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2019 IEEE International Conference on Bioinformatics and Biomedicine (BIBM)

Nov. 18 2019 to Nov. 21 2019

San Diego, CA, USA

ISBN: 978-1-7281-1867-3

Table of Contents

pp. 1-2

pp. 1-9

pp. 1-32

Artificial Intelligence for Public Health

pp. 1-2

by Kristin P. Bennett

Bioinformatics: a Servant or the Queen of Molecular Biology?

pp. 3-4

by Pavel Pevzner

Maintaining Intracellular Acid-Base Homeostasis is Probably at the Core of Cancer Formation, Progression and Metastasis

pp. 5-5

Domain Randomization for Macromolecule Structure Classification and Segmentation in Electron Cyro-tomograms

pp. 6-11

by Chengqian Che, Zhou Xian, Xiangrui Zeng, Xin Gao, Min Xu

A deep neural network approach using distributed representations of RNA sequence and structure for identifying binding site of RNA-binding proteins

pp. 12-17

by Lei Deng, Youzhi Liu, Yechuan Shi, Hui Liu

DKCirc2GO: Predicting Gene Ontology of circRNAs Using Dual KATZ Approach

pp. 18-23

by Lei Deng, Xin Sun, Wei Lin, Jingpu Zhang

Identification of protein hot regions by integrated machine learning algorithm

pp. 24-29

by Jing Hu, Haomin Gan, Xiaolong Zhang, Nansheng Chen

Identifying Near-Native Protein Structures via Anomaly Detection

pp. 30-35

by Sivani Tadepalli, Nasrin Akhter, Daniel Barbará, Amarda Shehu

DMCTOP: Topology Prediction of Alpha-Helical Transmembrane Protein Based on Deep Multi-Scale Convolutional Neural Network

pp. 36-43

by Han Wang, Yuning Yang, Jiawen Yu, Xi Wang, Dawei Zhao, Dong Xu, Pingping Sun

An Application of Random Walk Resampling to Phylogenetic HMM Inference and Learning

pp. 44-51

by Wei Wang, Qiqige Wuyun, Kevin J. Liu

Regularized Adversarial Training (RAT) for Robust Cellular Electron Cryo Tomograms Classification

pp. 1-6

by Xindi Wu, Yijun Mao, Haohan Wang, Xiangrui Zeng, Xin Gao, Eric P. Xing, Min Xu

PNAB: Prediction of protein-nucleic acid binding affinity using heterogeneous ensemble models

pp. 58-63

by Wenyi Yang, Lei Deng

AttentionDTA: prediction of drug–target binding affinity using attention model

pp. 64-69

by Qichang Zhao, Fen Xiao, Mengyun Yang, Yaohang Li, Jianxin Wang

Non-Negative Matrix Factorization for Selection of Near-Native Protein Tertiary Structures

pp. 70-73

by Nasrin Akhter, Raviteja Vangara, Gopinath Chennupati, Boian S. Alexandrov, Hristo Djidjev, Amarda Shehu

D2VCB: A Hybrid Deep Neural Network for the Prediction of in-vivo Protein-DNA Binding from Combined DNA Sequence

pp. 74-77

by Lei Deng, Hui Wu, Hui Liu

Detecting somatic mutations with high accuracy in plasma cell-free DNA with TNER2

pp. 78-81

by Shibing Deng, Joy Hsu, Jadwiga Bienkowska, Paul A. Rejto, Tao Xie

A Deep Neural Network for Antimicrobial Peptide Recognition

pp. 82-85

by Jianyuan Lin, Xiangxiang Zeng, Yun Zuo, Ying Ju, Xiangrong Liu

Predicting protein functions through non-negative matrix factorization regularized by protein-protein interaction network and gene functional information

pp. 86-89

by Wei Peng, Lun Li, Wei Dai, Jielin Du, Wei Lan

MUFold-Contact and TPCref: New Methods for Protein Structure Contact Prediction and Refinement

pp. 90-93

by Jeffrey Ruffolo, Zhaoyu Li, Yi Shang

B-cell Epitope Prediction Method based on Deep Ensemble Architecture and Sequences

