5 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…
BioLangFusion: Multimodal Fusion of DNA, mRNA, and Protein Language Models
Amina Mollaysa, Artem Moskale, Pushpak Pati +3
We present BioLangFusion, a simple approach for integrating pre-trained DNA, mRNA, and protein language models into unified molecular representations. Motivated by the central dogm…
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…
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…