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Supplementary materials of HILab publications

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* co-first authors. # corresponding authors.

GraCEImpute: a novel graph clustering autoencoder approach for imputation of single-cell RNA-seq data.

TaiChiNet: combining PCA-based diluted inter-and intra-BERT layers to represent anti-coronavirus peptides.

PepLand: a large-scale pre-trained peptide representation model for a comprehensive landscape of both canonical and non-canonical amino acids.

TrailGate: An Enhanced Network Intrusion Detection Framework Integrating Transformer-BiGRU with Data Augmentation and Confident Learning.

Crystall2: Pan-cancer remaining lifespan estimation via the multi-head self-attention regression network with adversarial learning.

FairCare: adversarial training of a heterogeneous graph neural network with attention mechanism to learn fair representations of electronic health records.

MolFeSCue: Enhancing Molecular Property Prediction in Data-Limited and Imbalanced Contexts using Few-Shot and Contrastive Learning.

Kewei Li, Yusi Fan, Yaqing Liu, Hongmei Liu, Gongyou Zhang, Meiyu Duan*, Lan Huang, Fengfeng Zhou*. "Generating the transcriptional regulation view of transcriptomic features for prediction task and dark biomarker detection on small datasets". JoVE - Journal of Visualized Experiments, Accepted, 2023.
HealthModel-mqTrans source code and pre-trained model: HealthModel-mqTrans-v1-02.rar

GANSamples: A Generative Adversarial Network with Conditional Encoder for Biomolecular Structured Data Augmentation.

ChemDT: a deep learning framework for detection and translation of chemical names from scanned documents.

GANSamples-ac4C: Enhancing ac4C Site Prediction via Gener-ative Adversarial Networks and Transfer Learning.

DeepOr: orchestrating representation learning and feature selection for clinical health status predictions.

Orchestrating information across tissues via a novel multitask GAT framework to improve quantitative gene regulation relation modeling for survival analysis.

EpiTEAmDNA: sequence feature representation via transfer learning and ensemble learning for identifying multiple DNA epigenetic modification types across species.

OCMR is All You Need for Chemical Structure Recognition.

Reconstructing the Cytokine View for the Multi-view Prediction of COVID-19 Mortality.

GSRNet, a multi-scale convolutional network to predict genomic signals and regions via DNABERT embedding and adversarial training.

Data augmentation algorithm for miRNA omics-based classifications.

msDAWG: Extracting useful features for classification of raw mass spectra via dual autoencoder WGAN with self-attention.

EvaGoNet: embedding original features in the VAE-WGANgp network for binary classifications.

Integration of lncRNAs, protein-coding genes and pathology images for detecting metastatic melanoma.

LazAE: learning the latent features for the classifications of single-cell RNA-seq samples with zero-inflated negative binomial distribution as the autoencoder loss.

HLAB: learning the BiLSTM features from the ProBERT-encoded proteins for the class I HLA binding peptide prediction.

A polygenic stacking classifier revealed the complicated platelet transcriptomic landscape of adult immune thrombocytopenia.

Computational characterization of undifferentially expressed genes with altered transcription regulations in lung cancers.

Transforming OMIC features for classification using Siamese convolutional networks.

ConvCPP: Cell-penetrating peptide prediction algorithm based on convolution neural network.

AcneTyper: an automatic diagnosis method of dermoscopic acne image via self-ensemble and stacking.

Zoo, selecting transcriptomic and methylomic biomarkers by ensembling animal-inspired swarm intelligence feature selec-tion algorithms.

A novel position-specific encoding algorithm (SeqPose) of nucleotide sequences and its application for detecting enhancers.

DiaMole: a mole detection and segmentation software for mobile phone skin images.

A comprehensive evaluation of a network feature construction algorithm FeCO3 based on inter-feature correlation coefficients.

RetinalVasNet: Integrating DenseNet and UNet for the Retinal Microvasculature Segmentation using the Multi-Proportion Channel Data of the Fundus Images.

