Xin Gao
Orcid: 0000-0002-7108-3574Affiliations:
- King Abdullah University of Science and Technology, Computer, Electrical and Mathematical Sciences and Engineering Division, Thuwal, Saudi Arabia
- Carnegie Mellon University, School of Computer Science, Pittsburgh, PA, USA (2009 - 2010)
- University of Waterloo, ON, Canada (PhD 2009)
According to our database1,
Xin Gao
authored at least 222 papers
between 2007 and 2024.
Collaborative distances:
Collaborative distances:
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Bibliography
2024
Personalized and privacy-preserving federated heterogeneous medical image analysis with PPPML-HMI.
Comput. Biol. Medicine, February, 2024
PractiCPP: a deep learning approach tailored for extremely imbalanced datasets in cell-penetrating peptide prediction.
Bioinform., February, 2024
IEEE ACM Trans. Audio Speech Lang. Process., 2024
Rethinking Scientific Summarization Evaluation: Grounding Explainable Metrics on Facet-aware Benchmark.
CoRR, 2024
Leveraging Professional Radiologists' Expertise to Enhance LLMs' Evaluation for Radiology Reports.
CoRR, 2024
PepHarmony: A Multi-View Contrastive Learning Framework for Integrated Sequence and Structure-Based Peptide Encoding.
CoRR, 2024
2023
MMCL-CDR: enhancing cancer drug response prediction with multi-omics and morphology images contrastive representation learning.
Bioinform., December, 2023
Cross-Parametric Generative Adversarial Network-Based Magnetic Resonance Image Feature Synthesis for Breast Lesion Classification.
IEEE J. Biomed. Health Informatics, November, 2023
RPI-CapsuleGAN: Predicting RNA-protein interactions through an interpretable generative adversarial capsule network.
Pattern Recognit., September, 2023
MULGA, a unified multi-view graph autoencoder-based approach for identifying drug-protein interaction and drug repositioning.
Bioinform., September, 2023
Spatom: a graph neural network for structure-based protein-protein interaction site prediction.
Briefings Bioinform., September, 2023
Graph Neural Network and Spatiotemporal Transformer Attention for 3D Video Object Detection From Point Clouds.
IEEE Trans. Pattern Anal. Mach. Intell., August, 2023
Spectrum-irrelevant fine-grained representation for visible-infrared person re-identification.
Comput. Vis. Image Underst., July, 2023
DeepSTF: predicting transcription factor binding sites by interpretable deep neural networks combining sequence and shape.
Briefings Bioinform., July, 2023
Briefings Bioinform., May, 2023
Briefings Bioinform., May, 2023
A universal framework for single-cell multi-omics data integration with graph convolutional networks.
Briefings Bioinform., May, 2023
Multi-modality attribute learning-based method for drug-protein interaction prediction based on deep neural network.
Briefings Bioinform., May, 2023
TriNet: A tri-fusion neural network for the prediction of anticancer and antimicrobial peptides.
Patterns, March, 2023
Neural Comput. Appl., February, 2023
Follow the Timeline! Generating an Abstractive and Extractive Timeline Summary in Chronological Order.
ACM Trans. Inf. Syst., January, 2023
IEEE ACM Trans. Comput. Biol. Bioinform., 2023
Author Correction: The high-dimensional space of human diseases built from diagnosis records and mapped to genetic loci.
Nat. Comput. Sci., 2023
CryoAlign: feature-based method for global and local 3D alignment of EM density maps.
CoRR, 2023
CoRR, 2023
Opportunities and Challenges for ChatGPT and Large Language Models in Biomedicine and Health.
CoRR, 2023
CoRR, 2023
CoRR, 2023
Efficient automatic segmentation for multi-level pulmonary arteries: The PARSE challenge.
CoRR, 2023
Audit to Forget: A Unified Method to Revoke Patients' Private Data in Intelligent Healthcare.
CoRR, 2023
Drug Synergistic Combinations Predictions via Large-Scale Pre-Training and Graph Structure Learning.
CoRR, 2023
Follow the Timeline! Generating Abstractive and Extractive Timeline Summary in Chronological Order.
CoRR, 2023
Proceedings of the Sixteenth ACM International Conference on Web Search and Data Mining, 2023
Proceedings of the 46th International ACM SIGIR Conference on Research and Development in Information Retrieval, 2023
Topology-Preserving Computed Tomography Super-Resolution Based on Dual-Stream Diffusion Model.
Proceedings of the Medical Image Computing and Computer Assisted Intervention - MICCAI 2023, 2023
Proceedings of the 29th ACM SIGKDD Conference on Knowledge Discovery and Data Mining, 2023
Learn to Encode Heterogeneous Data: A Heterogeneous Aware Network for Multi-Future Trajectory Prediction.
Proceedings of the International Joint Conference on Neural Networks, 2023
Proceedings of the IEEE International Conference on Bioinformatics and Biomedicine, 2023
Proceedings of the 61st Annual Meeting of the Association for Computational Linguistics (Volume 1: Long Papers), 2023
Proceedings of the Thirty-Seventh AAAI Conference on Artificial Intelligence, 2023
Towards Efficient and Domain-Agnostic Evasion Attack with High-Dimensional Categorical Inputs.
