Search Results for author: Sheng Wang

Found 67 papers, 34 papers with code

Pathway2Text: Dataset and Method for Biomedical Pathway Description Generation

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.

named-entity-recognition Named Entity Recognition +2

Textomics: A Dataset for Genomics Data Summary Generation

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.

BLIAM: Literature-based Data Synthesis for Synergistic Drug Combination Prediction

no code implementations14 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.

Data Augmentation Language Modelling

ChatCAD: Interactive Computer-Aided Diagnosis on Medical Image using Large Language Models

no code implementations14 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.

Decision Making Lesion Segmentation +1

RCPS: Rectified Contrastive Pseudo Supervision for Semi-Supervised Medical Image Segmentation

1 code implementation13 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.

Contrastive Learning Image Segmentation +2

Robust One-shot Segmentation of Brain Tissues via Image-aligned Style Transformation

1 code implementation26 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.

One-Shot Segmentation

CELLS: A Parallel Corpus for Biomedical Lay Language Generation

1 code implementation7 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.

Explanation Generation Retrieval +1

Modern Tontine with Transaction Costs

no code implementations20 Sep 2022 Lin He, Zongxia Liang, Sheng Wang

The wealth of the retiree is divided into a bequest account and a tontine account.

POPDx: An Automated Framework for Patient Phenotyping across 392,246 Individuals in the UK Biobank Study

1 code implementation23 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.

Patient Phenotyping

Brain-Aware Replacements for Supervised Contrastive Learning in Detection of Alzheimer's Disease

1 code implementation11 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.

Contrastive Learning Data Augmentation

E2Efold-3D: End-to-End Deep Learning Method for accurate de novo RNA 3D Structure Prediction

1 code implementation4 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.

A fully differentiable ligand pose optimization framework guided by deep learning and traditional scoring functions

no code implementations27 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.

Graph-in-Graph Network for Automatic Gene Ontology Description Generation

no code implementations10 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.

Hedging option books using neural-SDE market models

1 code implementation31 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.

Eye-gaze-guided Vision Transformer for Rectifying Shortcut Learning

no code implementations25 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.

Spatial Attention-based Implicit Neural Representation for Arbitrary Reduction of MRI Slice Spacing

no code implementations23 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.


ProTranslator: zero-shot protein function prediction using textual description

no code implementations20 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.

Machine Translation Multi-Label Classification +1

Follow My Eye: Using Gaze to Supervise Computer-Aided Diagnosis

1 code implementation6 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.

Estimating risks of option books using neural-SDE market models

1 code implementation15 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.

Adaptive Transfer Learning for Plant Phenotyping

no code implementations14 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.

BIG-bench Machine Learning GPR +2

SurvODE: Extrapolating Gene Expression Distribution for Early Cancer Identification

1 code implementation30 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.

Irregular Time Series Time Series Analysis

Domain Generalization for Mammography Detection via Multi-style and Multi-view Contrastive Learning

1 code implementation21 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.

Contrastive Learning Domain Generalization +2

GraphPrompt: Biomedical Entity Normalization Using Graph-based Prompt Templates

no code implementations13 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.

Joint Progressive and Coarse-to-fine Registration of Brain MRI via Deformation Field Integration and Non-Rigid Feature Fusion

1 code implementation25 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.

Leveraging the Cell Ontology to classify unseen cell types

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.

Combined Trojan Y Chromosome Strategy and Sterile Insect Technique to Eliminate Mosquitoes: Modelling and Analysis

no code implementations17 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.

UniFaceGAN: A Unified Framework for Temporally Consistent Facial Video Editing

no code implementations12 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.

3D Reconstruction Face Reenactment +3

Shallow Feature Matters for Weakly Supervised Object Localization

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.

Pseudo Label Weakly-Supervised Object Localization

DisenHAN: Disentangled Heterogeneous Graph Attention Network for Recommendation

1 code implementation21 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.

Collaborative Filtering Graph Attention +1

Arbitrage-free neural-SDE market models

1 code implementation24 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.

Time Series Analysis

EBM-Fold: Fully-Differentiable Protein Folding Powered by Energy-based Models

no code implementations11 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.

Denoising Protein Folding +1

Towards Accurate Active Camera Localization

1 code implementation8 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.

Camera Localization Pose Estimation +1

On the Efficiency of K-Means Clustering: Evaluation, Optimization, and Algorithm Selection

no code implementations13 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.

High-Fidelity 3D Digital Human Head Creation from RGB-D Selfies

2 code implementations12 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.

Detecting and repairing arbitrage in traded option prices

1 code implementation21 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.

Density Estimation

Boosting Ant Colony Optimization via Solution Prediction and Machine Learning

no code implementations29 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.

BIG-bench Machine Learning Combinatorial Optimization

STADB: A Self-Thresholding Attention Guided ADB Network for Person Re-identification

1 code implementation7 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.

Person Re-Identification

Task-agnostic Temporally Consistent Facial Video Editing

no code implementations3 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.

3D Reconstruction Video Editing

mr2NST: Multi-Resolution and Multi-Reference Neural Style Transfer for Mammography

no code implementations25 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.

Lesion Detection Style Transfer

Analysis of Indexing Structures for Immutable Data

2 code implementations4 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.


PointASNL: Robust Point Clouds Processing using Nonlocal Neural Networks with Adaptive Sampling

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.

3D Point Cloud Classification Semantic Segmentation

Re-balancing Variational Autoencoder Loss for Molecule Sequence Generation

1 code implementation1 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.

PANDA: Facilitating Usable AI Development

no code implementations26 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.

Autonomous Driving

Rafiki: Machine Learning as an Analytics Service System

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.

BIG-bench Machine Learning Hyperparameter Optimization +2

ForkBase: An Efficient Storage Engine for Blockchain and Forkable Applications

no code implementations14 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

Adaptive Graph Convolutional Neural Networks

2 code implementations10 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.

Metric Learning

Folding membrane proteins by deep transfer learning

no code implementations28 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.

Transfer Learning

Robust Contextual Bandit via the Capped-$\ell_{2}$ norm

no code implementations17 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.

Decision Making

Predicting membrane protein contacts from non-membrane proteins by deep transfer learning

no code implementations24 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).

Transfer Learning

Accurate De Novo Prediction of Protein Contact Map by Ultra-Deep Learning Model

1 code implementation2 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.

Protein Folding

Deep Learning At Scale and At Ease

no code implementations25 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.

Image Classification

AUC-maximized Deep Convolutional Neural Fields for Sequence Labeling

no code implementations17 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.

Feature Learning based Deep Supervised Hashing with Pairwise Labels

1 code implementation12 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.

Image Retrieval Retrieval

MRFalign: Protein Homology Detection through Alignment of Markov Random Fields

no code implementations12 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.

Multiple Sequence Alignment

Protein Contact Prediction by Integrating Joint Evolutionary Coupling Analysis and Supervised Learning

no code implementations10 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.

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