Spatial Transcriptomics

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Period ending 2026-09-21

4 new papers

A weekly snapshot of new work published in Spatial Transcriptomics.

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. 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

  2. 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

  3. 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

  4. GRAFT: Biological Graph and Hypergraph Benchmarks for Linked Gene Expression and Phenotypic Trait Prediction in Arabidopsis thaliana

    Jun 25, 2026Manuel Serna-Aguilera, Vanshika Jindal, Fiona L. Goggin +53D Plant PhenotypingPhenotypes

  5. 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

  6. AI-Assisted Computational Reproducibility on the FABRIC Testbed

    Jun 24, 2026Komal Thareja, Paul Ruth, Berent Aldikacti +1ReproducibilityHigh-Performance Computing

  7. 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

  8. KG-TRACE: A Neuro-Symbolic Framework for Mechanistic Grounding in Antimicrobial Resistance Prediction

    Jun 24, 2026Naman Garg, Sarika Jain, Sourav Yadav +4GenomicsClinical Prediction

  9. JASPR: Joint Spatial Representation learning of histology and spatial genomics for improved virtual genomic screening and clinical prognostication

    Jun 24, 2026Marija Pizurica, Eric Zimmermann, Neil Tenenholtz +5Spatial TranscriptomicsComputational Pathology

  10. ParaPairAudioBench: Paralinguistic Pairwise Audio Benchmark for LALM-as-a-Judge

    Jun 23, 2026Jisu Jeon, Seungyeon Jwa, Joosung Lee +6Paralinguistic CuesLarge Audio Language Models

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

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

  12. 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

  13. Contrastive and Adaptive Multi-modal Masked Autoencoder for Spatial Transcriptomics

    Jun 19, 2026Joohyeok Kim, Taejin Jeong, Jinyeong Kim +1Spatial TranscriptomicsWhole-Slide Images

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

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

  15. How Post-Training Shapes Biological Reasoning Models

    Jun 15, 2026Lukas Fesser, Hanlin Zhang, Michelle M. Li +5BiologicalLarge Reasoning Models

  16. Structured Nonparametric Variational Inference for Dependent Latent Modeling

    Jun 13, 2026Yuda Shao, Zhiling Gu, Shan YuVariational InferenceLatent Variable

  17. Cluster LOCO: Feature Importance For Interpreting Clusters

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

  18. HiST: A Hierarchical Sparse Transformer for Cross-Modal Spatial Transcriptomics Modeling

    Jun 12, 2026Weiyi Wu, Xinwen Xu, Xingjian Diao +4Spatial TranscriptomicsSpatio-Temporal Transformers

  19. Is It You or Your Environment? A Bayesian Inference Framework for Genomically-Anchored Personalized Physiological Interpretation

    Jun 11, 2026Aruna Dey, Suraj BiswasPhysiological DataBayesian

  20. 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

  21. 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

  22. CisTransCell: Single-Cell Perturbation Prediction via Gene Function, Regulatory Control, and Cellular Context

    Jun 10, 2026Wei Zhang, Xun Jiang, Yuesi Xi +1Single-Cell Perturbation PredictionSpatial Transcriptomics

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

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

  24. Finding Multiple Interpretations in Datasets

    Jun 10, 2026Matthew Chak, Paul AndersonData MiningSpatial Transcriptomics

  25. Skill-Augmented AI Agents for Medical Research Analysis: An Exploratory Multi-Model Human Evaluation in an NSCLC Transcriptomic Biomarker Task

    Jun 10, 2026Qianyu Yao, Fei Sun, Bocheng Huang +10Spatial TranscriptomicsArtificial Intelligence Systems

  26. 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

  27. 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

  28. Knowledge Graphs and Reasoning LLMs for Finding Simple Yet Effective Transcriptomic Perturbation Predictors

    Jun 7, 2026Jake Fawkes, Liam Hodgson, Jason HartfordBiomedical Knowledge GraphSpatial Transcriptomics

  29. SNR-ST-Mix: Sample-specific Neighborhood Regression Mixup for Augmented Spatial Transcriptomics Imputation with Deep Neural Network

    Jun 7, 2026Hongyi Yu, Yaoyu Fang, Jiahe Qian +3Spatial TranscriptomicsSynthetic Data Augmentation

  30. GIFT: LLM-Guided State-Reward Interface for Financial Reinforcement Learning

    Jun 7, 2026Yanyan Wu, Boyi Zhang, Yanlin Liu +10Portfolio OptimizationDeep Reinforcement Learning

  31. The Dark Regulome: Disentangling Predictability from Regulation in Genomic Foundation Models

    Jun 5, 2026Chahat Baranwal, Aaditya Baranwal, Lakshya Nitin TandonGene-Regulatory NetworksGenomics

