized in the direction that benefits all the correlated captions. We conducted extensive experiments on two datasets using four commonly used encoder and decoder architectures. Experimental results demonstrate the effectiveness of the proposed method. The code is available at https://github.com/PRIS-CV/Caption-Feature-Space-Regularization.

0 citations0 reviewsNo code linkedOpen access
preprint2022arXiv

Category Guided Attention Network for Brain Tumor Segmentation in MRI

Objective: Magnetic resonance imaging (MRI) has been widely used for the analysis and diagnosis of brain diseases. Accurate and automatic brain tumor segmentation is of paramount importance for radiation treatment. However, low tissue contrast in tumor regions makes it a challenging task.Approach: We propose a novel segmentation network named Category Guided Attention U-Net (CGA U-Net). In this model, we design a Supervised Attention Module (SAM) based on the attention mechanism, which can capture more accurate and stable long-range dependency in feature maps without introducing much computational cost. Moreover, we propose an intra-class update approach to reconstruct feature maps by aggregating pixels of the same category. Main results: Experimental results on the BraTS 2019 datasets show that the proposed method outperformers the state-of-the-art algorithms in both segmentation performance and computational complexity. Significance: The CGA U-Net can effectively capture the global semantic information in the MRI image by using the SAM module, while significantly reducing the computational cost. Code is available at https://github.com/delugewalker/CGA-U-Net.

0 citations0 reviewsNo code linkedOpen access
preprint2022arXiv

Hyperspectral image reconstruction for spectral camera based on ghost imaging via sparsity constraints using V-DUnet

Spectral camera based on ghost imaging via sparsity constraints (GISC spectral camera) obtains three-dimensional (3D) hyperspectral information with two-dimensional (2D) compressive measurements in a single shot, which has attracted much attention in recent years. However, its imaging quality and real-time performance of reconstruction still need to be further improved. Recently, deep learning has shown great potential in improving the reconstruction quality and reconstruction speed for computational imaging. When applying deep learning into GISC spectral camera, there are several challenges need to be solved: 1) how to deal with the large amount of 3D hyperspectral data, 2) how to reduce the influence caused by the uncertainty of the random reference measurements, 3) how to improve the reconstructed image quality as far as possible. In this paper, we present an end-to-end V-DUnet for the reconstruction of 3D hyperspectral data in GISC spectral camera. To reduce the influence caused by the uncertainty of the measurement matrix and enhance the reconstructed image quality, both differential ghost imaging results and the detected measurements are sent into the network's inputs. Compared with compressive sensing algorithm, such as PICHCS and TwIST, it not only significantly improves the imaging quality with high noise immunity, but also speeds up the reconstruction time by more than two orders of magnitude.

0 citations0 reviewsNo code linkedOpen access
preprint2022arXiv

Label-enhanced Prototypical Network with Contrastive Learning for Multi-label Few-shot Aspect Category Detection

Multi-label aspect category detection allows a given review sentence to contain multiple aspect categories, which is shown to be more practical in sentiment analysis and attracting increasing attention. As annotating large amounts of data is time-consuming and labor-intensive, data scarcity occurs frequently in real-world scenarios, which motivates multi-label few-shot aspect category detection. However, research on this problem is still in infancy and few methods are available. In this paper, we propose a novel label-enhanced prototypical network (LPN) for multi-label few-shot aspect category detection. The highlights of LPN can be summarized as follows. First, it leverages label description as auxiliary knowledge to learn more discriminative prototypes, which can retain aspect-relevant information while eliminating the harmful effect caused by irrelevant aspects. Second, it integrates with contrastive learning, which encourages that the sentences with the same aspect label are pulled together in embedding space while simultaneously pushing apart the sentences with different aspect labels. In addition, it introduces an adaptive multi-label inference module to predict the aspect count in the sentence, which is simple yet effective. Extensive experimental results on three datasets demonstrate that our proposed model LPN can consistently achieve state-of-the-art performance.

