7 papers
HyperHELM: Hyperbolic Hierarchy Encoding for mRNA Language Modeling
Max van Spengler, Artem Moskalev, Tommaso Mansi +2
Language models are increasingly applied to biological sequences like proteins and mRNA, yet their default Euclidean geometry may mismatch the hierarchical structures inherent to b…
Multimodal Modeling of CRISPR-Cas12 Activity Using Foundation Models and Chromatin Accessibility Data
Azim Dehghani Amirabad, Yanfei Zhang, Artem Moskalev +5
Predicting guide RNA (gRNA) activity is critical for effective CRISPR-Cas12 genome editing but remains challenging due to limited data, variation across protospacer adjacent motifs…
InfoSEM: A Deep Generative Model with Informative Priors for Gene Regulatory Network Inference
Tianyu Cui, Song-Jun Xu, Artem Moskalev +4
Inferring Gene Regulatory Networks (GRNs) from gene expression data is crucial for understanding biological processes. While supervised models are reported to achieve high performa…
Probing Equivariance and Symmetry Breaking in Convolutional Networks
Sharvaree Vadgama, Mohammad Mohaiminul Islam, Domas Buracas +3
In this work, we explore the trade-offs of explicit structural priors, particularly group equivariance. We address this through theoretical analysis and a comprehensive empirical s…
Geometric Hyena Networks for Large-scale Equivariant Learning
Artem Moskalev, Mangal Prakash, Junjie Xu +3
Processing global geometric context while preserving equivariance is crucial when modeling biological, chemical, and physical systems. Yet, this is challenging due to the computati…
Beyond Sequence: Impact of Geometric Context for RNA Property Prediction
Junjie Xu, Artem Moskalev, Tommaso Mansi +2
Accurate prediction of RNA properties, such as stability and interactions, is crucial for advancing our understanding of biological processes and developing RNA-based therapeutics.…