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Caleb N. Ellington · SciRah

Researcher profile · Semantic Scholar

Caleb N. Ellington

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Caleb N. Ellington — researcher profile on SciRah

h-index: 7
Works: 23
Citations: 172

Most-cited papers

A Large-Scale Foundation Model for RNA Function and Structure Prediction
Shuxian Zou, Tian-Hua Tao, Sazan Mahbub, Caleb N. Ellington +6 more
2024bioRxiv31 citations Open access
Semantic Scholar
AttentionPert: accurately modeling multiplexed genetic perturbations with multi-scale effects
Ding Bai, Caleb N. Ellington, Shentong Mo, Le Song +1 more
2024bioRxiv21 citations Open access
Semantic Scholar
Accurate and General DNA Representations Emerge from Genome Foundation Models at Scale
Caleb N. Ellington, Ning Sun, Nicholas Ho, Tian-Hua Tao +6 more
2025bioRxiv20 citations Open access
Semantic Scholar
Scaling Dense Representations for Single Cell with Transcriptome-Scale Context
Nicholas Ho, Caleb N. Ellington, Jinyu Hou, Sohan Addagudi +8 more
2024bioRxiv19 citations Open access
Semantic Scholar
Multi-task Learning of Order-Consistent Causal Graphs
Xin-Shi Chen, Haoran Sun, Caleb N. Ellington, E. Xing +1 more
2021Neural Information Processing Systems19 citations
Semantic Scholar
Foundation Models Improve Perturbation Response Prediction
Elijah Cole, Geert-Jan Huizing, Sohan Addagudi, Nicholas Ho +16 more
2026bioRxiv9 citations Open access
Semantic Scholar
Contextualized Machine Learning
Benjamin J. Lengerich, Caleb N. Ellington, Andrea Rubbi, M. Kellis +1 more
2023arXiv.org9 citations
Semantic Scholar
Scaling Structure Aware Virtual Screening to Billions of Molecules with SPRINT
Andrew T. McNutt, Abhinav K. Adduri, Caleb N. Ellington, Monica T. Dayao +3 more
2024arXiv.org7 citations
Semantic Scholar
Contextualized Policy Recovery: Modeling and Interpreting Medical Decisions with Adaptive Imitation Learning
J. Deuschel, Caleb N. Ellington, Benjamin J. Lengerich, Yingtao Luo +2 more
2023International Conference on Machine Learning7 citations Open access
Semantic Scholar
NOTMAD: Estimating Bayesian Networks with Sample-Specific Structures and Parameters
Benjamin J. Lengerich, Caleb N. Ellington, Bryon Aragam, E. Xing +1 more
2021arXiv.org7 citations
Semantic Scholar
Automated interpretable discovery of heterogeneous treatment effectiveness: A COVID-19 case study
Benjamin J. Lengerich, M. Nunnally, Y. Aphinyanaphongs, Caleb N. Ellington +1 more
2021medRxiv6 citations Open access
Semantic Scholar
Learning to estimate sample-specific transcriptional networks for 7,000 tumors
Caleb N. Ellington, Benjamin J. Lengerich, T. Watkins, Jie-Ying Yang +5 more
2025bioRxiv5 citations Open access
Semantic Scholar
Uncertainty-Aware Discrete Diffusion Improves Protein Design
Sazan Mahbub, Christoph Feinauer, Caleb N. Ellington, Le Song +1 more
2025bioRxiv3 citations Open access
Semantic Scholar
Contextualized: Heterogeneous Modeling Toolbox
Caleb N. Ellington, Benjamin J. Lengerich, W. Lo, A. Alvarez +3 more
2024Journal of Open Source Software3 citations Open access
Semantic Scholar
Rapid and Reproducible Multimodal Biological Foundation Model Development with AIDO.ModelGenerator
Caleb N. Ellington, Dian Li, Shuxian Zou, Elijah Cole +4 more
2025bioRxiv2 citations Open access
Semantic Scholar
Interpretable adenylation domain specificity prediction using protein language models
Abhinav K. Adduri, Andrew T. McNutt, Caleb N. Ellington, Krish Suraparaju +9 more
2025bioRxiv2 citations Open access
Semantic Scholar
Patient-Specific Models of Treatment Effects Explain Heterogeneity in Tuberculosis
Ethan Wu, Caleb N. Ellington, Benjamin J. Lengerich, E. Xing
2024arXiv.org2 citations
Semantic Scholar
Retrieval-Augmented Interpretable Learning: Towards Task-Specific Zero-Shot Models in Healthcare
Sazan Mahbub, Caleb N. Ellington, Zhi-Yuan Li, Yi-Xin Yang +3 more
2026arXiv.org1 citations
Semantic Scholar
Using AI to Build AI: AIDO.Builder Enables Autonomous Machine Learning Model Building for Biomedicine
Han Guo, Youwei Liang, Xingyi Cheng, Caleb N. Ellington +3 more
2026bioRxiv1 citations Open access
Semantic Scholar
Cell-Level Virtual Screening
Caleb N. Ellington, Sohan Addagudi, Jia-Qi Wang, Benjamin J. Lengerich +1 more
2026bioRxiv0 citations Open access
Semantic Scholar
FACET: Factorized Asymmetric Conditioning for Efficient Transport in High-Fidelity Fluorescence Microscopy Synthesis
Sazan Mahbub, Caleb N. Ellington, E. Xing
20260 citations
Semantic Scholar
Context-Adaptive Inference: A Unified Statistical and Foundation-Model View
Yue-Ting Yao, Caleb N. Ellington, Jing-Yu Jia, Bai-Yang Chen +8 more
2026arXiv.org0 citations
Semantic Scholar
From One to Zero: RAG-IM Adapts Language Models for Interpretable Zero-Shot Predictions on Clinical Tabular Data
Sazan Mahbub, Caleb N. Ellington, Sina Alinejad, K. Wen +3 more
0 citations
Semantic Scholar

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