pp. 94-97

by Pingping Sun, Yang Yu, Rui Wang, Mingjun Cheng, Zhiguo Zhou, Hui Sun

A Weighted Voting Algorithm for Detecting Reliable Common Lines in Single Particle Cryo-EM

pp. 98-101

by Xiangwen Wang, Yonggang Lu, Zhenyu Lu, Xingcheng Ran, Jiaxuan Liu

Win-win Cooperation: A Novel Dual-Modal Dual-Label Algorithm for Membrane Proteins Function Pre-screen

pp. 102-106

by Yi Zhang, Zhecheng Zhang, Hao Cheng, Hengyang Lu, Lei Zhang, Chongjun Wang, Junyuan Xie

A Protein Complex Identification Algorithm Based on essential protein

pp. 107-110

by Junmin Zhao, Jingpu Zhang, Bin Yang, Yuanyuan Ma

DoRC: Discovery of rare cells from ultra-large scRNA-seq data

pp. 111-116

by Xiang Chen, Fang-Xiang Wu, Jin Chen, Min Li

Protein Ubiquitylation and Sumoylation Site Prediction Based on Ensemble and Transfer Learning

pp. 117-123

by Fei He, Rui Wang, Yanxin Gao, Duolin Wang, Yang Yu, Dong Xu, Xiaowei Zhao

Drug and disease similarity calculation platform for drug repositioning

pp. 124-129

by Lan Huang, HuiMin Luo, Mengyun Yang, Fang-Xiang Wu, Jianxin Wang

Supervised prediction of aging-related genes from a context-specific protein interaction subnetwork

pp. 130-137

by Qi Li, Tijana Milenković

Pattern formation analysis by colored Petri nets with quantitative manipulation of a gene

pp. 138-144

by Fei Liu, Ena Yamamoto, Katsunobu Shirahama, Tsubasa Saitoh, Shuhei Aoyama, Yumiko Harada, Ryutaro Murakami, Hiroshi Matsuno

Predicting circRNA-disease associations using deep generative adversarial network based on multi-source fusion information

pp. 145-152

by Lei Wang, Zhu-Hong You, Li-Ping Li, Kai Zheng, Yan-Bin Wang

Predicting Drug-Disease Treatment Associations Based on Topological Similarity and Singular Value Decomposition

pp. 153-158

by Guangsheng Wu, Juan Liu

Predicting LncRNA-disease Association by Autoencoder and Rotation Forest

pp. 159-164

by Jincai Yang, Shunping Ma, Xingpeng Jiang

CoPath: discovering cooperative driver pathways using greedy mutual exclusivity and bi-clustering

pp. 165-170

by Ziying Yang, Guoxian Yu, Jiantao Yu, Maozu Guo, Jun Wang

DMIL-III: Isoform-isoform interaction prediction using deep multi-instance learning method

pp. 171-176

by Jie Zeng, Guoxian Yu, Jun Wang, Maozu Guo, Xiangliang Zhang

Predicting Disease-related RNA Associations based on Graph Convolutional Attention Network

pp. 177-182

by Jinli Zhang, Xiaohua Hu, Zongli Jiang, Bo Song, Wei Quan, Zheng Chen

Prediction of Microbe-Drug Associations Based on KATZ Measure

pp. 183-187

by Lingzhi Zhu, Guihua Duan, Cheng Yan, Jianxin Wang

Network Analysis of Antibiotic Resistance Identifies Compelling Mutations across Pathways

pp. 188-192

by Kimia Ameri, Kathryn Cooper

Identifying functional evolution processes according to the pathological stages of colorectal cancer

pp. 193-196

by Bolin Chen, Manting Yang, Li Gao, Xuequn Shang

Multi-Classification of Cancer Samples Based on Co-Expression Analyses

pp. 197-201

by Hongyang Jiang, Qiang Huang, Liang Chen, Zhi Li, Ying Xu, Huiyan Sun, Yi Chang

