2024
Ambiguities in neural-network-based hyperedge prediction.
J. Appl. Comput. Topol., October, 2024
Semantic Similarities Using Classical Embeddings in Quantum NLP.
Proceedings of the IEEE International Conference on Quantum Computing and Engineering, 2024
2023
FLUXestimator: a webserver for predicting metabolic flux and variations using transcriptomics data.
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Nucleic Acids Res., July, 2023
<i>Special Issue</i> Computational Network Biology: Modeling, Analysis, and Control (CNB-MAC) Workshop (2022).
J. Comput. Biol., July, 2023
Acid-Base Homeostasis and Implications to the Phenotypic Behaviors of Cancer.
Genom. Proteom. Bioinform., 2023
Generalized Matrix Local Low Rank Representation by Random Projection and Submatrix Propagation.
Proceedings of the 29th ACM SIGKDD Conference on Knowledge Discovery and Data Mining, 2023
2022
PLUS: Predicting cancer metastasis potential based on positive and unlabeled learning.
PLoS Comput. Biol., 2022
Response to 'Letter to the Editor: on the stability and internal consistency of component-wise sparse mixture regression based clustering', Zhang <i>et al.</i>.
Briefings Bioinform., 2022
Bias aware probabilistic Boolean matrix factorization.
Proceedings of the Uncertainty in Artificial Intelligence, 2022
Provable Second-Order Riemannian Gauss-Newton Method for Low-Rank Tensor Estimation <sup>‖</sup>.
Proceedings of the IEEE International Conference on Acoustics, 2022
2021
Principled Hyperedge Prediction with Structural Spectral Features and Neural Networks.
CoRR, 2021
IRIS-FGM: an integrative single-cell RNA-Seq interpretation system for functional gene module analysis.
Bioinform., 2021
Spatially and Robustly Hybrid Mixture Regression Model for Inference of Spatial Dependence.
Proceedings of the IEEE International Conference on Data Mining, 2021
2020
Corrections to "IsoTree: A New Framework for de novo Transcriptome Assembly from RNA-seq Reads".
IEEE ACM Trans. Comput. Biol. Bioinform., 2020
IsoTree: A New Framework for de novo Transcriptome Assembly from RNA-seq Reads.
IEEE ACM Trans. Comput. Biol. Bioinform., 2020
IRIS3: integrated cell-type-specific regulon inference server from single-cell RNA-Seq.
Nucleic Acids Res., 2020
Denoising individual bias for a fairer binary submatrix detection.
CoRR, 2020
Supervised clustering of high dimensional data using regularized mixture modeling.
CoRR, 2020
A New Algorithm using Component-wise Adaptive Trimming For Robust Mixture Regression.
CoRR, 2020
QUBIC2: a novel and robust biclustering algorithm for analyses and interpretation of large-scale RNA-Seq data.
Bioinform., 2020
Geometric All-way Boolean Tensor Decomposition.
Proceedings of the Advances in Neural Information Processing Systems 33: Annual Conference on Neural Information Processing Systems 2020, 2020
Denoising Individual Bias for Fairer Binary Submatrix Detection.
Proceedings of the CIKM '20: The 29th ACM International Conference on Information and Knowledge Management, 2020
A data denoising approach to optimize functional clustering of single cell RNA-sequencing data.
Proceedings of the IEEE International Conference on Bioinformatics and Biomedicine, 2020
Fast and Efficient Boolean Matrix Factorization by Geometric Segmentation.
Proceedings of the Thirty-Fourth AAAI Conference on Artificial Intelligence, 2020
2019
Robust tests for gene-environment interaction in case-control and case-only designs.
Comput. Stat. Data Anal., 2019
MEBF: a fast and efficient Boolean matrix factorization method.
CoRR, 2019
DTA-SiST: de novo transcriptome assembly by using simplified suffix trees.
BMC Bioinform., 2019
M3S: a comprehensive model selection for multi-modal single-cell RNA sequencing data.
BMC Bioinform., 2019
2018
MRHCA: a nonparametric statistics based method for hub and co-expression module identification in large gene co-expression network.
Quant. Biol., 2018
DTAST: A Novel Radical Framework for de Novo Transcriptome Assembly Based on Suffix Trees.
Proceedings of the Intelligent Computing Theories and Application, 2018
2017
QUBIC: a bioconductor package for qualitative biclustering analysis of gene co-expression data.
Bioinform., 2017
IsoTree: De Novo Transcriptome Assembly from RNA-Seq Reads - (Extended Abstract).
Proceedings of the Bioinformatics Research and Applications - 13th International Symposium, 2017
2016
PUEPro: A Computational Pipeline for Prediction of Urine Excretory Proteins.
Proceedings of the Advanced Data Mining and Applications - 12th International Conference, 2016
2015
Stresses drive a cancer's initiation, progression and metastasis: Critical comments on the book "Cancer Bioinformatics".
J. Bioinform. Comput. Biol., 2015
2014
Population dynamics inside cancer biomass driven by repeated hypoxia-reoxygenation cycles.
Quant. Biol., 2014