Xin Gao

According to our database1, Xin Gao authored at least 136 papers between 2007 and 2021.

Collaborative distances:
  • Dijkstra number2 of four.
  • Erdős number3 of four.



In proceedings 
PhD thesis 


Online presence:



Analysis of the effects of related fingerprints on molecular similarity using an eigenvalue entropy approach.
J. Cheminformatics, 2021

Robust and ultrafast fiducial marker correspondence in electron tomography by a two-stage algorithm considering local constraints.
Bioinform., 2021

Approximate Kernel Selection via Matrix Approximation.
IEEE Trans. Neural Networks Learn. Syst., 2020

A Rapid, Accurate and Machine-Agnostic Segmentation and Quantification Method for CT-Based COVID-19 Diagnosis.
IEEE Trans. Medical Imaging, 2020

Joint Prediction of Breast Cancer Histological Grade and Ki-67 Expression Level Based on DCE-MRI and DWI Radiomics.
IEEE J. Biomed. Health Informatics, 2020

Guest Editorial for Selected Papers from BIOKDD 2018 and DMBIH 2018.
IEEE ACM Trans. Comput. Biol. Bioinform., 2020

AttPNet: Attention-Based Deep Neural Network for 3D Point Set Analysis.
Sensors, 2020

A unified linear convergence analysis of k-SVD.
Memetic Comput., 2020

DTiGEMS+: drug-target interaction prediction using graph embedding, graph mining, and similarity-based techniques.
J. Cheminformatics, 2020

SenWave: Monitoring the Global Sentiments under the COVID-19 Pandemic.
CoRR, 2020

Learning to Stop While Learning to Predict.
CoRR, 2020

Multichannel Deep Attention Neural Networks for the Classification of Autism Spectrum Disorder Using Neuroimaging and Personal Characteristic Data.
Complex., 2020

Impact of data preprocessing on cell-type clustering based on single-cell RNA-seq data.
BMC Bioinform., 2020

Spark-based parallel calculation of 3D fourier shell correlation for macromolecule structure local resolution estimation.
BMC Bioinform., 2020

RepAHR: an improved approach for de novo repeat identification by assembly of the high-frequency reads.
BMC Bioinform., 2020

iPAC: a genome-guided assembler of isoforms via phasing and combing paths.
Bioinform., 2020

Formal axioms in biomedical ontologies improve analysis and interpretation of associated data.
Bioinform., 2020

gep2pep: a bioconductor package for the creation and analysis of pathway-based expression profiles.
Bioinform., 2020

Novel algorithms for efficient subsequence searching and mapping in nanopore raw signals towards targeted sequencing.
Bioinform., 2020

Proteome-level assessment of origin, prevalence and function of leucine-aspartic acid (LD) motifs.
Bioinform., 2020

DeepSimulator1.5: a more powerful, quicker and lighter simulator for Nanopore sequencing.
Bioinform., 2020

PUB-SalNet: A Pre-Trained Unsupervised Self-Aware Backpropagation Network for Biomedical Salient Segmentation.
Algorithms, 2020

Automated Counting of Colony Forming Units Using Deep Transfer Learning From a Model for Congested Scenes Analysis.
IEEE Access, 2020

Automatic and Interpretable Model for Periodontitis Diagnosis in Panoramic Radiographs.
Proceedings of the Medical Image Computing and Computer Assisted Intervention - MICCAI 2020, 2020

RNA Secondary Structure Prediction By Learning Unrolled Algorithms.
Proceedings of the 8th International Conference on Learning Representations, 2020

When sparse coding meets ranking: a joint framework for learning sparse codes and ranking scores.
Neural Comput. Appl., 2019

Accelerating flash calculation through deep learning methods.
J. Comput. Phys., 2019

Deep Learning Deepens the Analysis of Alternative Splicing.
Genom. Proteom. Bioinform., 2019

In Memory of Vladimir B. Bajic (1952-2019).
Genom. Proteom. Bioinform., 2019

Deep learning in bioinformatics: introduction, application, and perspective in big data era.
CoRR, 2019

Fine-grained alignment of cryo-electron subtomograms based on MPI parallel optimization.
BMC Bioinform., 2019

DeeReCT-PolyA: a robust and generic deep learning method for PAS identification.
Bioinform., 2019

PredMP: a web server for de novo prediction and visualization of membrane proteins.
Bioinform., 2019

Promoter analysis and prediction in the human genome using sequence-based deep learning models.
Bioinform., 2019

