Bayesian Approximation of RNA Folding Times
Dominik Scheuer, Frederic Runge, Jörg K.H. Franke, Michael T. Wolfinger, Christoph Flamm, Frank Hutter
SPACE: Your Genomic Profile Predictor is a Powerful DNA Foundation Model
Jiwei Zhu, Zhao Yang, Bing Su
Flexible Models of Functional Annotations to Variant Effects using Accelerated Linear Algebra
Alan Nawzad Amin, Andres Potapczynski, Andrew Gordon Wilson
arowana: a transformer-based training framework for RNA basecalling and modification detection
Yuk Kei Wan, Christopher Hendra, Bing Shao Chia, Wei Leong Chew, Jonathan Goeke
A Comprehensive Library for RNA Structure-Function Modeling
Luis Wyss, Vincent Mallet, Carlos Oliver, Wissam Karroucha, Karsten Borgwardt
Benchmarking Fine-Tuned RNA Language Models for Branch Point Prediction
Pablo Rodenas Ruiz, Ali Saadat, Timothy T. Tran, Oliver Müller Smedt, Peng Zhang, Jacques Fellay
EvoFlow-RNA: Generating and Representing non-coding RNA with a Language Model
Sawan Patel, Fred Zhangzhi Peng, Keith Fraser, Adam David Friedman, Pranam Chatterjee, Sherwood Yao
Crypto-ncRNA: Non-coding RNA (ncRNA) Based Encryption Algorithm
WangXu, YiquanWang, Tin-Yeh Huang
Decision Tree Induction with Dynamic Feature Generation: A Framework for Interpretable DNA Sequence Analysis
Nicolas Huynh, Krzysztof Kacprzyk, Ryan M Sheridan, David L. Bentley, Mihaela van der Schaar
FFPEnet: Somatic variant calling in FFPE tumor samples using deep transfer learning
Kiran Krishnamachari, Anders Jacobsen Skanderup
Zero-Shot Extrapolation in State-Space Models for Long-Range Genomics
Matvei Popov, Aymen Kallala, Anirudha Ramesh
ProtRNA: A Protein-derived RNA Language Model by Cross-Modality Transfer Learning
Ruoxi Zhang, Ben Ma, Gang Xu, Jianpeng Ma
Character-level Tokenizations as Powerful Inductive Biases for RNA Foundational Models
Adrian Morales-Pastor, Raquel Vázquez-Reza, Miłosz Wieczór, Clàudia Valverde, Manel Gil-Sorribes, Bertran Miquel-Oliver, Alvaro Ciudad Serrano, Alexis Molina
Protriever: End-to-End Differentiable Protein Homology Search for Fitness Prediction
Ruben Weitzman, Peter Mørch Groth, Aoi Otani, Yarin Gal, Debora Susan Marks, Pascal Notin
Campolina: A Deep Neural Framework for Accurate Segmentation of Nanopore Signals
Sara Bakić, Kresimir Friganovic, Bryan Hooi, Mile Sikic
Re-purposing GNNome: Genome Assembly Postprocessing (GAP)
Joshua Emmanuel Teo, Martin Schmitz
VirProBERT: A Sequence Language Model for Predicting Viral Hosts
Blessy Antony, Maryam Haghani, Anuj Karpatne, T. Murali
MoXGATE: Modality-Aware Cross-Attention for Multi-Omic Gastrointestinal Cancer Subtype Classification
Sajib Acharjee Dip
