HypoGeneAgent: A Hypothesis Language Agent for Gene-Set Cluster Resolution Selection Using Perturb-seq Datasets
Fuente:
arXiv
Saved in:
| Main Authors: | Yuan, Ying, Ge, Xing-Yue Monica, Waterman, Aaron Archer, Biancalani, Tommaso, Richmond, David, Pandit, Yogesh, Singh, Avtar, Littman, Russell, Liu, Jin, Huetter, Jan-Christian, Ermakov, Vladimir |
|---|---|
| Format: | Preprint |
| Published: |
2025
|
| Subjects: | |
| Online Access: | |
| Tags: |
Add Tag
No Tags, Be the first to tag this record!
|
Similar Items
Contextualizing biological perturbation experiments through language
by: Wu, Menghua, et al.
Published: (2025)
by: Wu, Menghua, et al.
Published: (2025)
Efficient Fine-Tuning of Single-Cell Foundation Models Enables Zero-Shot Molecular Perturbation Prediction
by: Maleki, Sepideh, et al.
Published: (2024)
by: Maleki, Sepideh, et al.
Published: (2024)
Group Contrastive Learning for Weakly Paired Multimodal Data
by: Gorla, Aditya, et al.
Published: (2026)
by: Gorla, Aditya, et al.
Published: (2026)
Understanding Reinforcement Learning-Based Fine-Tuning of Diffusion Models: A Tutorial and Review
by: Uehara, Masatoshi, et al.
Published: (2024)
by: Uehara, Masatoshi, et al.
Published: (2024)
Gene Set Summarization using Large Language Models
by: Joachimiak, Marcin P., et al.
Published: (2023)
by: Joachimiak, Marcin P., et al.
Published: (2023)
Simultaneously Infer Cell Pseudotime,Velocity Field and Gene Interaction from Multi-Branch scRNA-seq Data with scPN
by: Zhou, Zhen, et al.
Published: (2024)
by: Zhou, Zhen, et al.
Published: (2024)
InfoSEM: A Deep Generative Model with Informative Priors for Gene Regulatory Network Inference
by: Cui, Tianyu, et al.
Published: (2025)
by: Cui, Tianyu, et al.
Published: (2025)
SOWAHA as a Cancer Suppressor Gene Influence Metabolic Reprogramming
by: Yi, Xiaohong, et al.
Published: (2024)
by: Yi, Xiaohong, et al.
Published: (2024)
Spatially-extended Flow Phixer (SpeF-Phixer): A Spatially Extended $φ$-Mixing Framework for Gene Regulatory Causal Inference in Spatial Gene Field
by: Nagasaka, Toru, et al.
Published: (2025)
by: Nagasaka, Toru, et al.
Published: (2025)
WGTDA: A Topological Perspective to Biomarker Discovery in Gene Expression Data
by: Nyase, Ndivhuwo, et al.
Published: (2024)
by: Nyase, Ndivhuwo, et al.
Published: (2024)
HyperADRs: A Hierarchical Hypergraph Framework for Drug-Gene-ADR Prediction
by: Cai, Ze, et al.
Published: (2025)
by: Cai, Ze, et al.
Published: (2025)
GeneFEAST: the pivotal, gene-centric step in functional enrichment analysis interpretation
by: Taylor, Avigail, et al.
Published: (2023)
by: Taylor, Avigail, et al.
Published: (2023)
GenoHoption: Bridging Gene Network Graphs and Single-Cell Foundation Models
by: Cheng, Jiabei, et al.
Published: (2024)
by: Cheng, Jiabei, et al.
Published: (2024)
Integrative Prognostic Modeling of Breast Cancer Survival with Gene Expression and Clinical Data
by: Amevor, Robert, et al.
Published: (2025)
by: Amevor, Robert, et al.
Published: (2025)
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)
RatGene: Gene deletion-addition algorithms using growth to production ratio for growth-coupled production in constraint-based metabolic networks
by: Ma, Yier, et al.
Published: (2024)
by: Ma, Yier, et al.
Published: (2024)
GeneFlow: Translation of Single-cell Gene Expression to Histopathological Images via Rectified Flow
by: Wang, Mengbo, et al.
Published: (2025)
by: Wang, Mengbo, et al.
Published: (2025)
Inference-Time Alignment in Diffusion Models with Reward-Guided Generation: Tutorial and Review
by: Uehara, Masatoshi, et al.
Published: (2025)
by: Uehara, Masatoshi, et al.
Published: (2025)
Optimizing Gene-Based Testing for Antibiotic Resistance Prediction
by: Hagerman, David, et al.
Published: (2025)
by: Hagerman, David, et al.
Published: (2025)
Sparse Autoencoders Reveal Interpretable Structure in Small Gene Language Models
by: Guan, Haoxiang, et al.
Published: (2025)
by: Guan, Haoxiang, et al.
Published: (2025)
BioBO: Biology-informed Bayesian Optimization for Perturbation Design
by: Li, Yanke, et al.
Published: (2025)
by: Li, Yanke, et al.
