Xiucai Ye 研究室

主宰者：Xiucai Ye

筑波大学

AI 要約（直近 5 年の研究成果）

Xiucai Ye研究室は、機械学習と深層学習を生命科学の幅広い問題に応用する研究を展開しています。主たる関心は、医薬品開発に関わる分子・ペプチドの性質予測や、がんなどの疾患メカニズムの解明です。特に、タンパク質と薬物分子の相互作用、ペプチドの膜透過性や毒性、抗菌性ペプチドの設計といった課題に取り組んでいます。これらの問題は従来、時間と費用がかかる実験的検証が必要とされていましたが、計算機予測によって迅速かつ効率的にスクリーニングできる手法の開発を目指しています。手法としては、事前学習済みのタンパク質言語モデルや大規模言語モデルと、グラフニューラルネットワーク、変分自己符号化器、拡散モデルなどの先進的な深層学習技術を組み合わせています。分子データは化学構造、アミノ酸配列、画像情報など複数の表現形式から特徴を抽出する多模態学習のアプローチを採用しています。また、マルチオミクスデータからのがん亜型分類や遺伝子発現解析など、生物医学的な大規模データを統合・解析する研究も進めており、臨床応用を想定した実践的な知見を得ることに注力しています。さらに、プライバシー保護を考慮した分散学習や、交通予測・感染症予測といった社会的課題への応用研究も並行して行われています。これら多岐にわたるテーマを通じて、同研究室は計算手法による科学的発見と社会への実装を橋渡しする研究拠点としての役割を果たしています。

※ AI（Claude）が、公開されている論文要旨から研究の問い・手法・主要な発見を事実情報として抽出・再構成して自動生成しています。誤りを含む可能性があるため、正確性は研究室公式情報でご確認ください。

外部リンク

研究成果（75 件）

[2026] LLM-Enhanced Knowledge Distillation for Sequence-Based Protein-Ligand Interaction Prediction
DOI: https://doi.org/10.1109/jbhi.2026.3686853
[2026] Multi-Source Graphs and Dual KAN-Transformers for Next POI Recommendation
DOI: https://doi.org/10.1109/jiot.2026.3704841
[2026] RFD-ML: Robust federated defense via meta-learning
DOI: https://doi.org/10.1016/j.asoc.2026.115183
[2025] MOFormer: navigating the antimicrobial peptide design space with Pareto-based multi-objective transformer
DOI: https://doi.org/10.1093/bib/bbaf376
[2025] BiFDR: Brain-Inspired Federated Diffusion Transformer with Reinforcement for privacy-preserving molecular generation
DOI: https://doi.org/10.1016/j.jbi.2025.104910
[2025] Deciphering cancer therapy resistance via patient-level single-cell transcriptomics with CellResDB
DOI: https://doi.org/10.1038/s42003-025-08457-2
[2025] EAFL-ALP: Energy-Efficient Asynchronous Federated Learning With Adaptive Layered Personalization for Vehicular Networks
DOI: https://doi.org/10.1109/jiot.2025.3594026
[2025] Hybrid quantum-classical-quantum convolutional neural networks
DOI: https://doi.org/10.1038/s41598-025-13417-1
[2025] Integration of pre-trained protein language models with equivariant graph neural networks for peptide toxicity prediction
DOI: https://doi.org/10.1186/s12915-025-02329-1
[2025] Deep Feature Learning for Multi-Omics Clustering Using Supervised Variational Autoencoders with Clinical Information
DOI: https://doi.org/10.1109/ijcnn64981.2025.11227970