Proceedings of the Thirty-Seventh AAAI Conference on Artificial Intelligence, 2023
2022
Annotating TSSs in Multiple Cell Types Based on DNA Sequence and RNA-seq Data via DeeReCT-TSS.
Genom. Proteom. Bioinform., October, 2022
SD2: spatially resolved transcriptomics deconvolution through integration of dropout and spatial information.
Bioinform., October, 2022
Preventing Sensitive Information Leakage From Mobile Sensor Signals via Integrative Transformation.
IEEE Trans. Mob. Comput., 2022
A Framework for Deep Multitask Learning With Multiparametric Magnetic Resonance Imaging for the Joint Prediction of Histological Characteristics in Breast Cancer.
IEEE J. Biomed. Health Informatics, 2022
Person Re-Identification by Context-Aware Part Attention and Multi-Head Collaborative Learning.
IEEE Trans. Inf. Forensics Secur., 2022
Special issue on computational biology and bioinformatic applications to the COVID-19 pandemic.
Quant. Biol., 2022
An interpretable deep learning workflow for discovering subvisual abnormalities in CT scans of COVID-19 inpatients and survivors.
Nat. Mach. Intell., 2022
Nucleic Acids Res., 2022
<i>iFeatureOmega: </i> an integrative platform for engineering, visualization and analysis of features from molecular sequences, structural and ligand data sets.
Nucleic Acids Res., 2022
PointSite: A Point Cloud Segmentation Tool for Identification of Protein Ligand Binding Atoms.
J. Chem. Inf. Model., 2022
DeeReCT-APA: Prediction of Alternative Polyadenylation Site Usage Through Deep Learning.
Genom. Proteom. Bioinform., 2022
Identification of DNA modification sites based on elastic net and bidirectional gated recurrent unit with convolutional neural network.
Biomed. Signal Process. Control., 2022
Bioinform., 2022
Bioinform., 2022
NASMDR: a framework for miRNA-drug resistance prediction using efficient neural architecture search and graph isomorphism networks.
Briefings Bioinform., 2022
Briefings Bioinform., 2022
RBP-TSTL is a two-stage transfer learning framework for genome-scale prediction of RNA-binding proteins.
Briefings Bioinform., 2022
Impact of computational approaches in the fight against COVID-19: an AI guided review of 17 000 studies.
Briefings Bioinform., 2022
Briefings Bioinform., 2022
Briefings Bioinform., 2022
Self-supervised contrastive learning for integrative single cell RNA-seq data analysis.
Briefings Bioinform., 2022
Discovering trends and hotspots of biosafety and biosecurity research via machine learning.
Briefings Bioinform., 2022
RPI-MDLStack: Predicting RNA-protein interactions through deep learning with stacking strategy and LASSO.
Appl. Soft Comput., 2022
Prolificacy Assessment of Spermatozoan via State-of-the-Art Deep Learning Frameworks.
IEEE Access, 2022
Proceedings of the SIGIR '22: The 45th International ACM SIGIR Conference on Research and Development in Information Retrieval, Madrid, Spain, July 11, 2022
Proceedings of the Advances in Neural Information Processing Systems 35: Annual Conference on Neural Information Processing Systems 2022, 2022
Rolling Bearing Fault Diagnosis Based on Deep Adversarial Networks with Convolutional Layer and Wasserstein Distance.
Proceedings of the 27th International Conference on Automation and Computing, 2022
Unsupervised Multi-Task Learning for 3D Subtomogram Image Alignment, Clustering and Segmentation.
Proceedings of the 2022 IEEE International Conference on Image Processing, 2022
Proceedings of the 2022 Conference on Empirical Methods in Natural Language Processing, 2022
Proceedings of the 31st ACM International Conference on Information & Knowledge Management, 2022
AdvCat: Domain-Agnostic Robustness Assessment for Cybersecurity-Critical Applications with Categorical Inputs.
Proceedings of the IEEE International Conference on Big Data, 2022
2021
ReFeaFi: Genome-wide prediction of regulatory elements driving transcription initiation.
PLoS Comput. Biol., 2021
Stable maintenance of hidden switches as a strategy to increase the gene expression stability.
Nat. Comput. Sci., 2021
Mob. Networks Appl., 2021
DTi2Vec: Drug-target interaction prediction using network embedding and ensemble learning.
J. Cheminformatics, 2021
Analysis of the effects of related fingerprints on molecular similarity using an eigenvalue entropy approach.
J. Cheminformatics, 2021
QAUST: Protein Function Prediction Using Structure Similarity, Protein Interaction, and Functional Motifs.
Genom. Proteom. Bioinform., 2021
Genom. Proteom. Bioinform., 2021
NeuralPolish: a novel Nanopore polishing method based on alignment matrix construction and orthogonal Bi-GRU Networks.
Bioinform., 2021
A novel constrained reconstruction model towards high-resolution subtomogram averaging.
Bioinform., 2021
Robust and ultrafast fiducial marker correspondence in electron tomography by a two-stage algorithm considering local constraints.