0 citations0 reviewsNo code linkedOpen access
preprint2022arXiv

Learning as Conversation: Dialogue Systems Reinforced for Information Acquisition

We propose novel AI-empowered chat bots for learning as conversation where a user does not read a passage but gains information and knowledge through conversation with a teacher bot. Our information-acquisition-oriented dialogue system employs a novel adaptation of reinforced self-play so that the system can be transferred to various domains without in-domain dialogue data, and can carry out conversations both informative and attentive to users. Our extensive subjective and objective evaluations on three large public data corpora demonstrate the effectiveness of our system to deliver knowledge-intensive and attentive conversations and help end users substantially gain knowledge without reading passages. Our code and datasets are publicly available for follow-up research.

0 citations0 reviewsNo code linkedOpen access
preprint2022arXiv

ScAN: Suicide Attempt and Ideation Events Dataset

Suicide is an important public health concern and one of the leading causes of death worldwide. Suicidal behaviors, including suicide attempts (SA) and suicide ideations (SI), are leading risk factors for death by suicide. Information related to patients' previous and current SA and SI are frequently documented in the electronic health record (EHR) notes. Accurate detection of such documentation may help improve surveillance and predictions of patients' suicidal behaviors and alert medical professionals for suicide prevention efforts. In this study, we first built Suicide Attempt and Ideation Events (ScAN) dataset, a subset of the publicly available MIMIC III dataset spanning over 12k+ EHR notes with 19k+ annotated SA and SI events information. The annotations also contain attributes such as method of suicide attempt. We also provide a strong baseline model ScANER (Suicide Attempt and Ideation Events Retriever), a multi-task RoBERTa-based model with a retrieval module to extract all the relevant suicidal behavioral evidences from EHR notes of an hospital-stay and, and a prediction module to identify the type of suicidal behavior (SA and SI) concluded during the patient's stay at the hospital. ScANER achieved a macro-weighted F1-score of 0.83 for identifying suicidal behavioral evidences and a macro F1-score of 0.78 and 0.60 for classification of SA and SI for the patient's hospital-stay, respectively. ScAN and ScANER are publicly available.

0 citations0 reviewsNo code linkedOpen access
preprint2022arXiv

TransBTSV2: Towards Better and More Efficient Volumetric Segmentation of Medical Images

Transformer, benefiting from global (long-range) information modeling using self-attention mechanism, has been successful in natural language processing and computer vision recently. Convolutional Neural Networks, capable of capturing local features, are difficult to model explicit long-distance dependencies from global feature space. However, both local and global features are crucial for dense prediction tasks, especially for 3D medical image segmentation. In this paper, we present the further attempt to exploit Transformer in 3D CNN for 3D medical image volumetric segmentation and propose a novel network named TransBTSV2 based on the encoder-decoder structure. Different from TransBTS, the proposed TransBTSV2 is not limited to brain tumor segmentation (BTS) but focuses on general medical image segmentation, providing a stronger and more efficient 3D baseline for volumetric segmentation of medical images. As a hybrid CNN-Transformer architecture, TransBTSV2 can achieve accurate segmentation of medical images without any pre-training, possessing the strong inductive bias as CNNs and powerful global context modeling ability as Transformer. With the proposed insight to redesign the internal structure of Transformer block and the introduced Deformable Bottleneck Module to capture shape-aware local details, a highly efficient architecture is achieved with superior performance. Extensive experimental results on four medical image datasets (BraTS 2019, BraTS 2020, LiTS 2017 and KiTS 2019) demonstrate that TransBTSV2 achieves comparable or better results compared to the state-of-the-art methods for the segmentation of brain tumor, liver tumor as well as kidney tumor. Code will be publicly available at https://github.com/Wenxuan-1119/TransBTS.