OPA2Vec: combining formal and informal content of biomedical ontologies to improve similarity-based prediction.
Bioinform., 2019

AuTom-dualx: a toolkit for fully automatic fiducial marker-based alignment of dual-axis tilt series with simultaneous reconstruction.
Bioinform., 2019

A joint method for marker-free alignment of tilt series in electron tomography.
Bioinform., 2019

Systematic selection of chemical fingerprint features improves the Gibbs energy prediction of biochemical reactions.
Bioinform., 2019

GCN-MF: Disease-Gene Association Identification By Graph Convolutional Networks and Matrix Factorization.
Proceedings of the 25th ACM SIGKDD International Conference on Knowledge Discovery & Data Mining, 2019

Domain Randomization for Macromolecule Structure Classification and Segmentation in Electron Cyro-tomograms.
Proceedings of the 2019 IEEE International Conference on Bioinformatics and Biomedicine, 2019

Transmembrane Topology Identification by Fusing Evolutionary and Co-evolutionary Information with Cascaded Bidirectional Transformers.
Proceedings of the 10th ACM International Conference on Bioinformatics, 2019

Confidence Weighted Multitask Learning.
Proceedings of the Thirty-Third AAAI Conference on Artificial Intelligence, 2019

Approximate Kernel Selection with Strong Approximate Consistency.
Proceedings of the Thirty-Third AAAI Conference on Artificial Intelligence, 2019

Linear Kernel Tests via Empirical Likelihood for High-Dimensional Data.
Proceedings of the Thirty-Third AAAI Conference on Artificial Intelligence, 2019

Multiscale and Multimodal Analysis for Computational Biology.
IEEE ACM Trans. Comput. Biol. Bioinform., 2018

A Slice-based <sup>13</sup>C-detected NMR Spin System Forming and Resonance Assignment Method.
IEEE ACM Trans. Comput. Biol. Bioinform., 2018

WaveNano: a signal-level nanopore base-caller via simultaneous prediction of nucleotide labels and move labels through bi-directional WaveNets.
Quant. Biol., 2018

RIDDLE: Race and ethnicity Imputation from Disease history with Deep LEarning.
PLoS Comput. Biol., 2018

Functional interrogation of Plasmodium genus metabolism identifies species- and stage-specific differences in nutrient essentiality and drug targeting.
PLoS Comput. Biol., 2018

PromID: human promoter prediction by deep learning.
CoRR, 2018

On the Decision Boundary of Deep Neural Networks.
CoRR, 2018

SupportNet: solving catastrophic forgetting in class incremental learning with support data.
CoRR, 2018

Onto2Vec: joint vector-based representation of biological entities and their ontology-based annotations.
Bioinform., 2018

DLBI: deep learning guided Bayesian inference for structure reconstruction of super-resolution fluorescence microscopy.
Bioinform., 2018

DEEPre: sequence-based enzyme EC number prediction by deep learning.
Bioinform., 2018

DeepSimulator: a deep simulator for Nanopore sequencing.
Bioinform., 2018

A fast fiducial marker tracking model for fully automatic alignment in electron tomography.
Bioinform., 2018

An accurate and rapid continuous wavelet dynamic time warping algorithm for end-to-end mapping in ultra-long nanopore sequencing.
Bioinform., 2018

Robust Asymmetric Recommendation via Min-Max Optimization.
Proceedings of the 41st International ACM SIGIR Conference on Research & Development in Information Retrieval, 2018

Robust Cost-Sensitive Learning for Recommendation with Implicit Feedback.
Proceedings of the 2018 SIAM International Conference on Data Mining, 2018

Bandit Online Learning on Graphs via Adaptive Optimization.
Proceedings of the Twenty-Seventh International Joint Conference on Artificial Intelligence, 2018

Convergence Analysis of Gradient Descent for Eigenvector Computation.
Proceedings of the Twenty-Seventh International Joint Conference on Artificial Intelligence, 2018

Feature Decomposition Based Saliency Detection in Electron Cryo-Tomograms.
Proceedings of the IEEE International Conference on Bioinformatics and Biomedicine, 2018

Randomized Kernel Selection With Spectra of Multilevel Circulant Matrices.
Proceedings of the Thirty-Second AAAI Conference on Artificial Intelligence, 2018

Robust Online Multi-Task Learning with Correlative and Personalized Structures.
IEEE Trans. Knowl. Data Eng., 2017

