ICLR 2025 Workshop AI4NA Submissions

MoXGATE: Modality-Aware Cross-Attention for Multi-Omic Gastrointestinal Cancer Subtype Classification
Sajib Acharjee Dip
- Published: 05 Mar 2025, Last Modified: 16 Apr 2025
- ICLR 2025 AI4NA Poster
- Readers: Everyone
VirProBERT: A Sequence Language Model for Predicting Viral Hosts
Blessy Antony, Maryam Haghani, Anuj Karpatne, T. Murali
- Published: 05 Mar 2025, Last Modified: 16 Apr 2025
- ICLR 2025 AI4NA Poster
- Readers: Everyone
Re-purposing GNNome: Genome Assembly Postprocessing (GAP)
Joshua Emmanuel Teo, Martin Schmitz
- Published: 05 Mar 2025, Last Modified: 16 Apr 2025
- ICLR 2025 AI4NA Poster
- Readers: Everyone
Campolina: A Deep Neural Framework for Accurate Segmentation of Nanopore Signals
Sara Bakić, Kresimir Friganovic, Bryan Hooi, Mile Sikic
- Published: 05 Mar 2025, Last Modified: 16 Apr 2025
- ICLR 2025 AI4NA Oral
- Readers: Everyone
RiboGen: RNA Sequence and Structure Co-Generation with Equivariant Multiflow
Dana Rubin, Allan Dos Santos Costa, Manvitha Ponnapati, JOSEPH JACOBSON
- Published: 05 Mar 2025, Last Modified: 16 Apr 2025
- ICLR 2025 AI4NA Oral
- Readers: Everyone
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
- Published: 05 Mar 2025, Last Modified: 16 Apr 2025
- ICLR 2025 AI4NA Poster
- Readers: Everyone
Differentiable Folding for Nearest Neighbor Model Optimization
Ryan Krueger, Sharon Aviran, David Mathews, Jeffrey Zuber, Max Ward
- Published: 05 Mar 2025, Last Modified: 16 Apr 2025
- ICLR 2025 AI4NA Poster
- Readers: Everyone
scContrast: A contrastive learning based approach for encoding single-cell gene expression data
Winston Yuxiang Li, Ghulam Murtaza, Ritambhara Singh
- Published: 05 Mar 2025, Last Modified: 16 Apr 2025
- ICLR 2025 AI4NA Poster
- Readers: Everyone
Long-range gene expression prediction with token alignment of large language model
Edouardo Honig, Huixin Zhan, Ying Nian Wu, Zijun Frank Zhang
- Published: 05 Mar 2025, Last Modified: 16 Apr 2025
- ICLR 2025 AI4NA Poster
- Readers: Everyone
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
- Published: 05 Mar 2025, Last Modified: 16 Apr 2025
- ICLR 2025 AI4NA Poster
- Readers: Everyone
Understanding DNA Discrete Diffusion for Engineering Regulatory DNA Sequences
Anirban Sarkar, Yijie Kang, Nirali Somia, Peter K Koo
- Published: 05 Mar 2025, Last Modified: 16 Apr 2025
- ICLR 2025 AI4NA Poster
- Readers: Everyone
Accelerating Aptamer Discovery using a Transformer Based T5 Model: A Preliminary Study
Soniya, Runjhun Saran Narayan, Apurva Narayan
- Published: 05 Mar 2025, Last Modified: 16 Apr 2025
- ICLR 2025 AI4NA Poster
- Readers: Everyone
GENATATOR: de novo Gene Annotation With DNA Language Model
Aleksei Shmelev, Artem Shadskiy, Yuri Kuratov, Mikhail Burtsev, Olga Kardymon, Veniamin Fishman
- Published: 05 Mar 2025, Last Modified: 16 Apr 2025
- ICLR 2025 AI4NA Poster
- Readers: Everyone
siRNA-mRNA dual diffusion model for RNAi drug design
Zhiqi Ma, Xubin Zheng
- Published: 05 Mar 2025, Last Modified: 16 Apr 2025
- ICLR 2025 AI4NA Poster
- Readers: Everyone
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
- Published: 05 Mar 2025, Last Modified: 16 Apr 2025
- ICLR 2025 AI4NA Poster
- Readers: Everyone
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
- Published: 05 Mar 2025, Last Modified: 16 Apr 2025
- ICLR 2025 AI4NA Poster
- Readers: Everyone
ProtRNA: A Protein-derived RNA Language Model by Cross-Modality Transfer Learning
Ruoxi Zhang, Ben Ma, Gang Xu, Jianpeng Ma
- Published: 05 Mar 2025, Last Modified: 16 Apr 2025
- ICLR 2025 AI4NA Poster
- Readers: Everyone
Gumbel-Softmax Score and Flow Matching for Discrete Biological Sequence Generation
Sophia Tang, Yinuo Zhang, Alexander Tong, Pranam Chatterjee
- Published: 05 Mar 2025, Last Modified: 16 Apr 2025
- ICLR 2025 AI4NA Poster
- Readers: Everyone
On inputs to deep learning for RNA 3D structure prediction
Marcell Szikszai, Marcin Magnus, Sachin Kadyan, Elena Rivas
- Published: 05 Mar 2025, Last Modified: 16 Apr 2025
- ICLR 2025 AI4NA Poster
- Readers: Everyone
From Mutation to Degradation: Predicting Nonsense-Mediated mRNA Decay with NMDEP
Ali Saadat, Jacques Fellay
- Published: 05 Mar 2025, Last Modified: 16 Apr 2025
- ICLR 2025 AI4NA Oral
- Readers: Everyone
Zero-Shot Extrapolation in State-Space Models for Long-Range Genomics
Matvei Popov, Aymen Kallala, Anirudha Ramesh
- Published: 05 Mar 2025, Last Modified: 16 Apr 2025
- ICLR 2025 AI4NA Poster
- Readers: Everyone
FFPEnet: Somatic variant calling in FFPE tumor samples using deep transfer learning
Kiran Krishnamachari, Anders Jacobsen Skanderup
- Published: 05 Mar 2025, Last Modified: 16 Apr 2025
- ICLR 2025 AI4NA Poster
- Readers: Everyone
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
- Published: 05 Mar 2025, Last Modified: 16 Apr 2025
- ICLR 2025 AI4NA Poster
- Readers: Everyone
Crypto-ncRNA: Non-coding RNA (ncRNA) Based Encryption Algorithm
WangXu, YiquanWang, Tin-Yeh Huang
- Published: 05 Mar 2025, Last Modified: 03 Jun 2025
- ICLR 2025 AI4NA Poster
- Readers: Everyone
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
- Published: 05 Mar 2025, Last Modified: 16 Apr 2025
- ICLR 2025 AI4NA Poster
- Readers: Everyone