0 citations0 reviewsNo code linkedOpen access
preprint2021arXiv

A prognostic dynamic model applicable to infectious diseases providing easily visualized guides -- A case study of COVID-19 in the UK

A reasonable prediction of infectious diseases transmission process under different disease control strategies is an important reference point for policy makers. Here we established a dynamic transmission model via Python and realized comprehensive regulation of disease control measures. We classified government interventions into three categories and introduced three parameters as descriptions for the key points in disease control, these being intraregional growth rate, interregional communication rate, and detection rate of infectors. Our simulation predicts the infection by COVID-19 in the UK would be out of control in 73 days without any interventions; at the same time, herd immunity acquisition will begin from the epicentre. After we introduced government interventions, single intervention is effective in disease control but at huge expense while combined interventions would be more efficient, among which, enhancing detection number is crucial in control strategy of COVID-19. In addition, we calculated requirements for the most effective vaccination strategy based on infection number in real situation. Our model was programmed with iterative algorithms, and visualized via cellular automata, it can be applied to similar epidemics in other regions if the basic parameters are inputted, and is able to synthetically mimick the effect of multiple factors in infectious disease control.

0 citations0 reviewsNo code linkedOpen access
preprint2020arXiv

Birth-Burst in Evolving Networks

The evolution of complex networks is governed by both growing rules and internal properties. Most evolving network models (e.g. preferential attachment) emphasize on the growing strategy, while neglecting the characteristics of individual nodes. In this study, we analyzed a widely studied network: the evolving protein-protein interaction (PPI) network. We discovered the critical contribution of individual nodes, occurring particularly at their birth. Specifically, a node is born with a fitness value - a measurement of its intrinsic significance. Upon the introduction of a node with a large fitness into the network, a corresponding high birth-degree is determined accordingly, leading to an abrupt increase of connectivity in the network. The degree fraction of these large (hub) nodes does not decay away with the network evolution, while keeping a constant influence over the lifetime. Here we developed the birth-burst model, an adaptation of the fitness model, to simulate degree-burst and phase-transition in the network evolution.

0 citations0 reviewsNo code linkedOpen access
preprint2020arXiv

Calibrating Structured Output Predictors for Natural Language Processing

We address the problem of calibrating prediction confidence for output entities of interest in natural language processing (NLP) applications. It is important that NLP applications such as named entity recognition and question answering produce calibrated confidence scores for their predictions, especially if the system is to be deployed in a safety-critical domain such as healthcare. However, the output space of such structured prediction models is often too large to adapt binary or multi-class calibration methods directly. In this study, we propose a general calibration scheme for output entities of interest in neural-network based structured prediction models. Our proposed method can be used with any binary class calibration scheme and a neural network model. Additionally, we show that our calibration method can also be used as an uncertainty-aware, entity-specific decoding step to improve the performance of the underlying model at no additional training cost or data requirements. We show that our method outperforms current calibration techniques for named-entity-recognition, part-of-speech and question answering. We also improve our model's performance from our decoding step across several tasks and benchmark datasets. Our method improves the calibration and model performance on out-of-domain test scenarios as well.

0 citations0 reviewsNo code linkedOpen access
preprint2020arXiv

Conversational Machine Comprehension: a Literature Review

Conversational Machine Comprehension (CMC), a research track in conversational AI, expects the machine to understand an open-domain natural language text and thereafter engage in a multi-turn conversation to answer questions related to the text. While most of the research in Machine Reading Comprehension (MRC) revolves around single-turn question answering (QA), multi-turn CMC has recently gained prominence, thanks to the advancement in natural language understanding via neural language models such as BERT and the introduction of large-scale conversational datasets such as CoQA and QuAC. The rise in interest has, however, led to a flurry of concurrent publications, each with a different yet structurally similar modeling approach and an inconsistent view of the surrounding literature. With the volume of model submissions to conversational datasets increasing every year, there exists a need to consolidate the scattered knowledge in this domain to streamline future research. This literature review attempts at providing a holistic overview of CMC with an emphasis on the common trends across recently published models, specifically in their approach to tackling conversational history. The review synthesizes a generic framework for CMC models while highlighting the differences in recent approaches and intends to serve as a compendium of CMC for future researchers.

