Transformers in single-cell omics: a review and new perspectives
Recent efforts to construct reference maps of cellular phenotypes have expanded the
volume and diversity of single-cell omics data, providing an unprecedented resource for …
volume and diversity of single-cell omics data, providing an unprecedented resource for …
Optimal transport for single-cell and spatial omics
C Bunne, G Schiebinger, A Krause, A Regev… - Nature Reviews …, 2024 - nature.com
High-throughput single-cell profiling provides an unprecedented ability to uncover the
molecular states of millions of cells. These technologies are, however, destructive to cells …
molecular states of millions of cells. These technologies are, however, destructive to cells …
Evaluating the Utilities of Foundation Models in Single-cell Data Analysis
Abstract Large Language Models (LLMs) or foundation models have made significant
strides in both industrial and scientific domains. In this paper, we evaluate the performance …
strides in both industrial and scientific domains. In this paper, we evaluate the performance …
Profiling cell identity and tissue architecture with single-cell and spatial transcriptomics
GS Gulati, JP D'Silva, Y Liu, L Wang… - … Reviews Molecular Cell …, 2024 - nature.com
Single-cell transcriptomics has broadened our understanding of cellular diversity and gene
expression dynamics in healthy and diseased tissues. Recently, spatial transcriptomics has …
expression dynamics in healthy and diseased tissues. Recently, spatial transcriptomics has …
Foundation model for advancing healthcare: Challenges, opportunities, and future directions
Foundation model, which is pre-trained on broad data and is able to adapt to a wide range
of tasks, is advancing healthcare. It promotes the development of healthcare artificial …
of tasks, is advancing healthcare. It promotes the development of healthcare artificial …
James German and the Quest to Understand Human RECQ Helicase Deficiencies
RJ Monnat Jr - Cells, 2024 - mdpi.com
James German's work to establish the natural history and cancer risk associated with Bloom
syndrome (BS) has had a strong influence on the generation of scientists and clinicians …
syndrome (BS) has had a strong influence on the generation of scientists and clinicians …
Establishing a conceptual framework for holistic cell states and state transitions
SM Rafelski, JA Theriot - Cell, 2024 - cell.com
Cell states were traditionally defined by how they looked, where they were located, and what
functions they performed. In this post-genomic era, the field is largely focused on a …
functions they performed. In this post-genomic era, the field is largely focused on a …
Poseidon: Efficient Foundation Models for PDEs
We introduce Poseidon, a foundation model for learning the solution operators of PDEs. It is
based on a multiscale operator transformer, with time-conditioned layer norms that enable …
based on a multiscale operator transformer, with time-conditioned layer norms that enable …
[HTML][HTML] Integrating single-cell RNA-seq datasets with substantial batch effects
Integration of single-cell RNA-sequencing (scRNA-seq) datasets has become a standard
part of the analysis, with conditional variational autoencoders (cVAE) being among the most …
part of the analysis, with conditional variational autoencoders (cVAE) being among the most …
Perspectives on benchmarking foundation models for network biology
CV Theodoris - Quantitative Biology, 2024 - Wiley Online Library
Transfer learning has revolutionized fields including natural language understanding and
computer vision by leveraging large‐scale general datasets to pretrain models with …
computer vision by leveraging large‐scale general datasets to pretrain models with …