A comprehensive survey of foundation models in medicine

W Khan, S Leem, KB See, JK Wong… - IEEE Reviews in …, 2025 - ieeexplore.ieee.org
Foundation models (FMs) are large-scale deeplearning models that are developed using
large datasets and self-supervised learning methods. These models serve as a base for …

Provable in-context learning of linear systems and linear elliptic pdes with transformers

F Cole, Y Lu, R O'Neill, T Zhang - arxiv preprint arxiv:2409.12293, 2024 - arxiv.org
Foundation models for natural language processing, powered by the transformer
architecture, exhibit remarkable in-context learning (ICL) capabilities, allowing pre-trained …

Characterizing uncertainty in predictions of genomic sequence-to-activity models

A Bajwa, R Rastogi, P Kathail… - Machine Learning …, 2024 - proceedings.mlr.press
Genomic sequence-to-activity models are increasingly utilized to understand gene
regulatory syntax and probe the functional consequences of regulatory variation. Current …

Causal Representation Learning from Multimodal Biological Observations

Y Sun, L Kong, G Chen, L Li, G Luo, Z Li… - arxiv preprint arxiv …, 2024 - arxiv.org
Prevalent in biological applications (eg, human phenotype measurements), multimodal
datasets can provide valuable insights into the underlying biological mechanisms. However …

Bridging biomolecular modalities for knowledge transfer in bio-language models

M Prakash, A Moskalev, PA DiMaggio, S Combs… - bioRxiv, 2024 - biorxiv.org
In biology, messenger RNA (mRNA) plays a crucial role in gene expression and protein
synthesis. Accurate predictive modeling of mRNA properties can greatly enhance our …

DNA Language Models for RNA Analyses

S Du, L Liang, J Li, C Kingsford - openreview.net
Genomic Language Models (gLMs), encompassing DNA models, RNA models, and
multimodal models, are becoming widely used for the analysis of biological sequences …