Nonnegative Matrix Factorization for Dynamic Modules in Cancer Attribute Temporal Networks

pp. 202-206

by Dongyuan Li, Xiaoke Ma

Ensemble Classifier based on gene synergistic network improves breast cancer outcome prediction

pp. 207-210

by Bo Lu, Xiong-Hui Zhou

HNEDTI: Prediction of drug-target interaction based on heterogeneous network embedding

pp. 211-214

by Zhangli Lu, Yake Wang, Min Zeng, Min Li

Detecting protein complex based on hierarchical compressing network embedding

pp. 215-218

by Xiangmao Meng, Xiaoqing Peng, Fang-Xiang Wu, Min Li

A Novel Algorithm for Prioritizing Disease Candidate Genes from the Weighted PPI Network

pp. 219-222

by Xiwei Tang, Bihai Zhao, Xiao Qiu

Algorithms for inferring multiple microbial networks

pp. 223-227

by Sahar Tavakoli, Shibu Yooseph

Measuring Disease Similarity Based on Multiple Heterogeneous Disease Information Networks

pp. 228-231

by Ling Tian, Jianliang Gao, Jianxin Wang, Ying Wang, Bo Song, Xiaohua Hu

BnBeeEpi: An Approach of Epistasis Mining Based on Artificial Bee Colony Algorithm Optimizing Bayesian Network

pp. 232-239

by Chen Yang, Hui Gao, Xuan Yang, Suiyu Huang, Yulong Kan, Jianxiao Liu

Hypergraph Clustering Based on Intra-class Scatter Matrix for Mining Higher-order Microbial Module

pp. 240-243

by Limin Yu, Xianjun Shen, Xingpeng Jiang, Jincai Yang, Yujuan Yang, Duo Zhong

Metabolite Identification Using Artificial Neural Network

pp. 244-248

by Ziling Fan, Kian Ghaffari, Amber Alley, Habtom W. Ressom

Ant Colony Optimization with Self-Evolving Parameter for Detecting Epistatic Interactions

pp. 249-254

by Boxin Guan, Yuzhai Zhao, Yuan Li, Ying Yin

A knowledge driven mutual information-based analytical framework for the identification of rumen metabolites

pp. 255-260

by Mengyuan Wang, Huiru Zheng, Haiying Wang, Richard J. Dewhurst, Rainer Roehe

A Global Similarity Learning for Clustering of Single-Cell RNA-Seq Data

pp. 261-266

by Xiaoshu Zhu, Lilu Guo, Yunpei Xu, Hong-Dong Li, Xingyu Liao, Fang-Xiang Wu, Xiaoqing Peng

Integrative Analysis of DNA Methylation and Gene Expression Patterns in Tissues from Hepatocellular Carcinoma Patients

pp. 267-274

by Megan E. Barefoot, Yifan Chen, Rency S. Varghese, Yuan Zhou, Habtom W. Ressom

Efficient Shared Peak Counting in Database Peptide Search Using Compact Data Structure for Fragment-Ion Index

pp. 275-278

by Muhammad Haseeb, Fahad Saeed

FaceSNPs: Identifying Face-Related SNPs from the Human Genome

pp. 279-282

by Somadina Mbadiwe, Jeremy Dawson, Donald Adjeroh

SOF: An Efficient String Graph Construction Algorithm

pp. 283-287

by S. M. Iqbal Morshed, Shibu Yooseph

LysoPhD: predicting functional prophages in bacterial genomes from high-throughput sequencing

pp. 1-5

by Qi Niu, Shao-Liang Peng, Xiang-Li-Lan Zhang, Shuai-Cheng Li, Ying Xu, Xiang-Cheng Xie, Yi-Gang Tong

