1 code implementation • Findings (NAACL) 2022 • Junwei Yang, Zequn Liu, Ming Zhang, Sheng Wang
Collectively, we envision our method will become an important benchmark for evaluating Graph2Text methods and advance biomedical research for complex diseases.
1 code implementation • ACL 2022 • Mu-Chun Wang, Zixuan Liu, Sheng Wang
We further illustrate how Textomics can be used to advance other applications, including evaluating scientific paper embeddings and generating masked templates for scientific paper understanding.
no code implementations • 14 Feb 2023 • Cai Yang, Addie Woicik, Hoifung Poon, Sheng Wang
Instead of obtaining features from language models, we propose BLIAM, a literature-based data synthesis approach to directly generate training data points that are interpretable and model-agnostic to downstream applications.
no code implementations • 14 Feb 2023 • Sheng Wang, Zihao Zhao, Xi Ouyang, Qian Wang, Dinggang Shen
Large language models (LLMs) have recently demonstrated their potential in clinical applications, providing valuable medical knowledge and advice.
1 code implementation • 13 Jan 2023 • Xiangyu Zhao, Zengxin Qi, Sheng Wang, Qian Wang, Xuehai Wu, Ying Mao, Lichi Zhang
However, learning a robust representation from numerous unlabeled images remains challenging due to potential noise in pseudo labels and insufficient class separability in feature space, which undermines the performance of current semi-supervised segmentation approaches.
1 code implementation • 26 Nov 2022 • Jinxin Lv, Xiaoyu Zeng, Sheng Wang, Ran Duan, Zhiwei Wang, Qiang Li
In this paper, we propose a novel image-aligned style transformation to reinforce the dual-model iterative learning for robust one-shot segmentation of brain tissues.
1 code implementation • 7 Nov 2022 • Yue Guo, Wei Qiu, Gondy Leroy, Sheng Wang, Trevor Cohen
Recent lay language generation systems have used Transformer models trained on a parallel corpus to increase health information accessibility.
1 code implementation • 14 Oct 2022 • Zequn Liu, Kefei Duan, Junwei Yang, Hanwen Xu, Ming Zhang, Sheng Wang
Meta-path, a sequence of node types and edge types, is the core technique to embed HINs.
no code implementations • 20 Sep 2022 • Lin He, Zongxia Liang, Sheng Wang
The wealth of the retiree is divided into a bequest account and a tontine account.
1 code implementation • 23 Aug 2022 • Lu Yang, Sheng Wang, Russ B. Altman
We describe a method for phenotype recognition that imputes phenotype codes for all UK Biobank participants.
no code implementations • 12 Aug 2022 • Xiangyu Zhao, Di Zang, Sheng Wang, Zhenrong Shen, Kai Xuan, Zeyu Wei, Zhe Wang, Ruizhe Zheng, Xuehai Wu, Zheren Li, Qian Wang, Zengxin Qi, Lichi Zhang
To address these issues, we propose a novel medical image inpainting model named TBI-GAN to synthesize TBI MR scans with paired brain label maps.
1 code implementation • 11 Jul 2022 • Mehmet Saygın Seyfioğlu, Zixuan Liu, Pranav Kamath, Sadjyot Gangolli, Sheng Wang, Thomas Grabowski, Linda Shapiro
On top of BAR, we propose using a soft-label-capable supervised contrastive loss, aiming to learn the relative similarity of representations that reflect how mixed are the synthetic MRIs using our soft labels.
1 code implementation • 4 Jul 2022 • Tao Shen, Zhihang Hu, Zhangzhi Peng, Jiayang Chen, Peng Xiong, Liang Hong, Liangzhen Zheng, YiXuan Wang, Irwin King, Sheng Wang, Siqi Sun, Yu Li
When E2Efold-3D is coupled with the experimental techniques, the RNA structure prediction field can be greatly advanced.
no code implementations • 27 Jun 2022 • Zechen Wang, Liangzhen Zheng, Sheng Wang, Mingzhi Lin, Zhihao Wang, Adams Wai-Kin Kong, Yuguang Mu, Yanjie Wei, Weifeng Li
In this work, we propose a fully differentiable framework for ligand pose optimization based on a hybrid scoring function (SF) combined with a multi-layer perceptron (DeepRMSD) and the traditional AutoDock Vina SF.
no code implementations • 10 Jun 2022 • Fenglin Liu, Bang Yang, Chenyu You, Xian Wu, Shen Ge, Adelaide Woicik, Sheng Wang
This task aims to automatically generate a sentence that describes the function of a GO term belonging to one of the three categories, i. e., molecular function, biological process, and cellular component.
