Spatial Transcriptomics

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Period ending 2026-09-21

4 new papers

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Period ending 2026-09-14

3 new papers

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Period ending 2026-09-07

1 new paper

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177 papers

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  1. Forgotten Words: Benchmarking NeoBERT for Dementia Detection in Low-Resource Conversational Filipino and English Speech

    May 25, 2026Rez Samantha Z. Floresca, Edric Castel C. Hao, Hannah Grachiella Buñales +3Mild Cognitive ImpairmentAlzheimer

  2. Benchmarking Pathology Foundation Models for Spatial Domain Understanding

    May 25, 2026Bokai Zhao, Yiyang Zhang, Yuanchi Zhu +6Pathology Foundation ModelsComputational Pathology

  3. AnnotateMissense: a genome-wide annotation and benchmarking framework for missense pathogenicity prediction

    May 23, 2026Muhammad Muneeb, David B. AscherGenomics

  4. 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

  5. BlockFormer\textit{BlockFormer} : Transformer-based inference from interaction maps

    May 20, 2026Eloïse Touron, Pedro L. C. Rodrigues, Julyan Arbel +2GenomicsMixformer

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

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

  7. 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

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

    May 20, 2026Kisung YouPrincipal Component AnalysisGeneralized U-Statistics

  9. AgentCo-op: Retrieval-Based Synthesis of Interoperable Multi-Agent Workflows

    May 19, 2026Shuaike Shen, Wenduo Cheng, Shike Wang +2Multi-Agent WorkflowsScientific Agents

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

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

  11. FLAG: Foundation model representation with Latent diffusion Alignment via Graph for spatial gene expression prediction

    May 18, 2026Qi Si, Penglei Wang, Yushuai Wu +5Spatial TranscriptomicsSpatio-Temporal Correlations

  12. Multiscale Supervised Unbalanced Optimal Transport Flow Matching

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

  13. STS: Efficient Sparse Attention with Speculative Token Sparsity

    May 15, 2026Ceyu Xu, Jiangnan Yu, Yongji Wu +1Dynamic Sparse AttentionLLM Inference Efficiency

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

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

  15. Reading the Cell, Designing the Cure: Perturbation-Conditioned Molecular Diffusion for Function-Oriented Drug Design

    May 14, 2026Ziyu Xu, Zijian Zhang, Liang Wang +4Drug DesignSpatial Transcriptomics

  16. 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

  17. AttnGen: Attention-Guided Saliency Learning for Interpretable Genomic Sequence Classification

    May 13, 2026Rayhaneh Shabani Nia, Ali KarkehabadiGenomicsAttention-Guided Transunet

  18. Texture Regenerating and Grafting Using Genome-Driven Neural Cellular Automata

    May 13, 2026Mirela-Magdalena Catrina, Ioana Cristina Plajer, Alexandra BăicoianuNeural Cellular AutomataGenomics

  19. 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

  20. Bridging the Modality Bottleneck in Pathology MIL through Virtual Molecular Staining

    May 12, 2026Yucheng Xing, Pei Liu, Jingying Ma +6Computational PathologyMultiple Instance Learning

  21. RNA-FM: Flow-Matching Generative Model for Genome-wide RNA-Seq Prediction

    May 12, 2026Yaxuan Song, Jianan Fan, Tianyi Wang +4Spatial TranscriptomicsMessenger Rna

  22. Learning predictive models for combinations of heterogeneous proteomic data sources

    May 9, 2026Michal Valko, Richard Pelikan, Miloš HauskrechtMulti-Omic FrameworkSpatial Transcriptomics

  23. MicroFuse: Protein-to-Genome Expert Fusion for Microbial Operon Reasoning

    May 9, 2026Seungik ChoGenomicsProtein Data Bank

  24. Prototype Guided Post-pretraining for Single-Cell Representation Learning

    May 8, 2026Sachini Weerasekara, Natasha Darras, Sagar Kamarthi +2Spatial TranscriptomicsModel Pretraining

  25. Feature Dimensionality Outweighs Model Complexity in Breast Cancer Subtype Classification Using TCGA-BRCA Gene Expression Data

    May 7, 2026Meena Al HasaniNon-Small Cell Lung CancerHigh-Dimensional Data

  26. OmicsLM: A Multimodal Large Language Model for Multi-Sample Omics Reasoning

    May 7, 2026Maciej Sypetkowski, Joanna Krawczyk, Łukasz Smoliński +4Multi-Omic FrameworkSpatial Transcriptomics

  27. Wisteria: A Unified Multi-Scale Feature Learning Framework for DNA Language Model

    May 7, 2026Weihua Wang, Haoji Li, Feilong Bao +2GenomicsSequence Modeling

  28. Transformed Latent Variable Multi-Output Gaussian Processes

    May 6, 2026Xiaoyu Jiang, Xinxing Shi, Sokratia Georgaka +2Gaussian ProcessLatent Variable