A Bidirectional Fuzzy Index and Approximate Search Algorithm for Next Generation Sequencing

pp. 293-297

by Wei Quan, Guangri Quan, Bo Liu, Yadong Wang

Graph-structured Sparse Mixed Models for Genetic Association with Confounding Factors Correction

pp. 298-302

by Haohan Wang, Changpeng Lu, Wei Wu, Eric P. Xing

DeepAtom: A Framework for Protein-Ligand Binding Affinity Prediction

pp. 303-310

by Yanjun Li, Mohammad A. Rezaei, Chenglong Li, Xiaolin Li

DeepDock: Enhancing Ligand-protein Interaction Prediction by a Combination of Ligand and Structure Information

pp. 311-317

by Zhirui Liao, Ronghui You, Xiaodi Huang, Xiaojun Yao, Tao Huang, Shanfeng Zhu

TOP: Towards Better Toxicity Prediction by Deep Molecular Representation Learning

pp. 318-325

by Yuzhong Peng, Ziqiao Zhang, Qizhi Jiang, Jihong Guan, Shuigeng Zhou

Molecular Graph Generation with Deep Reinforced Multitask Network and Adversarial Imitation Learning

pp. 326-329

by Chenrui Zhang, Xiaoqing Lyu, Yifeng Huang, Zhi Tang, Zhenming Liu

Accelerating Large-Scale Molecular Similarity Search through Exploiting High Performance Computing

pp. 330-333

by Chun Jiang Zhu, Tan Zhu, Haining Li, Jinbo Bi, Minghu Song

Multi-Stage Probabilistic Bipartite Graph Algorithm - Effect of Herbal Medicines on the Gut Ecosystem

pp. 334-341

by Suganya Chandrababu, Dhundy R Bastola

Knowledge Abstraction Matching for Medical Question Answering

pp. 342-347

by Jun Chen, Jingbo Zhou, Zhenhui Shi, Bin Fan, Chengliang Luo

Automatic ICD code assignment utilizing textual descriptions and hierarchical structure of ICD code

pp. 348-353

by Yuwen Chen, Jiangtao Ren

Drug-drug Interaction Prediction with Graph Representation Learning

pp. 354-361

by Xin Chen, Xien Liu, Ji Wu

OverlapLDA: A Generative Approach for Literature-Based Discovery

pp. 362-369

by Juncheng Ding, Wei Jin

Hierarchical Question-Aware Context Learning with Augmented Data for Biomedical Question Answering

pp. 370-375

by Yongping Du, Wenyang Guo, Yiliang Zhao

Recognizing Nested Named Entity in Biomedical Texts: A Neural Network Model with Multi-Task Learning

pp. 376-381

by Hao Fei, Yafeng Ren, Donghong Ji

Predicting gene-disease associations via graph embedding and graph convolutional networks

pp. 382-389

by Lvxing Zhu, Zhaolin Hong, Haoran Zheng

An attention-based neural network basecaller for Oxford Nanopore sequencing data

pp. 390-394

by Neng Huang, Fan Nie, Peng Ni, Feng Luo, Jianxin Wang

CTGA: Graph-based Biomedical Literature Search

pp. 395-400

by Tianwen Jiang, Zhihan Zhang, Tong Zhao, Bing Qin, Ting Liu, Nitesh V. Chawla, Meng Jiang

Y-SPCR: A new dimensionality reduction method for gene expression data classification

pp. 401-408

by Jie Li, Zhun Zhao, Li Zhou, Yadong Wang

Automatic Tongue Image Segmentation For Real-Time Remote Diagnosis

pp. 409-414

by Xinlei Li, Dawei Yang, Yan Wang, Shuai Yang, Lizhe Qi, Fufeng Li, Zhongxue Gan, Wenqiang Zhang

Global Bank: A Guided Pathway of Encoding and Decoding for Pathological Image Analysis

pp. 415-422

by Hansheng Li, Baosheng Kang, Yuxin Kang, Feihong Liu, Wenli Hui, Qirong Bo, Chunbao Wang, Lin Yang, Lei Cui, Jun Feng

