The paper introduces IDiom, an autoregressive protein language model trained on a large dataset of intrinsically disordered protein regions (IDRs) from AlphaFold, and demonstrates that it can generate sequences matching natural IDR composition, motifs, and disorder. It further presents RL‑SAE, a reinforcement learning approach that uses sparse autoencoder features to steer generation toward specific functional patterns, achieving high activation of targeted features and improved predicted subcellular localization and transcriptional activity. The combination of IDiom and RL‑SAE allows interpretable, composable IDR design by explicitly controlling function‑associated sequence features.
By Jason X. Liu, Sebastian Ibarraran, Frank Hu, Soojung Yang, Xinyu A. Feng, Abigail Park, Anagha Aneesh, Lacramioara Bintu, Alexander R. Dunn, Grant M. Rotskoff
EvoLen is a tokenization method for DNA language models that incorporates evolutionary information to prioritize functional sequence patterns such as regulatory motifs. It groups DNA sequences by cross-species evolutionary signals, trains separate BPE tokenizers for each group, merges vocabularies with a rule that favors preserved patterns, and uses length-aware decoding with dynamic programming. Experiments show EvoLen better preserves functional motifs, differentiates genomic contexts, and aligns with evolutionary constraints while matching or surpassing standard BPE on various DNALM benchmarks.
By Nan Huang, Xiaoxiao Zhou, Junxia Cui, Mario Tapia-Pacheco, Tiffany Amariuta, Yang Li, Jingbo Shang
arXiv:2606. 10543v1 Announce Type: cross Abstract: Designing functional biological sequences requires navigating vast discrete spaces under strict evolutionary and biophysical constraints.
By Yogesh Verma, Dani Korpela, Harri L\"ahdesm\"aki, Vikas Garg
arXiv:2605. 15354v2 Announce Type: replace Abstract: Despite the success of foundation models in language and vision, molecular graph generation still lacks a unified framework for heterogeneous design tasks with reliable controllability.
By Yihan Zhu, Yuhan Liu, Weijiang Li, Tengfei Luo, Meng Jiang
VGAS: Variance-Reduced Guidance and Adaptive Selection for Training-Free Reward Alignment in Discrete Diffusion proposes a new inference-time framework that improves steering of frozen masked discrete diffusion models. By reducing the variance of guidance estimates, applying reward tilting to clean-token logits, and adapting the selection temperature at each step, VGAS addresses three default choices in existing pipelines. Experiments on regulatory DNA, protein, and small-molecule benchmarks show that VGAS achieves the best training-free reward performance and matches or surpasses reward-fine-tuned generators.
By Kwanyoung Kim
arXiv:2607. 19618v1 Announce Type: cross Abstract: Genomic language models achieve strong performance across regulatory-genomics tasks, yet what these models internally represent remains opaque, and the field lacks a principled procedure for verifying that an apparent ``concept'' inside a model is real rather than an artifact of sequence composition.
By Sarwan Ali