A comprehensive comparison of residue-level methylation levels with the regression-based gene-level methylation estimation by ReGear.

ZfaParallel: an improved R package to locate the optimal testing region for rare variant association tests using shared-memory parallel computing.

Accurate prediction of neoadjuvant chemotherapy pathological complete remission (pCR) for the four sub-types of breast cancer.

sefOri: selecting the best engineered sequence features to predict DNA replication origins. Submitted.
Accurate fatigue detection based on multiple facial morphological features. Submitted.
pyHIVE, a Health-related Image Feature Extraction system using Python. Submitted.
  • Manual of pyHIVE: pyHIVE-manual-v1-0-8.pdf
  • Python package of pyHIVE, including the example data and code: pyHIVE-1-0-8.tar.gz (32Mb)
  • Accurate fatigue detection based on multiple facial morphological features. Submitted.
    Selecting multiple biomarker subsets with similarly effective binary classification performances. Submitted.
  • Source code of kSolutionVis versoin 1.4 (single thread, windows): kSolutionVis_windows.rar
  • Source code of kSolutionVis versoin 1.4 (parallel, linux): kSolutionVis_Linux_parallel.rar
  • Supplementary materials: kSolutionVis-supp-r2u1.pdf
  • Any suggestions are welcome on improving the usabilities of kSolutionVis, and the user may contact Fengfeng Zhou, PI of HILab
  • Jiamei Liu, Cheng Xu, Weifeng Yang, Yayun Shu, Weiwei Zheng, Fengfeng Zhou#. Multiple similarly-well solutions exist for biomedical feature selection and classification problems. Scientific Reports 2017 Oct 9;7(1):12830.
  • Dataset and python codes for the difficult dataset ALL2: all2.zip
  • Dataset and python codes for the difficult dataset CNS: cns.zip
  • Rheumatoid arthritis and schizophrenia epigenetic biomarkers detected by a feature refining algorithm, TriVote. Submitted.
  • Manual of TriVote: TriVote-manual.pdf
  • Python package of TriVote, including the example data and code: TriVote-v1.rar (218Mb)
  • Ruixue Zhao, Ruochi Zhang, Tongyu Tang, Xin Feng, Jialiang Li, Yue Liu, Renxiang Zhu, Guangze Wang, Kangning Li, Wenyang Zhou, Yunfei Yang, Yuzhao Wang, Yuanjie Ba, Jiaojiao Zhang, Yang Liu, Fengfeng Zhou#. TriZ-a rotation-tolerant image feature and its application in endoscope-based disease diagnosis. Computers in Biology and Medicine 2018 Aug; 99(1) 182-190.
  • Dataset: TriZ-data-20180915.tar.gzTriZ-data-20180915.tar.gz (10Mb)
  • Ruiquan Ge, Guoqin Mai, R Zhang, X Wu, Q Wu, Fengfeng Zhou#. MUSTv2: an improved de novo miniature inverted repeat transposable element (MITE) detection program. Journal of Integrative Bioinformatics 2017 Aug 10;14(3).
  • Supplementary tables S1: MUSTv2-supp.pdf
  • The software MUSTv2: MUST.r2-4-002.Release.tar.gz
  • The simulated genome: before and after the insertions of 150 MITE copies.
  • The software NCBI BLAST version 2.2.11 may be downloaded from here or locally.
  • The software BLAT version 3.5 may be downloaded from here or locally.