1 code implementation • 31 May 2022 • Samuel N. Cohen, Christoph Reisinger, Sheng Wang
We study the capability of arbitrage-free neural-SDE market models to yield effective strategies for hedging options.
no code implementations • 25 May 2022 • Chong Ma, Lin Zhao, Yuzhong Chen, Lu Zhang, Zhenxiang Xiao, Haixing Dai, David Liu, Zihao Wu, Zhengliang Liu, Sheng Wang, Jiaxing Gao, Changhe Li, Xi Jiang, Tuo Zhang, Qian Wang, Dinggang Shen, Dajiang Zhu, Tianming Liu
To address this problem, we propose to infuse human experts' intelligence and domain knowledge into the training of deep neural networks.
no code implementations • 23 May 2022 • Xin Wang, Sheng Wang, Honglin Xiong, Kai Xuan, Zixu Zhuang, Mengjun Liu, Zhenrong Shen, Xiangyu Zhao, Lichi Zhang, Qian Wang
Magnetic resonance (MR) images collected in 2D clinical protocols typically have large inter-slice spacing, resulting in high in-plane resolution and reduced through-plane resolution.
1 code implementation • NAACL 2022 • Yu Zhang, Yu Meng, Xuan Wang, Sheng Wang, Jiawei Han
Discovering latent topics from text corpora has been studied for decades.
no code implementations • 20 Apr 2022 • Hanwen Xu, Sheng Wang
Here, we tackle this problem by annotating proteins to a function only based on its textual description so that we do not need to know any associated proteins for this function.
1 code implementation • 6 Apr 2022 • Sheng Wang, Xi Ouyang, Tianming Liu, Qian Wang, Dinggang Shen
In this paper, we demonstrate that the eye movement of radiologists reading medical images can be a new form of supervision to train the DNN-based computer-aided diagnosis (CAD) system.
1 code implementation • 15 Feb 2022 • Samuel N. Cohen, Christoph Reisinger, Sheng Wang
In this paper, we examine the capacity of an arbitrage-free neural-SDE market model to produce realistic scenarios for the joint dynamics of multiple European options on a single underlying.
no code implementations • 14 Jan 2022 • Jun Wu, Elizabeth A. Ainsworth, Sheng Wang, Kaiyu Guan, Jingrui He
Plant phenotyping (Guo et al. 2021; Pieruschka et al. 2019) focuses on studying the diverse traits of plants related to the plants' growth.
no code implementations • 12 Jan 2022 • Zixu Zhuang, Liping Si, Sheng Wang, Kai Xuan, Xi Ouyang, Yiqiang Zhan, Zhong Xue, Lichi Zhang, Dinggang Shen, Weiwu Yao, Qian Wang
Knee osteoarthritis (OA) is the most common osteoarthritis and a leading cause of disability.
1 code implementation • 30 Nov 2021 • Tong Chen, Sheng Wang
With the increasingly available large-scale cancer genomics datasets, machine learning approaches have played an important role in revealing novel insights into cancer development.
1 code implementation • 21 Nov 2021 • Zheren Li, Zhiming Cui, Sheng Wang, Yuji Qi, Xi Ouyang, Qitian Chen, Yuezhi Yang, Zhong Xue, Dinggang Shen, Jie-Zhi Cheng
Specifically, the backbone network is firstly trained with a multi-style and multi-view unsupervised self-learning scheme for the embedding of invariant features to various vendor-styles.
no code implementations • 13 Nov 2021 • Jiayou Zhang, Zhirui Wang, Shizhuo Zhang, Megh Manoj Bhalerao, Yucong Liu, Dawei Zhu, Sheng Wang
Biomedical entity normalization unifies the language across biomedical experiments and studies, and further enables us to obtain a holistic view of life sciences.
no code implementations • NeurIPS 2021 • Fenglin Liu, Chenyu You, Xian Wu, Shen Ge, Sheng Wang, Xu sun
KGAE consists of a pre-constructed knowledge graph, a knowledge-driven encoder and a knowledge-driven decoder.