  32. 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

  33. pp-adic Bi-Filtrations for Topological Machine Learning on Genomic Sequences

    Jun 4, 2026Tirtharaj Dash, Gunja SachdevaGenomicsTopological Deep Learning

  34. Cross-scale spatially-aware generative modeling of transcriptomic programs underlying neurodegenerative brain organization

    Jun 4, 2026Krishnakumar VaithianathanSpatial TranscriptomicsAlzheimer

  35. Multimarginal flow matching with optimal transport potentials

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

  36. Do Foundation Models See Biology? Evaluating Attention Coherence with Spatial Transcriptomics in Glioblastoma

    Jun 3, 2026Dilakshan Srikanthan, Amoon Jamzad, Paul Wilson +5Pathology Foundation ModelsSpatial Transcriptomics

  37. LDARNet: DNA Adaptive Representation Network with Learnable Tokenization for Genomic Modeling

    Jun 3, 2026Daria Ledneva, Denis KuznetsovGenomicsWireless Foundation Models

  38. GENEB: Why Genomic Models Are Hard to Compare

    Jun 3, 2026Daria Ledneva, Mikhail Nuridinov, Denis KuznetsovGenomicsModel Evaluation

  39. A Robust Optimization Approach to Sparse Principal Component Analysis

    Jun 2, 2026David Vävinggren, Francis Bach, André M. H. Teixeira +2Principal Component AnalysisSparsity

  40. 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

  41. A Fast Screening Approach for High-dimensional Outcomes and High-dimensional Predictors

    Jun 2, 2026Hongju Park, Zhenyao Ye, Shuo ChenHigh-Dimensional DataScreening

  42. Pathway-Structured Privileged Distillation for Deployable Computational Pathology

    Jun 1, 2026Yongxin Guo, Hao Lu, Onur Koyun +2Computational PathologySpatial Transcriptomics

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

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

  44. 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

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

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

  46. Plausibility Is Not Prediction: Contrastive Evidence for LLM-Based Cellular Perturbation Reasoning

    May 31, 2026Xinyu Yuan, Xixian Liu, Jianan Zhao +3Single-Cell Perturbation PredictionSpatial Transcriptomics

  47. On the Recoverability of Causal Relations from Bulk Gene Expression Data

    May 30, 2026Gongxu Luo, Boyang Sun, Kun ZhangGene-Regulatory NetworksSpatial Transcriptomics

  48. Annotation-Informed Block-Sparse Bayesian Modeling for cis-Expression Prediction

    May 30, 2026Lei Huang, Hui Shen, Kuan-Jui Su +9GenomicsLogistic Regression

  49. Agentic Authoring of Interactive Multiview Visualizations in Genomics

    May 29, 2026Astrid van den Brandt, Kiroong Choe, Sehi L'Yi +2Visual AnalyticsGenomics

  50. Cluster Analysis with Resampling for Validation and Exploration (CARVE)

    May 29, 2026Kai R. Wycik, Tiffany M. Tang, Tarek M. Zikry +1Image ClusteringCross Validation

  51. Effective Biological Representation Learning by Masking Gene Expression

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

  52. Spatial Transcriptomics-Guided Alignment Enhances Molecular Profiling in Pathology Foundation Model

    May 29, 2026Fengtao Zhou, Yingxue Xu, Zhengyu Zhang +20Pathology Foundation ModelsSpatial Transcriptomics

  53. Chem-PerturBridge: a harmonized compendium of small molecule perturbation transcriptomic effects

    May 29, 2026Artur Szałata, Olga Novitskaia, Maiia Shulman +3Single-Cell Perturbation PredictionSpatial Transcriptomics

  54. Position: Genomic Model Research Must Move Beyond Anecdotal Evaluation of Interpretability Methods

    May 29, 2026Shasha Zhou, Mingyu Huang, Ke LiGenomicsModel Interpretability

  55. IRIS: time-structured manifold projections

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

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

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

  57. ScaleMAP: Preserving Local Density and Neighborhood Structure in Low-Dimensional Embeddings

    May 28, 2026Rajas Poorna, Marcus T. CiceroneDimensionality ReductionNeighbors

  58. FPLIER: Federated Pathway-Level Information Extractor

    May 28, 2026Daniele Malpetti, Christian Berchtold, Francesco Gualdi +3Privacy-Preserving FrameworkSpatial Transcriptomics

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

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

  60. Geometry-First Generative Spatial Single-Cell Reconstruction

    May 27, 2026Ehtesamul Azim, Muhtasim Noor Alif, Tae Hyun Hwang +2Spatial TranscriptomicsDistance