Models, code, and papers for "Yidong Chen":

Multi-Perspective Neural Architecture for Recommendation System

Jul 12, 2018
Han Xiao, Yidong Chen, Xiaodong Shi

Currently, there starts a research trend to leverage neural architecture for recommendation systems. Though several deep recommender models are proposed, most methods are too simple to characterize users' complex preference. In this paper, for a fine-grain analysis, users' ratings are explained from multiple perspectives, based on which, we propose our neural architecture. Specifically, our model employs several sequential stages to encode the user and item into hidden representations. In one stage, the user and item are represented from multiple perspectives and in each perspective, the representations of user and item put attentions to each other. Last, we metric the output representations of final stage to approach the users' rating. Extensive experiments demonstrate that our method achieves substantial improvements against baselines.


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Hungarian Layer: Logics Empowered Neural Architecture

May 17, 2018
Han Xiao, Yidong Chen, Xiaodong Shi

Neural architecture is a purely numeric framework, which fits the data as a continuous function. However, lacking of logic flow (e.g. \textit{if, for, while}), traditional algorithms (e.g. \textit{Hungarian algorithm, A$^*$ searching, decision tress algorithm}) could not be embedded into this paradigm, which limits the theories and applications. In this paper, we reform the calculus graph as a dynamic process, which is guided by logic flow. Within our novel methodology, traditional algorithms could empower numerical neural network. Specifically, regarding the subject of sentence matching, we reformulate this issue as the form of task-assignment, which is solved by Hungarian algorithm. First, our model applies BiLSTM to parse the sentences. Then Hungarian layer aligns the matching positions. Last, we transform the matching results for soft-max regression by another BiLSTM. Extensive experiments show that our model outperforms other state-of-the-art baselines substantially.

* This is the draft submitting to ICML 2018. You could expect the final version, which is more perfect 

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Asynchronous "Events" are Better For Motion Estimation

Apr 24, 2019
Yuhu Guo, Han Xiao, Yidong Chen, Xiaodong Shi

Event-based camera is a bio-inspired vision sensor that records intensity changes (called event) asynchronously in each pixel. As an instance of event-based camera, Dynamic and Active-pixel Vision Sensor (DAVIS) combines a standard camera and an event-based camera. However, traditional models could not deal with the event stream asynchronously. To analyze the event stream asynchronously, most existing approaches accumulate events within a certain time interval and treat the accumulated events as a synchronous frame, which wastes the intensity change information and weakens the advantages of DAVIS. Therefore, in this paper, we present the first neural asynchronous approach to process event stream for event-based camera. Our method asynchronously extracts dynamic information from events by leveraging previous motion and critical features of gray-scale frames. To our best knowledge, this is the first neural asynchronous method to analyze event stream through a novel deep neural network. Extensive experiments demonstrate that our proposed model achieves remarkable improvements against the state-of-the-art baselines.

* Submitted at IJCAI 2019 

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Convolutional neural network models for cancer type prediction based on gene expression

Jun 18, 2019
Milad Mostavi, Yu-Chiao Chiu, Yufei Huang, Yidong Chen

Background Precise prediction of cancer types is vital for cancer diagnosis and therapy. Important cancer marker genes can be inferred through predictive model. Several studies have attempted to build machine learning models for this task however none has taken into consideration the effects of tissue of origin that can potentially bias the identification of cancer markers. Results In this paper, we introduced several Convolutional Neural Network (CNN) models that take unstructured gene expression inputs to classify tumor and non-tumor samples into their designated cancer types or as normal. Based on different designs of gene embeddings and convolution schemes, we implemented three CNN models: 1D-CNN, 2D-Vanilla-CNN, and 2D-Hybrid-CNN. The models were trained and tested on combined 10,340 samples of 33 cancer types and 731 matched normal tissues of The Cancer Genome Atlas (TCGA). Our models achieved excellent prediction accuracies (93.9-95.0%) among 34 classes (33 cancers and normal). Furthermore, we interpreted one of the models, known as 1D-CNN model, with a guided saliency technique and identified a total of 2,090 cancer markers (108 per class). The concordance of differential expression of these markers between the cancer type they represent and others is confirmed. In breast cancer, for instance, our model identified well-known markers, such as GATA3 and ESR1. Finally, we extended the 1D-CNN model for prediction of breast cancer subtypes and achieved an average accuracy of 88.42% among 5 subtypes. The codes can be found at https://github.com/chenlabgccri/CancerTypePrediction.