1 code implementation • 25 Sep 2021 • Jinxin Lv, Zhiwei Wang, Hongkuan Shi, Haobo Zhang, Sheng Wang, Yilang Wang, Qiang Li
Registration of brain MRI images requires to solve a deformation field, which is extremely difficult in aligning intricate brain tissues, e. g., subcortical nuclei, etc.
1 code implementation • Nature Communications 2021 • Sheng Wang, Angela Oliveira Pisco, Aaron McGeever, Maria Brbic, Marinka Zitnik, Spyros Darmanis, Jure Leskovec, Jim Karkanias, Russ B. Altman
Single cell technologies are rapidly generating large amounts of data that enables us to understand biological systems at single-cell resolution.
1 code implementation • EMNLP 2021 • Zequn Liu, Shukai Wang, Yiyang Gu, Ruiyi Zhang, Ming Zhang, Sheng Wang
Unfortunately, the lack of large-scale terminology definition dataset hinders the process toward definition generation.
no code implementations • 17 Aug 2021 • Jingjing Lyu, Musong Gu, Sheng Wang
Sterile insect technique has been successfully applied in the control of agricultural pests, however, it has a limited ability to control mosquitoes.
no code implementations • 12 Aug 2021 • Meng Cao, HaoZhi Huang, Hao Wang, Xuan Wang, Li Shen, Sheng Wang, Linchao Bao, Zhifeng Li, Jiebo Luo
Compared with the state-of-the-art facial image editing methods, our framework generates video portraits that are more photo-realistic and temporally smooth.
no code implementations • 5 Aug 2021 • Qin Wang, Jun Wei, Boyuan Wang, Zhen Li1, Sheng Wang, Shuguang Cu
Protein secondary structure prediction (PSSP) is essential for protein function analysis.
1 code implementation • CVPR 2021 • Jun Wei, Qin Wang, Zhen Li, Sheng Wang, S. Kevin Zhou, Shuguang Cui
In practice, our SPOL model first generates the CAMs through a novel element-wise multiplication of shallow and deep feature maps, which filters the background noise and generates sharper boundaries robustly.
1 code implementation • 21 Jun 2021 • Yifan Wang, Suyao Tang, Yuntong Lei, Weiping Song, Sheng Wang, Ming Zhang
In this paper, we propose a novel disentangled heterogeneous graph attention network DisenHAN for top-$N$ recommendation, which learns disentangled user/item representations from different aspects in a heterogeneous information network.
1 code implementation • 24 May 2021 • Samuel N. Cohen, Christoph Reisinger, Sheng Wang
Modelling joint dynamics of liquid vanilla options is crucial for arbitrage-free pricing of illiquid derivatives and managing risks of option trade books.
no code implementations • 11 May 2021 • Jiaxiang Wu, Shitong Luo, Tao Shen, Haidong Lan, Sheng Wang, Junzhou Huang
In this paper, we propose a fully-differentiable approach for protein structure optimization, guided by a data-driven generative network.
no code implementations • 10 May 2021 • Liangzhen Zheng, Haidong Lan, Tao Shen, Jiaxiang Wu, Sheng Wang, Wei Liu, Junzhou Huang
Protein structure prediction has been a grand challenge for over 50 years, owing to its broad scientific and application interests.
no code implementations • 8 Mar 2021 • Tu Gu, Kaiyu Feng, Gao Cong, Cheng Long, Zheng Wang, Sheng Wang
Learned indices have been proposed to replace classic index structures like B-Tree with machine learning (ML) models.
1 code implementation • ICCV 2021 • Zhihao Yuan, Xu Yan, Yinghong Liao, Ruimao Zhang, Sheng Wang, Zhen Li, Shuguang Cui
Compared with the visual grounding on 2D images, the natural-language-guided 3D object localization on point clouds is more challenging.