Multi-instance dictionary learning via multivariate performance measure optimization.
Pattern Recognit., 2017

Learning from Weak and Noisy Labels for Semantic Segmentation.
IEEE Trans. Pattern Anal. Mach. Intell., 2017

Learning gene regulatory networks from gene expression data using weighted consensus.
Neurocomputing, 2017

K-nearest uphill clustering in the protein structure space.
Neurocomputing, 2017

Genome-scale regression analysis reveals a linear relationship for promoters and enhancers after combinatorial drug treatment.
Bioinform., 2017

Sequence2Vec: a novel embedding approach for modeling transcription factor binding affinity landscape.
Bioinform., 2017

Gracob: a novel graph-based constant-column biclustering method for mining growth phenotype data.
Bioinform., 2017

FeaBoost: Joint Feature and Label Refinement for Semantic Segmentation.
Proceedings of the Thirty-First AAAI Conference on Artificial Intelligence, 2017

A Sequence-Based Dynamic Ensemble Learning System for Protein Ligand-Binding Site Prediction.
IEEE ACM Trans. Comput. Biol. Bioinform., 2016

DESM: portal for microbial knowledge exploration systems.
Nucleic Acids Res., 2016

MRE: a web tool to suggest foreign enzymes for the biosynthesis pathway design with competing endogenous reactions in mind.
Nucleic Acids Res., 2016

Large margin classification with indefinite similarities.
Mach. Learn., 2016

CMsearch: simultaneous exploration of protein sequence space and structure space improves not only protein homology detection but also protein structure prediction.
Bioinform., 2016

Optimizing Multivariate Performance Measures from Multi-View Data.
Proceedings of the Thirtieth AAAI Conference on Artificial Intelligence, 2016

Markov State Models Reveal a Two-Step Mechanism of miRNA Loading into the Human Argonaute Protein: Selective Binding followed by Structural Re-arrangement.
PLoS Comput. Biol., 2015

Max-min distance nonnegative matrix factorization.
Neural Networks, 2015

Sparse structure regularized ranking.
Multim. Tools Appl., 2015

Regularized maximum correntropy machine.
Neurocomputing, 2015

Feature selection and multi-kernel learning for adaptive graph regularized nonnegative matrix factorization.
Expert Syst. Appl., 2015

Maximum mutual information regularized classification.
Eng. Appl. Artif. Intell., 2015

An integrated structure- and system-based framework to identify new targets of metabolites and known drugs.
Bioinform., 2015

Distinct profiling of antimicrobial peptide families.
Bioinform., 2015

Finding optimal interaction interface alignments between biological complexes.
Bioinform., 2015

Parameter estimation methods for gene circuit modeling from time-series mRNA data: a comparative study.
Briefings Bioinform., 2015

Social Image Parsing by Cross-Modal Data Refinement.
Proceedings of the Twenty-Fourth International Joint Conference on Artificial Intelligence, 2015

Partially Labeled Data Tuple Can Optimize Multivariate Performance Measures.
Proceedings of the 24th ACM International Conference on Information and Knowledge Management, 2015

Pairwise structure alignment specifically tuned for surface pockets and interaction interfaces.
Proceedings of the 6th ACM Conference on Bioinformatics, 2015

Compare local pocket and global protein structure models by small structure patterns.
Proceedings of the 6th ACM Conference on Bioinformatics, 2015

Noise-Robust Semi-Supervised Learning by Large-Scale Sparse Coding.
Proceedings of the Twenty-Ninth AAAI Conference on Artificial Intelligence, 2015

Efficient Active Learning of Halfspaces via Query Synthesis.
Proceedings of the Twenty-Ninth AAAI Conference on Artificial Intelligence, 2015

Feature selection and multi-kernel learning for sparse representation on a manifold.
Neural Networks, 2014

Bayesian Peak Picking for NMR Spectra.
Genom. Proteom. Bioinform., 2014

Beyond cross-domain learning: Multiple-domain nonnegative matrix factorization.
Eng. Appl. Artif. Intell., 2014

Learning manifold to regularize nonnegative matrix factorization.
CoRR, 2014

Modeling DNA affinity landscape through two-round support vector regression with weighted degree kernels.
BMC Syst. Biol., 2014

LigandRFs: random forest ensemble to identify ligand-binding residues from sequence information alone.
BMC Bioinform., 2014

Semi-supervised sparse coding.
Proceedings of the 2014 International Joint Conference on Neural Networks, 2014