続きを表示（残り 65 件）

[2025] CSI-FL: Communication-Sensing Integrated Federated Learning Framework for Heterogeneous IoV
DOI: https://doi.org/10.1109/tcss.2025.3573280
[2025] PKAN: Leveraging Kolmogorov–Arnold Networks and Multi-Modal Learning for Peptide Prediction With Advanced Language Models
DOI: https://doi.org/10.1109/jbhi.2025.3561846
[2025] Spatio-temporal epidemic forecasting using mobility data with LSTM networks and attention mechanism
DOI: https://doi.org/10.1038/s41598-025-94089-9
[2025] OmniClust: A versatile clustering toolkit for single-cell and spatial transcriptomics data
DOI: https://doi.org/10.1016/j.ymeth.2025.03.007
[2025] MultiCycPermea: accurate and interpretable prediction of cyclic peptide permeability using a multimodal image-sequence model
DOI: https://doi.org/10.1186/s12915-025-02166-2
[2025] DRL-UPPS: User Trajectory Privacy Protection Strategy Based on Deep Reinforcement Learning in Mobile Crowdsensing
DOI: https://doi.org/10.1109/tcss.2025.3543289
[2025] Image-based generation for molecule design with SketchMol
DOI: https://doi.org/10.1038/s42256-025-00982-3
[2025] BlackHole-DTP: a distributed trajectory privacy protection strategy with deep trajectory training and data blackhole
DOI: https://doi.org/10.1093/comjnl/bxaf129
[2024] CLOP-hERG: The Contrastive Learning Optimized Pre-trained Model for Representation Learning in Predicting Drug-Induced hERG Channel Blockers
DOI: https://doi.org/10.47852/medin42022049
[2024] Multi-party collaborative drug discovery via federated learning
DOI: https://doi.org/10.1016/j.compbiomed.2024.108181
[2024] Selecting interpretable features for cancer subtyping on multi-omics data
DOI: https://doi.org/10.1109/bibm62325.2024.10821783
[2024] DTS-AdapSTNet: an adaptive spatiotemporal neural networks for traffic prediction with multi-graph fusion
DOI: https://doi.org/10.7717/peerj-cs.2527
[2024] Robust feature learning using contractive autoencoders for multi-omics clustering in cancer subtyping
DOI: https://doi.org/10.1016/j.ymeth.2024.11.013
[2024] Lightweight privacy-preserving authenticated key agreements using physically unclonable functions for internet of drones
DOI: https://doi.org/10.1016/j.jisa.2024.103915
[2024] PCDP-CRLPPM: a classified regional location privacy-protection model based on personalized clustering with differential privacy in data management
DOI: https://doi.org/10.1093/comjnl/bxae118
[2024] Mapping autophagy-related membrane contact site proteins and complexes with AutoMCS Navigator
DOI: https://doi.org/10.1080/15548627.2024.2394291
[2024] IEA-DP: Information Entropy-driven Adaptive Differential Privacy Protection Scheme for social networks
DOI: https://doi.org/10.1007/s11227-024-06202-w
[2024] CodLncScape Provides a Self‐Enriching Framework for the Systematic Collection and Exploration of Coding LncRNAs (Adv. Sci. 22/2024)
DOI: https://doi.org/10.1002/advs.202470129
[2024] An interpretable deep learning model predicts RNA–small molecule binding sites
DOI: https://doi.org/10.1016/j.future.2024.05.029
[2024] Integrated convolution and self-attention for improving peptide toxicity prediction
DOI: https://doi.org/10.1093/bioinformatics/btae297
[2024] CodLncScape Provides a Self‐Enriching Framework for the Systematic Collection and Exploration of Coding LncRNAs
DOI: https://doi.org/10.1002/advs.202400009
[2024] DiffSeqMol: A Non-Autoregressive Diffusion-Based Approach for Molecular Sequence Generation and Optimization
DOI: https://doi.org/10.2174/0115748936285493240307071916
[2024] CLOP-hERG: The Contrastive Learning Optimized Pre-trained Model for Representation Learning in Predicting Drug-Induced hERG Channel Blockers
DOI: https://doi.org/10.47852/bonviewmedin42022049
[2024] Identification of Spatial Domains, Spatially Variable Genes, and Genetic Association Studies of Alzheimer Disease with an Autoencoder-based Fuzzy Clustering Algorithm
DOI: https://doi.org/10.2174/0115748936278884240102094058
[2024] Stitch-Able Split Learning Assisted Multi-UAV Systems
DOI: https://doi.org/10.1109/ojcs.2024.3447773
[2024] A BERT-based model for the prediction of lncRNA subcellular localization in Homo sapiens
DOI: https://doi.org/10.1016/j.ijbiomac.2024.130659
[2023] m5U-SVM: identification of RNA 5-methyluridine modification sites based on multi-view features of physicochemical features and distributed representation
DOI: https://doi.org/10.1186/s12915-023-01596-0
[2023] Unravelling cancer subtype-specific driver genes in single-cell transcriptomics data with CSDGI
DOI: https://doi.org/10.1371/journal.pcbi.1011450
[2023] Multi-omics clustering based on interpretable and discriminative features for cancer subtyping
DOI: https://doi.org/10.1109/bibm58861.2023.10386005
[2023] FIAMol-AB: A feature fusion and attention-based deep learning method for enhanced antibiotic discovery
DOI: https://doi.org/10.1016/j.compbiomed.2023.107762
[2023] Pick-up point recommendation strategy based on user incentive mechanism
DOI: https://doi.org/10.7717/peerj-cs.1692
[2023] Adaptive learning embedding features to improve the predictive performance of SARS-CoV-2 phosphorylation sites
