Single-Cell Rna Sequencing

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  1. Static analysis-guided agentic AI translation enables Rust as a full stack bioinformatics language

    Aug 13, 2026Johan HenrikssonSingle-Cell Rna Sequencing

  2. Uncertainty-Aware Deep Learning for Genomics Applications: Insights from an Empirical Study

    Aug 11, 2026Sepideh Saran, Mahsa Ghanbari, Uwe OhlerGenomicsBayesian Neural Networks

  3. CosMAP: Contrastive Manifold Approximation and Projection for Dimensionality Reduction of Omics and Genealogical Data

    Aug 11, 2026Fenosoa Randrianjatovo, Maya Saleh, Simon Girard +1Dimensionality ReductionSingle-Cell Rna Sequencing

  4. Idea Search: Guiding Tree Search with Ideas to Explore Diverse Scientific Methods

    Aug 9, 2026Xuefei Julie Wang, Hao Cui, Michael P. Brenner +1Tree SearchScientific Discovery

  5. VOICE: A Vision-Omics Foundation Model Integrating Direct and Retrieval-Based Prediction of In-situ Single-Cell Gene Expression

    Aug 8, 2026Xin Luo, Yicheng Tao, Haoxuan Zeng +6Spatial TranscriptomicsSingle-Cell Rna Sequencing

  6. BioM-JEPA: joint-embedding prediction of graph-connected gene blocks in single cells

    Aug 6, 2026Yuhao Wang, Zelin Zang, Yuxuan Liu +2Single-Cell Rna SequencingJoint-Embedding Predictive Architectures

  7. CohortHijack: Robustness of Single Cell Annotation to Companion Cell Removal

    Aug 6, 2026Arash Vashagh, Yasmin VashaghSingle-Cell Rna SequencingHijacking

  8. Scaling an Autoregressive Transformer for Single-Cell Generation

    Aug 3, 2026Aleksandr Sharipov, Yusif Mukhtarov, Igor MolybogAutoregressive TransformersSingle-Cell Rna Sequencing

  9. Beyond Gene Reconstruction: Learning Cell Representations through Complementary Transcriptomic Views

    Aug 2, 2026Jiaqi Xiong, Yuntao hu, Yu Zheng +3Single-Cell Rna SequencingSpatial Transcriptomics

  10. Improving scDiffusion with Sparsity-Biased Classifier-Free Guidance

    Jul 31, 2026Yu Song, Hao Sun, Ikuko Nishikawa +1Single-Cell Rna Sequencing

  11. When Does Deep Representation Learning Help Single-Cell Clustering? A Sensitivity-Aware Diagnostic Benchmark for Biomedical AI Pipelines

    Jul 28, 2026Nguyen Thanh Phong, Truong Viet Vu, Nguyen Ha Thu +4Single-Cell Rna SequencingImage Clustering

  12. SCTA: An Agentic Framework for Stable and Interpretable Target Gene Discovery from Single-Cell RNA Sequencing

    Jul 26, 2026Shuyu Chen, Chen Zhu, Ye Zhang +3Single-Cell Rna Sequencing

  13. Distributional Determinantal Point Process for Repulsive Clustering of Distributions

    Jul 23, 2026Khai Nguyen, Yang Ni, Elizabeth Juarez-Colunga +1Determinantal Point ProcessMixture Models

  14. Making Single-Cell Data Distillation Auditable: Traceable Real-Cell Coresets via Discrete Min--Max Selection

    Jul 20, 2026Yaodi Luo, Peize He, Lingbei Meng +4Single-Cell Rna SequencingGeometry-Aware Uncertainty Coresets

  15. SpaCellAgent: A Self-Evolving LLM-Based Multi-Agent Framework for Trajectory Analysis

    Jul 8, 2026Songhan Wang, Haoang Chi, He Li +6Single-Cell Rna SequencingTrajectory Prediction

  16. Data-Driven Soft Labeling Scales DNA Read Classification to Whole-Body Cell-Type Deconvolution

    Jul 6, 2026Dmytro Rizdvanetskyi, Nathan Roos, Pavlo LutsikSingle-Cell Rna SequencingMulti-Label Classification

  17. HASSL: Hierarchy-Aware Self-Supervised Learning Framework for Single Cell Microscopy

    Jul 5, 2026Julius Riel, Vishwa Mohan Singh, Sai Anirudh Aryasomayajula +10Single-Cell Rna SequencingSelf-Supervised

  18. Resolving superposition in AI for interpretability and cross-modal alignment in patient-neuronal images

    Jun 30, 2026Jisung Park, Seohyeon Kang, Daeun Yoo +8Neuroimaging ModelsImplicit Neural Representations

  19. scKDGM: KAN-guided Dynamic Graph Masked Learning for Single-Cell RNA-seq Clustering

    Jun 26, 2026Jun Tang, Pengwei Hu, Sicong Gao +3Single-Cell Rna SequencingGraph Representation Learning

  20. PerturbCellRL: Verifier-Guided Reinforcement Learning for Single-Cell Perturbation Prediction

    Jun 26, 2026Dongxia Wu, Mingyu Li, Yuhui Zhang +4Single-Cell Perturbation PredictionSingle-Cell Rna Sequencing

