Caleb N. Ellington

This paper introduces CellVS-Net, a cell-level virtual screening model that outperforms existing methods on two benchmarks, demonstrating its viability as an alternative to molecular-level drug screening.

AIDO.Builder automates biomedical model development by generating executable pipelines, selecting strategies, and iteratively refining models without manual intervention.

This study evaluates foundation models for predicting cellular responses to perturbations, finding that some pretrained embeddings improve predictions while others do not.

AIDO.ModelGenerator enables rapid, reproducible multimodal foundation model development by integrating datasets, pre-trained models, and experiment recipes to improve biological predictions.

This paper introduces an uncertainty-aware discrete diffusion model for protein design, improving sequence generation from 3D structures by incorporating position-specific uncertainty and pretrained models.

The paper introduces contextualized network inference to estimate sample-specific transcriptional networks for 7000 tumors, improving accuracy and enabling novel prognostic subtyping.

The paper introduces MASPR, a machine learning method using protein language models to predict adenylation domain substrate specificities, enabling the prediction of hybrid NRP-PK natural products.

This paper introduces AIDO.DNA, a DNA language model that improves representation of DNA sequences across multiple tasks by scaling model size and training data.

This paper introduces AIDO.RNA, a large-scale foundation model for RNA function and structure prediction, achieving state-of-the-art performance on multiple tasks.

The paper introduces AIDO.Cell, a series of dense Transformer models pre-trained on human single-cell RNA-seq data, achieving state-of-the-art results in clustering, classification, and perturbation modeling.

AttentionPert predicts gene expression under multiplexed genetic perturbations and generalizes to unseen conditions, outperforming existing methods in accuracy and handling diverse perturbations.