DOI: https://doi.org/10.1093/bioinformatics/btad627
[2023] PPDF-FedTMI: A Federated Learning-based Transport Mode Inference Model with Privacy-Preserving Data Fusion
DOI: https://doi.org/10.1016/j.simpat.2023.102845
[2023] Collaborative analysis for drug discovery by federated learning on non-IID data
DOI: https://doi.org/10.1016/j.ymeth.2023.09.001
[2023] Multi-omics clustering for cancer subtyping based on latent subspace learning
DOI: https://doi.org/10.1016/j.compbiomed.2023.107223
[2023] Multi-view Network Embedding with Structure and Semantic Contrastive Learning
DOI: https://doi.org/10.1109/icme55011.2023.00154
[2023] Common and Unique Features Learning in Multi-view Network Embedding
DOI: https://doi.org/10.1109/ijcnn54540.2023.10191682
[2023] MRMD3.0: A Python Tool and Webserver for Dimensionality Reduction and Data Visualization via an Ensemble Strategy
DOI: https://doi.org/10.1016/j.jmb.2023.168116
[2023] Molecular language models: RNNs or transformer?
DOI: https://doi.org/10.1093/bfgp/elad012
[2023] A novel Sybil attack detection scheme in mobile IoT based on collaborate edge computing
DOI: https://doi.org/10.1186/s13638-023-02233-8
[2023] Bidirectional k-nearest neighbor spatial crowdsourcing allocation protocol based on edge computing
DOI: https://doi.org/10.7717/peerj-cs.1244
[2023] Quantum Algorithm for Regularized Spectral Clustering
DOI: https://doi.org/10.1145/3587716.3587718
[2023] Interactive gene identification for cancer subtyping based on multi-omics clustering
DOI: https://doi.org/10.1016/j.ymeth.2023.02.005
[2023] LSEC: Large-scale spectral ensemble clustering
DOI: https://doi.org/10.3233/ida-216240
[2022] SiameseCPP: a sequence-based Siamese network to predict cell-penetrating peptides by contrastive learning
DOI: https://doi.org/10.1093/bib/bbac545
[2022] Enhanced Authenticated Key Agreement for Surgical Applications in a Tactile Internet Environment
DOI: https://doi.org/10.3390/s22207941
[2022] ToxinMI
DOI: https://doi.org/10.1145/3538641.3561492
[2022] Knowledge distillation-based privacy-preserving data analysis
DOI: https://doi.org/10.1145/3538641.3561482
[2022] iLoc-miRNA: extracellular/intracellular miRNA prediction using deep BiLSTM with attention mechanism
DOI: https://doi.org/10.1093/bib/bbac395
[2022] Successive Trajectory Privacy Protection with Semantics Prediction Differential Privacy
DOI: https://doi.org/10.3390/e24091172
[2022] Missing Value Imputation With Low-Rank Matrix Completion in Single-Cell RNA-Seq Data by Considering Cell Heterogeneity
DOI: https://doi.org/10.3389/fgene.2022.952649
[2022] Divide-and-conquer based large-scale spectral clustering
DOI: https://doi.org/10.1016/j.neucom.2022.06.006
[2022] Sequential reinforcement active feature learning for gene signature identification in renal cell carcinoma
DOI: https://doi.org/10.1016/j.jbi.2022.104049
[2022] Multi-View Federated Learning with Data Collaboration
DOI: https://doi.org/10.1145/3529836.3529904
[2022] Extracellular vesicles derived from Wharton’s Jelly mesenchymal stem cells inhibit the tumor environment via the miR-125b/HIF1α signaling pathway
DOI: https://doi.org/10.1038/s41598-022-17767-y
[2022] Distortion-free PCA on sample space for highly variable gene detection from single-cell RNA-seq data
DOI: https://doi.org/10.1007/s11704-022-1172-z
[2022] Ensemble Learning for Cluster Number Detection Based on Shared Nearest Neighbor Graph and Spectral Clustering
DOI: https://doi.org/10.1109/ijcnn55064.2022.9892958
[2022] NerLTR-DTA: drug–target binding affinity prediction based on neighbor relationship and learning to rank
DOI: https://doi.org/10.1093/bioinformatics/btac048
[2022] Multiview network embedding for drug-target Interactions prediction by consistent and complementary information preserving
DOI: https://doi.org/10.1093/bib/bbac059
[2022] Anonymous Dynamic Group Authenticated Key Agreements Using Physical Unclonable Functions for Internet of Medical Things
DOI: https://doi.org/10.1109/jiot.2022.3149117
[2022] ToxIBTL: prediction of peptide toxicity based on information bottleneck and transfer learning
DOI: https://doi.org/10.1093/bioinformatics/btac006
[2021] Better Performance with Transformer: CPPFormer in the PrecisePrediction of Cell-penetrating Peptides
DOI: https://doi.org/10.2174/0929867328666210920103140
[2021] Spectral Clustering Joint Deep Embedding Learning by Autoencoder
DOI: https://doi.org/10.1109/ijcnn52387.2021.9533825
[2021] iDNA-MT: Identification DNA Modification Sites in Multiple Species by Using Multi-Task Learning Based a Neural Network Tool
DOI: https://doi.org/10.3389/fgene.2021.663572
[2021] ATSE: a peptide toxicity predictor by exploiting structural and evolutionary information based on graph neural network and attention mechanism
DOI: https://doi.org/10.1093/bib/bbab041

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AI 要約（直近 5 年の研究成果）

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関連研究室(8 件)

研究成果（75 件）

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