Bioinform., 2021
2020
Poly(A)-DG: A deep-learning-based domain generalization method to identify cross-species Poly(A) signal without prior knowledge from target species.
PLoS Comput. Biol., November, 2020
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
IEEE ACM Trans. Comput. Biol. Bioinform., 2020
Sensors, 2020
Few-shot learning for classification of novel macromolecular structures in cryo-electron tomograms.
PLoS Comput. Biol., 2020
DTiGEMS+: drug-target interaction prediction using graph embedding, graph mining, and similarity-based techniques.
J. Cheminformatics, 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
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
Proceedings of the 37th International Conference on Machine Learning, 2020
Proceedings of the 8th International Conference on Learning Representations, 2020
2019
When sparse coding meets ranking: a joint framework for learning sparse codes and ranking scores.
Neural Comput. Appl., 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
Bioinform., 2019
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
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
Proceedings of the Thirty-Third AAAI Conference on Artificial Intelligence, 2019
Proceedings of the Thirty-Third AAAI Conference on Artificial Intelligence, 2019
Proceedings of the Thirty-Third AAAI Conference on Artificial Intelligence, 2019
2018
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
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
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
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
Proceedings of the 41st International ACM SIGIR Conference on Research & Development in Information Retrieval, 2018
Proceedings of the 2018 SIAM International Conference on Data Mining, 2018
Proceedings of the Twenty-Seventh International Joint Conference on Artificial Intelligence, 2018
Proceedings of the Twenty-Seventh International Joint Conference on Artificial Intelligence, 2018
Proceedings of the IEEE International Conference on Bioinformatics and Biomedicine, 2018
Proceedings of the Thirty-Second AAAI Conference on Artificial Intelligence, 2018
2017
IEEE Trans. Knowl. Data Eng., 2017
Multi-instance dictionary learning via multivariate performance measure optimization.
Pattern Recognit., 2017
IEEE Trans. Pattern Anal. Mach. Intell., 2017
Learning gene regulatory networks from gene expression data using weighted consensus.
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
Proceedings of the 2017 ACM on Multimedia Conference, 2017
Proceedings of the Thirty-First AAAI Conference on Artificial Intelligence, 2017
2016
A Sequence-Based Dynamic Ensemble Learning System for Protein Ligand-Binding Site Prediction.
IEEE ACM Trans. Comput. Biol. Bioinform., 2016
MRE: a web tool to suggest foreign enzymes for the biosynthesis pathway design with competing endogenous reactions in mind.
Nucleic Acids Res., 2016
CMsearch: simultaneous exploration of protein sequence space and structure space improves not only protein homology detection but also protein structure prediction.
Bioinform., 2016
Proceedings of the Thirtieth AAAI Conference on Artificial Intelligence, 2016
2015
BMC Bioinform., December, 2015
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
Feature selection and multi-kernel learning for adaptive graph regularized nonnegative matrix factorization.
Expert Syst. Appl., 2015
Eng. Appl. Artif. Intell., 2015
An integrated structure- and system-based framework to identify new targets of metabolites and known drugs.
Bioinform., 2015
Bioinform., 2015
Parameter estimation methods for gene circuit modeling from time-series mRNA data: a comparative study.
Briefings Bioinform., 2015
Proceedings of the Twenty-Fourth International Joint Conference on Artificial Intelligence, 2015
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
Proceedings of the Twenty-Ninth AAAI Conference on Artificial Intelligence, 2015
Proceedings of the Twenty-Ninth AAAI Conference on Artificial Intelligence, 2015
2014
Neural Networks, 2014
Eng. Appl. Artif. Intell., 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
Proceedings of the 2014 International Joint Conference on Neural Networks, 2014
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
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
Proceedings of the Sixth Asian Conference on Machine Learning, 2014
Proceedings of the Twenty-Eighth AAAI Conference on Artificial Intelligence, 2014
2013
Joint learning and weighting of visual vocabulary for bag-of-feature based tissue classification.
Pattern Recognit., 2013
Recent Advances in Computational Methods for Nuclear Magnetic Resonance Data Processing.
Genom. Proteom. Bioinform., 2013
BMC Bioinform., 2013
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
2012
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
Combining automated peak tracking in SAR by NMR with structure-based backbone assignment from <sup>15</sup>N-NOESY.
BMC Bioinform., 2012
Bioinform., 2012
WaVPeak: picking NMR peaks through wavelet-based smoothing and volume-based filtering.
Bioinform., 2012
Proceedings of the 21st International Conference on Pattern Recognition, 2012
2011
Towards Fully Automated Structure-Based NMR Resonance Assignment of <sup>15</sup>N-Labeled Proteins From Automatically Picked Peaks.
J. Comput. Biol., 2011
J. Bioinform. Comput. Biol., 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
2010
Proceedings of the Research in Computational Molecular Biology, 2010
2009
J. Bioinform. Comput. Biol., 2009
2008
Proceedings of the Research in Computational Molecular Biology, 2008
Proceedings of the Proceedings 16th International Conference on Intelligent Systems for Molecular Biology (ISMB), 2008
2007
Proceedings of the Frontiers in Algorithmics, First Annual International Workshop, 2007