Mihir Bafna
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View article: Generating functional and multistate proteins with a multimodal diffusion transformer
Generating functional and multistate proteins with a multimodal diffusion transformer Open
Generating proteins with the full diversity and complexity of functions found in nature is a grand challenge in protein design. Here, we present ProDiT, a multimodal diffusion model that unifies sequence and structure modeling paradigms to…
View article: Sparse autoencoders uncover biologically interpretable features in protein language model representations
Sparse autoencoders uncover biologically interpretable features in protein language model representations Open
Foundation models in biology—particularly protein language models (PLMs)—have enabled ground-breaking predictions in protein structure, function, and beyond. However, the “black-box” nature of these representations limits transparency and …
View article: CLARIFY: cell–cell interaction and gene regulatory network refinement from spatially resolved transcriptomics
CLARIFY: cell–cell interaction and gene regulatory network refinement from spatially resolved transcriptomics Open
Motivation Gene regulatory networks (GRNs) in a cell provide the tight feedback needed to synchronize cell actions. However, genes in a cell also take input from, and provide signals to other neighboring cells. These cell–cell interactions…
View article: DeepViFi
DeepViFi Open
We consider the problem of identifying viral reads in human host genome data. We pose the problem as open-set classification as reads can originate from unknown sources such as bacterial and fungal genomes. Sequence-matching methods have l…