* 34 pages, 5 figures, This paper was presented at ICIBM June, 2019 at Ohio Columbus, and will be published in BMC Genomics journal. Keywords: Deep Learning; Convolutional Neural Networks, The Cancer Genome Atlas; Cancer type prediction; Cancer gene markers; Breast cancer subtype prediction 

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Context-Based Dynamic Pricing with Online Clustering

Feb 17, 2019
Sentao Miao, Xi Chen, Xiuli Chao, Jiaxi Liu, Yidong Zhang

We consider a context-based dynamic pricing problem of online products which have low sales. Sales data from Alibaba, a major global online retailer, illustrate the prevalence of low-sale products. For these products, existing single-product dynamic pricing algorithms do not work well due to insufficient data samples. To address this challenge, we propose pricing policies that concurrently perform clustering over products and set individual pricing decisions on the fly. By clustering data and identifying products that have similar demand patterns, we utilize sales data from products within the same cluster to improve demand estimation and allow for better pricing decisions. We evaluate the algorithms using the regret, and the result shows that when product demand functions come from multiple clusters, our algorithms significantly outperform traditional single-product pricing policies. Numerical experiments using a real dataset from Alibaba demonstrate that the proposed policies, compared with several benchmark policies, increase the revenue. The results show that online clustering is an effective approach to tackling dynamic pricing problems associated with low-sale products. Our algorithms were further implemented in a field study at Alibaba with 40 products for 30 consecutive days, and compared to the products which use business-as-usual pricing policy of Alibaba. The results from the field experiment show that the overall revenue increased by 10.14%.


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Deep Semantic Role Labeling with Self-Attention

Dec 05, 2017
Zhixing Tan, Mingxuan Wang, Jun Xie, Yidong Chen, Xiaodong Shi

Semantic Role Labeling (SRL) is believed to be a crucial step towards natural language understanding and has been widely studied. Recent years, end-to-end SRL with recurrent neural networks (RNN) has gained increasing attention. However, it remains a major challenge for RNNs to handle structural information and long range dependencies. In this paper, we present a simple and effective architecture for SRL which aims to address these problems. Our model is based on self-attention which can directly capture the relationships between two tokens regardless of their distance. Our single model achieves F$_1=83.4$ on the CoNLL-2005 shared task dataset and F$_1=82.7$ on the CoNLL-2012 shared task dataset, which outperforms the previous state-of-the-art results by $1.8$ and $1.0$ F$_1$ score respectively. Besides, our model is computationally efficient, and the parsing speed is 50K tokens per second on a single Titan X GPU.

* Accepted by AAAI-2018 

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GSAE: an autoencoder with embedded gene-set nodes for genomics functional characterization

May 21, 2018
Hung-I Harry Chen, Yu-Chiao Chiu, Tinghe Zhang, Songyao Zhang, Yufei Huang, Yidong Chen