Published: (2025)
Hypergraph Representations of scRNA-seq Data for Improved Clustering with Random Walks
by: He, Wan, et al.
Published: (2025)
by: He, Wan, et al.
Published: (2025)
Gene-associated Disease Discovery Powered by Large Language Models
by: Chang, Jiayu, et al.
Published: (2024)
by: Chang, Jiayu, et al.
Published: (2024)
Assessing the Utility of Large Language Models for Phenotype-Driven Gene Prioritization in Rare Genetic Disorder Diagnosis
by: Kim, Junyoung, et al.
Published: (2024)
by: Kim, Junyoung, et al.
Published: (2024)
Reconstructing Noisy Gene Regulation Dynamics Using Extrinsic-Noise-Driven Neural Stochastic Differential Equations
by: Zhang, Jiancheng, et al.
Published: (2025)
by: Zhang, Jiancheng, et al.
Published: (2025)
Harnessing Diet and Gene Expression Insights through a Centralized Nutrigenomics Database to Improve Public Health
by: Hai, Fahmida, et al.
Published: (2025)
by: Hai, Fahmida, et al.
Published: (2025)
Gene-environment interplay and public policies
by: Muslimova, Dilnoza, et al.
Published: (2025)
by: Muslimova, Dilnoza, et al.
Published: (2025)
Quantum Generative Modeling of Single-Cell transcriptomes: Capturing Gene-Gene and Cell-Cell Interactions
by: Romero, Selim, et al.
Published: (2025)
by: Romero, Selim, et al.
Published: (2025)
drGT: Attention-Guided Gene Assessment of Drug Response Utilizing a Drug-Cell-Gene Heterogeneous Network
by: Inoue, Yoshitaka, et al.
Published: (2024)
by: Inoue, Yoshitaka, et al.
Published: (2024)
Association in Facial Phenotype, Gene, Disease: A Dataset for Explainable Rare Genetic Diseases Diagnosis
by: Song, Jie, et al.
Published: (2025)
by: Song, Jie, et al.
Published: (2025)
KINDLE: Knowledge-Guided Distillation for Prior-Free Gene Regulatory Network Inference
by: Peng, Rui, et al.
Published: (2025)
by: Peng, Rui, et al.
Published: (2025)
GRiNS: A Python Library for Simulating Gene Regulatory Network Dynamics
by: Harlapur, Pradyumna, et al.
Published: (2025)
by: Harlapur, Pradyumna, et al.
Published: (2025)
Subspace Tensor Orthogonal Rotation Model (STORM) for Batch Alignment, Cell Type Deconvolution, and Gene Imputation in Spatial Transcriptomic Data
by: Cottrell, Sean, et al.
Published: (2026)
by: Cottrell, Sean, et al.
Published: (2026)
DNA Language Model and Interpretable Graph Neural Network Identify Genes and Pathways Involved in Rare Diseases
by: Saadat, Ali, et al.
Published: (2024)
by: Saadat, Ali, et al.
Published: (2024)
Markovian Promoter Models: A Mechanistic Alternative to Hill Functions in Gene Regulatory Networks
by: Wu, Tianyu
Published: (2025)
by: Wu, Tianyu
Published: (2025)
DBgDel: Database-Enhanced Gene Deletion Framework for Growth-Coupled Production in Genome-Scale Metabolic Models
by: Yang, Ziwei, et al.
Published: (2024)
by: Yang, Ziwei, et al.
Published: (2024)
A Closed-Form Solution to the 2-Sample Problem for Quantifying Changes in Gene Expression using Bayes Factors
by: Hoerbst, Franziska, et al.
Published: (2024)
by: Hoerbst, Franziska, et al.
Published: (2024)
AssayBench: An Assay-Level Virtual Cell Benchmark for LLMs and Agents
by: De Brouwer, Edward, et al.
Published: (2026)
by: De Brouwer, Edward, et al.
Published: (2026)
RankByGene: Gene-Guided Histopathology Representation Learning Through Cross-Modal Ranking Consistency
by: Huang, Wentao, et al.
Published: (2024)
by: Huang, Wentao, et al.
Published: (2024)
Advancing Gene Selection in Oncology: A Fusion of Deep Learning and Sparsity for Precision Gene Selection
by: Krishna, Akhila, et al.
Published: (2024)
by: Krishna, Akhila, et al.
Published: (2024)
Similar Items
-
Contextualizing biological perturbation experiments through language
by: Wu, Menghua, et al.
Published: (2025) -
Efficient Fine-Tuning of Single-Cell Foundation Models Enables Zero-Shot Molecular Perturbation Prediction
by: Maleki, Sepideh, et al.
Published: (2024) -
Group Contrastive Learning for Weakly Paired Multimodal Data
by: Gorla, Aditya, et al.
Published: (2026) -
Understanding Reinforcement Learning-Based Fine-Tuning of Diffusion Models: A Tutorial and Review
by: Uehara, Masatoshi, et al.
Published: (2024) -
Gene Set Summarization using Large Language Models
by: Joachimiak, Marcin P., et al.
Published: (2023)