A New Approach to Batch Effect Removal Based on Distribution Matching in Latent Space

pp. 423-430

by Huaqing Li, Haluk Dogan, Juan Cui

de novo repeat detection based on the third generation sequencing reads

pp. 431-436

by Xingyu Liao, Xiankai Zhang, Fang-Xiang Wu, Jianxin Wang

Early Prediction of Vital Signs Using Generative Boosting via LSTM Networks

pp. 437-444

by Shiyu Liu, Jia Yao, Mehul Motani

Structural Network Embedding using Multi-modal Deep Auto-encoders for Predicting Drug-drug Interactions

pp. 445-450

by Shichao Liu, Ziyang Huang, Yang Qiu, Yi-Ping Phoebe Chen, Wen Zhang

Detection of Cell Types from Single-cell RNA-seq Data using Similarity via Kernel Preserving Learning Embedding

pp. 451-457

by Zeming Liu, Feng Liu, Chengzhi Hong, Meng Gao, Yi-Ping Phoebe Chen, Shichao Liu, Wen Zhang

Predicting Disease Genes Using Connectivity and Functional Features

pp. 458-465

by Lorenzo Madeddu, Giovanni Stilo, Paola Velardi

OnTimeURB: Multi-Cloud Resource Brokering for Bioinformatics Workflows

pp. 466-473

by Ashish Pandey, Zhen Lyu, Trupti Joshi, Prasad Calyam

Statistical Linear Models in Virus Genomic Alignment-free Classification: Application to Hepatitis C Viruses

pp. 474-481

by Amine M. Remita, Abdoulaye Baniré Diallo

Active Learning with Deep Pre-trained Models for Sequence Tagging of Clinical and Biomedical Texts

pp. 482-489

by Artem Shelmanov, Vadim Liventsev, Danil Kireev, Nikita Khromov, Alexander Panchenko, Irina Fedulova, Dmitry V. Dylov

A General Fine-tuned Transfer Learning Model for Predicting Clinical Task Acrossing Diverse EHRs Datasets

pp. 490-495

by Zhe Sun, Shaoliang Peng, Yaning Yang, Xiaoqi Wang, Fei Li

Distantly Supervised Biomedical Named Entity Recognition with Dictionary Expansion

pp. 496-503

by Xuan Wang, Yu Zhang, Qi Li, Xiang Ren, Jingbo Shang, Jiawei Han

Predicting gene-disease associations from the heterogeneous network using graph embedding

pp. 504-511

by Xiaochan Wang, Yuchong Gong, Jing Yi, Wen Zhang

An Active Gene Annotation Corpus and Its Application on Anti-epilepsy Drug Discovery

pp. 512-519

by Yuxing Wang, Kaiyin Zhou, Jin-Dong Kim, Kevin B. Cohen, Mina Gachloo, Yuxin Ren, Shanghui Nie, Xuan Qin, Panzhong Lu, Jingbo Xia

Deep Inductive Matrix Completion for Biomedical Interaction Prediction

pp. 520-527

by Haohan Wang, Yibing Wei, Mengxin Cao, Min Xu, Wei Wu, Eric P. Xing

Drug Target Interaction Prediction using Multi-task Learning and Co-attention

pp. 528-533

by Yuyou Weng, Chen Lin, Xiangxiang Zeng, Yun Liang

Acceleration of the Pair-HMM forward algorithm on FPGA with cloud integration for GATK

pp. 534-541

by Rick Wertenbroek, Yann Thoma

Identifying Common Driver Pathways based on Pan-cancer Data

pp. 542-547

by Jingli Wu, Ke Pan, Kai Zhu, Qirong Cai

MHCherryPan. a novel model to predict the binding affinity of pan-specific class I HLA-peptide

pp. 548-554

by Xuezhi Xie, Yuanyuan Han, Kaizhong Zhang

LncPred-IEL: A Long Non-coding RNA Prediction Method using Iterative Ensemble Learning

pp. 555-562

by Yanzhen Xu, Xiaohan Zhao, Shuai Liu, Shichao Liu, Yanqing Niu, Wen Zhang, Leyi Wei

Semi-Supervised Attention-Guided CycleGAN for Data Augmentation on Medical Images

pp. 563-568

by Zhenghua Xu, Chang Qi, Guizhi Xu

Continuous Pain Assessment Using Ensemble Feature Selection from Wearable Sensor Data

pp. 569-576

by Fan Yang, Tanvi Banerjee, Mark J. Panaggio, Daniel M. Abrams, Nirmish R. Shah

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