  21. Reconstructing the Developmental Trajectory of Adipocytes in Human Adipose Tissue Using Single-Cell RNA Sequencing

    Jun 26, 2026Weny S. M Sitinjak, Humasak Tommy Argo SimanjuntakSingle-Cell Rna Sequencing

  22. scBench-Long: Verifiable Benchmarking of Long-Horizon Single-Cell Biology

    Jun 25, 2026Ian Diks, Zhen Yang, Arjun Banerjee +2Single-Cell Rna SequencingNon-Small Cell Lung Cancer

  23. Re-mixing Embeddings for Patient Augmentation in Data Scarce Multiple Instance Learning

    Jun 24, 2026Muhammed Furkan Dasdelen, Fatih Ozlugedik, Anastasia Litinetskaya +3Synthetic Data AugmentationMultiple Instance Learning

  24. Stable-Shift: Biologically Structured Prediction of Transcriptional Responses to Unseen Gene Perturbations

    Jun 22, 2026Sajib Acharjee Dip, Liqing ZhangSpatial TranscriptomicsSingle-Cell Rna Sequencing

  25. Privacy-preserving federated tensor decomposition of single-cell immune data: recovering multicellular programs across institutions

    Jun 22, 2026Axel Faes, Stephanie M. van den Berg, Maryam Amir HaeriSingle-Cell Rna SequencingSpatial Transcriptomics

  26. scGTN: Deep Siamese Graph Transformer Network for Single-cell RNA Sequencing Clustering

    Jun 17, 2026Jinke Wu, Yifan Wang, Siyu Yi +5Single-Cell Rna Sequencing

  27. Cluster LOCO: Feature Importance For Interpreting Clusters

    Jun 12, 2026Claire M. He, Genevera I. AllenFeature ImportanceImage Clustering

  28. scLLM-DSC: LLM-Knowledge Enhanced Cross-Modal Deep Structural Clustering for Single-Cell RNA Sequencing

    Jun 11, 2026Ping Xu, Pengjiang Li, Tian Du +6Single-Cell Rna SequencingSpatial Transcriptomics

  29. OCOO-T : A Simple and Scalable Virtual Cell Model for Transcriptional Perturbation Response Prediction

    Jun 11, 2026Danning Jiang, Zheming An, Yalong Zhao +1Single-Cell Perturbation PredictionSingle-Cell Rna Sequencing

  30. CellNet -- Localizing Cells using Sparse and Noisy Point Annotations

    Jun 10, 2026Benjamin Eckhardt, Dmytro Fishman, Stuart Fawke +3MicroscopySingle-Cell Rna Sequencing

  31. Patient-Level Diagnosis of Acute Myeloid Leukemia via Deep Learning Analysis of Bone Marrow Smear

    Jun 9, 2026Yuqi Ma, Tianyi Wang, Weihua Meng +6Acute Myeloid LeukemiaMultiple Instance Learning

  32. Integrating gene regulatory priors into Transformer attention with scTransformer for interpretable scRNA-seq analysis

    Jun 8, 2026Mikele Milia, Louis Fabrice Tshimanga, Henning Mueller +2Single-Cell Rna SequencingTransformer Attention

  33. Single-Cell Cross-Modal Transfer by Adversarial Fine-Tuning of Foundation Models

    Jun 4, 2026Joseph Boyd, Matthew Lyon, Martino Mansoldo +2Single-Cell Rna SequencingSpatial Transcriptomics

  34. Multimarginal flow matching with optimal transport potentials

    Jun 3, 2026Raghav Kansal, David Crair, Nghia Nguyen +2Conditional Flow MatchingOptimal Transport

  35. BRIDGE: Biological Evidence Refinement and Heterogeneous Dynamic Gating for Gene Regulatory Networks

    Jun 2, 2026Ziyang Dong, Shanwen Tan, Hengchuang Yin +5Gene-Regulatory NetworksSingle-Cell Rna Sequencing

  36. A Biconvex Formulation for Stable Transport of Mixture Models with a Unique Solution

    Jun 1, 2026Yeganeh Marghi, Kelly Jin, Uygar SümbülOptimal TransportMixture Models

  37. GC-MoE: Genomics-Guided Cell-Type-Specific Mixture of Experts for Histology-Based Single-Cell Spatial Transcriptomics

    Jun 1, 2026Kaito Shiku, Ahtisham Fazeel Abbasi, Ryoma Bise +4Spatial TranscriptomicsSingle-Cell Rna Sequencing

  38. Science Earth: Towards A Planet-Scale Operating System for AI-Native Scientific Discovery

    May 31, 2026Zhe Zhao, Haibin Wen, Yingcheng Wu +10Scientific DiscoveryAutoresearch

  39. Effective Biological Representation Learning by Masking Gene Expression

    May 29, 2026Kian Kenyon-Dean, Alina Selega, Ihab Bendidi +5Spatial TranscriptomicsSingle-Cell Rna Sequencing

  40. IRIS: time-structured manifold projections

    May 29, 2026Brian Ondov, Chia-Hsuan Chang, Weipeng Zhou +6Single-Cell Rna SequencingTime-Series Classification

