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Software for Promoting Open Health Data Science

Software Developed in The Hu Lab

Software Developed in The Hu Lab

Software Developed in The Hu Lab

27: Software Web:  GraphBAN: An inductive graph-based approach for enhanced prediction of compound-protein interactions




26: Software Web:  CL-MFAP: A contrastive learning-based multimodal foundation model for molecular property prediction and antibiotic screening

Software Developed in The Hu Lab

Software Developed in The Hu Lab

Description: GraphBAN: An inductive graph-based approach for enhanced prediction of compound-protein interactions

Citation: Hadipour et al. 2025. Nature Communications


Description: CL-MFAP: A contrastive learning-based multimodal foundation model for molecular property prediction and antibiotic screening

Citation: Zhou et al.  ICLR 2025


25: Software Web:  An interpretable deep geometric learning model to predict the effects of mutations on protein–protein interactions using large-scale protein language model


24: Software Web: Conditional Probabilistic Diffusion Model Driven Synthetic Radiogenomic Applications



23: Software Web:  Investigating Alignment-Free Machine Learning Methods for HIV-1 Subtype Classification 



22: Software Web:   A cross-cohort analysis of dental plaque microbiome in early childhood caries


21: Software Web:  ST-CellSeg: Cell segmentation for imaging-based spatial transcriptomics using multiscale manifold learning 


20. Software Web: iNGNN-DTI: prediction of drug – target interaction with interpretable nested graph geural network and pretrained molecule models


19. Software Web:  Conditional Generative Adversarial Network Driven Radiomic Prediction of Mutation Status Based on Magnetic Resonance Imaging of Breast Cancer 


18 .Software Web:  A self-knowledge distillation-driven CNN-LSTM model for predicting disease outcomes using longitudinal microbiome data 


17. Software Web:  scGMM-VGAE: A Gaussian mixture model-based variational graph autoencoder algorithm for clustering single-cell RNA-seq data 


16. Software Web:  ABT-MPNN: an atom-bond transformer-based message-passing neural network for molecular property prediction



15. Software Web   Deep learning-based MRI-genomic mapping




14. Software Web:  Molecular Property Prediction based on Bimodal Supervised Contrast Learning





13. Software Web:  Machine Learning Model trained on a High-Throughput Antibacterial Screen





12. Software Web: Multiomics-based deep tensor survival model for time-to-event prediction

11. Software Web: Self-supervised deep learning models for CT image segmentation 








10. Software Web: Semi-Supervised Deep Generative Models for Image Segmentation




9. Software Web: A re-trainable deep learning tool for single cell RNA-sequencing based cell type labeling 



​8. Software Web: Deep learning-driven algorithm for clustering small molecules




7. Software Web: Sparse Matrix Profile DenseNet for COVID-19 Diagnosis 


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6. Software Web: Deep learning-driven algorithm for predicting drug mechanism of action




5. Software Web: Computational prediction of the pathogenic status of cancer-specific somatic variants 




4. Software Web: Bayesian tensor factorization-drive breast cancer subtyping by integrating multi-omics data 





3. Software Web: DTF: Deep tensor factorization for predicting anticancer drug synergy 


2. Software Web: Matrix profile-guided attention LSTM model for forecasting COVID-19 cases



1. Software Web: An OpenMP based tool for finding LCS of DNA sequence data 





Description: A deep learning model to evaluate the impact of mutations on PPIs

Citation: Zhang et al. 2025. Journal of Cheminformatics


Description: Diffusion model for synthetic image generation.

Citation: Chen et al. 2024. Plos Computational Biology


Description: Sequence based AI algorithm for HIV-1 subtype classification.

Citation: Wade et al. 2024. Bioinformatics Sciences


Description: Pipeline for meta-analysis of microbiome data.

Citation: Khan et al. 2024. iScience


Description: Manifold learning for cell segmentation

Citation: Li et al. 2024. Plos Computational Biology


Description:  GNN for drug-target interaction prediction

Citation: Sun et al. 2024, Bioinformatics



Description:  Generative AI for MRI imaging generation

Citation:  Huang et al. 2024, Journal of Translational Medicine



Description:  Longitudinal Microbiome data analysis

Citation: Fung et al. 2023. Bioinformatics Advances


Description:  Clustering analysis of scRNA-seq data

Citation: Lin et al. 2023. Machine Learning: Science and Technology


Description:  An atom-bond transformer for molecular property predictions.

Citation:  Liu et al. 2022, Journal of Cheminformatics


Description   Radiogenomic association of deep MR imaging features with genomic profiles and clinical characteristics in breast cancer.

Citation:  Liu et al. 2023 Biomarker Research


Description:   A bimodal supervised contrastive learning (BSCL) framework to integrate the SMILES string and the molecular graph in a unified network.to predict molecular property.   
Citation:  Sun et al. 2022, IEEE BIBM 


Description:  A Machine Learning Model trained on a High-Throughput Antibacterial Screen Increases the Hit Rate of Drug Discovery
Citation:  Rahman, liu et al. 2022, Plos Computational Biology. 


Description:  Tightly integrated multiomics-based deep tensor survival model for time-to-event prediction
Citation:  Zhang et al. 2022, Bioinformatics 


Description: Self-supervised deep learning model for COVID-19 lung CT image segmentation highlighting putative causal relationship among age, underlying disease, and COVID-19​
Citation: Fung et al. 2021, Journal of Translational Medicine


Description: Semi-Supervised COVID-19 CT Image Segmentation Using Deep Generative Models 

Citation: Zammit et al. 2022, BMC Bioinformatics 


Description: ChrNet: A re-trainable chromosome-based 1D convolutional neural network for predicting immune cell types
Citation: Jia et al. 2021, Genomics


Description: Deep clustering of small molecules at large-scale via variational autoencoder embedding and K-means Citation: Hadipour et al. 2022, BMC Bioinformatics 


Description: A Two-dimensional Sparse Matrix Profile DenseNet for COVID-19 Diagnosis Using Chest CT Images
Citation: Liu et al. 2020, IEEE Access


Description: Deep learning-driven prediction of drug mechanism of action from large-scale chemical-genetic interaction profiles 

Citation: Liu et al. 2022, Journal of Cheminformatics
 

Description: Computational prediction of the pathogenic status of cancer-specific somatic variants 

Citation: Feizi et al. 2022, Frontiers in Genetics  


Description: Bayesian tensor factorization-drive breast cancer subtyping by integrating multi-omics data 

Citation: Liu et al. 2022, Journal of Biomedical Informatics  


Description: A new algorithm integrating tensor factorization and deep learning to predict anticancer drug combinations
Citation: Sun et al. 2020, Bioinformatics


Description: A novel matrix profile-guided attention LSTM model for forecasting COVID-19 cases in USA 

Citation: Liu et al. 2021, Frontiers in Public Health  


Description: This repository contains three parallel implementation of the LCS algorithm in MPI, OpenMP, and hybrid MPI-OpenMP platforms. 

Citation: Shikder et al. 2019, BMC Research Notes.

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