2 citations · 2 across the 11 of their papers we have counts for
14 papers
Disentangling Marginal Capacity from Geometry in Optimal-Transport Label Transfer
Ali Khodabandeh Yalabadi, Azim Dehghani Amirabad, Artem Moskalev +4
Optimal transport (OT) is widely used to align distributions and transfer labels between unpaired source and target data, but source-target composition shifts can cause rare classe…
VCLMU: Mechanism-Centric Virtual Cell World Modeling for Perturbation Response
Yuwei Miao, Azim Dehghani Amirabad, Scott Oloff +3
Predicting cellular responses to genetic perturbations is a central capability for virtual cells and a key step toward computational modeling of biological interventions. Most exis…
Predictor-Guided Latent Space Codon Optimization for Maximizing Protein Expression
Alberto Caron, Tianyu Cui, Dmytro S. Lituiev +13
Codon optimization, the process of selecting synonymous codons to improve mRNA translation efficiency and protein expression, is central to therapeutic protein production and mRNA…
PaSTel: Anchoring Histology in Spatial Transcriptomics via Multi-Scale Hierarchical Bio-Prior Contrastive Pretraining
Azim Dehghani Amirabad, Junchao Zhu, Pushpak Pati +3
Spatial transcriptomics (ST) links tissue morphology with molecular programs, motivating multimodal pretraining methods that align histology images with gene expression. However, e…
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…
BioBO: Biology-informed Bayesian Optimization for Perturbation Design
Yanke Li, Tianyu Cui, Tommaso Mansi +2
Efficient design of genomic perturbation experiments is crucial for accelerating drug discovery and therapeutic target identification, yet exhaustive perturbation of the human geno…
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…
HELM: Hierarchical Encoding for mRNA Language Modeling
Mehdi Yazdani-Jahromi, Mangal Prakash, Tommaso Mansi +2
Messenger RNA (mRNA) plays a crucial role in protein synthesis, with its codon structure directly impacting biological properties. While Language Models (LMs) have shown promise in…
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.…
SE(3)-Hyena Operator for Scalable Equivariant Learning
Artem Moskalev, Mangal Prakash, Rui Liao +1
Modeling global geometric context while maintaining equivariance is crucial for accurate predictions in many fields such as biology, chemistry, or vision. Yet, this is challenging…
Cardiac ultrasound simulation for autonomous ultrasound navigation
Abdoul Aziz Amadou, Laura Peralta, Paul Dryburgh +11
Ultrasound is well-established as an imaging modality for diagnostic and interventional purposes. However, the image quality varies with operator skills as acquiring and interpreti…