  41. CellBRIDGE: Learning Cellular Trajectories via Interaction-Aware Alignment

    May 28, 2026Silas Ruhrberg Estévez, Nicolas Huynh, Tennison Liu +4Single-Cell Rna SequencingGene-Regulatory Networks

  42. AutoScientists: Self-Organizing Agent Teams for Long-Running Scientific Experimentation

    May 27, 2026Shanghua Gao, Ada Fang, Marinka ZitnikScientific AgentsArtificial Intelligence Agents

  43. From Snapshots to Trajectories: Learning Single-Cell Gene Expression Dynamics via Conditional Flow Matching

    May 21, 2026Siyu Pu, Qingqing Long, Xiaohan Huang +7Single-Cell Rna SequencingConditional Flow Matching

  44. Modeling Temporal scRNA-seq Data with Latent Gaussian Process and Optimal Transport

    May 20, 2026Mehmet Yigit Balik, Harri LähdesmäkiSingle-Cell Rna SequencingGaussian Process

  45. Multi-Modal Machine Learning for Population- and Subject-Specific lncRNA-Type 2 Diabetes Association Analysis

    May 20, 2026Ashwani Siwach, Sanjeev Narayan Sharma, Sunil Datt SharmaSingle-Cell Rna SequencingMessenger Rna

  46. Scale-Calibrated Median-of-Means for Robust Distributed Principal Component Analysis

    May 20, 2026Kisung YouPrincipal Component AnalysisGeneralized U-Statistics

  47. scHelix: Asymmetric Dual-Stream Integration via Explicit Gene-Level Disentanglement

    May 18, 2026Xichen Yan, Zelin Zang, Changxi Chi +8Single-Cell Rna SequencingDual-Stream

  48. Multiscale Supervised Unbalanced Optimal Transport Flow Matching

    May 15, 2026Qiangwei Peng, Lezhi Chen, Peijie ZhouSingle-Cell Rna SequencingOptimal Transport

  49. Towards Label-Free Single-Cell Phenotyping Using Multi-Task Learning

    May 14, 2026Saqib Nazir, Ardhendu BeheraAcute Myeloid LeukemiaSingle-Cell Rna Sequencing

  50. DUET: Dual-Paradigm Adaptive Expert Triage with Single-cell Inductive Prior for Spatial Transcriptomics Prediction

    May 13, 2026Junchao Zhu, Ruining Deng, Junlin Guo +11Spatial TranscriptomicsSingle-Cell Rna Sequencing

  51. scShapeBench: Discovering geometry from high dimensional scRNAseq data

    May 12, 2026Andrew J Steindl, João Felipe Rocha, Brian Tshilengi Di Bassinga +13Single-Cell Rna SequencingStatistical Shape Model

  52. When Does Gene Regulatory Network Inference Break? A Controlled Diagnostic Study of Causal and Correlational Methods on Single-Cell Data

    May 6, 2026Miguel Fernandez-de-Retana, Ruben Sanchez-Corcuera, Unai Zulaika +2Gene-Regulatory NetworksSingle-Cell Rna Sequencing

  53. FL-Sailer: Efficient and Privacy-Preserving Federated Learning for Scalable Single-Cell Epigenetic Data Analysis via Adaptive Sampling

    May 6, 2026Guangyi Zhang, Yi Dai, Yiyun He +1Federated LearningSingle-Cell Rna Sequencing

  54. Donor-Aware scRNA-seq Benchmarks for IBD Classification

    May 5, 2026Jonathan MuhireSingle-Cell Rna SequencingCross Validation

  55. Towards Universal Gene Regulatory Network Inference: Unlocking Generalizable Regulatory Knowledge in Single-cell Foundation Models

    May 1, 2026Jiaxin Qi, Hang Li, Yan Cui +2Gene-Regulatory NetworksSingle-Cell Rna Sequencing

  56. A multi-stage soft computing framework for complex disease modelling and decision support: A liver cirrhosis case study

    Apr 26, 2026Xueyuan Huang, Yuheng Wang, Yuanzhi He +8Multi-Omic FrameworkCholangiocarcinoma

  57. Turtle shell clustering: A mixture approach to discriminative clustering with applications to flow cytometry and other data

    Apr 25, 2026Mackenzie R. Neal, Paul D. McNicholas, Arthur WhiteImage ClusteringSingle-Cell Rna Sequencing

  58. Relative Entropy Estimation in Function Space: Theory and Applications to Trajectory Inference

    Apr 22, 2026Chao Wang, Luca Nepote, Giulio Franzese +1Single-Cell Rna SequencingKullback-Leibler Divergence

  59. SMART: A Spectral Transfer Approach to Multi-Task Learning

    Apr 22, 2026Boxin Zhao, Mladen Kolar, Jinchi LvTransfer LearningMulti--Task Learning

  60. scpFormer: A Foundation Model for Unified Representation and Integration of the Single-Cell Proteomics

    Apr 21, 2026Qifeng Zhou, Lei Yu, Yuzhi Guo +5Single-Cell Rna SequencingMixformer