0 citations0 reviewsNo code linkedOpen access
preprint2020arXiv

Deep Neural Network for Analysis of DNA Methylation Data

Many researches demonstrated that the DNA methylation, which occurs in the context of a CpG, has strong correlation with diseases, including cancer. There is a strong interest in analyzing the DNA methylation data to find how to distinguish different subtypes of the tumor. However, the conventional statistical methods are not suitable for analyzing the highly dimensional DNA methylation data with bounded support. In order to explicitly capture the properties of the data, we design a deep neural network, which composes of several stacked binary restricted Boltzmann machines, to learn the low dimensional deep features of the DNA methylation data. Experiments show these features perform best in breast cancer DNA methylation data cluster analysis, comparing with some state-of-the-art methods.

0 citations0 reviewsNo code linkedOpen access
preprint2020arXiv

Ghost imaging based on Y-net: a dynamic coding and conjugate-decoding approach

Ghost imaging incorporating deep learning technology has recently attracted much attention in the optical imaging field. However, deterministic illumination and multiple exposure are still essential in most scenarios. Here we propose a ghost imaging scheme based on a novel conjugate-decoding deep learning framework (Y-net), which works well under both deterministic and indeterministic illumination. Benefited from the end-to-end characteristic of our network, the image of a sample can be achieved directly from a pair of correlated speckles collected by the detectors, and the sample is illuminated only once in the experiment. The spatial distribution of the speckles encoding the sample in the experiment can be completely different from that of the simulation speckles for training, as long as the statistical characteristics of the speckles remain unchanged. This approach is particularly important to high-resolution x-ray ghost imaging applications due to its potential for improving image quality and reducing radiation damage. And the idea of conjugate-decoding network may also be applied to other learning-based imaging

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preprint2020arXiv

Histogram Transform-based Speaker Identification

A novel text-independent speaker identification (SI) method is proposed. This method uses the Mel-frequency Cepstral coefficients (MFCCs) and the dynamic information among adjacent frames as feature sets to capture speaker's characteristics. In order to utilize dynamic information, we design super-MFCCs features by cascading three neighboring MFCCs frames together. The probability density function (PDF) of these super-MFCCs features is estimated by the recently proposed histogram transform~(HT) method, which generates more training data by random transforms to realize the histogram PDF estimation and recedes the commonly occurred discontinuity problem in multivariate histograms computing. Compared to the conventional PDF estimation methods, such as Gaussian mixture models, the HT model shows promising improvement in the SI performance.

0 citations0 reviewsNo code linkedOpen access
preprint2020arXiv

Language Identification with Deep Bottleneck Features

In this paper we proposed an end-to-end short utterances speech language identification(SLD) approach based on a Long Short Term Memory (LSTM) neural network which is special suitable for SLD application in intelligent vehicles. Features used for LSTM learning are generated by a transfer learning method. Bottle-neck features of a deep neural network (DNN) which are trained for mandarin acoustic-phonetic classification are used for LSTM training. In order to improve the SLD accuracy of short utterances a phase vocoder based time-scale modification(TSM) method is used to reduce and increase speech rated of the test utterance. By splicing the normal, speech rate reduced and increased utterances, we can extend length of test utterances so as to improved improved the performance of the SLD system. The experimental results on AP17-OLR database shows that the proposed methods can improve the performance of SLD, especially on short utterance with 1s and 3s durations.

0 citations0 reviewsNo code linkedOpen access
preprint2020arXiv

Large-scale Gastric Cancer Screening and Localization Using Multi-task Deep Neural Network

Gastric cancer is one of the most common cancers, which ranks third among the leading causes of cancer death. Biopsy of gastric mucosa is a standard procedure in gastric cancer screening test. However, manual pathological inspection is labor-intensive and time-consuming. Besides, it is challenging for an automated algorithm to locate the small lesion regions in the gigapixel whole-slide image and make the decision correctly.To tackle these issues, we collected large-scale whole-slide image dataset with detailed lesion region annotation and designed a whole-slide image analyzing framework consisting of 3 networks which could not only determine the screening result but also present the suspicious areas to the pathologist for reference. Experiments demonstrated that our proposed framework achieves sensitivity of 97.05% and specificity of 92.72% in screening task and Dice coefficient of 0.8331 in segmentation task. Furthermore, we tested our best model in real-world scenario on 10,315 whole-slide images collected from 4 medical centers.

