Continuous Diffusion Transformers for Designing Synthetic Regulatory Elements
Fuente:
arXiv
Saved in:
| Main Authors: | Liu, Jonathan, Ghods, Kia |
|---|---|
| Format: | Preprint |
| Published: |
2026
|
| Subjects: | |
| Online Access: | |
| Tags: |
Add Tag
No Tags, Be the first to tag this record!
|
Similar Items
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)
Derivative-Free Guidance in Continuous and Discrete Diffusion Models with Soft Value-Based Decoding
by: Li, Xiner, et al.
Published: (2024)
by: Li, Xiner, 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)
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)
HybriDNA: A Hybrid Transformer-Mamba2 Long-Range DNA Language Model
by: Ma, Mingqian, et al.
Published: (2025)
by: Ma, Mingqian, 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)
DiscDiff: Latent Diffusion Model for DNA Sequence Generation
by: Li, Zehui, et al.
Published: (2024)
by: Li, Zehui, et al.
Published: (2024)
Multi-Dimensional Spectral Geometry of Biological Knowledge in Single-Cell Transformer Representations
by: Kendiukhov, Ihor
Published: (2026)
by: Kendiukhov, Ihor
Published: (2026)
PETRA: Pretrained Evolutionary Transformer for SARS-CoV-2 Mutation Prediction
by: Zou, Xu
Published: (2025)
by: Zou, Xu
Published: (2025)
Learning to Discover Regulatory Elements for Gene Expression Prediction
by: Su, Xingyu, et al.
Published: (2025)
by: Su, Xingyu, et al.
Published: (2025)
stMCDI: Masked Conditional Diffusion Model with Graph Neural Network for Spatial Transcriptomics Data Imputation
by: Li, Xiaoyu, et al.
Published: (2024)
by: Li, Xiaoyu, 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)
Foundation Models for AI-Enabled Biological Design
by: Moldwin, Asher, et al.
Published: (2025)
by: Moldwin, Asher, et al.
Published: (2025)
Exploring the Potentials and Challenges of Using Large Language Models for the Analysis of Transcriptional Regulation of Long Non-coding RNAs
by: Wang, Wei, et al.
Published: (2024)
by: Wang, Wei, et al.
Published: (2024)
GenoTEX: An LLM Agent Benchmark for Automated Gene Expression Data Analysis
by: Liu, Haoyang, et al.
Published: (2024)
by: Liu, Haoyang, et al.
Published: (2024)
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)
GeneZip: Region-Aware Compression for Long Context DNA Modeling
by: Zhao, Jianan, et al.
Published: (2026)
by: Zhao, Jianan, et al.
Published: (2026)
Classification of autoimmune diseases from Peripheral blood TCR repertoires by multimodal multi-instance learning
by: Zhang, Ruihao, et al.
Published: (2025)
by: Zhang, Ruihao, 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)
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)
Genomic Next-Token Predictors are In-Context Learners
by: Breslow, Nathan, et al.
Published: (2025)
by: Breslow, Nathan, 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)
scSiameseClu: A Siamese Clustering Framework for Interpreting single-cell RNA Sequencing Data
by: Xu, Ping, et al.
Published: (2025)
by: Xu, Ping, et al.
Published: (2025)
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)
Toward a Team of AI-made Scientists for Scientific Discovery from Gene Expression Data
by: Liu, Haoyang, et al.
Published: (2024)
by: Liu, Haoyang, et al.
Published: (2024)
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)
MergeDNA: Context-aware Genome Modeling with Dynamic Tokenization through Token Merging
by: Li, Siyuan, et al.
Published: (2025)
by: Li, Siyuan, et al.
Published: (2025)
FGBERT: Function-Driven Pre-trained Gene Language Model for Metagenomics
by: Duan, ChenRui, et al.
Published: (2024)
by: Duan, ChenRui, et al.
Published: (2024)
DeepVRegulome: DNABERT-based deep-learning framework for predicting the functional impact of short genomic variants on the human regulome
by: Dutta, Pratik, et al.
Published: (2025)
by: Dutta, Pratik, et al.
Published: (2025)
SynthPert: Enhancing LLM Biological Reasoning via Synthetic Reasoning Traces for Cellular Perturbation Prediction
by: Phillips, Lawrence, et al.
Published: (2025)
by: Phillips, Lawrence, et al.
Published: (2025)
Quantum-Boosted High-Fidelity Deep Learning
by: Wang, Feng-ao, et al.
Published: (2025)
by: Wang, Feng-ao, et al.
Published: (2025)
GenoBERT: A Language Model for Accurate Genotype Imputation
by: Huang, Lei, et al.
Published: (2026)
by: Huang, Lei, et al.
Published: (2026)
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)
LPDP: Inference-Time Reward Control for Variable-Length DNA Generation with Edit Flows
by: Kim, Jeongchan, et al.
Published: (2026)
by: Kim, Jeongchan, et al.
Published: (2026)
Interpretable DNA Sequence Classification via Dynamic Feature Generation in Decision Trees
by: Huynh, Nicolas, et al.
Published: (2026)
by: Huynh, Nicolas, et al.
Published: (2026)
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)
WFR-MFM: One-Step Inference for Dynamic Unbalanced Optimal Transport
by: Wang, Xinyu, et al.
Published: (2026)
by: Wang, Xinyu, et al.
Published: (2026)
Knowledge Graph Sparsification for GNN-based Rare Disease Diagnosis
by: Cara, Premt, et al.
Published: (2025)
by: Cara, Premt, et al.
Published: (2025)
DNABERT-2: Fine-Tuning a Genomic Language Model for Colorectal Gene Enhancer Classification
by: King, Darren, et al.
Published: (2025)
by: King, Darren, et al.
Published: (2025)
Highly Accurate Disease Diagnosis and Highly Reproducible Biomarker Identification with PathFormer
by: Dong, Zehao, et al.
Published: (2024)
by: Dong, Zehao, et al.
Published: (2024)
Similar Items
-
Ctrl-DNA: Controllable Cell-Type-Specific Regulatory DNA Design via Constrained RL
by: Chen, Xingyu, et al.
Published: (2025) -
Derivative-Free Guidance in Continuous and Discrete Diffusion Models with Soft Value-Based Decoding
by: Li, Xiner, et al.
Published: (2024) -
SpaDiT: Diffusion Transformer for Spatial Gene Expression Prediction using scRNA-seq
by: Li, Xiaoyu, et al.
Published: (2024) -
Single Cells Are Spatial Tokens: Transformers for Spatial Transcriptomic Data Imputation
by: Wen, Hongzhi, et al.
Published: (2023) -
HybriDNA: A Hybrid Transformer-Mamba2 Long-Range DNA Language Model
by: Ma, Mingqian, et al.
Published: (2025)