Bioinformatics tools have been developed to interpret gene expression data at the gene set level, and these gene set based analyses improve the biologists' capability to discover functional relevance of their experiment design. While elucidating gene set individually, inter gene sets association is rarely taken into consideration. Deep learning, an emerging machine learning technique in computational biology, can be used to generate an unbiased combination of gene set, and to determine the biological relevance and analysis consistency of these combining gene sets by leveraging large genomic data sets. In this study, we proposed a gene superset autoencoder (GSAE), a multi-layer autoencoder model with the incorporation of a priori defined gene sets that retain the crucial biological features in the latent layer. We introduced the concept of the gene superset, an unbiased combination of gene sets with weights trained by the autoencoder, where each node in the latent layer is a superset. Trained with genomic data from TCGA and evaluated with their accompanying clinical parameters, we showed gene supersets' ability of discriminating tumor subtypes and their prognostic capability. We further demonstrated the biological relevance of the top component gene sets in the significant supersets. Using autoencoder model and gene superset at its latent layer, we demonstrated that gene supersets retain sufficient biological information with respect to tumor subtypes and clinical prognostic significance. Superset also provides high reproducibility on survival analysis and accurate prediction for cancer subtypes.

* Accepted for presentation in the International Conference on Intelligent Biology and Medicine (ICIBM 2018) at Los Angeles, CA, USA. Currently under consideration for publication in a Supplement Issue of BMC Systems Biology 

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Predicting drug response of tumors from integrated genomic profiles by deep neural networks

May 20, 2018
Yu-Chiao Chiu, Hung-I Harry Chen, Tinghe Zhang, Songyao Zhang, Aparna Gorthi, Li-Ju Wang, Yufei Huang, Yidong Chen

The study of high-throughput genomic profiles from a pharmacogenomics viewpoint has provided unprecedented insights into the oncogenic features modulating drug response. A recent screening of ~1,000 cancer cell lines to a collection of anti-cancer drugs illuminated the link between genotypes and vulnerability. However, due to essential differences between cell lines and tumors, the translation into predicting drug response in tumors remains challenging. Here we proposed a DNN model to predict drug response based on mutation and expression profiles of a cancer cell or a tumor. The model contains a mutation and an expression encoders pre-trained using a large pan-cancer dataset to abstract core representations of high-dimension data, followed by a drug response predictor network. Given a pair of mutation and expression profiles, the model predicts IC50 values of 265 drugs. We trained and tested the model on a dataset of 622 cancer cell lines and achieved an overall prediction performance of mean squared error at 1.96 (log-scale IC50 values). The performance was superior in prediction error or stability than two classical methods and four analog DNNs of our model. We then applied the model to predict drug response of 9,059 tumors of 33 cancer types. The model predicted both known, including EGFR inhibitors in non-small cell lung cancer and tamoxifen in ER+ breast cancer, and novel drug targets. The comprehensive analysis further revealed the molecular mechanisms underlying the resistance to a chemotherapeutic drug docetaxel in a pan-cancer setting and the anti-cancer potential of a novel agent, CX-5461, in treating gliomas and hematopoietic malignancies. Overall, our model and findings improve the prediction of drug response and the identification of novel therapeutic options.

* Accepted for presentation in the International Conference on Intelligent Biology and Medicine (ICIBM 2018) at Los Angeles, CA, USA. Currently under consideration for publication in a Supplement Issue of BMC Genomics 

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Multiple-Human Parsing in the Wild

Mar 15, 2018
Jianshu Li, Jian Zhao, Yunchao Wei, Congyan Lang, Yidong Li, Terence Sim, Shuicheng Yan, Jiashi Feng

Human parsing is attracting increasing research attention. In this work, we aim to push the frontier of human parsing by introducing the problem of multi-human parsing in the wild. Existing works on human parsing mainly tackle single-person scenarios, which deviates from real-world applications where multiple persons are present simultaneously with interaction and occlusion. To address the multi-human parsing problem, we introduce a new multi-human parsing (MHP) dataset and a novel multi-human parsing model named MH-Parser. The MHP dataset contains multiple persons captured in real-world scenes with pixel-level fine-grained semantic annotations in an instance-aware setting. The MH-Parser generates global parsing maps and person instance masks simultaneously in a bottom-up fashion with the help of a new Graph-GAN model. We envision that the MHP dataset will serve as a valuable data resource to develop new multi-human parsing models, and the MH-Parser offers a strong baseline to drive future research for multi-human parsing in the wild.

* The first two authors are with equal contribution 

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