InfoSEM: A Deep Generative Model with Informative Priors for Gene Regulatory Network Inference
Tianyu Cui, Song-Jun Xu, Artem Moskalev, Shuwei Li, Tommaso Mansi, Mangal Prakash, Rui Liao
HyperGenie: A method for predicting enzymatic gene essentiality using hypergraph neural networks and genome-scale metabolic models
Panayiotis Ioannou, Iulia Duta, Suraj Verma, Pietro Cicuta, Pietro Lio, Claudio Angione
RNAlign: Alignment of tumor and cell line transcriptomes using conditional VAEs
Jacob Alvarez, Kiran Krishnamachari, Anders Jacobsen Skanderup
HARMONY: A Multi-Representation Framework for RNA Property Prediction
Junjie Xu, Artem Moskalev, Tommaso Mansi, Mangal Prakash, Rui Liao
From Mutation to Degradation: Predicting Nonsense-Mediated Decay with NMDEP
Ali Saadat, Jacques Fellay
On inputs to deep learning for RNA 3D structure prediction
Marcell Szikszai, Marcin Magnus, Sachin Kadyan, Elena Rivas
Gumbel-Softmax Score and Flow Matching for Discrete Biological Sequence Generation
Sophia Tang, Yinuo Zhang, Alexander Tong, Pranam Chatterjee
siRNA-mRNA dual diffusion model for RNAi drug design
Zhiqi Ma, Xubin Zheng
GENATATOR: de novo Gene Annotation With DNA Language Model
Aleksei Shmelev, Artem Shadskiy, Yuri Kuratov, Mikhail Burtsev, Olga Kardymon, Veniamin Fishman
Accelerating Aptamer Discovery using a Transformer Based T-5 Model: A Preliminary Study
Soniya, Runjhun Saran Narayan, Apurva Narayan
Understanding DNA Discrete Diffusion for Engineering Regulatory DNA Sequences
Anirban Sarkar, Yijie Kang, Nirali Somia, Peter K Koo
Enhancing DNA Foundation Models to Address Masking Inefficiencies
Monireh Safari, Pablo Andres Millan Arias, Scott C. Lowe, Lila Kari, Angel X Chang, Graham W. Taylor
Long-range gene expression prediction with token alignment of large language model
Edouardo Honig, Huixin Zhan, Zijun Frank Zhang, Ying Nian Wu
scContrast: A contrastive learning based approach for encoding single-cell gene expression data
Winston Yuxiang Li, Ghulam Murtaza, Ritambhara Singh
Differentiable Folding for Nearest Neighbor Model Optimization
Ryan Krueger, Sharon Aviran, David Mathews, Jeffrey Zuber, Max Ward
RNAGym: Benchmarks for RNA Fitness and Structure Prediction
Rohit Arora, Murphy Angelo, Christian Andrew Choe, Aaron W Kollasch, Fiona Qu, Courtney A. Shearer, Ruben Weitzman, Artem Gazizov, Sarah Gurev, Erik Xie, Debora Susan Marks, Pascal Notin
RiboGen: RNA Sequence and Structure Co-Generation with Equivariant Multiflow
Dana Rubin, Allan Dos Santos Costa, Joseph Jacobson, Manvitha Ponnapati