0 citations0 reviewsNo code linkedOpen access
preprint2020arXiv

Neural Data-to-Text Generation with Dynamic Content Planning

Neural data-to-text generation models have achieved significant advancement in recent years. However, these models have two shortcomings: the generated texts tend to miss some vital information, and they often generate descriptions that are not consistent with the structured input data. To alleviate these problems, we propose a Neural data-to-text generation model with Dynamic content Planning, named NDP for abbreviation. The NDP can utilize the previously generated text to dynamically select the appropriate entry from the given structured data. We further design a reconstruction mechanism with a novel objective function that can reconstruct the whole entry of the used data sequentially from the hidden states of the decoder, which aids the accuracy of the generated text. Empirical results show that the NDP achieves superior performance over the state-of-the-art on ROTOWIRE dataset, in terms of relation generation (RG), content selection (CS), content ordering (CO) and BLEU metrics. The human evaluation result shows that the texts generated by the proposed NDP are better than the corresponding ones generated by NCP in most of time. And using the proposed reconstruction mechanism, the fidelity of the generated text can be further improved significantly.

0 citations0 reviewsNo code linkedOpen access
preprint2020arXiv

Ontology-based annotation and analysis of COVID-19 phenotypes

The epidemic of COVID-19 has caused an unpredictable and devastated disaster to the public health in different territories around the world. Common phenotypes include fever, cough, shortness of breath, and chills. With more cases investigated, other clinical phenotypes are gradually recognized, for example, loss of smell, and loss of tastes. Compared with discharged or cured patients, severe or died patients often have one or more comorbidities, such as hypertension, diabetes, and cardiovascular disease. In this study, we systematically collected and analyzed COVID-19-related clinical phenotypes from 70 articles. The commonly occurring 17 phenotypes were classified into different groups based on the Human Phenotype Ontology (HPO). Based on the HP classification, we systematically analyze three nervous phenotypes (loss of smell, loss of taste, and headache) and four abdominal phenotypes (nausea, vomiting, abdominal pain, and diarrhea) identified in patients, and found that patients from Europe and USA turned to have higher nervous phenotypes and abdominal phenotypes than patients from Asia. A total of 23 comorbidities were found to commonly exist among COVID-19 patients. Patients with these comorbidities such as diabetes and kidney failure had worse outcomes compared with those without these comorbidities.

0 citations0 reviewsNo code linkedOpen access
preprint2020arXiv

Ontology-based systematic classification and analysis of coronaviruses, hosts, and host-coronavirus interactions towards deep understanding of COVID-19

Given the existing COVID-19 pandemic worldwide, it is critical to systematically study the interactions between hosts and coronaviruses including SARS-Cov, MERS-Cov, and SARS-CoV-2 (cause of COVID-19). We first created four host-pathogen interaction (HPI)-Outcome postulates, and generated a HPI-Outcome model as the basis for understanding host-coronavirus interactions (HCI) and their relations with the disease outcomes. We hypothesized that ontology can be used as an integrative platform to classify and analyze HCI and disease outcomes. Accordingly, we annotated and categorized different coronaviruses, hosts, and phenotypes using ontologies and identified their relations. Various COVID-19 phenotypes are hypothesized to be caused by the backend HCI mechanisms. To further identify the causal HCI-outcome relations, we collected 35 experimentally-verified HCI protein-protein interactions (PPIs), and applied literature mining to identify additional host PPIs in response to coronavirus infections. The results were formulated in a logical ontology representation for integrative HCI-outcome understanding. Using known PPIs as baits, we also developed and applied a domain-inferred prediction method to predict new PPIs and identified their pathological targets on multiple organs. Overall, our proposed ontology-based integrative framework combined with computational predictions can be used to support fundamental understanding of the intricate interactions between human patients and coronaviruses (including SARS-CoV-2) and their association with various disease outcomes.

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