Multi-Dimensional Spectral Geometry of Biological Knowledge in Single-Cell Transformer Representations
Fuente:
arXiv
Saved in:
| Main Author: | Kendiukhov, Ihor |
|---|---|
| Format: | Preprint |
| Published: |
2026
|
| Subjects: | |
| Online Access: | |
| Tags: |
Add Tag
No Tags, Be the first to tag this record!
|
Similar Items
Scaling Laws for Masked-Reconstruction Transformers on Single-Cell Transcriptomics
by: Kendiukhov, Ihor
Published: (2026)
by: Kendiukhov, Ihor
Published: (2026)
Systematic Evaluation of Single-Cell Foundation Model Interpretability Reveals Attention Captures Co-Expression Rather Than Unique Regulatory Signal
by: Kendiukhov, Ihor
Published: (2026)
by: Kendiukhov, Ihor
Published: (2026)
Causal Circuit Tracing Reveals Distinct Computational Architectures in Single-Cell Foundation Models: Inhibitory Dominance, Biological Coherence, and Cross-Model Convergence
by: Kendiukhov, Ihor
Published: (2026)
by: Kendiukhov, Ihor
Published: (2026)
What Topological and Geometric Structure Do Biological Foundation Models Learn? Evidence from 141 Hypotheses
by: Kendiukhov, Ihor
Published: (2026)
by: Kendiukhov, Ihor
Published: (2026)
Discovery of a Hematopoietic Manifold in scGPT Yields a Method for Extracting Performant Algorithms from Biological Foundation Model Internals
by: Kendiukhov, Ihor
Published: (2026)
by: Kendiukhov, Ihor
Published: (2026)
Sparse autoencoders reveal organized biological knowledge but minimal regulatory logic in single-cell foundation models: a comparative atlas of Geneformer and scGPT
by: Kendiukhov, Ihor
Published: (2026)
by: Kendiukhov, Ihor
Published: (2026)
Single Cells Are Spatial Tokens: Transformers for Spatial Transcriptomic Data Imputation
by: Wen, Hongzhi, et al.
Published: (2023)
by: Wen, Hongzhi, et al.
Published: (2023)
xTrimoGene: An Efficient and Scalable Representation Learner for Single-Cell RNA-Seq Data
by: Gong, Jing, et al.
Published: (2023)
by: Gong, Jing, et al.
Published: (2023)
Gene Incremental Learning for Single-Cell Transcriptomics
by: Qi, Jiaxin, et al.
Published: (2025)
by: Qi, Jiaxin, et al.
Published: (2025)
Celler:A Genomic Language Model for Long-Tailed Single-Cell Annotation
by: Zhao, Huan, et al.
Published: (2025)
by: Zhao, Huan, et al.
Published: (2025)
Enhanced Gene Selection in Single-Cell Genomics: Pre-Filtering Synergy and Reinforced Optimization
by: Zhang, Weiliang, et al.
Published: (2024)
by: Zhang, Weiliang, et al.
Published: (2024)
Open World Knowledge Aided Single-Cell Foundation Model with Robust Cross-Modal Cell-Language Pre-training
by: Wang, Haoran, et al.
Published: (2026)
by: Wang, Haoran, et al.
Published: (2026)
Soft-Evidence Fused Graph Neural Network for Cancer Driver Gene Identification across Multi-View Biological Graphs
by: Chen, Bang, et al.
Published: (2025)
by: Chen, Bang, et al.
Published: (2025)
BSM: Small but Powerful Biological Sequence Model for Genes and Proteins
by: Xiang, Weixi, et al.
Published: (2024)
by: Xiang, Weixi, et al.
Published: (2024)
F5C-finder: An Explainable and Ensemble Biological Language Model for Predicting 5-Formylcytidine Modifications on mRNA
by: Wang, Guohao, et al.
Published: (2024)
by: Wang, Guohao, et al.
Published: (2024)
Knowledge Graph Sparsification for GNN-based Rare Disease Diagnosis
by: Cara, Premt, et al.
Published: (2025)
by: Cara, Premt, et al.
Published: (2025)
Absorb & Escape: Overcoming Single Model Limitations in Generating Genomic Sequences
by: Li, Zehui, et al.
Published: (2024)
by: Li, Zehui, et al.
Published: (2024)
Single-cell Curriculum Learning-based Deep Graph Embedding Clustering
by: Li, Huifa, et al.
Published: (2024)
by: Li, Huifa, et al.
Published: (2024)
How Private Are DNA Embeddings? Inverting Foundation Model Representations of Genomic Sequences
by: Ouaari, Sofiane, et al.
Published: (2026)
by: Ouaari, Sofiane, et al.
Published: (2026)
Dy-mer: An Explainable DNA Sequence Representation Scheme using Dictionary Learning
by: Peng, Zhiyuan, et al.
Published: (2024)
by: Peng, Zhiyuan, et al.
Published: (2024)
Continuous Diffusion Transformers for Designing Synthetic Regulatory Elements
by: Liu, Jonathan, et al.
Published: (2026)
by: Liu, Jonathan, et al.