  29. 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

  30. HEXST: Hexagonal Shifted-Window Transformer for Spatial Transcriptomics Gene Expression Prediction

    May 6, 2026Keunho Byeon, Jin Tae KwakSpatial TranscriptomicsSpatio-Temporal Transformers

  31. 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

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

    May 5, 2026Jonathan MuhireSingle-Cell Rna SequencingCross Validation

  33. AdaGraph: A Graph-Native Clustering Algorithm That Overcomes the Curse of Dimensionality and Enables Scientific Discovery

    May 5, 2026Ahmed ElmahdiImage ClusteringSpatial Transcriptomics

  34. 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

  35. Simple Self-Conditioning Adaptation for Masked Diffusion Models

    Apr 28, 2026Michael Cardei, Huu Binh Ta, Ferdinando FiorettoMasked Diffusion Language ModelsDiscrete Diffusion Model

  36. Mining Negative Sequential Patterns to Improve Viral Genomic Feature Representation and Classification

    Apr 28, 2026Wenxi Zhu, Wensheng Gan, Zhenlian QiGenomics

  37. 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

  38. Leveraging Spatial Transcriptomics as Alternative to Manual Annotations for Deep Learning-Based Nuclei Analysis

    Apr 26, 2026Kazuya Nishimura, Ryoma Bise, Haruka Hirose +1Spatial TranscriptomicsComputational Pathology

  39. 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

  40. StackFeat RL: Reinforcement Learning over Iterative Dual Criterion Feature Selection for Stable Biomarker Discovery

    Apr 24, 2026A. Yermekov, D. A. Herrera-MartíFeature SelectionFeature Learning

  41. CHRep: Cross-modal Histology Representation and Post-hoc Calibration for Spatial Gene Expression Prediction

    Apr 23, 2026Changfan Wang, Xinran Wang, Donghai Liu +4Spatial TranscriptomicsComputational Pathology

  42. 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

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

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

  44. 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

  45. Audio Spoof Detection with GaborNet

    Apr 21, 2026Waldek MaciejkoMel-Frequency Cepstral CoefficientConvolutional

  46. Intervention-Aware Multiscale Representation Learning from Imaging Phenomics and Perturbation Transcriptomics

    Apr 19, 2026Jiayuan Chen, Ruoqi Liu, Zishan Gu +1Spatial TranscriptomicsPhenotypes

  47. SAVE: A Generalizable Framework for Multi-Condition Single-Cell Generation with Gene Block Attention

    Apr 18, 2026Jiahao Li, Jiayi Dong, Peng Ye +3Single-Cell Rna SequencingHigh-Fidelity Conditional Generation

  48. Structure as Computation: Developmental Generation of Minimal Neural Circuits

    Apr 16, 2026Duan ZhouSynaptic PlasticityMinimal

  49. Transcriptomic Models for Immunotherapy Response Prediction Show Limited Cross-cohort Generalisability

    Apr 7, 2026Yuheng Liang, Lucy Chhuo, Ahmadreza Argha +8Spatial Transcriptomics

  50. A Spectral Decomposition Framework for Multiscale Nonlinear Dimensionality Reduction

    Apr 2, 2026Zeyang Huang, Angelos Chatzimparmpas, Thomas Höllt +1Dimensionality ReductionMultiscale

  51. i-IF-Learn: Iterative Feature Selection and Unsupervised Learning for High-Dimensional Complex Data

    Mar 25, 2026Chen Ma, Wanjie Wang, Shuhao FanFeature SelectionUnsupervised

  52. Spatial Transcriptomics as Images for Large-Scale Pretraining

    Mar 13, 2026Yishun Zhu, Jiaxin Qi, Jian Wang +2Spatial TranscriptomicsSpatial Patching

  53. Multimodal Feature Prototype Learning for Interpretable and Discriminative Cancer Survival Prediction

    Oct 7, 2025Shuo Jiang, Zhuwen Chen, Liaoman Xu +6Survival PredictionsMulti-Modal Representation Learning

  54. Variational Learning of Disentangled Representations

    Jun 20, 2025Yuli Slavutsky, Ozgur Beker, David Blei +1VariationalCovariate Shift

  55. Leveraging Natural Language Processing to Unravel the Mystery of Life: A Review of NLP Approaches in Genomics, Transcriptomics, and Proteomics

    Jun 2, 2025Ella Rannon, David BursteinGenomicsSpatial Transcriptomics

  56. scDataset: Scalable Data Loading for Deep Learning on Large-Scale Single-Cell Omics

    Jun 2, 2025Davide D'Ascenzo, Sebastiano Cultrera di MontesanoSingle-Cell Rna SequencingBenchmark Datasets

  57. Cross-Cluster Weighted Forests

    May 17, 2021Maya Ramchandran, Rajarshi Mukherjee, Giovanni ParmigianiRandom ForestImage Clustering