Large margin image set representation and classification.
Proceedings of the 2014 International Joint Conference on Neural Networks, 2014

Minimum Information Loss Based Multi-kernel Learning for Flagellar Protein Recognition in Trypanosoma Brucei.
Proceedings of the 2014 IEEE International Conference on Data Mining Workshops, 2014

Quick Mining of Isomorphic Exact Large Patterns from Large Graphs.
Proceedings of the 2014 IEEE International Conference on Data Mining Workshops, 2014

Adding Robustness to Support Vector Machines Against Adversarial Reverse Engineering.
Proceedings of the 23rd ACM International Conference on Conference on Information and Knowledge Management, 2014

Support vector machines with indefinite kernels.
Proceedings of the Sixth Asian Conference on Machine Learning, 2014

Supervised Transfer Sparse Coding.
Proceedings of the Twenty-Eighth AAAI Conference on Artificial Intelligence, 2014

Joint learning and weighting of visual vocabulary for bag-of-feature based tissue classification.
Pattern Recognit., 2013

Multiple graph regularized nonnegative matrix factorization.
Pattern Recognit., 2013

Discriminative sparse coding on multi-manifolds.
Knowl. Based Syst., 2013

Recent Advances in Computational Methods for Nuclear Magnetic Resonance Data Processing.
Genom. Proteom. Bioinform., 2013

Non-negative matrix factorization by maximizing correntropy for cancer clustering.
BMC Bioinform., 2013

Poly(A) motif prediction using spectral latent features from human DNA sequences.
Bioinform., 2013

A framework for scalable parameter estimation of gene circuit models using structural information.
Bioinform., 2013

Assessing protein conformational sampling methods based on bivariate lag-distributions of backbone angles.
Briefings Bioinform., 2013

ProClusEnsem: Predicting membrane protein types by fusing different modes of pseudo amino acid composition.
Comput. Biol. Medicine, 2012

ProDis-ContSHC: learning protein dissimilarity measures and hierarchical context coherently for protein-protein comparison in protein database retrieval.
BMC Bioinform., 2012

Multiple graph regularized protein domain ranking.
BMC Bioinform., 2012

Combining automated peak tracking in SAR by NMR with structure-based backbone assignment from <sup>15</sup>N-NOESY.
BMC Bioinform., 2012

Protein domain recurrence and order can enhance prediction of protein functions.
Bioinform., 2012

WaVPeak: picking NMR peaks through wavelet-based smoothing and volume-based filtering.
Bioinform., 2012

Adaptive graph regularized Nonnegative Matrix Factorization via feature selection.
Proceedings of the 21st International Conference on Pattern Recognition, 2012

Bag-of-Features Based Medical Image Retrieval via Multiple Assignment and Visual Words Weighting.
IEEE Trans. Medical Imaging, 2011

Towards Fully Automated Structure-Based NMR Resonance Assignment of <sup>15</sup>N-Labeled Proteins From Automatically Picked Peaks.
J. Comput. Biol., 2011

Error Tolerant NMR Backbone Resonance Assignment and Automated Structure Generation.
J. Bioinform. Comput. Biol., 2011

A protein-dependent side-chain rotamer library.
BMC Bioinform., 2011

An efficient parallel stochastic simulation method for analysis of nonviral gene delivery systems.
Proceedings of the Computational Methods in Systems Biology, 9th International Conference, 2011

Combining ambiguous chemical shift mapping with structure-based backbone and NOE assignment from <sup>15</sup>N-NOESY.
Proceedings of the ACM International Conference on Bioinformatics, 2011

Towards Automated Structure-Based NMR Resonance Assignment.
Proceedings of the Research in Computational Molecular Biology, 2010

Towards Automating Protein Structure Determination from NMR Data.
PhD thesis, 2009

Predicting Local Quality of a Sequence-Structure Alignment.
J. Bioinform. Comput. Biol., 2009

PICKY: a novel SVD-based NMR spectra peak picking method.
Bioinform., 2009

Rapid and Accurate Protein Side Chain Prediction with Local Backbone Information.
Proceedings of the Research in Computational Molecular Biology, 2008

Designing succinct structural alphabets.
Proceedings of the Proceedings 16th International Conference on Intelligent Systems for Molecular Biology (ISMB), 2008

New Algorithms for the Spaced Seeds.
Proceedings of the Frontiers in Algorithmics, First Annual International Workshop, 2007