Published: (2026)
DOGMA: Weaving Structural Information into Data-centric Single-cell Transcriptomics Analysis
by: Zhang, Ru, et al.
Published: (2026)
by: Zhang, Ru, et al.
Published: (2026)
Foundation Models for AI-Enabled Biological Design
by: Moldwin, Asher, et al.
Published: (2025)
by: Moldwin, Asher, et al.
Published: (2025)
Knowledge-guided Contextual Gene Set Analysis Using Large Language Models
by: Wang, Zhizheng, et al.
Published: (2025)
by: Wang, Zhizheng, et al.
Published: (2025)
DP-DCAN: Differentially Private Deep Contrastive Autoencoder Network for Single-cell Clustering
by: Li, Huifa, et al.
Published: (2023)
by: Li, Huifa, et al.
Published: (2023)
scASDC: Attention Enhanced Structural Deep Clustering for Single-cell RNA-seq Data
by: Min, Wenwen, et al.
Published: (2024)
by: Min, Wenwen, et al.
Published: (2024)
PETRA: Pretrained Evolutionary Transformer for SARS-CoV-2 Mutation Prediction
by: Zou, Xu
Published: (2025)
by: Zou, Xu
Published: (2025)
eDOC: Explainable Decoding Out-of-domain Cell Types with Evidential Learning
by: Wu, Chaochen, et al.
Published: (2024)
by: Wu, Chaochen, et al.
Published: (2024)
SpaDiT: Diffusion Transformer for Spatial Gene Expression Prediction using scRNA-seq
by: Li, Xiaoyu, et al.
Published: (2024)
by: Li, Xiaoyu, et al.
Published: (2024)
HybriDNA: A Hybrid Transformer-Mamba2 Long-Range DNA Language Model
by: Ma, Mingqian, et al.
Published: (2025)
by: Ma, Mingqian, et al.
Published: (2025)
Ctrl-DNA: Controllable Cell-Type-Specific Regulatory DNA Design via Constrained RL
by: Chen, Xingyu, et al.
Published: (2025)
by: Chen, Xingyu, et al.
Published: (2025)
SynLeaF: A Dual-Stage Multimodal Fusion Framework for Synthetic Lethality Prediction Across Pan- and Single-Cancer Contexts
by: Xing, Zheming, et al.
Published: (2026)
by: Xing, Zheming, et al.
Published: (2026)
Identification of Prognostic Biomarkers for Stage III Non-Small Cell Lung Carcinoma in Female Nonsmokers Using Machine Learning
by: Zheng, Huili, et al.
Published: (2024)
by: Zheng, Huili, et al.
Published: (2024)
Graph Structure Learning for Tumor Microenvironment with Cell Type Annotation from non-spatial scRNA-seq data
by: Huang, Yu-An, et al.
Published: (2025)
by: Huang, Yu-An, et al.
Published: (2025)
Explainable AI Methods for Multi-Omics Analysis: A Survey
by: Hussein, Ahmad, et al.
Published: (2024)
by: Hussein, Ahmad, et al.
Published: (2024)
SToFM: a Multi-scale Foundation Model for Spatial Transcriptomics
by: Zhao, Suyuan, et al.
Published: (2025)
by: Zhao, Suyuan, et al.
Published: (2025)
UniPTMs: The First Unified Multi-type PTM Site Prediction Model via Master-Slave Architecture-Based Multi-Stage Fusion Strategy and Hierarchical Contrastive Loss
by: Lin, Yiyu, et al.
Published: (2025)
by: Lin, Yiyu, et al.
Published: (2025)
A Multi-Label Temporal Convolutional Framework for Transcription Factor Binding Characterization
by: Demurtas, Pietro, et al.
Published: (2026)
by: Demurtas, Pietro, et al.
Published: (2026)
CRADLE-VAE: Enhancing Single-Cell Gene Perturbation Modeling with Counterfactual Reasoning-based Artifact Disentanglement
by: Baek, Seungheun, et al.
Published: (2024)
by: Baek, Seungheun, et al.
Published: (2024)
Omni-DNA: A Unified Genomic Foundation Model for Cross-Modal and Multi-Task Learning
by: Li, Zehui, et al.
Published: (2025)
by: Li, Zehui, et al.
Published: (2025)
Similar Items
-
Scaling Laws for Masked-Reconstruction Transformers on Single-Cell Transcriptomics
by: Kendiukhov, Ihor
Published: (2026) -
Systematic Evaluation of Single-Cell Foundation Model Interpretability Reveals Attention Captures Co-Expression Rather Than Unique Regulatory Signal
by: Kendiukhov, Ihor
Published: (2026) -
Causal Circuit Tracing Reveals Distinct Computational Architectures in Single-Cell Foundation Models: Inhibitory Dominance, Biological Coherence, and Cross-Model Convergence
by: Kendiukhov, Ihor
Published: (2026) -
What Topological and Geometric Structure Do Biological Foundation Models Learn? Evidence from 141 Hypotheses
by: Kendiukhov, Ihor
Published: (2026) -
Discovery of a Hematopoietic Manifold in scGPT Yields a Method for Extracting Performant Algorithms from Biological Foundation Model Internals
by: Kendiukhov, Ihor
Published: (2026)