1 code implementation • 8 Dec 2020 • Qihang Fang, Yingda Yin, Qingnan Fan, Fei Xia, Siyan Dong, Sheng Wang, Jue Wang, Leonidas Guibas, Baoquan Chen
These approaches localize the camera in the discrete pose space and are agnostic to the localization-driven scene property, which restricts the camera pose accuracy in the coarse scale.
no code implementations • 13 Oct 2020 • Sheng Wang, Yuan Sun, Zhifeng Bao
This paper presents a thorough evaluation of the existing methods that accelerate Lloyd's algorithm for fast k-means clustering.
2 code implementations • 12 Oct 2020 • Linchao Bao, Xiangkai Lin, Yajing Chen, Haoxian Zhang, Sheng Wang, Xuefei Zhe, Di Kang, HaoZhi Huang, Xinwei Jiang, Jue Wang, Dong Yu, Zhengyou Zhang
We present a fully automatic system that can produce high-fidelity, photo-realistic 3D digital human heads with a consumer RGB-D selfie camera.
1 code implementation • 21 Aug 2020 • Samuel N. Cohen, Christoph Reisinger, Sheng Wang
In addition, we show that removing arbitrage from prices data by our repair method can improve model calibration with enhanced robustness and reduced calibration error.
no code implementations • 29 Jul 2020 • Yuan Sun, Sheng Wang, Yunzhuang Shen, Xiao-Dong Li, Andreas T. Ernst, Michael Kirley
In the first phase of our ML-ACO algorithm, an ML model is trained using a set of small problem instances where the optimal solution is known.
1 code implementation • 7 Jul 2020 • Bo Jiang, Sheng Wang, Xiao Wang, Aihua Zheng
Specifically, STADB first obtains an attention map by channel-wise pooling and returns a drop mask by thresholding the attention map.
no code implementations • 3 Jul 2020 • Meng Cao, Hao-Zhi Huang, Hao Wang, Xuan Wang, Li Shen, Sheng Wang, Linchao Bao, Zhifeng Li, Jiebo Luo
Compared with the state-of-the-art facial image editing methods, our framework generates video portraits that are more photo-realistic and temporally smooth.
no code implementations • 25 May 2020 • Sheng Wang, Jiayu Huo, Xi Ouyang, Jifei Che, Xuhua Ren, Zhong Xue, Qian Wang, Jie-Zhi Cheng
However, the image styles of different vendors are very distinctive, and there may exist domain gap among different vendors that could potentially compromise the universal applicability of one deep learning model.
no code implementations • ECCV 2020 • Jinyu Yang, Weizhi An, Sheng Wang, Xinliang Zhu, Chaochao Yan, Junzhou Huang
Unsupervised domain adaptation enables to alleviate the need for pixel-wise annotation in the semantic segmentation.
Ranked #22 on
Domain Adaptation
on SYNTHIA-to-Cityscapes
2 code implementations • 4 Mar 2020 • Cong Yue, Zhongle Xie, Meihui Zhang, Gang Chen, Beng Chin Ooi, Sheng Wang, Xiaokui Xiao
We establish the worst-case guarantees of each index in terms of these five metrics, and we experimentally evaluate all indexes in a large variety of settings.
Databases
1 code implementation • CVPR 2020 • Xu Yan, Chaoda Zheng, Zhen Li, Sheng Wang, Shuguang Cui
Extensive experiments verify the robustness and superiority of our approach in point clouds processing tasks regardless of synthesis data, indoor data, and outdoor data with or without noise.
Ranked #20 on
Semantic Segmentation
on S3DIS
1 code implementation • 1 Oct 2019 • Chaochao Yan, Sheng Wang, Jinyu Yang, Tingyang Xu, Junzhou Huang
We investigate the posterior collapse problem of current RNN-based VAEs for molecule sequence generation.
no code implementations • 26 Apr 2018 • Jinyang Gao, Wei Wang, Meihui Zhang, Gang Chen, H. V. Jagadish, Guoliang Li, Teck Khim Ng, Beng Chin Ooi, Sheng Wang, Jingren Zhou
In many complex applications such as healthcare, subject matter experts (e. g. Clinicians) are the ones who appreciate the importance of features that affect health, and their knowledge together with existing knowledge bases are critical to the end results.