  • Dongli Ma, Shan Zhong, Xiaorong Liu, Huirong Mai, Guoqin Mai, Cheng Xu, Fengfeng Zhou#. CD3D and PRKCQ work together to discriminate between B-cell and T-cell acute lymphoblastic leukemia. Computers in Biology and Medicine 77, 16-22.
  • Supplementary material: bALLt-supp-r2.pdf

  • Ruiquan Ge, Guoqin Mai, Pu Wang, Manli Zhou, Youxi Luo, Y Cai, Fengfeng Zhou#. CRISPRdigger: detecting CRISPRs with better direct repeat annotations. Scientific Reports, 2016; 6: 32942.
  • CRISPR annotation pipeline version 1.007: CRISPRdigger-pipe-v1-007.rar
  • A package including all the dependent softwares (~350MB): CRISPRdigger-software.rar
  • The pipeline may also be found at GitHub: CRISPRdigger

  • Guoqin Mai, Ruiquan Ge, Guoquan Sun, Qinghan Meng, Fengfeng Zhou#. A comprehensive curation demonstrates the dynamic evolutionary patterns of prokaryotic CRISPRs. BioMed Research International 2016; 2016: 7237053.
  • Supplementary information: caCRISPR-supp.pdf
  • Curated CRISPR annotations in FASTA: caCRISPR_20151001.fna
  • Curated CRISPR annotations in GFF3: caCRISPR_20151001.gff3.rar
  • DR sequences of curated CRISPR annotations: caCRISPR_dbDR_20151001.fasta
  • Spacer sequences of curated CRISPR annotations: caCRISPR_dbSpacer_20151001.fasta

  • SubLasso: a feature selection and classification R package with a fixed feature subset. Submitted.
  • Supplementary information: SubLasso-supp.pdf
  • R packages: SubLasso_1.2.zip (windows) and SubLasso_1.2.tar.gz (linux)
  • Manual: SubLasso.pdf
  • Example dataset: GSE9574.rar
  • Example R scripts: exSubLasso.R and testSubLasso.R

    Miaomiao Zhao, Zhao Zhang, Guoqin Mai, Youxi Luo, Fengfeng Zhou#. jEcho: an Evolved weight vector to CHaracterize the protein's post-translational modification mOtifs. Interdisciplinary Sciences: Computational Life Sciences 7 (2), 194-199.
  • Supplementary table S1 and figure S1: jEcho-supp.pdf
  • Software: jEcho.v1

    Zhao Zhang, Ze Wang, Guoqin Mai, Youxi Luo, Miaomiao Zhao, Fengfeng Zhou#. Evolutionary optimization of transcription factor binding motif detection. Advance in Structural Bioinformatics 827, 261-274.
  • Supplementary figure S1: bDNA-supp.pdf

    Pi Guo, Youxi Luo, Guoqin Mai, Ming Zhang, Guoqing Wang, Miaomiao Zhao, Liming Gao, Fan Li, Fengfeng Zhou#. Gene Expression Profile based Classification Models of Psoriasis. Genomics.103(1):48-55, 2014.
  • Supplementary figures S1-S2 and tables S1-S2: cPsoriasis-supp.pdf
  • 3rd rank in the SBV IMPROVER Challenge 2012: cPsoriasis-SBV.pdf

    Meixue Yang, Bin Liu, Miaomiao Zhao, Fan Li, Guoqing Wang, Fengfeng Zhou#. Normalizing electrocardiograms of both healthy persons and cardiovascular disease patients for biometric authentication. PLoS ONE 8(8):e71523, 2013.
  • Supplementary table S1: STable1.pdf
  • Matlab source code: bECG-src.rar

  • Kaishi Li, Meixue Yang, Gaurav Sablok, Jianping Fan, Fengfeng Zhou#. Screening features to improve the class prediction of acute myeloid leukemia and myelodysplastic syndrome. Gene. 2013 Jan 10;512(2):348-54.
  • Supplementary data matrix: AML-MDS.data-matrix.1-00.arff.gz

    Legacy tools that were released in the other web sites
    Fengfeng Zhou, Ying Xu. cBar: a computer program to distinguish plasmid-derived from chromosomederived sequence fragments in metagenomics data. Bioinformatics, 2010 26(16):2051-2052.
  • Source code: cBar.1.2.tar.gz
  • Manual page: web.pdf



    © Fengfeng Zhou, Health Informatics Lab, College of Computer Science and Technology, Jilin University.
    Last update: April 13, 2024.