Morning Session (11:15-12:15)
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
Afternoon Session (16:05-17:05)
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