1 code implementation • PVLDB (The Proceedings of the VLDB Endowment) 2018 • Wei Wang, Sheng Wang, Jinyang Gao, Meihui Zhang, Gang Chen, Teck Khim Ng, Beng Chin Ooi
Second, expertise knowledge is required to optimize the training and inference procedures in terms of efficiency and effectiveness, which imposes heavy burden on the system users.
no code implementations • 14 Feb 2018 • Sheng Wang, Tien Tuan Anh Dinh, Qian Lin, Zhongle Xie, Meihui Zhang, Qingchao Cai, Gang Chen, Wanzeng Fu, Beng Chin Ooi, Pingcheng Ruan
By integrating the core application properties into the storage, ForkBase not only delivers high performance but also reduces development effort.
Databases Cryptography and Security Distributed, Parallel, and Cluster Computing
2 code implementations • 10 Jan 2018 • Ruoyu Li, Sheng Wang, Feiyun Zhu, Junzhou Huang
Graph Convolutional Neural Networks (Graph CNNs) are generalizations of classical CNNs to handle graph data such as molecular data, point could and social networks.
no code implementations • 28 Aug 2017 • Sheng Wang, Zhen Li, Yizhou Yu, Jinbo Xu
Computational elucidation of membrane protein (MP) structures is challenging partially due to lack of sufficient solved structures for homology modeling.
no code implementations • 17 Aug 2017 • Feiyun Zhu, Xinliang Zhu, Sheng Wang, Jiawen Yao, Junzhou Huang
In the critic updating, the capped-$\ell_{2}$ norm is used to measure the approximation error, which prevents outliers from dominating our objective.
no code implementations • 24 Apr 2017 • Zhen Li, Sheng Wang, Yizhou Yu, Jinbo Xu
Tested on 510 non-redundant MPs, our deep model (learned from only non-MPs) has top L/10 long-range contact prediction accuracy 0. 69, better than our deep model trained by only MPs (0. 63) and much better than a representative DCA method CCMpred (0. 47) and the CASP11 winner MetaPSICOV (0. 55).
1 code implementation • 2 Sep 2016 • Sheng Wang, Siqi Sun, Zhen Li, Renyu Zhang, Jinbo Xu
Using our predicted contacts as restraints, we can (ab initio) fold 208 of the 398 membrane proteins with TMscore>0. 5.
no code implementations • 25 Mar 2016 • Wei Wang, Gang Chen, Haibo Chen, Tien Tuan Anh Dinh, Jinyang Gao, Beng Chin Ooi, Kian-Lee Tan, Sheng Wang
The other is scalability, that is the deep learning system must be able to provision for a huge demand of computing resources for training large models with massive datasets.
1 code implementation • 2 Dec 2015 • Sheng Wang, Jian Peng, Jianzhu Ma, Jinbo Xu
Protein secondary structure (SS) prediction is important for studying protein structure and function.
Ranked #1 on
Protein Secondary Structure Prediction
on CullPDB
no code implementations • 17 Nov 2015 • Sheng Wang, Siqi Sun, Jinbo Xu
Our experimental results confirm that maximum-AUC greatly outperforms the other two training methods on 8-state secondary structure prediction and disorder prediction since their label distributions are highly imbalanced and also have similar performance as the other two training methods on the solvent accessibility prediction problem which has three equally-distributed labels.
1 code implementation • 12 Nov 2015 • Wu-Jun Li, Sheng Wang, Wang-Cheng Kang
For another common application scenario with pairwise labels, there have not existed methods for simultaneous feature learning and hash-code learning.
no code implementations • 12 Jan 2014 • Jianzhu Ma, Sheng Wang, Zhiyong Wang, Jinbo Xu
A sequence profile is usually represented as a position-specific scoring matrix (PSSM) or an HMM (Hidden Markov Model) and accordingly PSSM-PSSM or HMM-HMM comparison is used for homolog detection.
no code implementations • 10 Dec 2013 • Jianzhu Ma, Sheng Wang, Zhiyong Wang, Jinbo Xu
To further improve the accuracy of the estimated precision matrices, we employ a supervised learning method to predict contact probability from a variety of evolutionary and non-evolutionary information and then incorporate the predicted probability as prior into our GGL framework.